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Sample records for brassica rapa flc1

  1. QTL architecture of reproductive fitness characters in Brassica rapa

    PubMed Central

    2014-01-01

    Background Reproductive output is critical to both agronomists seeking to increase seed yield and to evolutionary biologists interested in understanding natural selection. We examine the genetic architecture of diverse reproductive fitness traits in recombinant inbred lines (RILs) developed from a crop (seed oil) × wild-like (rapid cycling) genotype of Brassica rapa in field and greenhouse environments. Results Several fitness traits showed strong correlations and QTL-colocalization across environments (days to bolting, fruit length and seed color). Total fruit number was uncorrelated across environments and most QTL affecting this trait were correspondingly environment-specific. Most fitness components were positively correlated, consistent with life-history theory that genotypic variation in resource acquisition masks tradeoffs. Finally, we detected evidence of transgenerational pleiotropy, that is, maternal days to bolting was negatively correlated with days to offspring germination. A QTL for this transgenerational correlation was mapped to a genomic region harboring one copy of FLOWERING LOCUS C, a genetic locus known to affect both days to flowering as well as germination phenotypes. Conclusions This study characterizes the genetic structure of important fitness/yield traits within and between generations in B. rapa. Several identified QTL are suitable candidates for fine-mapping for the improvement of yield in crop Brassicas. Specifically, brFLC1, warrants further investigation as a potential regulator of phenology between generations. PMID:24641198

  2. Unleashing the Genome of Brassica Rapa

    PubMed Central

    Tang, Haibao; Lyons, Eric

    2012-01-01

    The completion and release of the Brassica rapa genome is of great benefit to researchers of the Brassicas, Arabidopsis, and genome evolution. While its lineage is closely related to the model organism Arabidopsis thaliana, the Brassicas experienced a whole genome triplication subsequent to their divergence. This event contemporaneously created three copies of its ancestral genome, which had diploidized through the process of homeologous gene loss known as fractionation. By the fractionation of homeologous gene content and genetic regulatory binding sites, Brassica’s genome is well placed to use comparative genomic techniques to identify syntenic regions, homeologous gene duplications, and putative regulatory sequences. Here, we use the comparative genomics platform CoGe to perform several different genomic analyses with which to study structural changes of its genome and dynamics of various genetic elements. Starting with whole genome comparisons, the Brassica paleohexaploidy is characterized, syntenic regions with A. thaliana are identified, and the TOC1 gene in the circadian rhythm pathway from A. thaliana is used to find duplicated orthologs in B. rapa. These TOC1 genes are further analyzed to identify conserved non-coding sequences that contain cis-acting regulatory elements and promoter sequences previously implicated in circadian rhythmicity. Each “cookbook style” analysis includes a step-by-step walk-through with links to CoGe to quickly reproduce each step of the analytical process. PMID:22866056

  3. Targeted metabolite analysis and biological activity of Pieris brassicae fed with Brassica rapa var. rapa.

    PubMed

    Pereira, David M; Noites, Alexandra; Valentão, Patricia; Ferreres, Federico; Pereira, José A; Vale-Silva, Luis; Pinto, Eugénia; Andrade, Paula B

    2009-01-28

    For the first time, an insect-plant system, Pieris brassicae fed with Brassica rapa var. rapa, was tested for its biological capacity, namely, antioxidant (DPPH*, *NO, and O(2)*- radicals) and antimicrobial (bacteria and fungi) activities. Samples from the insect's life cycle (larvae, excrements, exuviae, and butterfly) were always found to be more efficient than the host plant. Also, P. brassicae materials, as well as its host plant, were screened for phenolics and organic acids. The host plant revealed higher amounts of both compounds. Two phenolic acids, ferulic and sinapic, as well as kaempferol 3-Osophoroside, were common to insect (larvae and excrements) and plant materials, with excrements being considerably richer. Detection of sulfated compounds in excrements, absent in host plant, revealed that metabolic processes in this species involved sulfation. Additionally, deacylation and deglycosilation were observed. All matrices presented the same organic acids qualitative profile, with the exception of excrements. PMID:19115952

  4. Characterization and effects of the replicated flowering time gene FLC in Brassica rapa.

    PubMed Central

    Schranz, M Eric; Quijada, Pablo; Sung, Si-Bum; Lukens, Lewis; Amasino, Richard; Osborn, Thomas C

    2002-01-01

    Functional genetic redundancy is widespread in plants and could have an important impact on phenotypic diversity if the multiple gene copies act in an additive or dosage-dependent manner. We have cloned four Brassica rapa homologs (BrFLC) of the MADS-box flowering-time regulator FLC, located at the top of chromosome 5 of Arabidopsis thaliana. Relative rate tests revealed no evidence for differential rates of evolution and the ratios of nonsynonymous-to-synonymous substitutions suggest BrFLC loci are not under strong purifying selection. BrFLC1, BrFLC2, and BrFLC3 map to genomic regions that are collinear with the top of At5, consistent with a polyploid origin. BrFLC5 maps near a junction of two collinear regions to Arabidopsis, one of which includes an FLC-like gene (AGL31). However, all BrFLC sequences are more closely related to FLC than to AGL31. BrFLC1, BrFLC2, and BrFLC5 cosegregate with flowering-time loci evaluated in populations derived by backcrossing late-flowering alleles from a biennial parent into an annual parent. Two loci segregating in a single backcross population affected flowering in a completely additive manner. Thus, replicated BrFLC genes appear to have a similar function and interact in an additive manner to modulate flowering time. PMID:12454088

  5. Secondary Metabolism in Brassica Rapa Under Hypergravity

    NASA Astrophysics Data System (ADS)

    Levine, Lanfang; Darnell, Rebecca; Allen, Joan; Musgrave, Mary; Bisbee, Patricia

    Effect of altered gravity on secondary metabolism is of critical importance not only from the viewpoint of plant evolution, but also of productivity (carbon partition between edible and non-edible parts), plant fitness, as well as culinary and nutraceutical values to human diet. Previous work found that lignin content decreases in microgravity as the need for mechanical support decreases, while the response of other small molecular secondary metabolites to microgravity varies. Our recent ISS experiment showed that 3-butenyl glucosinolate (a predominant glucosinolate in Brassica rapa) increased in stems of B. rapa grown in the microgravity conditions. To further elucidate the role of gravity in plant secondary metabolism, a series of hypergravity (the other end of gravity spectrum) experiments were carried out using the 24-ft centrifuge at Ames Research Center. Thirteen-day-old B. rapa L. (cv. Astroplants) were transferred to the Plant Growth Facility attached to the centrifuge following previous experimental conditions, and subsequently grown for 16 days. Plants were harvested, immediately frozen in liquid nitrogen, and lyophilized prior to analysis for glucosinolates and lignin. In general, glucosinolate concentration was the highest in stems, followed by leaves, then roots. Glucosinolate concentration was significantly lower in stems of the 2-g and 4-g plants - averaging 4.6 and 2.5 ng/g DW, respectively - compared with the stationary control plants, which averaged 7.9 ng/g DW. Similarly, there was a 2.2-fold and 7.5-fold decrease in 3-butenyl glucosinolate in roots of the 2-g and 4-g plants, respectively, compared with the control (2.6 ng/g DW). There was a significant decrease in 3-butenyl glucosinolate concentration in leaves of the 4-g compared to leaves of the control plants (2.6 and 4.5 ng/g DW, respectively); however, there was no effect of 2-g on leaf glucosinolate concentration. Increasing gravity from 1-g to 2-g to 4-g generally resulted in further

  6. Identification of Resistance to Peppery Leaf Spot among Brassica Juncea and Brassica Rapa Plant Introductions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Brassica leafy greens (Brassica juncea L. and B. rapa L.) represent one of the most economically important vegetable crop groups in the southeastern United States. In the last 10 years, numerous occurrences of a leaf spot disease on these leafy vegetables have been reported in several states. This...

  7. THE BRASSICA RAPA ELONGATED INTERNODE (EIN) GENE ENCODES PHYTOCHROME B

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The elongated internode (ein) mutation of Brassica rapa leads to a deficiency in immunochemically detectable phytochrome B. Molecular analysis of the PHYB gene from ein indicates a deletion in the flanking DNA 5' of the ATG start codon, which could interfere either with PHYB transcription or process...

  8. Phytotoxicity assay for seed production using Brassica rapa L.

    EPA Science Inventory

    Although pesticide drift can affect crop yield adversely, current plant testing protocols emphasize only the potential impacts on vegetative plant growth. The present study was conducted to determine whether a plant species with a short life cycle, such as Brassica rapa L. Wiscon...

  9. Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa.

    PubMed

    Cheng, Feng; Mandáková, Terezie; Wu, Jian; Xie, Qi; Lysak, Martin A; Wang, Xiaowu

    2013-05-01

    The genus Brassica includes several important agricultural and horticultural crops. Their current genome structures were shaped by whole-genome triplication followed by extensive diploidization. The availability of several crucifer genome sequences, especially that of Chinese cabbage (Brassica rapa), enables study of the evolution of the mesohexaploid Brassica genomes from their diploid progenitors. We reconstructed three ancestral subgenomes of B. rapa (n = 10) by comparing its whole-genome sequence to ancestral and extant Brassicaceae genomes. All three B. rapa paleogenomes apparently consisted of seven chromosomes, similar to the ancestral translocation Proto-Calepineae Karyotype (tPCK; n = 7), which is the evolutionarily younger variant of the Proto-Calepineae Karyotype (n = 7). Based on comparative analysis of genome sequences or linkage maps of Brassica oleracea, Brassica nigra, radish (Raphanus sativus), and other closely related species, we propose a two-step merging of three tPCK-like genomes to form the hexaploid ancestor of the tribe Brassiceae with 42 chromosomes. Subsequent diversification of the Brassiceae was marked by extensive genome reshuffling and chromosome number reduction mediated by translocation events and followed by loss and/or inactivation of centromeres. Furthermore, via interspecies genome comparison, we refined intervals for seven of the genomic blocks of the Ancestral Crucifer Karyotype (n = 8), thus revising the key reference genome for evolutionary genomics of crucifers. PMID:23653472

  10. Could nitrile derivatives of turnip (Brassica rapa) glucosinolates be hepato- or cholangiotoxic in cattle?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Turnip (Brassica rapa ssp. rapa) and rape (Brassica napus ssp. biennis) and other brassica forage crops are regarded as “safe” feed for cattle during late summer and fall in the North Island of New Zealand when high Pithomyces chartarum spore counts in pastures frequently lead to sporidesmin toxicit...

  11. Could nitrile derivatives of turnip (Brassica rapa) glucosinolates be Hepato-and/or cholangiotoxic in cattle?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Turnip (Brassica rapa ssp. rapa) and rape (Brassica napus ssp. biennis) and other brassica forage crops are generally regarded as “safe” feed for cattle during late summer and fall in New Zealand. However, when Pithomyces chartarum spore counts are high there are epidemics of sporidesmin toxicity (...

  12. Embryogenesis of brassica rapa l. under clinorotation

    NASA Astrophysics Data System (ADS)

    Popova, A.; Ivanenko, G.

    Investigation of reproductive development of higher plants in spaceflight represents scientific interest first of all with the necessity to work out the plant space technologies for creation of controlled life-support systems. In such systems mainly the higher plants are considered to be an important component that makes it necessary to obtain the several generations of higher plants with their full ontogenesis. As a rule, seeds obtained in three species of the higher plants in a series of experiments differ from the control by some parameters (Merkis, Laurinavichius, 1983; Musgrave et al., 1998; 2000; Levinskikh et all. 1999; Stankovich et al., 2002). It was shown, that immature embryos generated in microgravity were at a range of developmental stage, while the ground control embryos had all reached the premature stage of development (Kuang et al., 2003). Besides, the distinctions in a degree of nutrient substances accumulation in them were revealed (Kuang et al., 2000). Therefore, the elucidation of the possible reasons for distortion of plant reproduction in microgravity demands the further research. In this study we examined embryogenesis of higher plant Brassica rapa L. with an application of slow horizontal clinostats, that allows to deprive the plants the opportunity to perceive the gravitational stimulus. Some plants were clinorotated from the moment sowing of seeds; in other series the experiment plants were placed on clinostats after formation of flower buds. Temporal fixation of the material was used in these experiments, which allow to obtain material for studying of consecutive stages of embryogenesis. The development of 2-21 day-old embryos was studied. Comparative embryological analysis has shown a similarity in the main of process of embryo differentiation produced under clinorotation and in the stationary control. At the early stages of embryogenesis, the distortion in suspensor formation was observed more frequently. Embryos generated in

  13. Isolate Dependency of Brassica rapa Resistance QTLs to Botrytis cinerea.

    PubMed

    Zhang, Wei; Kwon, Soon-Tae; Chen, Fang; Kliebenstein, Daniel J

    2016-01-01

    Generalist necrotrophic pathogens including Botrytis cinerea cause significant yield and financial losses on Brassica crops. However, there is little knowledge about the mechanisms underlying the complex interactions encoded by both host and pathogen genomes in this interaction. This potentially includes multiple layers of plant defense and pathogen virulence mechanisms that could complicate in breeding broad spectrum resistance within Brassica species. Glucosinolates (GSLs) are a diverse group of defense metabolites that play a key role in interaction between Brassica and biotic attackers. In this study, we utilized a collection of diverse B. cinerea isolates to investigate resistance within the Brassica rapa R500 × IMB211 recombinant inbred line population. We tested variation on lesion development and glucosinolate accumulation in parental lines and all population lines. We then mapped quantitative trait loci (QTL) for both resistances to B. cinerea and defense metabolites in this population. Phenotypic analysis and QTL mapping demonstrate that the genetic basis of resistance to B. cinerea in B. rapa is isolate specific and polygenic with transgressive segregation that both parents contribute resistance alleles. QTLs controlling defensive GSLs are highly dependent on pathogen infection. An overlap of two QTLs identified between resistance to B. cinerea and defense metabolites also showed isolate specific effects. This work suggests that directly searching for resistance loci may not be the best approach at improving resistance in B. rapa to necrotrophic pathogen. PMID:26925079

  14. Isolate Dependency of Brassica rapa Resistance QTLs to Botrytis cinerea

    PubMed Central

    Zhang, Wei; Kwon, Soon-Tae; Chen, Fang; Kliebenstein, Daniel J.

    2016-01-01

    Generalist necrotrophic pathogens including Botrytis cinerea cause significant yield and financial losses on Brassica crops. However, there is little knowledge about the mechanisms underlying the complex interactions encoded by both host and pathogen genomes in this interaction. This potentially includes multiple layers of plant defense and pathogen virulence mechanisms that could complicate in breeding broad spectrum resistance within Brassica species. Glucosinolates (GSLs) are a diverse group of defense metabolites that play a key role in interaction between Brassica and biotic attackers. In this study, we utilized a collection of diverse B. cinerea isolates to investigate resistance within the Brassica rapa R500 × IMB211 recombinant inbred line population. We tested variation on lesion development and glucosinolate accumulation in parental lines and all population lines. We then mapped quantitative trait loci (QTL) for both resistances to B. cinerea and defense metabolites in this population. Phenotypic analysis and QTL mapping demonstrate that the genetic basis of resistance to B. cinerea in B. rapa is isolate specific and polygenic with transgressive segregation that both parents contribute resistance alleles. QTLs controlling defensive GSLs are highly dependent on pathogen infection. An overlap of two QTLs identified between resistance to B. cinerea and defense metabolites also showed isolate specific effects. This work suggests that directly searching for resistance loci may not be the best approach at improving resistance in B. rapa to necrotrophic pathogen. PMID:26925079

  15. Identification of expressed genes during infection of Chinese cabbage (Brassica rapa subsp. pekinensis) by Plasmodiophora brassicae.

    PubMed

    Sundelin, Thomas; Jensen, Dan F; Lübeck, Mette

    2011-01-01

    Plasmodiophora brassicae is an obligate, biotrophic pathogen causing the club-root disease of crucifers. Despite its importance as a plant pathogen, little is known about P. brassicae at the molecular level as most of its life cycle takes place inside the plant host, and axenic culturing is impossible. Discovery of genes expressed during infection and gene organization are the first steps toward a better understanding of the pathogen-host interaction. Here, suppression subtractive hybridization was used to search for the P. brassicae genes expressed during plant infection. One-hundred and forty ESTs were found of which 49% proved to be P. brassicae genes. Ten novel P. brassicae genes were identified, and the genomic sequences surrounding four of the ESTs were acquired using genome walking. Alignment of the ESTs and the genomic DNA sequences confirmed that P. brassicae genes are intron rich and that the introns are small. These results show that it is possible to discover new P. brassicae genes from a mixed pool of both plant and pathogen cDNA. The results also revealed that some of the P. brassicae genes expressed in Chinese cabbage (Brassica rapa subsp. pekinensis) were identical to the genes expressed in the infection of Arabidopsis plants, indicating that these genes play an important role in P. brassicae infection. PMID:21518080

  16. Genomic distribution of simple sequence repeats in Brassica rapa.

    PubMed

    Hong, Chang Pyo; Piao, Zhong Yun; Kang, Tae Wook; Batley, Jacqueline; Yang, Tae-Jin; Hur, Yoon-Kang; Bhak, Jong; Park, Beom-Seok; Edwards, David; Lim, Yong Pyo

    2007-06-30

    Simple Sequence Repeats (SSRs) represent short tandem duplications found within all eukaryotic organisms. To examine the distribution of SSRs in the genome of Brassica rapa ssp. pekinensis, SSRs from different genomic regions representing 17.7 Mb of genomic sequence were surveyed. SSRs appear more abundant in non-coding regions (86.6%) than in coding regions (13.4%). Comparison of SSR densities in different genomic regions demonstrated that SSR density was greatest within the 5'-flanking regions of the predicted genes. The proportion of different repeat motifs varied between genomic regions, with trinucleotide SSRs more prevalent in predicted coding regions, reflecting the codon structure in these regions. SSRs were also preferentially associated with gene-rich regions, with peri-centromeric heterochromatin SSRs mostly associated with retrotransposons. These results indicate that the distribution of SSRs in the genome is non-random. Comparison of SSR abundance between B. rapa and the closely related species Arabidopsis thaliana suggests a greater abundance of SSRs in B. rapa, which may be due to the proposed genome triplication. Our results provide a comprehensive view of SSR genomic distribution and evolution in Brassica for comparison with the sequenced genomes of A. thaliana and Oryza sativa. PMID:17646709

  17. Genetic analysis of interspecific incompatibility in Brassica rapa.

    PubMed

    Udagawa, H; Ishimaru, Y; Li, F; Sato, Y; Kitashiba, H; Nishio, T

    2010-08-01

    In interspecific pollination of Brassica rapa stigmas with Brassica oleracea pollen grains, pollen tubes cannot penetrate stigma tissues. This trait, called interspecific incompatibility, is similar to self-incompatibility in pollen tube behaviors of rejected pollen grains. Since some B. rapa lines have no interspecific incompatibility, genetic analysis of interspecific incompatibility was performed using two F(2) populations. Analysis with an F(2) population between an interspecific-incompatible line and a self-compatible cultivar 'Yellow sarson' having non-functional alleles of S-locus genes and MLPK, the stigmas of which are compatible with B. oleracea pollen grains, revealed no involvement of the S locus and MLPK in the difference of their interspecific incompatibility phenotypes. In QTL analysis of the strength of interspecific incompatibility, three peaks of LOD scores were found, but their LOD scores were as high as the threshold value, and the variance explained by each QTL was small. QTL analysis using another F(2) population derived from selected parents having the highest and lowest levels of interspecific incompatibility revealed five QTLs with high LOD scores, which did not correspond to those found in the former population. The QTL having the highest LOD score was found in linkage group A02. The effect of this QTL on interspecific incompatibility was confirmed by analyzing backcrossed progeny. Based on synteny of this QTL region with Arabidopsis thaliana chromosome 5, a possible candidate gene, which might be involved in interspecific incompatibility, is discussed. PMID:20414635

  18. Genetic diversity of allozymes in turnip (Brassica rapa L. var. rapa) from the Nordic area.

    PubMed

    Persson, K; Fält, A S; von Bothmer, R

    2001-01-01

    Genetic diversity and relationships based on isozymes were studied in 31 accessions of turnip (Brassica rapa L. var. rapa). The material included varieties, elite stocks, landraces and older turnip of slash-and-burn type from the Nordic area. A total of 9 isozyme loci and 26 alleles were studied. The isozyme systems were ACO, DIA, GPI, GOT, PGM, PGD and SKD. The level of heterozygosity was reduced in the landraces, but it was high for the variety group 'Ostersundom'. Turnip has a higher genetic variation than other crops within B. rapa and than in other species with the same breeding system. The genetic diversity showed that 18.7% of the genetic variation was within the accessions, and the total H tau value was 0.358. Gpi-I and Pgd-I showed the lowest variation compared with the other loci. The cluster analysis revealed five clusters, with one main cluster including 25 of the 31 accessions. The dendrogram indicated that the variety group 'Ostersundom' clustered together whereas the variety group 'Bortfelder' was associated with country of origin. The landraces were spread in different clusters. The 'slash-and-burn' type of turnip belonged to two groups. PMID:11525064

  19. Characterization of directly transformed weedy Brassica rapa and introgressed B. rapa with Bt cry1Ac and gfp genes.

    PubMed

    Moon, Hong S; Halfhill, Matthew D; Good, Laura L; Raymer, Paul L; Neal Stewart, C

    2007-07-01

    Crop to weed transgene flow, which could result in more competitive weed populations, is an agricultural biosafety concern. Crop Brassica napus to weedy Brassica rapa hybridization has been extensively characterized to better understand the transgene flow and its consequences. In this study, weedy accessions of B. rapa were transformed with Bacillus thuringiensis (Bt) cry1Ac- and green fluorescence protein (gfp)-coding transgenes using Agrobacterium to assess ecological performance of the wild biotype relative to introgressed hybrids in which the transgenic parent was the crop. Regenerated transgenic B. rapa events were characterized by progeny analysis, Bt protein enzyme-linked immunosorbent assay (ELISA), Southern blot analysis, and GFP expression assay. GFP expression level and Bt protein concentration were significantly different between independent transgenic B. rapa events. Similar reproductive productivity was observed in comparison between transgenic B. rapa events and B. rapa x B. napus introgressed hybrids in greenhouse and field experiments. In the greenhouse, Bt transgenic plants experienced significantly less herbivory damage from the diamondback moth (Plutella xylostella). No differences were found in the field experiment under ambient, low, herbivore pressure. Directly transformed transgenic B. rapa plants should be a helpful experimental control to better understand crop genetic load in introgressed transgenic weeds. PMID:17333014

  20. Phytotoxicity assay for seed production using Brassica rapa L.

    PubMed

    Olszyk, David; Pfleeger, Thomas; Lee, E Henry; Plocher, Milton

    2010-10-01

    Although pesticide drift can affect crop yield adversely, current plant testing protocols emphasize only the potential impacts on vegetative plant growth. The present study was conducted to determine whether a plant species with a short life cycle, such as Brassica rapa L. Wisconsin Fast Plants®, can be used to indicate potential effects on seed production of herbicides applied at relatively low levels (e.g., low field application rates [FAR]). The effects of ≤0.1 × FAR of aminopyralid, cloransulam, glyphosate, primisulfuron, or sulfometuron applied 14 d after emergence (DAE), were evaluated for B. rapa grown in mineral soil in pots under greenhouse conditions. Effects were expressed as the effective concentration of the herbicide producing a 25% reduction in a response (EC25) based on nonlinear regression. Brassica rapa seed dry weight was reduced by sulfometuron at an EC25 of 0.00014 × a field application rate (FAR) of 53 g active ingredient (a.i.) ha(-1), primisulfuron at 0.008 (experiment 1) or 0.0050 (experiment 2) × FAR of 40 g a.i. ha(-1), cloransulam at 0.022 × FAR of 18 g a.i. ha(-1), glyphosate at 0.0399 × FAR of 834 g a.i. ha(-1), and by aminopyralid at 0.005 × FAR of 123 g a.i. ha(-1), but only for 1 of 2 experiments. Reduced seed production occurred at less than the FAR that reduced shoot dry weight with sulfometuron and primisulfuron, whereas neither aminopyralid, cloransulam, nor glyphosate affected shoot dry weight. A short life cycle form of B. rapa could be used to indicate reduced seed production with plants grown only 1 week longer (∼35 DAE) than as the current vegetative vigor test for nontarget herbicide effects on plants. PMID:20872651

  1. NMR metabolomics of ripened and developing oilseed rape (Brassica napus) and turnip rape (Brassica rapa).

    PubMed

    Kortesniemi, Maaria; Vuorinen, Anssi L; Sinkkonen, Jari; Yang, Baoru; Rajala, Ari; Kallio, Heikki

    2015-04-01

    The oilseeds of the commercially important oilseed rape (Brassica napus) and turnip rape (Brassica rapa) were investigated with (1)H NMR metabolomics. The compositions of ripened (cultivated in field trials) and developing seeds (cultivated in controlled conditions) were compared in multivariate models using principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and orthogonal partial least squares discriminant analysis (OPLS-DA). Differences in the major lipids and the minor metabolites between the two species were found. A higher content of polyunsaturated fatty acids and sucrose were observed in turnip rape, while the overall oil content and sinapine levels were higher in oilseed rape. The genotype traits were negligible compared to the effect of the growing site and concomitant conditions on the oilseed metabolome. This study demonstrates the applicability of NMR-based analysis in determining the species, geographical origin, developmental stage, and quality of oilseed Brassicas. PMID:25442524

  2. Pollination and embryo development in Brassica rapa L. in microgravity

    NASA Technical Reports Server (NTRS)

    Kuang, A.; Popova, A.; Xiao, Y.; Musgrave, M. E.

    2000-01-01

    Plant reproduction under spaceflight conditions has been problematic in the past. In order to determine what aspect of reproductive development is affected by microgravity, we studied pollination and embryo development in Brassica rapa L. during 16 d in microgravity on the space shuttle (STS-87). Brassica is self-incompatible and requires mechanical transfer of pollen. Short-duration access to microgravity during parabolic flights on the KC-135A aircraft was used initially to confirm that equal numbers of pollen grains could be collected and transferred in the absence of gravity. Brassica was grown in the Plant Growth Facility flight hardware as follows. Three chambers each contained six plants that were 13 d old at launch. As these plants flowered, thin colored tape was used to indicate the date of hand pollination, resulting in silique populations aged 8-15 d postpollination at the end of the 16-d mission. The remaining three chambers contained dry seeds that germinated on orbit to produce 14-d-old plants just beginning to flower at the time of landing. Pollen produced by these plants had comparable viability (93%) with that produced in the 2-d-delayed ground control. Matched-age siliques yielded embryos of equivalent developmental stage in the spaceflight and ground control treatments. Carbohydrate and protein storage reserves in the embryos, assessed by cytochemical localization, were also comparable. In the spaceflight material, growth and development by embryos rescued from siliques 15 d after pollination lagged behind the ground controls by 12 d; however, in the subsequent generation, no differences between the two treatments were found. The results demonstrate that while no stage of reproductive development in Brassica is absolutely dependent upon gravity, lower embryo quality may result following development in microgravity.

  3. A novel detection system for the genetically modified canola (Brassica rapa) line RT73.

    PubMed

    Akiyama, Hiroshi; Makiyama, Daiki; Nakamura, Kosuke; Sasaki, Nobuhiro; Minegishi, Yasutaka; Mano, Junichi; Kitta, Kazumi; Ozeki, Yoshihiro; Teshima, Reiko

    2010-12-01

    The herbicide-tolerant genetically modified Roundup Ready canola (Brassica napus) line RT73 has been approved worldwide for use in animal feed and human food. However, RT73 Brassica rapa lines derived from interspecific crosses with RT73 B. napus have not been approved in Japan. Here, we report on a novel system using individual kernel analyses for the qualitative detection of RT73 B. rapa in canola grain samples. We developed a duplex real-time polymerase chain reaction (PCR) method to discriminate B. napus and B. rapa DNA using scatter plots of the end-point analyses; this method was able to discriminate a group comprising B. rapa and Brassica juncea from a group comprising B. napus, Brassica carinata, and Brassica oleracea. We also developed a duplex real-time PCR method for the simultaneous detection of an RT73-specific sequence and an endogenous FatA gene. Additionally, a DNA-extraction method using 96-well silica-membrane plates was developed and optimized for use with individual canola kernels. Our detection system could identify RT73 B. rapa kernels in canola grain samples enabling the accurate and reliable monitoring of RT73 B. rapa contamination in canola, thus playing a role in its governmental regulation in Japan. PMID:21049930

  4. Genetic Dissection of Leaf Development in Brassica rapa Using a Genetical Genomics Approach1[W

    PubMed Central

    Xiao, Dong; Wang, Huange; Basnet, Ram Kumar; Zhao, Jianjun; Lin, Ke; Hou, Xilin; Bonnema, Guusje

    2014-01-01

    The paleohexaploid crop Brassica rapa harbors an enormous reservoir of morphological variation, encompassing leafy vegetables, vegetable and fodder turnips (Brassica rapa, ssp. campestris), and oil crops, with different crops having very different leaf morphologies. In the triplicated B. rapa genome, many genes have multiple paralogs that may be regulated differentially and contribute to phenotypic variation. Using a genetical genomics approach, phenotypic data from a segregating doubled haploid population derived from a cross between cultivar Yellow sarson (oil type) and cultivar Pak choi (vegetable type) were used to identify loci controlling leaf development. Twenty-five colocalized phenotypic quantitative trait loci (QTLs) contributing to natural variation for leaf morphological traits, leaf number, plant architecture, and flowering time were identified. Genetic analysis showed that four colocalized phenotypic QTLs colocalized with flowering time and leaf trait candidate genes, with their cis-expression QTLs and cis- or trans-expression QTLs for homologs of genes playing a role in leaf development in Arabidopsis (Arabidopsis thaliana). The leaf gene BRASSICA RAPA KIP-RELATED PROTEIN2_A03 colocalized with QTLs for leaf shape and plant height; BRASSICA RAPA ERECTA_A09 colocalized with QTLs for leaf color and leaf shape; BRASSICA RAPA LONGIFOLIA1_A10 colocalized with QTLs for leaf size, leaf color, plant branching, and flowering time; while the major flowering time gene, BRASSICA RAPA FLOWERING LOCUS C_A02, colocalized with QTLs explaining variation in flowering time, plant architectural traits, and leaf size. Colocalization of these QTLs points to pleiotropic regulation of leaf development and plant architectural traits in B. rapa. PMID:24394778

  5. Genetic dissection of leaf development in Brassica rapa using a genetical genomics approach.

    PubMed

    Xiao, Dong; Wang, Huange; Basnet, Ram Kumar; Zhao, Jianjun; Lin, Ke; Hou, Xilin; Bonnema, Guusje

    2014-03-01

    The paleohexaploid crop Brassica rapa harbors an enormous reservoir of morphological variation, encompassing leafy vegetables, vegetable and fodder turnips (Brassica rapa, ssp. campestris), and oil crops, with different crops having very different leaf morphologies. In the triplicated B. rapa genome, many genes have multiple paralogs that may be regulated differentially and contribute to phenotypic variation. Using a genetical genomics approach, phenotypic data from a segregating doubled haploid population derived from a cross between cultivar Yellow sarson (oil type) and cultivar Pak choi (vegetable type) were used to identify loci controlling leaf development. Twenty-five colocalized phenotypic quantitative trait loci (QTLs) contributing to natural variation for leaf morphological traits, leaf number, plant architecture, and flowering time were identified. Genetic analysis showed that four colocalized phenotypic QTLs colocalized with flowering time and leaf trait candidate genes, with their cis-expression QTLs and cis- or trans-expression QTLs for homologs of genes playing a role in leaf development in Arabidopsis (Arabidopsis thaliana). The leaf gene Brassica rapa KIP-related protein2_A03 colocalized with QTLs for leaf shape and plant height; Brassica rapa Erecta_A09 colocalized with QTLs for leaf color and leaf shape; Brassica rapa Longifolia1_A10 colocalized with QTLs for leaf size, leaf color, plant branching, and flowering time; while the major flowering time gene, Brassica rapa flowering locus C_A02, colocalized with QTLs explaining variation in flowering time, plant architectural traits, and leaf size. Colocalization of these QTLs points to pleiotropic regulation of leaf development and plant architectural traits in B. rapa. PMID:24394778

  6. Development of Public Immortal Mapping Populations, Molecular Markers and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study we describe public immortal mapping populations of self-compatible lines, molecular markers, and linkage maps for Brassica rapa and B. oleracea. We propose that these resources are valuable reference tools for the Brassica community. The B. rapa population consists of 150 recombinant...

  7. Development of Public Immortal Mapping Populations, Molecular Markers, and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Past research efforts on genetic mapping in Brassica oleracea and Brassica rapa have been disconnected, utilizing separate mapping populations and different sets of molecular markers. Here we present public immortal mapping populations, molecular markers and linkage maps for rapid cycling B. rapa a...

  8. Transfer of auxinic herbicide resistance from Brassica kaber to Brassica juncea and Brassica rapa through embryo rescue.

    PubMed

    Mithila, J; Hall, J Christopher

    2013-01-01

    Auxinic herbicides are widely used in agriculture to selectively control broadleaf weeds. Prolonged use of auxinic herbicides has resulted in the evolution of resistance to these herbicides in some biotypes of Brassica kaber (wild mustard), a common weed in agricultural crops. In this study, auxinic herbicide resistance from B. kaber was transferred to Brassica juncea and Brassica rapa, two commercially important Brassica crops, by traditional breeding coupled with in vitro embryo rescue. A high frequency of embryo regeneration and hybrid plant establishment was achieved. Transfer of auxinic herbicide resistance from B. kaber to the hybrids was assessed by whole-plant screening of hybrids with dicamba, a widely used auxinic herbicide. Furthermore, the hybrids were tested for fertility (both pollen and pistil) and their ability to produce backcross progeny. The auxinic herbicide-resistant trait was introgressed into B. juncea by backcross breeding. DNA ploidy of the hybrids as well as of the backcross progeny was estimated by flow cytometry. Creation of auxinic herbicide-resistant Brassica crops by non-transgenic approaches should facilitate effective weed control, encourage less tillage, provide herbicide rotation options, minimize occurrence of herbicide resistance, and increase acceptance of these crops. PMID:23990700

  9. Polymorphism Identification and Improved Genome Annotation of Brassica rapa Through Deep RNA Sequencing

    PubMed Central

    Devisetty, Upendra Kumar; Covington, Michael F.; Tat, An V.; Lekkala, Saradadevi; Maloof, Julin N.

    2014-01-01

    The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system for this population and subsequent development of high-resolution genetic map. An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation. This is useful for accurate mRNA abundance and detection of expression QTL (eQTLs) in mapping populations. Deep RNA-Seq of two Brassica rapa genotypes—R500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)—using eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads. A total of 330,995 SNPs were identified in transcribed regions between the two genotypes with an average frequency of one SNP in every 200 bases. The deep RNA-Seq reassembled Brassica rapa transcriptome identified 44,239 protein-coding genes. Compared with current gene models of B. rapa, we detected 3537 novel transcripts, 23,754 gene models had structural modifications, and 3655 annotated proteins changed. Gaps in the current genome assembly of B. rapa are highlighted by our identification of 780 unmapped transcripts. All the SNPs, annotations, and predicted transcripts can be viewed at http://phytonetworks.ucdavis.edu/. PMID:25122667

  10. The elucidation of stress memory inheritance in Brassica rapa plants

    PubMed Central

    Bilichak, Andriy; Ilnytskyy, Yaroslav; Wóycicki, Rafal; Kepeshchuk, Nina; Fogen, Dawson; Kovalchuk, Igor

    2015-01-01

    Plants are able to maintain the memory of stress exposure throughout their ontogenesis and faithfully propagate it into the next generation. Recent evidence argues for the epigenetic nature of this phenomenon. Small RNAs (smRNAs) are one of the vital epigenetic factors because they can both affect gene expression at the place of their generation and maintain non-cell-autonomous gene regulation. Here, we have made an attempt to decipher the contribution of smRNAs to the heat-shock-induced transgenerational inheritance in Brassica rapa plants using sequencing technology. To do this, we have generated comprehensive profiles of a transcriptome and a small RNAome (smRNAome) from somatic and reproductive tissues of stressed plants and their untreated progeny. We have demonstrated that the highest tissue-specific alterations in the transcriptome and smRNAome profile are detected in tissues that were not directly exposed to stress, namely, in the endosperm and pollen. Importantly, we have revealed that the progeny of stressed plants exhibit the highest fluctuations at the smRNAome level but not at the transcriptome level. Additionally, we have uncovered the existence of heat-inducible and transgenerationally transmitted tRNA-derived small RNA fragments in plants. Finally, we suggest that miR168 and braAGO1 are involved in the stress-induced transgenerational inheritance in plants. PMID:25653665

  11. Enzymatic degradation of Congo Red by turnip (Brassica rapa) peroxidase.

    PubMed

    Ahmedi, Afaf; Abouseoud, Mahmoud; Couvert, Annabelle; Amrane, Abdeltif

    2012-01-01

    The enzyme peroxidase is known for its capacity to remove phenolic compounds and aromatic amines from aqueous solutions and also to decolourize textile effluents. This study aims at evaluating the potential of a turnip (Brassica rapa) peroxidase (TP) preparation in the discolouration of textile azo dyes and effluents. An azo dye, Congo Red (CR), was used as a model pollutant for treatment by the enzyme. The effects of various operating conditions like pH value, temperature, initial dye and hydrogen peroxide concentrations, contact time, and enzyme concentration were evaluated. The optimal conditions for maximal colour removal were at pH 2.0, 40 degrees C, 50 mM hydrogen peroxide, 50 mg/l CR dye, and TP activity of 0.45 U/ml within 10 min of incubation time. Analysis of the by-products from the enzymatic treatment by UV-Vis and IR spectroscopy showed no residual compounds in the aqueous phase and a precipitate of polymeric nature. PMID:23016283

  12. A Brassica rapa Linkage Map of EST-based SNP Markers for Identification of Candidate Genes Controlling Flowering Time and Leaf Morphological Traits

    PubMed Central

    Li, Feng; Kitashiba, Hiroyasu; Inaba, Kiyofumi; Nishio, Takeshi

    2009-01-01

    For identification of genes responsible for varietal differences in flowering time and leaf morphological traits, we constructed a linkage map of Brassica rapa DNA markers including 170 EST-based markers, 12 SSR markers, and 59 BAC sequence-based markers, of which 151 are single nucleotide polymorphism (SNP) markers. By BLASTN, 223 markers were shown to have homologous regions in Arabidopsis thaliana, and these homologous loci covered nearly the whole genome of A. thaliana. Synteny analysis between B. rapa and A. thaliana revealed 33 large syntenic regions. Three quantitative trait loci (QTLs) for flowering time were detected. BrFLC1 and BrFLC2 were linked to the QTLs for bolting time, budding time, and flowering time. Three SNPs in the promoter, which may be the cause of low expression of BrFLC2 in the early-flowering parental line, were identified. For leaf lobe depth and leaf hairiness, one major QTL corresponding to a syntenic region containing GIBBERELLIN 20 OXIDASE 3 and one major QTL containing BrGL1, respectively, were detected. Analysis of nucleotide sequences and expression of these genes suggested possible involvement of these genes in leaf morphological traits. PMID:19884167

  13. Field evaluation of leaf blight-resistant plant introductions of Brassica Juncea and Brassica Rapa and elucidation of inheritance of resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Brassica leafy greens (Brassica juncea and Brassica rapa) represent one of the most economically important vegetable crop groups in the southeastern United States. In the last 10 years, numerous occurrences of a leaf blight disease on these leafy vegetables have been reported in several states. One ...

  14. Comparative Analysis of Disease-Linked Single Nucleotide Polymorphic Markers from Brassica rapa for Their Applicability to Brassica oleracea

    PubMed Central

    Cho, Young-Il; Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Lee, Hye-Eun; Kim, Do-Sun

    2015-01-01

    Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH—developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP—based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS—derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species. PMID:25790283

  15. Morphology, Carbohydrate Composition and Vernalization Response in a Genetically Diverse Collection of Asian and European Turnips (Brassica rapa subsp. rapa)

    PubMed Central

    Zhang, Ningwen; Zhao, Jianjun; Lens, Frederic; de Visser, Joan; Menamo, Temesgen; Fang, Wen; Xiao, Dong; Bucher, Johan; Basnet, Ram Kumar; Lin, Ke; Cheng, Feng; Wang, Xiaowu; Bonnema, Guusje

    2014-01-01

    Brassica rapa displays enormous morphological diversity, with leafy vegetables, turnips and oil crops. Turnips (Brassica rapa subsp. rapa) represent one of the morphotypes, which form tubers and can be used to study the genetics underlying storage organ formation. In the present study we investigated several characteristics of an extensive turnip collection comprising 56 accessions from both Asia (mainly Japanese origin) and Europe. Population structure was calculated using data from 280 evenly distributed SNP markers over 56 turnip accessions. We studied the anatomy of turnip tubers and measured carbohydrate composition of the mature turnip tubers of a subset of the collection. The variation in 16 leaf traits, 12 tuber traits and flowering time was evaluated in five independent experiments for the entire collection. The effect of vernalization on flowering and tuber formation was also investigated. SNP marker profiling basically divided the turnip accessions into two subpopulations, with admixture, generally corresponding with geographical origin (Europe or Asia). The enlarged turnip tuber consists of both hypocotyl and root tissue, but the proportion of the two tissues differs between accessions. The ratio of sucrose to fructose and glucose differed among accessions, while generally starch content was low. The evaluated traits segregated in both subpopulations, with leaf shape, tuber colour and number of shoots per tuber explaining most variation between the two subpopulations. Vernalization resulted in reduced flowering time and smaller tubers for the Asian turnips whereas the European turnips were less affected by vernalization. PMID:25474111

  16. Anthocyanin biosynthesis for cold and freezing stress tolerance and desirable color in Brassica rapa.

    PubMed

    Ahmed, Nasar Uddin; Park, Jong-In; Jung, Hee-Jeong; Hur, Yoonkang; Nou, Ill-Sup

    2015-07-01

    Flavonoids are divided into several structural classes, including anthocyanins, which provide flower and leaf colors and other derivatives that play diverse roles in plant development and interactions with the environment. This study characterized four anthocyanidin synthase (ANS) genes of Brassica rapa, a structural gene of the anthocyanin biosynthetic pathway, and investigated their association with pigment formation, cold and freezing tolerance in B. rapa. Sequences of these genes were analyzed and compared with similar gene sequences from other species, and a high degree of homology with their respective functions was found. Organ-specific expression analysis revealed that these genes were only expressed in the colored portion of leaves of different lines of B. rapa. Conversely, B. rapa anthocyanidin synthase (BrANS) genes also showed responses to cold and freezing stress treatment in B. rapa. BrANSs were also shown to be regulated by two transcription factors, BrMYB2-2 and BrTT8, contrasting with anthocyanin accumulation and cold stress. Thus, the above results suggest the association of these genes with anthocyanin biosynthesis and cold and freezing stress tolerance and might be useful resources for development of cold-resistant Brassica crops with desirable colors as well. PMID:25504198

  17. Regulatory Network of Secondary Metabolism in Brassica rapa: Insight into the Glucosinolate Pathway

    PubMed Central

    Pino Del Carpio, Dunia; Basnet, Ram Kumar; Arends, Danny; Lin, Ke; De Vos, Ric C. H.; Muth, Dorota; Kodde, Jan; Boutilier, Kim; Bucher, Johan; Wang, Xiaowu; Jansen, Ritsert; Bonnema, Guusje

    2014-01-01

    Brassica rapa studies towards metabolic variation have largely been focused on the profiling of the diversity of metabolic compounds in specific crop types or regional varieties, but none aimed to identify genes with regulatory function in metabolite composition. Here we followed a genetical genomics approach to identify regulatory genes for six biosynthetic pathways of health-related phytochemicals, i.e carotenoids, tocopherols, folates, glucosinolates, flavonoids and phenylpropanoids. Leaves from six weeks-old plants of a Brassica rapa doubled haploid population, consisting of 92 genotypes, were profiled for their secondary metabolite composition, using both targeted and LC-MS-based untargeted metabolomics approaches. Furthermore, the same population was profiled for transcript variation using a microarray containing EST sequences mainly derived from three Brassica species: B. napus, B. rapa and B. oleracea. The biochemical pathway analysis was based on the network analyses of both metabolite QTLs (mQTLs) and transcript QTLs (eQTLs). Co-localization of mQTLs and eQTLs lead to the identification of candidate regulatory genes involved in the biosynthesis of carotenoids, tocopherols and glucosinolates. We subsequently focused on the well-characterized glucosinolate pathway and revealed two hotspots of co-localization of eQTLs with mQTLs in linkage groups A03 and A09. Our results indicate that such a large-scale genetical genomics approach combining transcriptomics and metabolomics data can provide new insights into the genetic regulation of metabolite composition of Brassica vegetables. PMID:25222144

  18. The first generation of a BAC-based physical map of Brassica rapa

    PubMed Central

    Mun, Jeong-Hwan; Kwon, Soo-Jin; Yang, Tae-Jin; Kim, Hye-Sun; Choi, Beom-Soon; Baek, Seunghoon; Kim, Jung Sun; Jin, Mina; Kim, Jin A; Lim, Myung-Ho; Lee, Soo In; Kim, Ho-Il; Kim, Hyungtae; Lim, Yong Pyo; Park, Beom-Seok

    2008-01-01

    Background The genus Brassica includes the most extensively cultivated vegetable crops worldwide. Investigation of the Brassica genome presents excellent challenges to study plant genome evolution and divergence of gene function associated with polyploidy and genome hybridization. A physical map of the B. rapa genome is a fundamental tool for analysis of Brassica "A" genome structure. Integration of a physical map with an existing genetic map by linking genetic markers and BAC clones in the sequencing pipeline provides a crucial resource for the ongoing genome sequencing effort and assembly of whole genome sequences. Results A genome-wide physical map of the B. rapa genome was constructed by the capillary electrophoresis-based fingerprinting of 67,468 Bacterial Artificial Chromosome (BAC) clones using the five restriction enzyme SNaPshot technique. The clones were assembled into contigs by means of FPC v8.5.3. After contig validation and manual editing, the resulting contig assembly consists of 1,428 contigs and is estimated to span 717 Mb in physical length. This map provides 242 anchored contigs on 10 linkage groups to be served as seed points from which to continue bidirectional chromosome extension for genome sequencing. Conclusion The map reported here is the first physical map for Brassica "A" genome based on the High Information Content Fingerprinting (HICF) technique. This physical map will serve as a fundamental genomic resource for accelerating genome sequencing, assembly of BAC sequences, and comparative genomics between Brassica genomes. The current build of the B. rapa physical map is available at the B. rapa Genome Project website for the user community. PMID:18549474

  19. Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa.

    PubMed

    Sun, Chao; Wu, Jian; Liang, Jianli; Schnable, James C; Yang, Wencai; Cheng, Feng; Wang, Xiaowu

    2015-11-01

    MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play essential roles in eukaryotes. Although the influence of whole-genome triplication (WGT) on protein-coding genes has been well documented in Brassica rapa, little is known about its impacts on MIRNAs. In this study, through generating a comprehensive annotation of 680 MIRNAs for B. rapa, we analyzed the evolutionary characteristics of these MIRNAs from different aspects in B. rapa. First, while MIRNAs and genes show similar patterns of biased distribution among subgenomes of B. rapa, we found that MIRNAs are much more overretained than genes following fractionation after WGT. Second, multiple-copy MIRNAs show significant sequence conservation than that of single-copy MIRNAs, which is opposite to that of genes. This indicates that increased purifying selection is acting upon these highly retained multiple-copy MIRNAs and their functional importance over singleton MIRNAs. Furthermore, we found the extensive divergence between pairs of miRNAs and their target genes following the WGT in B. rapa. In summary, our study provides a valuable resource for exploring MIRNA in B. rapa and highlights the impacts of WGT on the evolution of MIRNA. PMID:26527651

  20. Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis

    PubMed Central

    Zheng, Jin-shuang; Sun, Cheng-zhen; Zhang, Shu-ning; Hou, Xi-lin; Bonnema, Guusje

    2016-01-01

    A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis. PMID:27507974

  1. Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. chinensis.

    PubMed

    Zheng, Jin-Shuang; Sun, Cheng-Zhen; Zhang, Shu-Ning; Hou, Xi-Lin; Bonnema, Guusje

    2016-01-01

    A significant fraction of the nuclear DNA of all eukaryotes is comprised of simple sequence repeats (SSRs). Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. In this paper, we report the distribution characterization of mono-, di-, and tri-nucleotide SSRs in Brassica rapa ssp. chinensis. Fluorescence in situ hybridization was used to characterize the cytogenetic diversity of SSRs among morphotypes of B. rapa ssp. chinensis. The proportion of different SSR motifs varied among morphotypes of B. rapa ssp. chinensis, with tri-nucleotide SSRs being more prevalent in the genome of B. rapa ssp. chinensis. We determined the chromosomal locations of mono-, di-, and tri-nucleotide repeat loci. The results showed that the chromosomal distribution of SSRs in the different morphotypes is non-random and motif-dependent, and allowed us to characterize the relative variability in terms of SSR numbers and similar chromosomal distributions in centromeric/peri-centromeric heterochromatin. The differences between SSR repeats with respect to abundance and distribution indicate that SSRs are a driving force in the genomic evolution of B. rapa species. Our results provide a comprehensive view of the SSR sequence distribution and evolution for comparison among morphotypes B. rapa ssp. chinensis. PMID:27507974

  2. Mapping the Anthocyaninless (anl) Locus in Rapid-Cycling Brassica rapa (RBr) to Linkage Group R9

    PubMed Central

    Burdzinski, Carrie; Wendell, Douglas L

    2007-01-01

    Background Anthocyanins are flavonoid pigments that are responsible for purple coloration in the stems and leaves of a variety of plant species. Anthocyaninless (anl) mutants of Brassica rapa fail to produce anthocyanin pigments. In rapid-cycling Brassica rapa, also known as Wisconsin Fast Plants, the anthocyaninless trait, also called non-purple stem, is widely used as a model recessive trait for teaching genetics. Although anthocyanin genes have been mapped in other plants such as Arabidopsis thaliana, the anl locus has not been mapped in any Brassica species. Results We tested primer pairs known to amplify microsatellites in Brassicas and identified 37 that amplified a product in rapid-cycling Brassica rapa. We then developed three-generation pedigrees to assess linkage between the microsatellite markers and anl. 22 of the markers that we tested were polymorphic in our crosses. Based on 177 F2 offspring, we identified three markers linked to anl with LOD scores ≥ 5.0, forming a linkage group spanning 46.9 cM. Because one of these markers has been assigned to a known B. rapa linkage group, we can now assign the anl locus to B. rapa linkage group R9. Conclusion This study is the first to identify the chromosomal location of an anthocyanin pigment gene among the Brassicas. It also connects a classical mutant frequently used in genetics education with molecular markers and a known chromosomal location. PMID:17894874

  3. Inferring the Brassica rapa Interactome Using Protein–Protein Interaction Data from Arabidopsis thaliana

    PubMed Central

    Yang, Jianhua; Osman, Kim; Iqbal, Mudassar; Stekel, Dov J.; Luo, Zewei; Armstrong, Susan J.; Franklin, F. Chris H.

    2013-01-01

    Following successful completion of the Brassica rapa sequencing project, the next step is to investigate functions of individual genes/proteins. For Arabidopsis thaliana, large amounts of protein–protein interaction (PPI) data are available from the major PPI databases (DBs). It is known that Brassica crop species are closely related to A. thaliana. This provides an opportunity to infer the B. rapa interactome using PPI data available from A. thaliana. In this paper, we present an inferred B. rapa interactome that is based on the A. thaliana PPI data from two resources: (i) A. thaliana PPI data from three major DBs, BioGRID, IntAct, and TAIR. (ii) ortholog-based A. thaliana PPI predictions. Linking between B. rapa and A. thaliana was accomplished in three complementary ways: (i) ortholog predictions, (ii) identification of gene duplication based on synteny and collinearity, and (iii) BLAST sequence similarity search. A complementary approach was also applied, which used known/predicted domain–domain interaction data. Specifically, since the two species are closely related, we used PPI data from A. thaliana to predict interacting domains that might be conserved between the two species. The predicted interactome was investigated for the component that contains known A. thaliana meiotic proteins to demonstrate its usability. PMID:23293649

  4. Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana.

    PubMed

    Yang, Jianhua; Osman, Kim; Iqbal, Mudassar; Stekel, Dov J; Luo, Zewei; Armstrong, Susan J; Franklin, F Chris H

    2012-01-01

    Following successful completion of the Brassica rapa sequencing project, the next step is to investigate functions of individual genes/proteins. For Arabidopsis thaliana, large amounts of protein-protein interaction (PPI) data are available from the major PPI databases (DBs). It is known that Brassica crop species are closely related to A. thaliana. This provides an opportunity to infer the B. rapa interactome using PPI data available from A. thaliana. In this paper, we present an inferred B. rapa interactome that is based on the A. thaliana PPI data from two resources: (i) A. thaliana PPI data from three major DBs, BioGRID, IntAct, and TAIR. (ii) ortholog-based A. thaliana PPI predictions. Linking between B. rapa and A. thaliana was accomplished in three complementary ways: (i) ortholog predictions, (ii) identification of gene duplication based on synteny and collinearity, and (iii) BLAST sequence similarity search. A complementary approach was also applied, which used known/predicted domain-domain interaction data. Specifically, since the two species are closely related, we used PPI data from A. thaliana to predict interacting domains that might be conserved between the two species. The predicted interactome was investigated for the component that contains known A. thaliana meiotic proteins to demonstrate its usability. PMID:23293649

  5. Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives.

    PubMed

    Ramchiary, Nirala; Nguyen, Van Dan; Li, Xiaonan; Hong, Chang Pyo; Dhandapani, Vignesh; Choi, Su Ryun; Yu, Ge; Piao, Zhong Yun; Lim, Yong Pyo

    2011-10-01

    Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species. PMID:21768136

  6. Mitigation using a tandem construct containing a selectively unfit gene precludes establishment of Brassica napus transgenes in hybrids and backcrosses with weedy Brassica rapa.

    PubMed

    Al-Ahmad, Hani; Gressel, Jonathan

    2006-01-01

    Transgenic oilseed rape (Brassica napus) plants can interbreed with nearby weedy Brassica rapa, potentially enhancing the weediness and/or invasiveness of subsequent hybrid offspring. We have previously demonstrated that transgenic mitigation effectively reduces the fitness of the transgenic dwarf and herbicide-resistant B. napus volunteers. We now report the efficacy of such a tandem construct, including a primary herbicide-resistant gene and a dwarfing mitigator gene, to preclude the risks of gene establishment in the related weed B. rapa and its backcross progeny. The transgenically mitigated and non-transgenic B. rapa x B. napus interspecific hybrids and the backcrosses (BC(1)) with B. rapa were grown alone and in competition with B. rapa weed. The reproductive fitness of hybrid offspring progressively decreased with increased B. rapa genes in the offspring, illustrating the efficacy of the concept. The fitness of F(2) interspecific non-transgenic hybrids was between 50% and 80% of the competing weedy B. rapa, whereas the fitness of the comparable T(2) interspecific transgenic hybrids was never more than 2%. The reproductive fitness of the transgenic T(2) BC(1) mixed with B. rapa was further severely suppressed to 0.9% of that of the competing weed due to dwarfism. Clearly, the mitigation technology works efficiently in a rapeseed crop-weed system under biocontainment-controlled environments, but field studies should further validate its utility for minimizing the risks of gene flow. PMID:17177782

  7. Identification and characterization of stress resistance related genes of Brassica rapa.

    PubMed

    Ahmed, Nasar Uddin; Park, Jong-In; Jung, Hee-Jeong; Seo, Mi-Suk; Kumar, Thamilarasan Senthil; Lee, In-Ho; Nou, Ill-Sup

    2012-05-01

    Two biotic stress resistance related genes from the full-length cDNA library of Brassica rapa cv. Osome were identified from EST analysis and determined to be pathogenesis-related (PR) 12 Brassica defensin-like family protein (BrDLFP) and PR-10 Brassica Betv1 allergen family protein (BrBetv1AFP) after sequence analysis and homology study with other stress resistance related same family genes. In the expression analysis, both genes expressed in different organs and during all developmental growth stages in healthy plants. Expression of BrDLFP significantly increased and BrBetv1AFP gradually decreased after infection with Pectobacterium carotovorum subsp. carotovorum in Chinese cabbage. Expression of these two genes significantly changed after cold, salt, drought and ABA stress treatments. These two PR genes may therefore be involved in the plant resistance against biotic and abiotic stresses. PMID:22286206

  8. The high-throughput sequencing of small RNAs profiling in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra.

    PubMed

    Ghani, Muhammad Awais; Li, Junxing; Rao, Linli; Raza, Muhammad Ammar; Cao, Liwen; Yu, Ningning; Zou, Xiaoxia; Chen, Liping

    2015-03-01

    Small RNAs play an important role in maintaining the genome reconstruction and stability in the plant. However, little is known regarding the role of small RNAs during the process of wide hybridisation and chromosome doubling. Therefore, the changes in the small RNAs were assessed during the formation of an allodiploid (genome: AB) and its allotetraploid (genome: AABB) between Brassica rapa (♀) and Brassica nigra (♂) in the present study. Here, the experimental methods described in details, RNA-seq data (available at Gene Expression Omnibus database under GSE61872) and analysis published by Ghani et al. [1]. The study showed that small RNAs play an important role in maintaining the genome stability, and regulate gene expression which induces the phenotype variation in the formation of an allotetraploid. This may play an important role in the occurrence of heterosis in the allotetraploid. PMID:26484138

  9. Identification and expression analysis of WRKY family genes under biotic and abiotic stresses in Brassica rapa.

    PubMed

    Kayum, Md Abdul; Jung, Hee-Jeong; Park, Jong-In; Ahmed, Nasar Uddin; Saha, Gopal; Yang, Tae-Jin; Nou, Ill-Sup

    2015-02-01

    WRKY proteins constitute one of the largest transcription factor families in higher plants, and they are involved in multiple biological processes such as plant development, metabolism, and responses to biotic and abiotic stresses. Genes of this family have been well documented in response to many abiotic and biotic stresses in many plant species, but not yet against Pectobacterium carotovorum subsp. carotovorum and Fusarium oxysporum f.sp. conglutinans in any of the plants. Moreover, potentiality of a specific gene may vary depending on stress conditions and genotypes. To identify stress resistance-related potential WRKY genes of Brassica rapa, we analyzed their expressions against above-mentioned pathogens and cold, salt, and drought stresses in B. rapa. Stress resistance-related functions of all Brassica rapa WRKY (BrWRKY) genes were firstly analyzed through homology study with existing biotic and abiotic stress resistance-related WRKY genes of other plant species and found a high degree of homology. We then identified all BrWRKY genes in a Br135K microarray dataset, which was created by applying low-temperature stresses to two contrasting Chinese cabbage doubled haploid (DH) lines, Chiifu and Kenshin, and selected 41 BrWRKY genes with high and differential transcript abundance levels. These selected genes were further investigated under cold, salt, and drought stresses as well as after infection with P. carotovorum subsp. carotovorum and F. oxysporum f.sp. conglutinans in B. rapa. The selected genes showed an organ-specific expression, and 22 BrWRKY genes were differentially expressed in Chiifu compared to Kenshin under cold and drought stresses. Six BrWRKY genes were more responsive in Kenshin compared to Chiffu under salt stress. In addition, eight BrWRKY genes showed differential expression after P. carotovorum subsp. carotovorum infection and five genes after F. oxysporum f.sp. conglutinans infection in B. rapa. Thus, the differentially expressed Br

  10. Gene ontology based characterization of expressed sequence tags (ESTs) of Brassica rapa cv. Osome.

    PubMed

    Arasan, Senthil Kumar Thamil; Park, Jong-In; Ahmed, Nasar Uddin; Jung, Hee-Jeong; Lee, In-Ho; Cho, Yong-Gu; Lim, Yong-Pyo; Kang, Kwon-Kyoo; Nou, Ill-Sup

    2013-07-01

    Chinese cabbage (Brassica rapa) is widely recognized for its economic importance and contribution to human nutrition but abiotic and biotic stresses are main obstacle for its quality, nutritional status and production. In this study, 3,429 Express Sequence Tag (EST) sequences were generated from B. rapa cv. Osome cDNA library and the unique transcripts were classified functionally using a gene ontology (GO) hierarchy, Kyoto encyclopedia of genes and genomes (KEGG). KEGG orthology and the structural domain data were obtained from the biological database for stress related genes (SRG). EST datasets provided a wide outlook of functional characterization of B. rapa cv. Osome. In silico analysis revealed % 83 of ESTs to be well annotated towards reeds one dimensional concept. Clustering of ESTs returned 333 contigs and 2,446 singlets, giving a total of 3,284 putative unigene sequences. This dataset contained 1,017 EST sequences functionally annotated to stress responses and from which expression of randomly selected SRGs were analyzed against cold, salt, drought, ABA, water and PEG stresses. Most of the SRGs showed differentially expression against these stresses. Thus, the EST dataset is very important for discovering the potential genes related to stress resistance in Chinese cabbage, and can be of useful resources for genetic engineering of Brassica sp. PMID:23898551

  11. Characterization and stress-induced expression analysis of Alfin-like transcription factors in Brassica rapa.

    PubMed

    Kayum, Md Abdul; Park, Jong-In; Ahmed, Nasar Uddin; Jung, Hee-Jeong; Saha, Gopal; Kang, Jong-Goo; Nou, Ill-Sup

    2015-08-01

    The Alfin-like (AL) transcription factors (TFs) family is involved in many developmental processes, including the growth and development of roots, root hair elongation, meristem development, etc. However, stress resistance-related function and the regulatory mechanism of these TFs have yet to be elucidated. This study identified 15 Brassica rapa AL (BrAL) TFs from BRAD database, analyzed the sequences and profiled their expression first time in response to Fusarium oxysporum f. sp. conglutinans and Pectobacterium carotovorum subsp. carotovorum in fection, cold, salt and drought stresses in B. rapa. Structural and phylogenetic analyses of 15 BrAL TFs revealed four distinct groups (groups I-IV) with AL TFs of Arabidopsis thaliana. In the expression analyses, ten BrAL TFs showed responsive expression after F. oxysporum f. sp. conglutinans infection, while all BrAL TFs showed responses under cold, salt and drought stresses in B. rapa. Interestingly, ten BrAL TFs showed responses to both biotic and abiotic stress factors tested here. The differentially expressed BrAL TFs thus represent potential resources for molecular breeding of Brassica crops resistant against abiotic and biotic stresses. Our findings will also help to elucidate the complex regulatory mechanism of AL TFs in stress resistance and provide a foundation for further functional genomics studies and applications. PMID:25618423

  12. Hybridisation and introgression between Brassica napus and B. rapa in the Netherlands.

    PubMed

    Luijten, S H; Schidlo, N S; Meirmans, P G; de Jong, T J

    2015-01-01

    We used flow cytometry, chromosome counting and AFLP markers to investigate gene flow from the crop plant oilseed rape, Brassica napus (AACC) to wild B. rapa (AA) in the Netherlands. From 89 B. napus source populations investigated, all near cropping fields or at transhipment sites, only 19 contained a B. rapa population within a 2.5-km radius. During our survey we found only three populations with F1 hybrids (AAC), as recognized by their nine extra chromosomes and by flow cytometry. These hybrids were all collected in mixed populations where the two species grew in close proximity. Populations with F1 hybrids were not close to crops, but instead were located on road verges with highly disturbed soils, in which both species were probably recruited from the soil seed bank. Many plants in the F2, BC1 or higher backcrosses are expected to carry one to eight C chromosomes. However, these plants were not observed among the hybrids. We further investigated introgression with molecular markers (AFLP) and compared sympatric B. rapa populations (near populations of B. napus) with control populations of B. rapa (no B. napus within at least 7 km). We found no difference between sympatric and control populations in the number of C markers in B. rapa, nor did we find that these sympatric populations closely resembled B. napus. Our data show that hybrids occur but also suggest no recent introgression of alleles from the crop plant B. napus into wild B. rapa in the Dutch populations studied. PMID:24889091

  13. Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa

    PubMed Central

    Rameneni, Jana Jeevan; Li, Xiaonan; Sivanandhan, Ganesan; Choi, Su Ryun; Pang, Wenxing; Im, Subin; Lim, Yong Pyo

    2016-01-01

    Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in Brassica rapa (B. rapa). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in B. rapa using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the B. rapa Aux/IAA (BrIAA) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of BrIAA with Arabidopsis thaliana, Oryza sativa and Zea mays identified 51 sister pairs including 15 same species (BrIAA—BrIAA) and 36 cross species (BrIAA—AtIAA) IAA genes. Among the 55 BrIAA genes, expression of 43 and 45 genes were verified using Genebank B. rapa ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of BrIAA genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the BrIAA genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between IAA genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in B. rapa. Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of Brassica crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in B. rapa. PMID

  14. Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa.

    PubMed

    Paul, Parameswari; Dhandapani, Vignesh; Rameneni, Jana Jeevan; Li, Xiaonan; Sivanandhan, Ganesan; Choi, Su Ryun; Pang, Wenxing; Im, Subin; Lim, Yong Pyo

    2016-01-01

    Auxins are the key players in plant growth development involving leaf formation, phototropism, root, fruit and embryo development. Auxin/Indole-3-Acetic Acid (Aux/IAA) are early auxin response genes noted as transcriptional repressors in plant auxin signaling. However, many studies focus on Aux/ARF gene families and much less is known about the Aux/IAA gene family in Brassica rapa (B. rapa). Here we performed a comprehensive genome-wide analysis and identified 55 Aux/IAA genes in B. rapa using four conserved motifs of Aux/IAA family (PF02309). Chromosomal mapping of the B. rapa Aux/IAA (BrIAA) genes facilitated understanding cluster rearrangement of the crucifer building blocks in the genome. Phylogenetic analysis of BrIAA with Arabidopsis thaliana, Oryza sativa and Zea mays identified 51 sister pairs including 15 same species (BrIAA-BrIAA) and 36 cross species (BrIAA-AtIAA) IAA genes. Among the 55 BrIAA genes, expression of 43 and 45 genes were verified using Genebank B. rapa ESTs and in home developed microarray data from mature leaves of Chiifu and RcBr lines. Despite their huge morphological difference, tissue specific expression analysis of BrIAA genes between the parental lines Chiifu and RcBr showed that the genes followed a similar pattern of expression during leaf development and a different pattern during bud, flower and siliqua development stages. The response of the BrIAA genes to abiotic and auxin stress at different time intervals revealed their involvement in stress response. Single Nucleotide Polymorphisms between IAA genes of reference genome Chiifu and RcBr were focused and identified. Our study examines the scope of conservation and divergence of Aux/IAA genes and their structures in B. rapa. Analyzing the expression and structural variation between two parental lines will significantly contribute to functional genomics of Brassica crops and we belive our study would provide a foundation in understanding the Aux/IAA genes in B. rapa. PMID

  15. A transposon insertion in FLOWERING LOCUS T is associated with delayed flowering in Brassica rapa.

    PubMed

    Zhang, Xueming; Meng, Lin; Liu, Bo; Hu, Yunyan; Cheng, Feng; Liang, Jianli; Aarts, Mark G M; Wang, Xiaowu; Wu, Jian

    2015-12-01

    Long days and vernalization accelerate the transition from vegetative growth to reproductive growth in Brassica rapa. Bolting before plants reach the harvesting stage is a serious problem in B. rapa vegetable crop cultivation. The genetic dissection of flowering time is important for breeding of premature bolting-resistant B. rapa crops. Using a recombinant inbred line (RIL) population, we twice detected two major quantitative trait loci (QTLs) for flowering time in two different growing seasons that were located on chromosomes A02 and A07, respectively. We hypothesized that an orthologue of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene, named as BrFT2, was the candidate gene underlying the QTL localized to A07. A transposon insertion in the second intron of BrFT2 was detected in one of the parental lines, which was predicted to generate a loss-of-function allele. Transcription analysis revealed that the BrFT2 transcript was not present in the parental line that harbored the mutated allele. RILs carrying only the mutated BrFT2 allele showed delayed flowering regardless of growing seasons when compared to RILs carrying the wild-type BrFT2 allele. These data suggest that BrFT2 is involved in flowering time regulation in controlling flowering time in B. rapa. PMID:26706072

  16. Competition affects gene flow from oilseed rape (female symbol) to Brassica rapa (male symbol).

    PubMed

    Johannessen, M M; Andersen, B A; Jørgensen, R B

    2006-05-01

    Unlike most studies on hybridisation between oilseed rape and Brassica rapa, this study focused on hybridisation with oilseed rape as the maternal parent. This is a key cross because, assuming that plastids are inherited maternally, F(1)-hybrid production with maternal oilseed rape (B. napus) is the only transgene escape route from transplastomic oilseed rape. We investigated such F(1)-hybrid production in winter oilseed rape co-cultivated with weedy B. rapa at three plant densities each with two proportions of the different species. The paternity of the progeny produced on oilseed rape was assessed, and several fitness parameters were determined in oilseed rape mother plants in order to correlate hybridisation and plant competition. At higher density, the vegetative fitness per mother plant decreased significantly, but the density only affected the frequency of F(1)-hybrids significantly (a decrease) in the treatment with equal proportions of each species. As to the proportions, at higher B. napus frequencies, there were fewer F(1)-hybrids per mother plant and a significant increase in most biomass components. Thus, B. rapa was the stronger competitor in its effect on both the vegetative and reproductive fitness in B. napus, and the hybridisation frequency. In conclusion, the relative frequency of the two species was a more influential parameter than the density. Hybridisation with B. napus as the female will be most likely at current field densities of B. napus and when B. rapa is an abundant weed. PMID:16508664

  17. Powdery mildew suppresses herbivore-induced plant volatiles and interferes with parasitoid attraction in Brassica rapa.

    PubMed

    Desurmont, Gaylord A; Xu, Hao; Turlings, Ted C J

    2016-09-01

    The co-occurrence of different antagonists on a plant can greatly affect infochemicals with ecological consequences for higher trophic levels. Here we investigated how the presence of a plant pathogen, the powdery mildew Erysiphe cruciferarum, on Brassica rapa affects (1) plant volatiles emitted in response to damage by a specialist herbivore, Pieris brassicae; (2) the attraction of the parasitic wasp Cotesia glomerata and (3) the performance of P. brassicae and C. glomerata. Plant volatiles were significantly induced by herbivory in both healthy and mildew-infected plants, but were quantitatively 41% lower for mildew-infected plants compared to healthy plants. Parasitoids strongly preferred Pieris-infested plants to dually-infested (Pieris + mildew) plants, and preferred dually infested plants over only mildew-infected plants. The performance of P. brassicae was unaffected by powdery mildew, but C. glomerata cocoon mass was reduced when parasitized caterpillars developed on mildew-infected plants. Thus, avoidance of mildew-infested plants may be adaptive for C. glomerata parasitoids, whereas P. brassicae caterpillars may suffer less parasitism on mildew-infected plants in nature. From a pest management standpoint, the concurrent presence of multiple plant antagonists can affect the efficiency of specific natural enemies, which may in turn have a negative impact on the regulation of pest populations. PMID:27043839

  18. Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

    PubMed Central

    2013-01-01

    Background Brassica rapa includes several important leaf vegetable crops whose production is often damaged by high temperature. Cis-natural antisense transcripts (cis-NATs) and cis-NATs-derived small interfering RNAs (nat-siRNAs) play important roles in plant development and stress responses. However, genome-wide cis-NATs in B. rapa are not known. The NATs and nat-siRNAs that respond to heat stress have never been well studied in B. rapa. Here, we took advantage of RNA-seq and small RNA (sRNA) deep sequencing technology to identify cis-NATs and heat responsive nat-siRNAs in B. rapa. Results Analyses of four RNA sequencing datasets revealed 1031 cis-NATs B. rapa ssp. chinensis cv Wut and B. rapa ssp. pekinensis cv. Bre. Based on sequence homology between Arabidopsis thaliana and B. rapa, 303 conserved cis-NATs in B. rapa were found to correspond to 280 cis-NATs in Arabidopsis; the remaining 728 novel cis-NATs were identified as Brassica-specific ones. Using six sRNA libraries, 4846 nat-siRNAs derived from 150 cis-NATs were detected. Differential expression analysis revealed that nat-siRNAs derived from 12 cis-NATs were responsive to heat stress, and most of them showed strand bias. Real-time PCR indicated that most of the transcripts generating heat-responsive nat-siRNAs were upregulated under heat stress, while the transcripts from the opposite strands of the same loci were downregulated. Conclusions Our results provide the first subsets of genome-wide cis-NATs and heat-responsive nat-siRNAs in B. rapa; these sRNAs are potentially useful for the genetic improvement of heat tolerance in B. rapa and other crops. PMID:24320882

  19. Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication

    PubMed Central

    2009-01-01

    Background Brassica rapa is one of the most economically important vegetable crops worldwide. Owing to its agronomic importance and phylogenetic position, B. rapa provides a crucial reference to understand polyploidy-related crop genome evolution. The high degree of sequence identity and remarkably conserved genome structure between Arabidopsis and Brassica genomes enables comparative tiling sequencing using Arabidopsis sequences as references to select the counterpart regions in B. rapa, which is a strong challenge of structural and comparative crop genomics. Results We assembled 65.8 megabase-pairs of non-redundant euchromatic sequence of B. rapa and compared this sequence to the Arabidopsis genome to investigate chromosomal relationships, macrosynteny blocks, and microsynteny within blocks. The triplicated B. rapa genome contains only approximately twice the number of genes as in Arabidopsis because of genome shrinkage. Genome comparisons suggest that B. rapa has a distinct organization of ancestral genome blocks as a result of recent whole genome triplication followed by a unique diploidization process. A lack of the most recent whole genome duplication (3R) event in the B. rapa genome, atypical of other Brassica genomes, may account for the emergence of B. rapa from the Brassica progenitor around 8 million years ago. Conclusions This work demonstrates the potential of using comparative tiling sequencing for genome analysis of crop species. Based on a comparative analysis of the B. rapa sequences and the Arabidopsis genome, it appears that polyploidy and chromosomal diploidization are ongoing processes that collectively stabilize the B. rapa genome and facilitate its evolution. PMID:19821981

  20. Shotgun Label-free Proteomic Analysis of Clubroot (Plasmodiophora brassicae) Resistance Conferred by the Gene Rcr1 in Brassica rapa.

    PubMed

    Song, Tao; Chu, Mingguang; Lahlali, Rachid; Yu, Fengqun; Peng, Gary

    2016-01-01

    Clubroot, caused by the plasmodiophorid pathogen Plasmodiophora brassicae, is one of the most serious diseases on Brassica crops worldwide and a major threat to canola production in western Canada. Host resistance is the key strategy for clubroot management on canola. Several clubroot resistance (CR) genes have been identified, but the mechanisms associated with these CR genes are poorly understood. In the current study, a label-free shotgun proteomic approach was used to profile and compare the proteomes of Brassica rapa carrying and not carrying the CR gene Rcr1 in response to P. brassicae infection. A total of 527 differentially accumulated proteins (DAPs) were identified between the resistant (with Rcr1) and susceptible (without Rcr1) samples, and functional annotation of these DAPs indicates that the perception of P. brassicae and activation of defense responses are triggered via an unique signaling pathway distinct from common modes of recognition receptors reported with many other plant-pathogen interactions; this pathway appears to act in a calcium-independent manner through a not-well-defined cascade of mitogen-activated protein kinases and may require the ubiquitin-26S proteasome found to be related to abiotic stresses, especially the cold-stress tolerance in other studies. Both up-regulation of defense-related and down-regulation of pathogenicity-related metabolism was observed in plants carrying Rcr1, and these functions may all contribute to the CR mediated by Rcr1. These results, combined with those of transcriptomic analysis reported earlier, improved our understanding of molecular mechanisms associated with Rcr1 and CR at large, and identified candidate metabolites or pathways related to specific resistance mechanisms. Deploying CR genes with different modes of action may help improve the durability of CR. PMID:27462338

  1. Genomic and transcriptomic alterations following hybridisation and genome doubling in trigenomic allohexaploid Brassica carinata × Brassica rapa.

    PubMed

    Xu, Y; Zhao, Q; Mei, S; Wang, J

    2012-09-01

    Allopolyploidisation is a prominent evolutionary force that involves two major events: interspecific hybridisation and genome doubling. Both events have important functional consequences in shaping the genomic architecture of the neo-allopolyploids. The respective effects of hybridisation and genome doubling upon genomic and transcriptomic changes in Brassica allopolyploids are unresolved. In this study, amplified fragment length polymorphism (AFLP), methylation-sensitive amplification polymorphism (MSAP) and cDNA-AFLP approaches were used to track genetic, epigenetic and transcriptional changes in both allohexaploid Brassica (ArArBcBcCcCc genome) and triploid hybrids (ArBcCc genome). Results from these groups were compared with each other and also to their parents Brassica carinata (BBCC genome) and Brassica rapa (AA genome). Rapid and dramatic genetic, DNA methylation and gene expression changes were detected in the triploid hybrids. During the shift from triploidy to allohexaploidy, some of the hybridisation-induced alterations underwent reversion. Additionally, novel genetic, epigenetic and transcriptional alterations were also detected. The proportions of A-genome-specific DNA methylation and gene expression alterations were significantly greater than those of BC-genome-specific alterations in the triploid hybrids. However, the two parental genomes were equally affected during the ploidy shift. Hemi-CCG methylation changes induced by hybridisation were recovered after genome doubling. Full-CG methylation changes were a more general process initiated in the hybrid and continued after genome doubling. These results indicate that genome doubling could ameliorate genomic and transcriptomic alterations induced by hybridisation and instigate additional alterations in trigenomic Brassica allohexaploids. Moreover, genome doubling also modified hybridisation-induced progenitor genome-biased alterations and epigenetic alteration characteristics. PMID:22309095

  2. Shotgun Label-free Proteomic Analysis of Clubroot (Plasmodiophora brassicae) Resistance Conferred by the Gene Rcr1 in Brassica rapa

    PubMed Central

    Song, Tao; Chu, Mingguang; Lahlali, Rachid; Yu, Fengqun; Peng, Gary

    2016-01-01

    Clubroot, caused by the plasmodiophorid pathogen Plasmodiophora brassicae, is one of the most serious diseases on Brassica crops worldwide and a major threat to canola production in western Canada. Host resistance is the key strategy for clubroot management on canola. Several clubroot resistance (CR) genes have been identified, but the mechanisms associated with these CR genes are poorly understood. In the current study, a label-free shotgun proteomic approach was used to profile and compare the proteomes of Brassica rapa carrying and not carrying the CR gene Rcr1 in response to P. brassicae infection. A total of 527 differentially accumulated proteins (DAPs) were identified between the resistant (with Rcr1) and susceptible (without Rcr1) samples, and functional annotation of these DAPs indicates that the perception of P. brassicae and activation of defense responses are triggered via an unique signaling pathway distinct from common modes of recognition receptors reported with many other plant–pathogen interactions; this pathway appears to act in a calcium-independent manner through a not-well-defined cascade of mitogen-activated protein kinases and may require the ubiquitin-26S proteasome found to be related to abiotic stresses, especially the cold-stress tolerance in other studies. Both up-regulation of defense-related and down-regulation of pathogenicity-related metabolism was observed in plants carrying Rcr1, and these functions may all contribute to the CR mediated by Rcr1. These results, combined with those of transcriptomic analysis reported earlier, improved our understanding of molecular mechanisms associated with Rcr1 and CR at large, and identified candidate metabolites or pathways related to specific resistance mechanisms. Deploying CR genes with different modes of action may help improve the durability of CR. PMID:27462338

  3. Functional analysis and tissue-differential expression of four FAD2 genes in amphidiploid Brassica napus derived from Brassica rapa and Brassica oleracea.

    PubMed

    Lee, Kyeong-Ryeol; In Sohn, Soo; Jung, Jin Hee; Kim, Sun Hee; Roh, Kyung Hee; Kim, Jong-Bum; Suh, Mi Chung; Kim, Hyun Uk

    2013-12-01

    Fatty acid desaturase 2 (FAD2), which resides in the endoplasmic reticulum (ER), plays a crucial role in producing linoleic acid (18:2) through catalyzing the desaturation of oleic acid (18:1) by double bond formation at the delta 12 position. FAD2 catalyzes the first step needed for the production of polyunsaturated fatty acids found in the glycerolipids of cell membranes and the triacylglycerols in seeds. In this study, four FAD2 genes from amphidiploid Brassica napus genome were isolated by PCR amplification, with their enzymatic functions predicted by sequence analysis of the cDNAs. Fatty acid analysis of budding yeast transformed with each of the FAD2 genes showed that whereas BnFAD2-1, BnFAD2-2, and BnFAD2-4 are functional enzymes, and BnFAD2-3 is nonfunctional. The four FAD2 genes of B. napus originated from synthetic hybridization of its diploid progenitors Brassica rapa and Brassica oleracea, each of which has two FAD2 genes identical to those of B. napus. The BnFAD2-3 gene of B. napus, a nonfunctional pseudogene mutated by multiple nucleotide deletions and insertions, was inherited from B. rapa. All BnFAD2 isozymes except BnFAD2-3 localized to the ER. Nonfunctional BnFAD2-3 localized to the nucleus and chloroplasts. Four BnFAD2 genes can be classified on the basis of their expression patterns. PMID:24029080

  4. The δ-cyclin expression at early stages of embryogenesis of Brassica rapa L. under clinorotation

    NASA Astrophysics Data System (ADS)

    Artemenko, O. A.; Popova, A. F.

    We present some results of comparison studying of Brassica embryo development and the δ-cyclin genes expression under slow horizontal clinorotation and in the laboratory control. Some backlog of the δ1-cyclin genes expression at early stages of embryogenesis under clinorotation was revealed in comparison with the laboratory control. The similar level of the δ3-cyclin expression at all stages of embryo formation (from one to nine days) in both variants is shown. Some delays in the rate of Brassica rapa embryo development under clinorotation in comparison with the laboratory control can be a result of decrease of a level and some backlog of the δ1-cyclin expression at early stages of embryogenesis.

  5. The Fate of Arabidopsis thaliana Homeologous CNSs and Their Motifs in the Paleohexaploid Brassica rapa

    PubMed Central

    Subramaniam, Sabarinath; Wang, Xiaowu; Freeling, Michael; Pires, J. Chris

    2013-01-01

    Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana–A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa. Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene, would be unlikely to lose function compared with a more redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, each mechanism of CNS loss was assigned a metric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not matter much to their detectability frequency), whereas those lost by inferred deletion or indels are approximately 75% likely to be nonfunctional. Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72% chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with “deletion” in its description, but base substitutions do cause loss. Similarly, proved-functional G-boxes go undetectable by deletion 82% of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a “deletion machine” in the Brassica lineage. PMID:23493633

  6. Reduction of EPSP synthase in transgenic wild turnip (Brassica rapa) weed via suppression of aroA.

    PubMed

    Kahrizi, Danial

    2014-12-01

    EPSPS is coded with the aroA gene, a key enzyme that catalyzes the penultimate step of shikimate pathway. The current study focuses on the suppression of aroA gene in weedy Brassica rapa. For this purpose B. rapa was transformed with double-stranded RNA interference construct designed to silence aroA gene. This developed in a significant decline in EPSPS (about 72 %) in T0 and T1 plants. In order to study the gene flow, the B. rapa control and B. napus plants were pollinated with T0 B. rapa. Results showed that in the next generation of challenging plants, the pollinated normal B. rapa showed the T1 symptoms and performance. Statistical analysis of data showed that knocking down of aroA will lead to a weakness and decreasing in investigated morphological, physiological and phonological characteristics. Meanwhile pollinated B. napus plant species have been not fertilized by T0 B. rapa. To conclude current result is the first evidence of aroA gene inhibition induces a high decrease in EPSPS protein in B. rapa. Also this result provides a basis for the future investigation in order to controlling B. rapa via molecular approach along with agronomical, biological and chemical methods regarding environmental considerations. PMID:25189653

  7. Comparative genomic in situ hybridization (cGISH) analysis of the genomic relationships among Sinapis arvensis, Brassica rapa and Brassica nigra.

    PubMed

    Mao, Shufang; Han, Yonghua; Wu, Xiaoming; An, Tingting; Tang, Jiali; Shen, Junjun; Li, Zongyun

    2012-06-01

    To further understand the relationships between the SS genome of Sinapis arvensis and the AA, BB genomes in Brassica, genomic DNA of Sinapis arvensis was hybridized to the metaphase chromosomes of Brassica nigra (BB genome), and the metaphase chromosomes and interphase nucleus of Brassica rapa (AA genome) by comparative genomic in situ hybridization (cGISH). As a result, every chromosome of B. nigra had signals along the whole chromosomal length. However, only half of the condensed heterochromatic areas in the interphase nucleus and the chromosomes showed rich signals in Brassica rapa. Interphase nucleus and the metaphase chromosomes of S. arvensis were simultaneously hybridized with digoxigenin-labeled genomic DNA of B. nigra and biotin-labeled genomic DNA of B. rapa. Signals of genomic DNA of B. nigra hybridized throughout the length of all chromosomes and all the condensed heterochromatic areas in the interphase nucleus, except chromosome 4, of which signals were weak in centromeric regions. Signals of the genomic DNA of B. rapa patterned the most areas of ten chromosomes and ten condensed heterochromatic areas, others had less signals. The results showed that the SS genome had homology with AA and BB genomes, but the homology between SS genome and AA genome was clearly lower than that between the SS genome and BB genome. PMID:22804340

  8. Chromosome elimination, addition and introgression in intertribal partial hybrids between Brassica rapa and Isatis indigotica

    PubMed Central

    Tu, Yuqin; Sun, Jian; Ge, Xianhong; Li, Zaiyun

    2009-01-01

    Background and Aims Partial hybrids with female-parent-type phenotypes and chromosome numbers but altered genomic compositions have been reported in wide crosses of several plants. In order to introgress desirable genes from a wild relative, Isatis indigotica (a dye and medicinal plant; 2n = 14), into Brassica crops, intertribal sexual hybridizations were carried out with B. rapa (2n = 20), and the resulting hybrids and their progenies were characterized. Methods Using genomic in situ hybridization (GISH) and amplified fragment length polymorphism (AFLP), chromosomal/genomic components of the hybrids and their progenies were analysed. Key Results Many hybrid plants were obtained from the mature seeds harvested from the B. rapa × I. indigotica cross, and these exhibited different morphological traits. However, the majority of them did not survive and only three plants grew to maturity. These three hybrids showed poor growth and much smaller stature than the two parents, but had some morphological traits and chemical composition of I. indigotica. One plant had 2n = 10, the haploid chromosome number of B. rapa, and was absolutely sterile. The other two plants had 20 and 22 somatic chromosomes and were male sterile but produced seeds following pollinations with B. rapa. All back-cross progenies over several generations maintained a B. rapa-type phenotype and also displayed some variations in morphological characters and fatty acid compositions. They were all 2n = 20 and showed good seed-set. The hybrid with 2n = 22 produced some progeny plants with 2n = 21 and 2n = 22. GISH detected two chromosomes of I. indigotica in the hybrid with 2n = 22 but none in the one with 2n = 20. AFLP bands specific for I. indigotica, novel for two parents or absent in B. rapa, were detected in the two hybrids and their progenies. These progeny plants were novel B. rapa types with an altered genomic constitution or alien additions. Conclusions Complete or partial chromosome elimination and

  9. Influence of microgravity on ultrastructure and storage reserves in seeds of Brassica rapa L

    NASA Technical Reports Server (NTRS)

    Kuang, A.; Xiao, Y.; McClure, G.; Musgrave, M. E.

    2000-01-01

    Successful plant reproduction under spaceflight conditions has been problematic in the past. During a 122 d opportunity on the Mir space station, full life cycles of Brassica rapa L. were completed in microgravity in a series of three experiments in the Svet greenhouse. Ultrastructural and cytochemical analyses of storage reserves in mature dry seeds produced in these experiments were compared with those of seeds produced during a high-fidelity ground control. Additional analyses were performed on developing Brassica embryos, 15 d post pollination, which were produced during a separate experiment on the Shuttle (STS-87). Seeds produced on Mir had less than 20% of the cotyledon cell number found in seeds harvested from the ground control. Cytochemical localization of storage reserves in mature cotyledons showed that starch was retained in the spaceflight material, whereas protein and lipid were the primary storage reserves in ground control seeds. Protein bodies in mature cotyledons produced in space were 44% smaller than those in the ground control seeds. Fifteen days after pollination, cotyledon cells from mature embryos formed in space had large numbers of starch grains, and protein bodies were absent, while in developing ground control seeds at the same stage, protein bodies had already formed and fewer starch grains were evident. These data suggest that both the late stage of seed development and maturation are changed in Brassica by growth in a microgravity environment. While gravity is not absolutely required for any step in the plant life cycle, seed quality in Brassica is compromised by development in microgravity.

  10. Plant Growth and Development: An Outline for a Unit Structured Around the Life Cycle of Rapid-Cycling Brassica Rapa.

    ERIC Educational Resources Information Center

    Becker, Wayne M.

    This outline is intended for use in a unit of 10-12 lectures on plant growth and development at the introductory undergraduate level as part of a course on organismal biology. The series of lecture outlines is structured around the life cycle of rapid-cycling Brassica rapa (RCBr). The unit begins with three introductory lectures on general plant…

  11. A Method to Teach Age-Specific Demography with Field Grown Rapid Cycling "Brassica rapa" (Wisconsin Fast Plants)

    ERIC Educational Resources Information Center

    Kelly, Martin G.; Terrana, Sebastian

    2004-01-01

    In this paper, we demonstrate that rapid cycling "Brassica rapa" (Wisconsin Fast Plants) can be used in inquiry-based, student ecological fieldwork. We are the first to describe age-specific survival for field-grown Fast Plants and identify life history traits associated with individual survival. This experiment can be adapted by educators as a…

  12. SNP diversity within and among Brassica rapa accessions reveals no geographic differentiation.

    PubMed

    Tanhuanpää, P; Erkkilä, M; Tenhola-Roininen, T; Tanskanen, J; Manninen, O

    2016-01-01

    Genetic diversity was studied in a collection of 61 accessions of Brassica rapa, which were mostly oil-type turnip rapes but also included two oil-type subsp. dichotoma and five subsp. trilocularis accessions, as well as three leaf-type subspecies (subsp. japonica, pekinensis, and chinensis) and five turnip cultivars (subsp. rapa). Two-hundred and nine SNP markers, which had been discovered by amplicon resequencing, were used to genotype 893 plants from the B. rapa collection using Illumina BeadXpress. There was great variation in the diversity indices between accessions. With STRUCTURE analysis, the plant collection could be divided into three groups that seemed to correspond to morphotype and flowering habit but not to geography. According to AMOVA analysis, 65% of the variation was due to variation within accessions, 25% among accessions, and 10% among groups. A smaller subset of the plant collection, 12 accessions, was also studied with 5727 GBS-SNPs. Diversity indices obtained with GBS-SNPs correlated well with those obtained with Illumina BeadXpress SNPs. The developed SNP markers have already been used and will be used in future plant breeding programs as well as in mapping and diversity studies. PMID:26694015

  13. The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa.

    PubMed

    Balesdent, Marie-Hélène; Fudal, Isabelle; Ollivier, Bénédicte; Bally, Pascal; Grandaubert, Jonathan; Eber, Frédérique; Chèvre, Anne-Marie; Leflon, Martine; Rouxel, Thierry

    2013-05-01

    Phytopathogenic fungi frequently contain dispensable chromosomes, some of which contribute to host range or pathogenicity. In Leptosphaeria maculans, the stem canker agent of oilseed rape (Brassica napus), the minichromosome was previously suggested to be dispensable, without evidence for any role in pathogenicity. Using genetic and genomic approaches, we investigated the inheritance and molecular determinant of an L. maculans-Brassica rapa incompatible interaction. Single gene control of the resistance was found, while all markers located on the L. maculans minichromosome, absent in the virulent parental isolate, co-segregated with the avirulent phenotype. Only one candidate avirulence gene was identified on the minichromosome, validated by complementation experiments and termed AvrLm11. The minichromosome was frequently lost following meiosis, but the frequency of isolates lacking it remained stable in field populations sampled at a 10-yr time interval, despite a yearly sexual stage in the L. maculans life cycle. This work led to the cloning of a new 'lost in the middle of nowhere' avirulence gene of L. maculans, interacting with a B. rapa resistance gene termed Rlm11 and introgressed into B. napus. It demonstrated the dispensability of the L. maculans minichromosome and suggested that its loss generates a fitness deficit. PMID:23406519

  14. GDSL esterase/lipase genes in Brassica rapa L.: genome-wide identification and expression analysis.

    PubMed

    Dong, Xiangshu; Yi, Hankuil; Han, Ching-Tack; Nou, Ill-Sup; Hur, Yoonkang

    2016-04-01

    GDSL esterase/lipase proteins (GELPs), a very large subfamily of lipolytic enzymes, have been identified in microbes and many plants, but only a few have been characterized with respect to their roles in growth, development, and stress responses. In Brassica crops, as in many other species, genome-wide systematic analysis and functional studies of these genes are still lacking. As a first step to study their function in B. rapa ssp. pekinensis (Chinese cabbage), we comprehensively identified all GELP genes in the genome. We found a total of 121 Brassica rapa GDSL esterase/lipase protein genes (BrGELPs), forming three clades in the phylogenetic analysis (two major and one minor), with an asymmetrical chromosomal distribution. Most BrGELPs possess four strictly conserved residues (Ser-Gly-Asn-His) in four separate conserved regions, along with short conserved and clade-specific blocks, suggesting functional diversification of these proteins. Detailed expression profiling revealed that BrGELPs were expressed in various tissues, including floral organs, implying that BrGELPs play diverse roles in various tissues and during development. Ten percent of BrGELPs were specifically expressed in fertile buds, rather than male-sterile buds, implying their involvement in pollen development. Analyses of EXL6 (extracellular lipase 6) expression and its co-expressed genes in both B. rapa and Arabidopsis, as well as knockdown of this gene in Arabidopsis, revealed that this gene plays an important role in pollen development in both species. The data described in this study will facilitate future investigations of other BrGELP functions. PMID:26423069

  15. High-throughput multiplex cpDNA resequencing clarifies the genetic diversity and genetic relationships among Brassica napus, Brassica rapa and Brassica oleracea.

    PubMed

    Qiao, Jiangwei; Cai, Mengxian; Yan, Guixin; Wang, Nian; Li, Feng; Chen, Binyun; Gao, Guizhen; Xu, Kun; Li, Jun; Wu, Xiaoming

    2016-01-01

    Brassica napus (rapeseed) is a recent allotetraploid plant and the second most important oilseed crop worldwide. The origin of B. napus and the genetic relationships with its diploid ancestor species remain largely unresolved. Here, chloroplast DNA (cpDNA) from 488 B. napus accessions of global origin, 139 B. rapa accessions and 49 B. oleracea accessions were populationally resequenced using Illumina Solexa sequencing technologies. The intraspecific cpDNA variants and their allelic frequencies were called genomewide and further validated via EcoTILLING analyses of the rpo region. The cpDNA of the current global B. napus population comprises more than 400 variants (SNPs and short InDels) and maintains one predominant haplotype (Bncp1). Whole-genome resequencing of the cpDNA of Bncp1 haplotype eliminated its direct inheritance from any accession of the B. rapa or B. oleracea species. The distribution of the polymorphism information content (PIC) values for each variant demonstrated that B. napus has much lower cpDNA diversity than B. rapa; however, a vast majority of the wild and cultivated B. oleracea specimens appeared to share one same distinct cpDNA haplotype, in contrast to its wild C-genome relatives. This finding suggests that the cpDNA of the three Brassica species is well differentiated. The predominant B. napus cpDNA haplotype may have originated from uninvestigated relatives or from interactions between cpDNA mutations and natural/artificial selection during speciation and evolution. These exhaustive data on variation in cpDNA would provide fundamental data for research on cpDNA and chloroplasts. PMID:26031705

  16. Mapping of quantitative trait loci for high level of self-incompatibility in Brassica rapa L.

    PubMed

    Hatakeyama, Katsunori; Horisaki, Atsushi; Niikura, Satoshi; Narusaka, Yoshihiro; Abe, Hiroshi; Yoshiaki, Hitoshi; Ishida, Masahiko; Fukuoka, Hiroyuki; Matsumoto, Satoru

    2010-04-01

    The level of self-incompatibility (SI) is important to the purity of F1 seeds produced using the SI system of Brassica vegetables. To analyze the genetic basis of the level of SI, we generated an F2 population derived from a cross between a turnip inbred line showing a high level of SI and a Chinese cabbage inbred line showing a low level, and evaluated the level of SI under insect pollination in two years. We constructed a detailed linkage map of Brassica rapa from the F2 progeny, consisting of SSR, SNP, indel, and CAPS loci segregating into 10 linkage groups covering approximately 700 cM. Five quantitative trait loci (QTL) for high-level SI were identified. The phenotypic variation explained by the QTL ranged between 7.2% and 23.8%. Two QTL were detected in both years. Mapping of SI-related genes revealed that these QTL were co-localized with SLG on R07 and MLPK on R03. This is the first report of QTL for high-level SI evaluated under insect pollination in a Brassica vegetable. Our results could be useful for the marker-assisted selection of parental lines with a stable SI. PMID:20616857

  17. Teaching Human Genetics with Mustard: Rapid Cycling "Brassica rapa" (Fast Plants Type) as a Model for Human Genetics in the Classroom Laboratory

    ERIC Educational Resources Information Center

    Wendell, Douglas L.; Pickard, Dawn

    2007-01-01

    We have developed experiments and materials to model human genetics using rapid cycling "Brassica rapa", also known as Fast Plants. Because of their self-incompatibility for pollination and the genetic diversity within strains, "B. rapa" can serve as a relevant model for human genetics in teaching laboratory experiments. The experiment presented…

  18. Patterns of evolutionary conservation of ascorbic acid-related genes following whole-genome triplication in Brassica rapa.

    PubMed

    Duan, Weike; Song, Xiaoming; Liu, Tongkun; Huang, Zhinan; Ren, Jun; Hou, Xilin; Du, Jianchang; Li, Ying

    2015-01-01

    Ascorbic acid (AsA) is an important antioxidant in plants and an essential vitamin for humans. Extending the study of AsA-related genes from Arabidopsis thaliana to Brassica rapa could shed light on the evolution of AsA in plants and inform crop breeding. In this study, we conducted whole-genome annotation, molecular-evolution and gene-expression analyses of all known AsA-related genes in B. rapa. The nucleobase-ascorbate transporter (NAT) gene family and AsA l-galactose pathway genes were also compared among plant species. Four important insights gained are that: 1) 102 AsA-related gene were identified in B. rapa and they mainly diverged 12-18 Ma accompanied by the Brassica-specific genome triplication event; 2) during their evolution, these AsA-related genes were preferentially retained, consistent with the gene dosage hypothesis; 3) the putative proteins were highly conserved, but their expression patterns varied; and 4) although the number of AsA-related genes is higher in B. rapa than in A. thaliana, the AsA contents and the numbers of expressed genes in leaves of both species are similar, the genes that are not generally expressed may serve as substitutes during emergencies. In summary, this study provides genome-wide insights into evolutionary history and mechanisms of AsA-related genes following whole-genome triplication in B. rapa. PMID:25552535

  19. Genome-Wide Comparative Analysis of 20 Miniature Inverted-Repeat Transposable Element Families in Brassica rapa and B. oleracea

    PubMed Central

    Sampath, Perumal; Murukarthick, Jayakodi; Izzah, Nur Kholilatul; Lee, Jonghoon; Choi, Hong-Il; Shirasawa, Kenta; Choi, Beom-Soon; Liu, Shengyi; Nou, Ill-Sup; Yang, Tae-Jin

    2014-01-01

    Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion. PMID:24747717

  20. Genome-wide comparative analysis of 20 miniature inverted-repeat transposable element families in Brassica rapa and B. oleracea.

    PubMed

    Sampath, Perumal; Murukarthick, Jayakodi; Izzah, Nur Kholilatul; Lee, Jonghoon; Choi, Hong-Il; Shirasawa, Kenta; Choi, Beom-Soon; Liu, Shengyi; Nou, Ill-Sup; Yang, Tae-Jin

    2014-01-01

    Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion. PMID:24747717

  1. Genetic control of immunity to Turnip mosaic virus (TuMV) pathotype 1 in Brassica rapa (Chinese cabbage).

    PubMed

    Lydiate, Derek J; Pilcher, Rachel L Rusholme; Higgins, Erin E; Walsh, John A

    2014-08-01

    Turnip mosaic virus (TuMV) is the major virus infecting crops of the genus Brassica worldwide. A dominant resistance gene, TuRB01b, that confers immunity to the virus isolate UK 1 (a representative pathotype 1 isolate of TuMV) on Brassica rapa was identified in the Chinese cabbage cultivar Tropical Delight. The TuRB01b locus was mapped to a 2.9-cM interval on B. rapa chromosome 6 (A6) that was flanked by RFLP markers pN101e1 and pW137e1. This mapping used a first backcross (B(1)) population segregating for the resistance gene at TuRB01b and sets of RFLP markers employed in previous mapping experiments in Brassica. Virus-plant interaction phenotypes were assayed in inbred progeny derived from B(1) individuals to allow different virus isolates to be tested. Comparative mapping confirmed that A6 of B. rapa was equivalent to chromosome 6 of Brassica napus (A6) and that the map position of TuRB01b in B. rapa could be identical to that of TuRB01 in B. napus. Detailed evaluation of plant-virus interactions showed that TuRB01 and TuRB01b had indistinguishable specificities to a range of TuMV isolates. The possibility that TuRB01 and TuRB01b represent similar or identical alleles at the same A genome resistance locus suggests that B. napus acquired TuRB01 from the B. rapa gene pool. PMID:25275757

  2. Influence of microgravity on ultrastructure and storage reserves in seeds of Brassica rapa L.

    PubMed

    Kuang, A; Xiao, Y; McClure, G; Musgrave, M E

    2000-06-01

    Successful plant reproduction under spaceflight conditions has been problematic in the past. During a 122 d opportunity on the Mir space station, full life cycles of Brassica rapa L. were completed in microgravity in a series of three experiments in the Svet greenhouse. Ultrastructural and cytochemical analyses of storage reserves in mature dry seeds produced in these experiments were compared with those of seeds produced during a high-fidelity ground control. Additional analyses were performed on developing Brassica embryos, 15 d post pollination, which were produced during a separate experiment on the Shuttle (STS-87). Seeds produced on Mir had less than 20% of the cotyledon cell number found in seeds harvested from the ground control. Cytochemical localization of storage reserves in mature cotyledons showed that starch was retained in the spaceflight material, whereas protein and lipid were the primary storage reserves in ground control seeds. Protein bodies in mature cotyledons produced in space were 44% smaller than those in the ground control seeds. Fifteen days after pollination, cotyledon cells from mature embryos formed in space had large numbers of starch grains, and protein bodies were absent, while in developing ground control seeds at the same stage, protein bodies had already formed and fewer starch grains were evident. These data suggest that both the late stage of seed development and maturation are changed in Brassica by growth in a microgravity environment. While gravity is not absolutely required for any step in the plant life cycle, seed quality in Brassica is compromised by development in microgravity. PMID:11543312

  3. Antioxidant capacities and polyphenolics of Chinese cabbage (Brassica rapa L. ssp. Pekinensis) leaves.

    PubMed

    Seong, Gi-Un; Hwang, In-Wook; Chung, Shin-Kyo

    2016-05-15

    Chinese cabbage (Brassica rapa L. ssp. Pekinensis) is a green leafy vegetable used mainly in kimchi, salted and fermented dishes. Consumer preference for the leaf portion differs according to the type of dishes. In this study, Chinese cabbage was divided into three parts, and their antioxidant activities were investigated through in vitro assays. The total phenolic contents (TPC), total flavonoid contents (TFC), and vitamin C contents were also determined as indicators of antioxidant contents. The phenolic acids and flavonoids were separated and identified using high performance liquid chromatography (HPLC) and liquid chromatography/mass spectrometry (LC/MS). The outer leaf had the strongest antioxidant activity with the maximum antioxidant contents, followed by the mid- and inner leaves. Principal component analysis (PCA) revealed that outer leaf is positively related to caffeic acid, p-coumaric acid, ferulic acid, and myricetin contents, whereas the mid- and inner leaves are negatively related to sinapic acid contents. PMID:26776015

  4. Herbaspirillum sp. strain GW103 alleviates salt stress in Brassica rapa L. ssp. pekinensis.

    PubMed

    Lee, Gun Woong; Lee, Kui-Jae; Chae, Jong-Chan

    2016-05-01

    Mutual interactions between plant and rhizosphere bacteria facilitate plant growth and reduce risks of biotic and abiotic stresses. The present study demonstrates alleviation of salt stress in Brassica rapa L. ssp. perkinensis (Chinese cabbage) by Herbaspirillum sp. strain GW103 isolated from rhizosphere soil of Phragmites australis. The strain was capable of producing plant beneficial factors, such as auxin, siderophore, and 1-aminocylopropane-1-carboxylic acid deaminase. Treatment of strain GW103 on Chinese cabbage under salt stress increased K(+)/Na(+) ratio in roots generating balance in the ratio of ion homeostasis and consequently contributed to the increase of biomass. In addition, root colonization potential of the strain was observed by green fluorescent protein (GFP)-tagging approach. These results strongly suggest the beneficial impact of strain GW103 by inducing the alleviation of salt stress and development of stress tolerance in Chinese cabbage via plant-microbe interaction. PMID:26358119

  5. Transcriptome Analysis of Brassica rapa Near-Isogenic Lines Carrying Clubroot-Resistant and -Susceptible Alleles in Response to Plasmodiophora brassicae during Early Infection.

    PubMed

    Chen, Jingjing; Pang, Wenxing; Chen, Bing; Zhang, Chunyu; Piao, Zhongyun

    2015-01-01

    Although Plasmodiophora brassicae is one of the most common pathogens worldwide, the causal agent of clubroot disease in Brassica crops, resistance mechanisms to it are still only poorly understood. To study the early defense response induced by P. brassicae infection, a global transcriptome profiling of the roots of two near-isogenic lines (NILs) of clubroot-resistant (CR BJN3-2) and clubroot-susceptible (BJN3-2) Chinese cabbage (Brassica rapa) was performed by RNA-seq. Among the 42,730 unique genes mapped to the reference genome of B. rapa, 1875, and 2103 genes were found to be up- and down-regulated between CR BJN3-2 and BJN3-2, respectively, at 0, 12, 72, and 96 h after inoculation (hai). Functional annotation showed that most of the differently expressed genes are involved in metabolism, transport, signal transduction, and defense. Of the genes assigned to plant-pathogen interactions, 151 showed different expression patterns between two NILs, including genes associated with pathogen-associated molecular patterns (PAMPs) and effectors recognition, calcium ion influx, hormone signaling, pathogenesis-related (PR) genes, transcription factors, and cell wall modification. In particular, the expression level of effector receptors (resistance proteins), PR genes involved in salicylic acid (SA) signaling pathway, were higher in clubroot-resistant NIL, while half of the PAMP receptors were suppressed in CR BJN3-2. This suggests that there was a more robust effector-triggered immunity (ETI) response in CR BJN3-2 and that SA signaling was important to clubroot resistance. The dataset generated by our transcriptome profiling may prove invaluable for further exploration of the different responses to P. brassicae between clubroot-resistant and clubroot-susceptible genotypes, and it will strongly contribute to a better understanding of the molecular mechanisms of resistance genes of B. rapa against P. brassicae infection. PMID:26779217

  6. Transcriptome Analysis of Brassica rapa Near-Isogenic Lines Carrying Clubroot-Resistant and –Susceptible Alleles in Response to Plasmodiophora brassicae during Early Infection

    PubMed Central

    Chen, Jingjing; Pang, Wenxing; Chen, Bing; Zhang, Chunyu; Piao, Zhongyun

    2016-01-01

    Although Plasmodiophora brassicae is one of the most common pathogens worldwide, the causal agent of clubroot disease in Brassica crops, resistance mechanisms to it are still only poorly understood. To study the early defense response induced by P. brassicae infection, a global transcriptome profiling of the roots of two near-isogenic lines (NILs) of clubroot-resistant (CR BJN3-2) and clubroot-susceptible (BJN3-2) Chinese cabbage (Brassica rapa) was performed by RNA-seq. Among the 42,730 unique genes mapped to the reference genome of B. rapa, 1875, and 2103 genes were found to be up- and down-regulated between CR BJN3-2 and BJN3-2, respectively, at 0, 12, 72, and 96 h after inoculation (hai). Functional annotation showed that most of the differently expressed genes are involved in metabolism, transport, signal transduction, and defense. Of the genes assigned to plant-pathogen interactions, 151 showed different expression patterns between two NILs, including genes associated with pathogen-associated molecular patterns (PAMPs) and effectors recognition, calcium ion influx, hormone signaling, pathogenesis-related (PR) genes, transcription factors, and cell wall modification. In particular, the expression level of effector receptors (resistance proteins), PR genes involved in salicylic acid (SA) signaling pathway, were higher in clubroot-resistant NIL, while half of the PAMP receptors were suppressed in CR BJN3-2. This suggests that there was a more robust effector-triggered immunity (ETI) response in CR BJN3-2 and that SA signaling was important to clubroot resistance. The dataset generated by our transcriptome profiling may prove invaluable for further exploration of the different responses to P. brassicae between clubroot-resistant and clubroot-susceptible genotypes, and it will strongly contribute to a better understanding of the molecular mechanisms of resistance genes of B. rapa against P. brassicae infection. PMID:26779217

  7. Ascorbic acid accumulates as a defense response to Turnip mosaic virus in resistant Brassica rapa cultivars.

    PubMed

    Fujiwara, Ayaka; Togawa, Satoko; Hikawa, Takahiro; Matsuura, Hideyuki; Masuta, Chikara; Inukai, Tsuyoshi

    2016-07-01

    We initially observed that Brassica rapa cultivars containing the Turnip mosaic virus (TuMV) resistance gene, Rnt1-1, accumulated a high level of endogenous ascorbic acid (AS) and dehydroascobic acid (DHA) when infected with TuMV. We here hypothesized a possible contribution of an elevated level of AS+DHA (TAA) to the Rnt1-1-mediated resistance, and conducted a series of experiments using B. rapa and Arabidopsis plants. The application of l-galactose (the key substrate in AS synthesis) to a susceptible cultivar could increase the TAA level ~2-fold, and simultaneously lead to some degree of enhanced viral resistance. To confirm some positive correlation between TAA levels and viral resistance, we analyzed two Arabidopsis knockout mutants (ao and vtc1) in the AS pathways; the TAA levels were significantly increased and decreased in ao and vtc1 plants, respectively. While the ao plants showed enhanced resistance to TuMV, vtc1 plants were more susceptible than the control, supporting our hypothesis. When we analyzed the expression profiles of the genes involved in the AS pathways upon TuMV infection, we found that the observed TAA increase was mainly brought about by the reduction of AS oxidation and activation of AS recycling. We then investigated the secondary signals that regulate endogenous TAA levels in response to viral infection, and found that jasmonic acid (JA) might play an important role in TAA accumulation. In conclusion, we reason that the elevated TAA accumulation in B. rapa plants would be at least partly mediated by the JA-dependent signaling pathway and may significantly contribute to viral resistance. PMID:27255930

  8. Genome-wide characterization of the CBF/DREB1 gene family in Brassica rapa.

    PubMed

    Lee, Sang-Choon; Lim, Myung-Ho; Yu, Jae-Gyeong; Park, Beom-Seok; Yang, Tae-Jin

    2012-12-01

    The C-repeat/dehydration-responsive element binding transcription factors (CBF/DREBs) are important proteins in involved in responses to abiotic stress in plants. We identified ten BrDREB1 genes belonging to the CBF/DREB1 gene family in the Brassica rapa whole genome sequence, whereas six genes are found in the Arabidopsis thaliana genome. The deduced amino acid sequences of the B. rapa genes showed conserved motifs shared with other known plant CBF/DREB1s. Comparative analysis revealed that nine of the BrDREB1 genes were derived from the recent genome triplication in the tribe Brassiceae and the other one was translocated. The nine genes were located in seven of the 12 macrosyntenic blocks that are triplicated counterparts of four Arabidopsis macrosyntenic blocks harboring six CBF/DREB1 genes: one gene on each of three blocks and three tandemly arrayed genes on another block. We inspected the expression patterns of eight BrDREB1 genes by RT-PCR and microarray database searches. All eight genes were highly up-regulated during cold (4 °C) treatment, and some of them were also responsive to salt (250 mM NaCl), drought (air drying), and ABA (100 μM) treatment. Microarray data for plant developmental stages revealed that BrDREB1C2 was highly expressed during a period of cold treatment for vernalization, similar to abiotic stress-inducible genes homologous to Bn28a, Bn47, Bn115, and BoRS1, but almost opposite of BrFLC genes. Taken together, the number of BrDREB1 genes increased to 10 by genome triplication and reorganization, providing additional functions in B. rapa abiotic stress responses and development, as distinct from their Arabidopsis homologs. PMID:23148914

  9. Isolation and functional characterisation of the genes encoding Δ(8)-sphingolipid desaturase from Brassica rapa.

    PubMed

    Li, Shu-Fen; Song, Li-Ying; Yin, Wei-Bo; Chen, Yu-Hong; Chen, Liang; Li, Ji-Lin; Wang, Richard R-C; Hu, Zan-Min

    2012-01-01

    Δ(8)-Sphingolipid desaturase is the key enzyme that catalyses desaturation at the C8 position of the long-chain base of sphingolipids in higher plants. There have been no previous studies on the genes encoding Δ(8)-sphingolipid desaturases in Brassica rapa. In this study, four genes encoding Δ(8)-sphingolipid desaturases from B. rapa were isolated and characterised. Phylogenetic analyses indicated that these genes could be divided into two groups: BrD8A, BrD8C and BrD8D in group I, and BrD8B in group II. The two groups of genes diverged before the separation of Arabidopsis and Brassica. Though the four genes shared a high sequence similarity, and their coding desaturases all located in endoplasmic reticulum, they exhibited distinct expression patterns. Heterologous expression in Saccharomyces cerevisiae revealed that BrD8A/B/C/D were functionally diverse Δ(8)-sphingolipid desaturases that catalyse different ratios of the two products 8(Z)- and 8(E)-C18-phytosphingenine. The aluminium tolerance of transgenic yeasts expressing BrD8A/B/C/D was enhanced compared with that of control cells. Expression of BrD8A in Arabidopsis changed the ratio of 8(Z):8(E)-C18-phytosphingenine in transgenic plants. The information reported here provides new insights into the biochemical functional diversity and evolutionary relationship of Δ(8)-sphingolipid desaturase in plants and lays a foundation for further investigation of the mechanism of 8(Z)- and 8(E)-C18-phytosphingenine biosynthesis. PMID:22293117

  10. Molecular characterization of BZR transcription factor family and abiotic stress induced expression profiling in Brassica rapa.

    PubMed

    Saha, Gopal; Park, Jong-In; Jung, Hee-Jeong; Ahmed, Nasar Uddin; Kayum, Md Abdul; Kang, Jong-Goo; Nou, Ill-Sup

    2015-07-01

    BRASSINAZOLE-RESISTANT (BZR) transcription factors (TFs) are primarily well known as positive regulators of Brassinosteroid (BR) signal transduction in different plants. BR is a plant specific steroid hormone, which has multiple stress resistance functions besides various growth regulatory roles. Being an important regulator of the BR synthesis, BZR TFs might have stress resistance related activities. However, no stress resistance related functional study of BZR TFs has been reported in any crop plants so far. Therefore, this study identified 15 BZR TFs of Brassica rapa (BrBZR) from a genome-wide survey and characterized them through sequence analysis and expression profiling against several abiotic stresses. Various systematic in silico analysis of these TFs validated the fundamental properties of BZRs, where a high degree of similarity also observed with recognized BZRs of other plant species from the comparison studies. In the organ specific expression analyses, 6 BrBZR TFs constitutively expressed in flower developmental stages indicating their flower specific functions. Subsequently, from the stress resistance related expression profiles differential transcript abundance levels were observed by 6 and 11 BrBZRs against salt and drought stresses, respectively. All BrBZRs showed several folds up-regulation against exogenous ABA treatment. All BrBZRs also showed differential expression against low temperature stress treatments and these TFs were proposed as transcriptional activators of CBF cold response pathway of B. rapa. Notably, three BrBZRs gave co-responsive expression against all the stresses tested here, suggesting their multiple stress resistance related functions. Thus, the findings would be helpful in resolving the complex regulatory mechanism of BZRs in stress resistance and further functional genomics study of these potential TFs in different Brassica crops. PMID:25931321

  11. Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa.

    PubMed

    Cheng, Feng; Sun, Chao; Wu, Jian; Schnable, James; Woodhouse, Margaret R; Liang, Jianli; Cai, Chengcheng; Freeling, Michael; Wang, Xiaowu

    2016-07-01

    Subgenome dominance is an important phenomenon observed in allopolyploids after whole genome duplication, in which one subgenome retains more genes as well as contributes more to the higher expressing gene copy of paralogous genes. To dissect the mechanism of subgenome dominance, we systematically investigated the relationships of gene expression, transposable element (TE) distribution and small RNA targeting, relating to the multicopy paralogous genes generated from whole genome triplication in Brassica rapa. The subgenome dominance was found to be regulated by a relatively stable factor established previously, then inherited by and shared among B. rapa varieties. In addition, we found a biased distribution of TEs between flanking regions of paralogous genes. Furthermore, the 24-nt small RNAs target TEs and are negatively correlated to the dominant expression of individual paralogous gene pairs. The biased distribution of TEs among subgenomes and the targeting of 24-nt small RNAs together produce the dominant expression phenomenon at a subgenome scale. Based on these findings, we propose a bucket hypothesis to illustrate subgenome dominance and hybrid vigor. Our findings and hypothesis are valuable for the evolutionary study of polyploids, and may shed light on studies of hybrid vigor, which is common to most species. PMID:26871271

  12. Optimization of extraction, characterization and antioxidant activity of polysaccharides from Brassica rapa L.

    PubMed

    Wang, Wei; Wang, Xiaoqing; Ye, Hong; Hu, Bing; Zhou, Li; Jabbar, Saqib; Zeng, Xiaoxiong; Shen, Wenbiao

    2016-01-01

    The root of Brassica rapa L. has been traditionally used as a Uyghur folk medicine to cure cough and asthma by Uyghur nationality in Xinjiang Uygur Autonomous Region of China. In the present study, therefore, extraction optimization, characterization and antioxidant activity in vitro of polysaccharides from the root of B. rapa L. (BRP) were investigated. The optimal extraction conditions with an extraction yield of 21.48 ± 0.41% for crude BRP were obtained as follows: extraction temperature 93°C, extraction time 4.3h and ratio of extraction solvent (water) to raw material 75 mL/g. The crude BRP was purified by chromatographic columns of DEAE-52 cellulose and Sephadex G-100, affording three purified fractions of BRP-1-1, BRP-2-1 and BRP-2-2 with average molecular weight of 1510, 1110 and 838 kDa, respectively. Monosaccharide composition analysis indicated that BRP-1-1 was composed of mannose, rhamnose, glucose, galactose and arabinose, BRP-2-1 was composed of rhamnose, galacturonic acid, galactose and arabinose, and BRP-2-2 was composed of rhamnose and galacturonic acid in a molar ratio of 1.27: 54.92. Furthermore, the crude BRP exhibited relatively higher antioxidant activity in vitro than purified fractions; hence, it could be used as a natural antioxidant in functional foods or medicines. PMID:26499088

  13. New insights into helitron transposable elements in the mesopolyploid species Brassica rapa.

    PubMed

    Fu, Donghui; Wei, Lijuan; Xiao, Meili; Hayward, Alice

    2013-12-15

    Helitrons are DNA transposable elements that are widely present in the genomes of diverse eukaryotic taxa. Helitrons are distinct from other transposons in their ability to capture gene fragments and their rolling-replication mechanism. Brassica rapa is a mesopolyploid species and one of the most important vegetable and oil crops globally. A total of 787 helitrons were identified in the B. rapa genome and were assigned to 662 families and 700 subfamilies. More than 21,806 repetitive sequences were found within the helitrons, whose G+C content correlated negatively to that of the host helitron. Each helitron contained an average of 2.9 gene fragments and 1.9 intact genes, of which the majority were annotated with binding functions in metabolic processes. In addition, a set of 114 nonredundant microRNAs were detected within 174 helitrons and predicted to regulate a set of 787 nonredundant target genes. These results suggest that helitrons contribute to genomic structural and transcriptional variation by capturing gene fragments and generating microRNAs. PMID:24055723

  14. Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication

    PubMed Central

    Dong, Heng; Liu, Dandan; Han, Tianyu; Zhao, Yuxue; Sun, Ji; Lin, Sue; Cao, Jiashu; Chen, Zhong-Hua; Huang, Li

    2015-01-01

    Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci. PMID:26596461

  15. Dissecting the complex molecular evolution and expression of polygalacturonase gene family in Brassica rapa ssp. chinensis.

    PubMed

    Liang, Ying; Yu, Youjian; Shen, Xiuping; Dong, Heng; Lyu, Meiling; Xu, Liai; Ma, Zhiming; Liu, Tingting; Cao, Jiashu

    2015-12-01

    Polygalacturonases (PGs) participate in pectin disassembly of cell wall and belong to one of the largest hydrolase families in plants. In this study, we identified 99 PG genes in Brassica rapa. Comprehensive analysis of phylogeny, gene structures, physico-chemical properties and coding sequence evolution demonstrated that plant PGs should be classified into seven divergent clades and each clade's members had specific sequence and structure characteristics, and/or were under specific selection pressures. Genomic distribution and retention rate analysis implied duplication events and biased retention contributed to PG family's expansion. Promoter divergence analysis using "shared motif method" revealed a significant correlation between regulatory and coding sequence evolution of PGs, and proved Clades A and E were of ancient origin. Quantitative real-time PCR analysis showed that expression patterns of PGs displayed group specificities in B. rapa. Particularly, nearly half of PG family members, especially those of Clades C, D and F, closely relates to reproductive development. Most duplicates showed similar expression profiles, suggesting dosage constraints accounted for preservation after duplication. Promoter-GUS assay further indicated PGs' extensive roles and possible redundancy during reproductive development. This work can provide a scientific classification of plant PGs, dissect the internal relationships between their evolution and expressions, and promote functional researches. PMID:26506823

  16. Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication.

    PubMed

    Dong, Heng; Liu, Dandan; Han, Tianyu; Zhao, Yuxue; Sun, Ji; Lin, Sue; Cao, Jiashu; Chen, Zhong-Hua; Huang, Li

    2015-01-01

    Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci. PMID:26596461

  17. The Endogenous Nitric Oxide Mediates Selenium-Induced Phytotoxicity by Promoting ROS Generation in Brassica rapa

    PubMed Central

    Hu, Liang-Bin; Li, You-Qin; Chen, Jian; Yang, Li-Fei

    2014-01-01

    Selenium (Se) is suggested as an emerging pollutant in agricultural environment because of the increasing anthropogenic release of Se, which in turn results in phytotoxicity. The most common consequence of Se-induced toxicity in plants is oxidative injury, but how Se induces reactive oxygen species (ROS) burst remains unclear. In this work, histofluorescent staining was applied to monitor the dynamics of ROS and nitric oxide (NO) in the root of Brassica rapa under Se(IV) stress. Se(IV)-induced faster accumulation of NO than ROS. Both NO and ROS accumulation were positively correlated with Se(IV)-induced inhibition of root growth. The NO accumulation was nitrate reductase (NR)- and nitric oxide synthase (NOS)-dependent while ROS accumulation was NADPH oxidase-dependent. The removal of NO by NR inhibitor, NOS inhibitor, and NO scavenger could alleviate Se(IV)-induced expression of Br_Rbohs coding for NADPH oxidase and the following ROS accumulation in roots, which further resulted in the amelioration of Se(IV)-induced oxidative injury and growth inhibition. Thus, we proposed that the endogenous NO played a toxic role in B. rapa under Se(IV) stress by triggering ROS burst. Such findings can be used to evaluate the toxic effects of Se contamination on crop plants. PMID:25333984

  18. Increased susceptibility to fungal disease accompanies adaptation to drought in Brassica rapa.

    PubMed

    O'Hara, Niamh B; Rest, Joshua S; Franks, Steven J

    2016-01-01

    Recent studies have demonstrated adaptive evolutionary responses to climate change, but little is known about how these responses may influence ecological interactions with other organisms, including natural enemies. We used a resurrection experiment in the greenhouse to examine the effect of evolutionary responses to drought on the susceptibility of Brassica rapa plants to a fungal pathogen, Alternaria brassicae. In agreement with previous studies in this population, we found an evolutionary shift to earlier flowering postdrought, which was previously shown to be adaptive. Here, we report the novel finding that postdrought descendant plants were also more susceptible to disease, indicating a rapid evolutionary shift to increased susceptibility. This was accompanied by an evolutionary shift to increased specific leaf area (thinner leaves) following drought. We found that flowering time and disease susceptibility displayed plastic responses to experimental drought treatments, but that this plasticity did not match the direction of evolution, indicating that plastic and evolutionary responses to changes in climate can be opposed. The observed evolutionary shift to increased disease susceptibility accompanying adaptation to drought provides evidence that even if populations can rapidly adapt in response to climate change, evolution in other traits may have ecological effects that could make species more vulnerable. PMID:26648585

  19. Gravity independence of seed-to-seed cycling in Brassica rapa

    NASA Technical Reports Server (NTRS)

    Musgrave, M. E.; Kuang, A.; Xiao, Y.; Stout, S. C.; Bingham, G. E.; Briarty, L. G.; Levenskikh, M. A.; Sychev, V. N.; Podolski, I. G.

    2000-01-01

    Growth of higher plants in the microgravity environment of orbital platforms has been problematic. Plants typically developed more slowly in space and often failed at the reproductive phase. Short-duration experiments on the Space Shuttle showed that early stages in the reproductive process could occur normally in microgravity, so we sought a long-duration opportunity to test gravity's role throughout the complete life cycle. During a 122-d opportunity on the Mir space station, full life cycles were completed in microgravity with Brassica rapa L. in a series of three experiments in the Svet greenhouse. Plant material was preserved in space by chemical fixation, freezing, and drying, and then compared to material preserved in the same way during a high-fidelity ground control. At sampling times 13 d after planting, plants on Mir were the same size and had the same number of flower buds as ground control plants. Following hand-pollination of the flowers by the astronaut, siliques formed. In microgravity, siliques ripened basipetally and contained smaller seeds with less than 20% of the cotyledon cells found in the seeds harvested from the ground control. Cytochemical localization of storage reserves in the mature embryos showed that starch was retained in the spaceflight material, whereas protein and lipid were the primary storage reserves in the ground control seeds. While these successful seed-to-seed cycles show that gravity is not absolutely required for any step in the plant life cycle, seed quality in Brassica is compromised by development in microgravity.

  20. Quantitative Trait Locus Analysis of Seed Germination and Seedling Vigor in Brassica rapa Reveals QTL Hotspots and Epistatic Interactions

    PubMed Central

    Basnet, Ram K.; Duwal, Anita; Tiwari, Dev N.; Xiao, Dong; Monakhos, Sokrat; Bucher, Johan; Visser, Richard G. F.; Groot, Steven P. C.; Bonnema, Guusje; Maliepaard, Chris

    2015-01-01

    The genetic basis of seed germination and seedling vigor is largely unknown in Brassica species. We performed a study to evaluate the genetic basis of these important traits in a B. rapa doubled haploid population from a cross of a yellow-seeded oil-type yellow sarson and a black-seeded vegetable-type pak choi. We identified 26 QTL regions across all 10 linkage groups for traits related to seed weight, seed germination and seedling vigor under non-stress and salt stress conditions illustrating the polygenic nature of these traits. QTLs for multiple traits co-localized and we identified eight hotspots for quantitative trait loci (QTL) of seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 mapped at the B. rapa Flowering Locus C (BrFLC2). Another hotspot on A05 with salt stress specific QTLs co-located with the B. rapa Fatty acid desaturase 2 (BrFAD2) locus. Epistatic interactions were observed between QTL hotspots for seed germination on A02 and A10 and with a salt tolerance QTL on A05. These results contribute to the understanding of the genetics of seed quality and seeding vigor in B. rapa and can offer tools for Brassica breeding. PMID:26648948

  1. Characterization of dihydroflavonol 4-reductase (DFR) genes and their association with cold and freezing stress in Brassica rapa.

    PubMed

    Ahmed, Nasar Uddin; Park, Jong-In; Jung, Hee-Jeong; Yang, Tae-Jin; Hur, Yoonkang; Nou, Ill-Sup

    2014-10-15

    Flavonoids including anthocyanins provide flower and leaf colors, as well as other derivatives that play diverse roles in plant development and interactions with the environment. Dihydroflavonol 4-reductase (DFR) is part of an important step in the flavonoid biosynthetic pathway of anthocyanins. This study characterized 12 DFR genes of Brassica rapa and investigated their association with anthocyanin coloration, as well as cold and freezing stress in several genotypes of B. rapa. Comparison of sequences of these genes with DFR gene sequences from other species revealed a high degree of homology. Constitutive expression of the genes in several pigmented and non-pigmented lines of B. rapa demonstrated correlation with anthocyanin accumulation for BrDFR8 and 9. Conversely, BrDFR2, 4, 8 and 9 only showed very high responses to cold stress in pigmented B. rapa samples. BrDFR1, 3, 5, 6 and 10 responded to cold and freezing stress treatments, regardless of pigmentation. BrDFRs were also shown to be regulated by two transcription factors, BrMYB2-2 and BrTT8, contrasting with anthocyanin accumulation and cold and freezing stress. Thus, the above results suggest that these genes are associated with anthocyanin biosynthesis and cold and freezing stress tolerance and might be useful resources for development of cold and/or freezing stress resistant Brassica crops with desirable colors as well. These findings may also facilitate exploration of the molecular mechanism that regulates anthocyanin biosynthesis and its response to abiotic stresses. PMID:25108127

  2. Application of in vitro pollination of opened ovaries to obtain Brassica oleracea L. × B. rapa L. hybrids.

    PubMed

    Sosnowska, Katarzyna; Cegielska-Taras, Teresa

    2014-01-01

    This study presents the results of experiments concerning: (1) interspecific hybridization of Brassica oleracea × Brassica rapa via application of in vitro placental pollination and (2) embryological analysis of the process of resynthesis of Brassica napus. In order to overcome certain stigma/style barriers, B. rapa pollen was placed in vitro on an opened B. oleracea ovary (with style removed). Pollinated ovaries were cultured on Murashige and Skoog (MS) medium. After 24-d culture, the developing embryos were isolated from immature seeds and transferred onto MS medium supplemented with 0.47 μM kinetin, 0.49 μM 1-naphthaleneacetic acid, and 10% (v/v) coconut water. When the embryos had turned green, they were immediately placed onto MS medium with 100 μM kinetin. After development of the seedling, plantlets were transferred to soil. Chromosome doubling was achieved after another week. Cytometric analysis of nuclear DNA confirmed the hybrid nature of the plants. Resynthesis of B. napus can be performed through interspecific hybridization of B. oleracea × B. rapa followed by embryo rescue and genome doubling. PMID:24719550

  3. Brassica rapa plants adapted to microgravity with reduced photosystem I and its photochemical activity

    NASA Technical Reports Server (NTRS)

    Jiao, Shunxing; Hilaire, Emmanuel; Paulsen, Avelina Q.; Guikema, James A.

    2004-01-01

    The photosynthetic apparatus contains several protein complexes, many of which are regulated by environmental conditions. In this study, the influences of microgravity on PSI and PSII in Brassica rapa plants grown aboard the space shuttle were examined. We found that Brassica plants grown in space had a normal level of growth relative to controls under similar conditions on Earth. Upon return to Earth, cotyledons were harvested and thylakoid membranes were isolated. Analysis of chlorophyll contents showed that the Chl a/b ratio (3.5) in flight cotyledons was much higher than a ratio of 2.42 in the ground controls. The flight samples also had a reduction of PSI complexes and a corresponding 30% decrease of PSI photochemical activity. Immunoblotting showed that the reaction centre polypeptides of PSI were more apparently decreased (e.g. by 24-33% for PsaA and PsaB, and 57% for PsaC) than the light-harvesting complexes. In comparison, the accumulation of PSII complex was less affected in microgravity, thus only a slight reduction in D1, D2 and LHCII was observed in protein blots. However, there was a 32% decrease of OEC1 in the flight samples, indicating a defective OEC subcomplex. In addition, an average 54% increase of the 54 kDa CF1-beta isoform was found in the flight samples, suggesting that space-grown plants suffered from certain stresses, consistent with implications of the increased Chl a/b ratio. Taken together, the results demonstrated that Brassica plants can adapt to spaceflight microgravity, but with significant alterations in chloroplast structures and photosynthetic complexes, and especially reduction of PSI and its activity.

  4. Construction of genetic linkage map and mapping of QTL for seed color in Brassica rapa.

    PubMed

    Kebede, Berisso; Cheema, Kuljit; Greenshields, David L; Li, Changxi; Selvaraj, Gopalan; Rahman, Habibur

    2012-12-01

    A genetic linkage map of Brassica rapa L. was constructed using recombinant inbred lines (RILs) derived from a cross between yellow-seeded cultivar Sampad and a yellowish brown seeded inbred line 3-0026.027. The RILs were evaluated for seed color under three conditions: field plot, greenhouse, and controlled growth chambers. Variation for seed color in the RILs ranged from yellow, like yellow sarson, to dark brown/black even though neither parent had shown brown/black colored seeds. One major QTL (SCA9-2) and one minor QTL (SCA9-1) on linkage group (LG) A9 and two minor QTL (SCA3-1, SCA5-1) on LG A3 and LG A5, respectively, were detected. These collectively explained about 67% of the total phenotypic variance. SCA9-2 mapped in the middle of LG A9, explained about 55% phenotypic variance, and consistently expressed in all environments. The second QTL on LG A9 was ~70 cM away from SCA9-2, suggesting that independent assortment of these QTLs is possible. A digenic epistatic interaction was found between the two main effect QTL on LG A9; and the epistasis × environment interaction was nonsignificant, suggesting stability of the interaction across the environments. The QTL effect on LG A9 was validated using simple sequence repeat (SSR) markers from the two QTL regions of this LG on a B(1)S(1) population (F(1) backcrossed to Sampad followed by self-pollination) segregating for brown and yellow seed color, and on their self-pollinated progenies (B(1)S(2)). The SSR markers from the QTL region SCA9-2 showed a stronger linkage association with seed color as compared with the marker from SCA9-1. This suggests that the QTL SCA9-2 is the major determinant of seed color in the A genome of B. rapa. PMID:23231600

  5. Functional divergence of BAK1 genes from Brassica rapa in regulating plant architecture.

    PubMed

    Zhang, S; Li, C; Li, Q; Wang, Q N; Huang, S H; Zhang, Y F; Wang, X F

    2015-01-01

    BAK1 is a co-receptor of BRI1 in early signaling pathways mediated by brassinosteroids (BRs) and is thought to play a major role in plant growth and development. As the role of BAK1 has not yet been fully elucidated then further research is required to explore its potential for use in genetic modification to improve crops. In this study, three BAK1 genes from the amphidiploid species Brassica rapa were isolated and their kinase functions were predicted following DNA sequence analysis. A bioinformatic analysis revealed that two genes, BrBAK1-1 and BrBAK1-8, shared a conserved kinase domain and 5 tandem leucine-rich repeats (LRRs) that are characteristic of a BAK1 receptor for BR perception, whereas the third gene, BrBAK1-3, was deficient for a signal peptide, but had 4 leucine zippers and 3 leucine-rich repeats (LRRs) in an extracellular domain. All three BrBAK1 kinases localized on the cellular membrane. Ectopic expression of each BrBAK1 gene in BR-insensitive (bri1-5 mutant) Arabidopsis plants indicated that BrBAK1-1 and BrBAK1-8 were functional homologues of AtBAK1 based on the rescue of growth in the bri1-5 mutant. Overexpression of BrBAK1-3 caused a severe dwarf phenotype resembling the phenotype of null BRI1 alleles. The results here suggest there are significant differences among the three BrBAK1 kinases for their effects on plant architecture. This conclusion has important implications for genetic modification of B. rapa. PMID:26600518

  6. Selenium Inhibits Root Elongation by Repressing the Generation of Endogenous Hydrogen Sulfide in Brassica rapa

    PubMed Central

    Zheng, Mei-Yu; Xian, Ming; Qi, Zhong-Qiang; Li, You-Qin; Hu, Liang-Bin; Chen, Jian; Yang, Li-Fei

    2014-01-01

    Selenium (Se) has been becoming an emerging pollutant causing severe phytotoxicity, which the biochemical mechanism is rarely known. Although hydrogen sulfide (H2S) has been suggested as an important exogenous regulator modulating plant physiological adaptions in response to heavy metal stress, whether and how the endogenous H2S regulates Se-induce phytotoxicity remains unclear. In this work, a self-developed specific fluorescent probe (WSP-1) was applied to track endogenous H2S in situ in the roots of Brassica rapa under Se(IV) stress. Se(IV)-induced root growth stunt was closely correlated with the inhibition of endogenous H2S generation in root tips. Se(IV) stress dampened the expression of most LCD and DCD homologues in the roots of B. rapa. By using various specific fluorescent probes for bio-imaging root tips in situ, we found that the increase in endogenous H2S by the application of H2S donor NaHS could significantly alleviate Se(IV)-induced reactive oxygen species (ROS) over-accumulation, oxidative impairment, and cell death in root tips, which further resulted in the recovery of root growth under Se(IV) stress. However, dampening the endogenous H2S could block the alleviated effect of NaHS on Se(IV)-induced phytotoxicity. Finally, the increase in endogenous H2S resulted in the enhancement of glutathione (GSH) in Se(IV)-treated roots, which may share the similar molecular mechanism for the dominant role of H2S in removing ROS by activating GSH biosynthesis in mammals. Altogether, these data provide the first direct evidences confirming the pivotal role of endogenous H2S in modulating Se(IV)-induced phytotoxicity in roots. PMID:25333279

  7. Genome-wide analysis of the MADS-box gene family in Brassica rapa (Chinese cabbage).

    PubMed

    Duan, Weike; Song, Xiaoming; Liu, Tongkun; Huang, Zhinan; Ren, Jun; Hou, Xilin; Li, Ying

    2015-02-01

    The MADS-box gene family is an ancient and well-studied transcription factor family that functions in almost every developmental process in plants. There are a number of reports about the MADS-box family in different plant species, but systematic analysis of the MADS-box transcription factor family in Brassica rapa (Chinese cabbage) is still lacking. In this study, 160 MADS-box transcription factors were identified from the entire Chinese cabbage genome and compared with the MADS-box factors from 21 other representative plant species. A detailed list of MADS proteins from these 22 species was sorted. Phylogenetic analysis of the BrMADS genes, together with their Arabidopsis and rice counterparts, showed that the BrMADS genes were categorised into type I (Mα, Mβ, Mγ) and type II (MIKC(C), MIKC*) groups, and the MIKC(C) proteins were further divided into 13 subfamilies. The Chinese cabbage type II group has 95 members, which is twice as much as the Arabidopsis type II group, indicating that the Chinese cabbage type II genes have been retained more frequently than the type I genes. Finally, RNA-seq transcriptome data and quantitative real-time PCR analysis revealed that BrMADS genes are expressed in a tissue-specific manner similar to Arabidopsis. Interestingly, a number of BrMIKC genes showed responses to different abiotic stress treatments, suggesting a function for some of the genes in these processes as well. Taken together, the characterization of the B. rapa MADS-box family presented here, will certainly help in the selection of appropriate candidate genes and further facilitate functional studies in Chinese cabbage. PMID:25216934

  8. Effects of the veterinary pharmaceutical salinomycin and its formulation on the plant Brassica rapa.

    PubMed

    Furtula, V; Stephenson, G L; Olaveson, K M; Chambers, P A

    2012-11-01

    Veterinary pharmaceuticals are emerging contaminants found throughout the environment, and their presence and effects are a matter of concern. The purpose of this study was to compare the phytotoxicity of salinomycin (pure compound = 96 %) and Sacox 120 (formulated product = 120 g salinomycin/kg) to the plant species Brassica rapa as well as to investigate salinomycin persistence in soil. Calculated EC/IC(50) values for salinomycin and Sacox 120 were 1.10 and 2.88 and 2.19 and 18.03 mg/kg, respectively, based on salinomycin concentration. For exposure of B. rapa to salinomycin, significant adverse effects were observed for growth end points at the greater concentrations. For the reproduction end point (i.e., number of buds), as well as root length and wet mass, significant differences were observed at the lower concentrations (stimulating growth) and adverse effects at the greater concentrations. This study confirmed that the toxic effects of Sacox 120 are attributable to the active ingredient salinomycin. Liquid chromatography-electrospray ionization-mass spectrometry analyses confirmed that exposure concentrations of salinomycin were 90 and 83 % of the nominal concentrations, respectively, in the soils amended with either pure or formulated product. At the end of the experiment, after 14 days, salinomycin concentrations for both tests (salinomycin and Sacox 120) decreased to 6.2 and 5.8 % of the nominal exposure concentrations, respectively. Detected salinomycin concentrations in plant shoots ranged from 3.47 to 41.0 ng/g dry shoot. This study shows the importance of using plants as tools to evaluate environmental risk and as a bridge to relate environment and human health risks. PMID:22961218

  9. Class-Specific Evolution and Transcriptional Differentiation of 14-3-3 Family Members in Mesohexaploid Brassica rapa.

    PubMed

    Chandna, Ruby; Augustine, Rehna; Kanchupati, Praveena; Kumar, Roshan; Kumar, Pawan; Arya, Gulab C; Bisht, Naveen C

    2016-01-01

    14-3-3s are highly conserved, multigene family proteins that have been implicated in modulating various biological processes. The presence of inherent polyploidy and genome complexity has limited the identification and characterization of 14-3-3 proteins from globally important Brassica crops. Through data mining of Brassica rapa, the model Brassica genome, we identified 21 members encoding 14-3-3 proteins namely, BraA.GRF14.a to BraA.GRF14.u. Phylogenetic analysis indicated that B. rapa contains both ε (epsilon) and non-ε 14-3-3 isoforms, having distinct intron-exon structural organization patterns. The non-ε isoforms showed lower divergence rate (Ks < 0.45) compared to ε protein isoforms (Ks > 0.48), suggesting class-specific divergence pattern. Synteny analysis revealed that mesohexaploid B. rapa genome has retained 1-5 orthologs of each Arabidopsis 14-3-3 gene, interspersed across its three fragmented sub-genomes. qRT-PCR analysis showed that 14 of the 21 BraA.GRF14 were expressed, wherein a higher abundance of non-ε transcripts was observed compared to the ε genes, indicating class-specific transcriptional bias. The BraA.GRF14 genes showed distinct expression pattern during plant developmental stages and in response to abiotic stress, phytohormone treatments, and nutrient deprivation conditions. Together, the distinct expression pattern and differential regulation of BraA.GRF14 genes indicated the occurrence of functional divergence of B. rapa 14-3-3 proteins during plant development and stress responses. PMID:26858736

  10. Class-Specific Evolution and Transcriptional Differentiation of 14-3-3 Family Members in Mesohexaploid Brassica rapa

    PubMed Central

    Chandna, Ruby; Augustine, Rehna; Kanchupati, Praveena; Kumar, Roshan; Kumar, Pawan; Arya, Gulab C.; Bisht, Naveen C.

    2016-01-01

    14-3-3s are highly conserved, multigene family proteins that have been implicated in modulating various biological processes. The presence of inherent polyploidy and genome complexity has limited the identification and characterization of 14-3-3 proteins from globally important Brassica crops. Through data mining of Brassica rapa, the model Brassica genome, we identified 21 members encoding 14-3-3 proteins namely, BraA.GRF14.a to BraA.GRF14.u. Phylogenetic analysis indicated that B. rapa contains both ε (epsilon) and non-ε 14-3-3 isoforms, having distinct intron-exon structural organization patterns. The non-ε isoforms showed lower divergence rate (Ks < 0.45) compared to ε protein isoforms (Ks > 0.48), suggesting class-specific divergence pattern. Synteny analysis revealed that mesohexaploid B. rapa genome has retained 1–5 orthologs of each Arabidopsis 14-3-3 gene, interspersed across its three fragmented sub-genomes. qRT-PCR analysis showed that 14 of the 21 BraA.GRF14 were expressed, wherein a higher abundance of non-ε transcripts was observed compared to the ε genes, indicating class-specific transcriptional bias. The BraA.GRF14 genes showed distinct expression pattern during plant developmental stages and in response to abiotic stress, phytohormone treatments, and nutrient deprivation conditions. Together, the distinct expression pattern and differential regulation of BraA.GRF14 genes indicated the occurrence of functional divergence of B. rapa 14-3-3 proteins during plant development and stress responses. PMID:26858736

  11. Gravity independence of seed-to-seed cycling in Brassica rapa.

    PubMed

    Musgrave, M E; Kuang, A; Xiao, Y; Stout, S C; Bingham, G E; Briarty, L G; Levenskikh, M A; Sychev, V N; Podolski, I G

    2000-02-01

    Growth of higher plants in the microgravity environment of orbital platforms has been problematic. Plants typically developed more slowly in space and often failed at the reproductive phase. Short-duration experiments on the Space Shuttle showed that early stages in the reproductive process could occur normally in microgravity, so we sought a long-duration opportunity to test gravity's role throughout the complete life cycle. During a 122-d opportunity on the Mir space station, full life cycles were completed in microgravity with Brassica rapa L. in a series of three experiments in the Svet greenhouse. Plant material was preserved in space by chemical fixation, freezing, and drying, and then compared to material preserved in the same way during a high-fidelity ground control. At sampling times 13 d after planting, plants on Mir were the same size and had the same number of flower buds as ground control plants. Following hand-pollination of the flowers by the astronaut, siliques formed. In microgravity, siliques ripened basipetally and contained smaller seeds with less than 20% of the cotyledon cells found in the seeds harvested from the ground control. Cytochemical localization of storage reserves in the mature embryos showed that starch was retained in the spaceflight material, whereas protein and lipid were the primary storage reserves in the ground control seeds. While these successful seed-to-seed cycles show that gravity is not absolutely required for any step in the plant life cycle, seed quality in Brassica is compromised by development in microgravity. PMID:10750897

  12. Transcriptome Analysis of Interspecific Hybrid between Brassica napus and B. rapa Reveals Heterosis for Oil Rape Improvement

    PubMed Central

    Zhang, Jinfang; Li, Guangrong; Li, Haojie; Pu, Xiaobin; Jiang, Jun; Chai, Liang; Zheng, Benchuan; Cui, Cheng; Yang, Zujun; Zhu, Yongqing; Jiang, Liangcai

    2015-01-01

    The hybrid between Brassica napus and B. rapa displays obvious heterosis in both growth performance and stress tolerances. A comparative transcriptome analysis for B. napus (AnAnCC genome), B. rapa (ArAr genome), and its hybrid F1 (AnArC genome) was carried out to reveal the possible molecular mechanisms of heterosis at the gene expression level. A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes. A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples. The coexistence of nonadditive DEGs including high-parent dominance, low-parent dominance, overdominance, and underdominance was observed in the gene action modes of F1 hybrid, which were potentially related to the heterosis. The coexistence of multiple gene actions in the hybrid was observed and provided a list of candidate genes and pathways for heterosis. The expression bias of transposable element-associated genes was also observed in the hybrid compared to their parents. The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement. PMID:26448924

  13. Transcriptome Analysis of Interspecific Hybrid between Brassica napus and B. rapa Reveals Heterosis for Oil Rape Improvement.

    PubMed

    Zhang, Jinfang; Li, Guangrong; Li, Haojie; Pu, Xiaobin; Jiang, Jun; Chai, Liang; Zheng, Benchuan; Cui, Cheng; Yang, Zujun; Zhu, Yongqing; Jiang, Liangcai

    2015-01-01

    The hybrid between Brassica napus and B. rapa displays obvious heterosis in both growth performance and stress tolerances. A comparative transcriptome analysis for B. napus (A(n)A(n)CC genome), B. rapa (A(r)A(r) genome), and its hybrid F1 (A(n)A(r)C genome) was carried out to reveal the possible molecular mechanisms of heterosis at the gene expression level. A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes. A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples. The coexistence of nonadditive DEGs including high-parent dominance, low-parent dominance, overdominance, and underdominance was observed in the gene action modes of F1 hybrid, which were potentially related to the heterosis. The coexistence of multiple gene actions in the hybrid was observed and provided a list of candidate genes and pathways for heterosis. The expression bias of transposable element-associated genes was also observed in the hybrid compared to their parents. The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement. PMID:26448924

  14. Heritability of floral volatiles and pleiotropic responses to artificial selection in Brassica rapa.

    PubMed

    Zu, Pengjuan; Blanckenhorn, Wolf U; Schiestl, Florian P

    2016-02-01

    The evolution of the vast diversity of floral volatiles is little understood, although they serve fundamental functions, such as pollinator attraction and herbivore deterrence. Floral volatiles are often species specific, yet highly variable and sensitive to environmental factors. To date, nothing is known about the heritability of floral volatiles, and whether individual compounds can evolve independently or solely in concert with the whole volatile bouquet. We conducted bi-directional artificial selection on four target floral volatiles to estimate heritability and correlated pleiotropic responses in the wild turnip (Brassica rapa). The realized heritability of the four target volatiles ranged from 20% to 45%. The average narrow-sense heritability of all 13 analyzed floral volatiles was 18% based on parent-offspring regressions. There were pleiotropic effects of the selected floral volatile compounds on other constituents of the floral scent bouquet, on flowering time and on some morphological traits. We found that the whole floral scent bouquet changed, even when there was selection only on single compounds, with the overall phenotypic covariance being unaffected. Our study demonstrates that floral scent can evolve rapidly under phenotypic selection, but with additional correlated responses in traits that are not direct targets of selection. PMID:26391626

  15. Comparative Transcriptome Analysis Reveals Heat-Responsive Genes in Chinese Cabbage (Brassica rapa ssp. chinensis)

    PubMed Central

    Wang, Aihua; Hu, Jihong; Huang, Xingxue; Li, Xia; Zhou, Guolin; Yan, Zhixiang

    2016-01-01

    Chinese cabbage (Brassica rapa ssp. chinensis) is an economically and agriculturally significant vegetable crop and is extensively cultivated throughout the world. Heat stress disturbs cellular homeostasis and causes visible growth inhibition of shoots and roots, severe retardation in growth and development, and even death. However, there are few studies on the transcriptome profiling of heat stress in non-heading Chinese cabbage. In this study, we investigated the transcript profiles of non-heading Chinese cabbage from heat-sensitive and heat-tolerant varieties “GHA” and “XK,” respectively, in response to high temperature using RNA sequencing (RNA seq). Approximately 625 genes were differentially expressed between the two varieties. The responsive genes can be divided into three phases along with the time of heat treatment: response to stimulus, programmed cell death and ribosome biogenesis. Differentially expressed genes (DEGs) were identified in the two varieties, including transcription factors (TFs), kinases/phosphatases, genes related to photosynthesis and effectors of homeostasis. Many TFs were involved in the heat stress response of Chinese cabbage, including NAC069 TF which was up-regulated at all the heat treatment stages. And their expression levels were also validated by quantitative real-time-PCR (qRT-PCR). These candidate genes will provide genetic resources for further improving the heat-tolerant characteristics in non-heading Chinese cabbage. PMID:27443222

  16. Comparative Transcriptome Analysis Reveals Heat-Responsive Genes in Chinese Cabbage (Brassica rapa ssp. chinensis).

    PubMed

    Wang, Aihua; Hu, Jihong; Huang, Xingxue; Li, Xia; Zhou, Guolin; Yan, Zhixiang

    2016-01-01

    Chinese cabbage (Brassica rapa ssp. chinensis) is an economically and agriculturally significant vegetable crop and is extensively cultivated throughout the world. Heat stress disturbs cellular homeostasis and causes visible growth inhibition of shoots and roots, severe retardation in growth and development, and even death. However, there are few studies on the transcriptome profiling of heat stress in non-heading Chinese cabbage. In this study, we investigated the transcript profiles of non-heading Chinese cabbage from heat-sensitive and heat-tolerant varieties "GHA" and "XK," respectively, in response to high temperature using RNA sequencing (RNA seq). Approximately 625 genes were differentially expressed between the two varieties. The responsive genes can be divided into three phases along with the time of heat treatment: response to stimulus, programmed cell death and ribosome biogenesis. Differentially expressed genes (DEGs) were identified in the two varieties, including transcription factors (TFs), kinases/phosphatases, genes related to photosynthesis and effectors of homeostasis. Many TFs were involved in the heat stress response of Chinese cabbage, including NAC069 TF which was up-regulated at all the heat treatment stages. And their expression levels were also validated by quantitative real-time-PCR (qRT-PCR). These candidate genes will provide genetic resources for further improving the heat-tolerant characteristics in non-heading Chinese cabbage. PMID:27443222

  17. Proteomic and gene expression analyses during bolting-related leaf color change in Brassica rapa.

    PubMed

    Zhang, Y W; Guo, M H; Tang, X B; Jin, D; Fang, Z Y

    2016-01-01

    Bolting and flowering are key processes during the growth and development of Chinese cabbage (Brassica rapa L. ssp pekinensis). Understanding the molecular mechanisms underlying bolting and flowering is of significance for improving production of the vegetable. A leaf-color change from bright green to gray-green has been observed following differentiation of the flowering stem and before bolting in the vegetable, and is considered to be a signal for bolting. Proteomics in meristem tissues of an inbred line (C30) were analyzed by two-dimensional electrophoresis during the transition period. We found that some proteins were specifically expressed while others were differentially expressed. Among these, 17 proteins were specifically expressed before the color change, 18 were specifically expressed after the color change, 21 were downregulated during the color change, and 29 were upregulated. Mass spectrometric analysis (MALDI-TOF-TOF/MS) was used to analyze 17 protein spots, and four proteins (subunit E1 of vacuolar-type H+ transporter ATPase, the large subunit of Rubicon, S-adenosylmethionine synthetase, and tubulin α-2) were identified. qPCR analysis was conducted to quantify the expression of genes encoding these proteins during the transitional period. The expression of BrVHA-E1, BrSAMS, BrrbcL, and BrTUA6 was significantly different before and after the leaf-color change, suggesting that these genes might be involved in regulating flower differentiation and bolting. PMID:27525926

  18. Effects of fixation protocol and gravistimulation on cytoskeletal organization in Brassica rapa roots

    NASA Astrophysics Data System (ADS)

    Edge, Andrea; Hasenstein, Karl H.

    2012-07-01

    In preparation for a flight experiment we have studied the optimization of the staining protocols for microtubules and actin filaments in Brassica rapa seedlings. Microtubules (MT) were stained with monoclonal antibody (mAb) YOL 1/34. F-actin (FA) staining was achieved with C4 mAb antibody. Fixative prepared more than three weeks before use produces specimens that stained poorly. Storage in fixative for more than four weeks resulted in noticeably poorer staining. Staining was best in cortical cells but more difficult and less consistent in cap cells, especially for FA. In addition, the quality of staining of root cap cells was dependent on the age of the formaldehyde. The organization of the MTs corresponded with previously published descriptions; FA was prominent in the stele with thick and numerous parallel bundles; cortical cells showed less dense and less directional organization of mostly thinner filaments. FA organization was determined by tissue rather than by differential elongation. The organization of MTs in cortical cells of curving roots was uniformly circular and perpendicular to the long cell axis despite different cell length. The effect of clinorotation around the horizontal axis and centrifugation on the cytoskeletal organization was inconsistent. (Supported by NASA grant NNX10AP91G)

  19. The Genetic Architecture of Ecophysiological and Circadian Traits in Brassica rapa

    PubMed Central

    Edwards, Christine E.; Ewers, Brent E.; Williams, David G.; Xie, Qiguang; Lou, Ping; Xu, Xiaodong; McClung, C. Robertson; Weinig, Cynthia

    2011-01-01

    Developmental mechanisms that enable perception of and response to the environment may enhance fitness. Ecophysiological traits typically vary depending on local conditions and contribute to resource acquisition and allocation, yet correlations may limit adaptive trait expression. Notably, photosynthesis and stomatal conductance vary diurnally, and the circadian clock, which is an internal estimate of time that anticipates diurnal light/dark cycles, may synchronize physiological behaviors with environmental conditions. Using recombinant inbred lines of Brassica rapa, we examined the quantitative-genetic architecture of ecophysiological and phenological traits and tested their association with the circadian clock. We also investigated how trait expression differed across treatments that simulated seasonal settings encountered by crops and naturalized populations. Many ecophysiological traits were correlated, and some correlations were consistent with expected biophysical constraints; for example, stomata jointly regulate photosynthesis and transpiration by affecting carbon dioxide and water vapor diffusion across leaf surfaces, and these traits were correlated. Interestingly, some genotypes had unusual combinations of ecophysiological traits, such as high photosynthesis in combination with low stomatal conductance or leaf nitrogen, and selection on these genotypes could provide a mechanism for crop improvement. At the genotypic and QTL level, circadian period was correlated with leaf nitrogen, instantaneous measures of photosynthesis, and stomatal conductance as well as with a long-term proxy (carbon isotope discrimination) for gas exchange, suggesting that gas exchange is partly regulated by the clock and thus synchronized with daily light cycles. The association between circadian rhythms and ecophysiological traits is relevant to crop improvement and adaptive evolution. PMID:21750258

  20. Effects of microgravityon the structural organization of Brassica rapa photosynthetic appartus

    NASA Astrophysics Data System (ADS)

    Adamchuk, N.; Kordyum, E.; Guikema, J.

    Leaf mesophyll cells of 13- and 15-day old Brassica rapa plants grown on board the space shuttle Columbia (STS-87) and in the ground control have been investigated using the methods of light and electron microscopy. 13-day old plants were fixed on orbit and 15-day old plants were fixed after landing. It was shown the essential differences in leaf mesophyll quantitative anatomical and ultrastructural characteristics between spaceflight and ground control variants. Both the volume of palisade parenchyma cells and a number of chloroplasts in those cells increased in spaceflight samples. Simultaneusly, a chloroplast size decreased together with increasing of a relative volume of stromal thylakoids, starch grains and plastoglobuli. It was also noted increasing of stromal thylakoid length. In the same time, both a total length of thylakoids in granae and the grana number diminished in space flight. In addition, the interthylakoid space could be expended and the thylakoid length was more variable in chloroplast granae on microgravity, that correlated with a shrinkage of thylakoids in granal stacks. The obtained data a er discussed with the questions on both the photosynthetic apparatus sensitivity to gravity and its adaptive possibility to microgravity.

  1. Anthocyanin accumulation and transcriptional regulation of anthocyanin biosynthesis in purple bok choy (Brassica rapa var. chinensis).

    PubMed

    Zhang, Yanjie; Chen, Guoping; Dong, Tingting; Pan, Yu; Zhao, Zhiping; Tian, Shibing; Hu, Zongli

    2014-12-24

    Bok choy (Brassica rapa var. chinensis) is an important dietary vegetable cultivated and consumed worldwide for its edible leaves. The purple cultivars rich in health-promoting anthocyanins are usually more eye-catching and valuable. Fifteen kinds of anthocyanins were separated and identified from a purple bok choy cultivar (Zi He) by high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. To investigate the molecular mechanisms underlying anthocyanin accumulation in bok choy, the expression profiles of anthocyanin biosynthetic and regulatory genes were analyzed in seedlings and leaves of the purple cultivar and the green cultivar (Su Zhouqing). Compared with the other tissues, BrTT8 and most of the anthocyanin biosynthetic genes were significantly up-regulated in the leaves and light-grown seedlings of Zi He. The results that heterologous expression of BrTT8 promotes the transcription of partial anthocyanin biosynthetic genes in regeneration shoots of tomato indicate that BrTT8 plays an important role in the regulation of anthocyanin biosynthesis. PMID:25419600

  2. Molecular cloning and characterization of the Dicer-like 2 gene from Brassica rapa.

    PubMed

    Yan, Fei; Peng, Jiejun; Lu, Yuwen; Lin, Lin; Zheng, Hongying; Chen, Hairu; Chen, Jianping; Adams, Michael J

    2009-07-01

    Dicer-like proteins (DCLs) are involved in small RNA-mediated development and viral defense in plants. In model plants, at least four DCLs have been found and a number of studies have helped to understand their function. However, the function of the Dicer or DCLs in other plants is still unclear. Here, we report the full-length cDNA sequence of Brassica rapa ssp. chinensis DCL2 (BrDCL2) gene, which contains a 4,179 bp open reading frame (ORF) encoding a protein of 1,392 amino acids. At the 3' end of BrDCL2, clones with three different lengths of 3' untranslated region were found. An alternative splice variant of BrDCL2, BrDCL2sv, in which one intron was retained between exon9 and exon10, was also cloned. Because of a change in the coding sequence resulting in a premature terminal codon, BrDCL2sv was expected to translate a short peptide containing the whole DEXHc domain. PMID:18607769

  3. Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa.

    PubMed

    Hammond, John P; Mayes, Sean; Bowen, Helen C; Graham, Neil S; Hayden, Rory M; Love, Christopher G; Spracklen, William P; Wang, Jun; Welham, Sue J; White, Philip J; King, Graham J; Broadley, Martin R

    2011-07-01

    Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement. PMID:21527424

  4. Effect of Diffusion on Discoloration of Congo Red by Alginate Entrapped Turnip (Brassica rapa) Peroxidase.

    PubMed

    Ahmedi, Afaf; Abouseoud, Mahmoud; Abdeltif, Amrane; Annabelle, Couvert

    2015-01-01

    Enzymatic discoloration of the diazo dye, Congo red (CR), by immobilized plant peroxidase from turnip "Brassica rapa" is investigated. Partially purified turnip peroxidase (TP) was immobilized by entrapment in spherical particles of calcium alginate and was assayed for the discoloration of aqueous CR solution. Experimental data revealed that pH, reaction time, temperature, colorant, and H2O2 concentration play a significant role in dye degradation. Maximum CR removal was found at pH 2.0, constant temperature of 40°C in the presence of 10 mM H2O2, and 180 mg/L of CR. More than 94% of CR was removed by alginate immobilized TP after 1 h of incubation in a batch process under optimal conditions. About 74% removal efficiency was retained after four recycles. Diffusional limitations in alginate beads such as effectiveness factor η, Thiele modulus Φ, and effective diffusion coefficients (D e ) of Congo red were predicted assuming a first-order biodegradation kinetic. Results showed that intraparticle diffusion resistance has a significant effect on the CR biodegradation rate. PMID:25734011

  5. Dynamics of storage reserve deposition during Brassica rapa L. pollen and seed development in microgravity

    NASA Technical Reports Server (NTRS)

    Kuang, A.; Popova, A.; McClure, G.; Musgrave, M. E.

    2005-01-01

    Pollen and seeds share a developmental sequence characterized by intense metabolic activity during reserve deposition before drying to a cryptobiotic form. Neither pollen nor seed development has been well studied in the absence of gravity, despite the importance of these structures in supporting future long-duration manned habitation away from Earth. Using immature seeds (3-15 d postpollination) of Brassica rapa L. cv. Astroplants produced on the STS-87 flight of the space shuttle Columbia, we compared the progress of storage reserve deposition in cotyledon cells during early stages of seed development. Brassica pollen development was studied in flowers produced on plants grown entirely in microgravity on the Mir space station and fixed while on orbit. Cytochemical localization of storage reserves showed differences in starch accumulation between spaceflight and ground control plants in interior layers of the developing seed coat as early as 9 d after pollination. At this age, the embryo is in the cotyledon elongation stage, and there are numerous starch grains in the cotyledon cells in both flight and ground control seeds. In the spaceflight seeds, starch was retained after this stage, while starch grains decreased in size in the ground control seeds. Large and well-developed protein bodies were observed in cotyledon cells of ground control seeds at 15 d postpollination, but their development was delayed in the seeds produced during spaceflight. Like the developing cotyledonary tissues, cells of the anther wall and filaments from the spaceflight plants contained numerous large starch grains, while these were rarely seen in the ground controls. The tapetum remained swollen and persisted to a later developmental stage in the spaceflight plants than in the ground controls, even though most pollen grains appeared normal. These developmental markers indicate that Brassica seeds and pollen produced in microgravity were physiologically younger than those produced in 1 g

  6. Use of airborne remote sensing to detect riverside Brassica rapa to aid in risk assessment of transgenic crops

    NASA Astrophysics Data System (ADS)

    Elliott, Luisa M.; Mason, David C.; Allainguillaume, Joel; Wilkinson, Mike J.

    2009-11-01

    High resolution descriptions of plant distribution have utility for many ecological applications but are especially useful for predictive modeling of gene flow from transgenic crops. Difficulty lies in the extrapolation errors that occur when limited ground survey data are scaled up to the landscape or national level. This problem is epitomized by the wide confidence limits generated in a previous attempt to describe the national abundance of riverside Brassica rapa (a wild relative of cultivated rapeseed) across the United Kingdom. Here, we assess the value of airborne remote sensing to locate B. rapa over large areas and so reduce the need for extrapolation. We describe results from flights over the river Nene in England acquired using Airborne Thematic Mapper (ATM) and Compact Airborne Spectrographic Imager (CASI) imagery, together with ground truth data. It proved possible to detect 97% of flowering B. rapa on the basis of spectral profiles. This included all stands of plants that occupied >2m square (>5 plants), which were detected using single-pixel classification. It also included very small populations (<5 flowering plants, 1-2m square) that generated mixed pixels, which were detected using spectral unmixing. The high detection accuracy for flowering B. rapa was coupled with a rather large false positive rate (43%). The latter could be reduced by using the image detections to target fieldwork to confirm species identity, or by acquiring additional remote sensing data such as laser altimetry or multitemporal imagery.

  7. Genome-wide survey and expression analysis of the PUB family in Chinese cabbage (Brassica rapa ssp. pekinesis).

    PubMed

    Wang, Cheng; Duan, Weike; Riquicho, Ali RamuliMaquina; Jing, Zange; Liu, Tongkun; Hou, Xilin; Li, Ying

    2015-12-01

    U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. Plant U-box (PUB) proteins play crucial regulatory roles in various developmental and physiological processes. Previously, 64 and 77 PUB genes have been identified in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), respectively. In this study, 101 putative PUB genes were identified in the Chinese cabbage (Brassica rapa ssp. pekinensis line Chiifu-401-42) genome and compared with other 15 representative plants. By specific protein domains and a phylogenetic analysis, the B. rapa PUB (BrPUB) gene family was subdivided into 10 groups. Localization of BrPUB genes showed an uneven distribution on the ten chromosomes of B. rapa. The orthologous and co-orthologous PUB gene pairs were identified between B. rapa and A. thaliana. RNA-seq transcriptome data of different tissues revealed tissue-specific and differential expression profiles of the BrPUBs, and quantitative real-time PCR analysis showed inverse gene expression patterns of the BrPUB-ARMs in response to cold and heat stresses. Altogether, the identification, classification, phylogenetic analysis, chromosome distribution, conserved motifs, and expression patterns of BrPUBs were predicted and analysed. Importantly, this study of BrPUBs provides a rich resource that will aid in the determination of PUB functions in plant development. PMID:26054324

  8. Cerium Oxide Nanoparticles and Bulk Cerium Oxide Leading to Different Physiological and Biochemical Responses in Brassica rapa.

    PubMed

    Ma, Xingmao; Wang, Qiang; Rossi, Lorenzo; Zhang, Weilan

    2016-07-01

    Cerium oxide nanoparticles (CeO2NPs) have been incorporated into many commercial products, and their potential release into the environment through the use and disposal of these products has caused serious concerns. Despite the previous efforts and rapid progress on elucidating the environmental impact of CeO2NPs, the long-term impact of CeO2NPs to plants, a key component of the ecosystem, is still not well understood. The potentially different impact of CeO2NPs and their bulk counterparts to plants is also unclear. The main objectives of this study were (1) to investigate whether continued irrigation with solutions containing different concentrations of CeO2NPs (0, 10, and 100 mg/L) would induce physiological and biochemical adjustments in Brassica rapa in soil growing conditions and (2) to determine whether CeO2NPs and bulk CeO2 particles exert different impacts on plants. The results indicated that bulk CeO2 at 10 and 100 mg/L enhanced plant biomass by 28% and 35%, respectively, while CeO2NPs at equivalent concentrations did not. While the bulk CeO2 treatment resulted in significantly higher concentrations of hydrogen peroxide (H2O2) in plant tissues at the vegetative stage, CeO2NPs led to significantly higher H2O2 levels in plant tissues at the floral stage. The activity of superoxide dismutase (SOD) in Brassica rapa also displayed a growth-stage dependent response to different sizes of CeO2 while catalase (CAT) activity was not affected by either size of CeO2 throughout the life cycle of Brassica rapa. Altogether, the results demonstrated that plant responses to CeO2 exposure varied with the particle sizes and the growth stages of plants. PMID:26691446

  9. Effect of enzyme-aided cell wall disintegration on protein extractability from intact and dehulled rapeseed (Brassica rapa L. and Brassica napus L.) press cakes.

    PubMed

    Rommi, Katariina; Hakala, Terhi K; Holopainen, Ulla; Nordlund, Emilia; Poutanen, Kaisa; Lantto, Raija

    2014-08-13

    Cell-wall- and pectin-degrading enzyme preparations were used to enhance extractability of proteins from rapeseed press cake. Rapeseed press cakes from cold pressing of intact Brassica rapa and partially dehulled Brassica napus seeds, containing 36-40% protein and 35% carbohydrates, were treated with pectinolytic (Pectinex Ultra SP-L), xylanolytic (Depol 740L), and cellulolytic (Celluclast 1.5L) enzyme preparations. Pectinex caused effective disintegration of embryonic cell walls through hydrolysis of pectic polysaccharides and glucans and increased protein extraction by up to 1.7-fold in comparison to treatment without enzyme addition. Accordingly, 56% and 74% of the total protein in the intact and dehulled press cakes was extracted. Light microscopy of the press cakes suggested the presence of pectins colocalized with proteins inside the embryo cells. Hydrolysis of these intracellular pectins and deconstruction of embryonic cell walls during Pectinex treatment were concluded to relate with enhanced protein release. PMID:25039585

  10. Investigating genotype specific response in photosynthetic behavior under drought stress and nitrogen limitation in Brassica rapa.

    NASA Astrophysics Data System (ADS)

    Pleban, J. R.; Mackay, D. S.; Ewers, B. E.; Weinig, C.; Aston, T.

    2015-12-01

    Challenges in terrestrial ecosystem modeling include characterizing the impact of stress on vegetation and the heterogeneous behavior of different species within the environment. In an effort to address these challenges the impacts of drought and nutrient limitation on the CO2 assimilation of multiple genotypes of Brassica rapa was investigated using the Farquhar Model (FM) of photosynthesis following a Bayesian parameterization and updating scheme. Leaf gas exchange and chlorophyll fluorescence measurements from an unstressed group (well-watered/well-fertilized) and two stressed groups (drought/well-fertilized and well-watered/nutrient limited) were used to estimate FM model parameters. Unstressed individuals were used to initialize Bayesian parameter estimation. Posterior mean estimates yielded a close fit with data as observed assimilation (An) closely matched predicted (Ap) with mean standard error for all individuals ranging from 0.8 to 3.1 μmol CO2 m-2 s-1. Posterior parameter distributions of the unstressed individuals were combined and fit to distributions to establish species level Bayesian priors of FM parameters for testing stress responses. Species level distributions of unstressed group identified mean maximum rates of carboxylation standardized to 25° (Vcmax25) as 101.8 μmol m-2 s-1 (± 29.0) and mean maximum rates of electron transport standardized to 25° (Jmax25) as 319.7 μmol m-2 s-1 (± 64.4). These updated priors were used to test the response of drought and nutrient limitations on assimilation. In the well-watered/nutrient limited group a decrease of 28.0 μmol m-2 s-1 was observed in mean estimate of Vcmax25, a decrease of 27.9 μmol m-2 s-1 in Jmax25 and a decrease in quantum yield from 0.40 mol photon/mol e- in unstressed individuals to 0.14 in the nutrient limited group. In the drought/well-fertilized group a decrease was also observed in Vcmax25 and Jmax25. The genotype specific unstressed and stressed responses were then used to

  11. Growth and antioxidant response of Brassica rapa var. rapa L. (turnip) irrigated with different compositions of paper and board mill (PBM) effluent.

    PubMed

    Iqbal, Shahid; Younas, Umer; Chan, Kim Wei; Saeed, Zohaib; Shaheen, Muhammad Ashraf; Akhtar, Naeem; Majeed, Abdul

    2013-05-01

    Current study presents the effect of irrigation with different compositions (0%, 20%, 40%, 60%, 80% and 100%) of PBM effluent on growth and antioxidant potential of Brassica rapa var. rapa L. plants. Seeds were exposed to different PBM effluent compositions, which resulted in significant decrease in their germination potential with elevated delay index. Significant changes in growth parameters (plant height, number of leaves and leaf area) were recorded for turnip plants at regular intervals (25, 50 and 75 d) as function of PBM effluent proportion. Response of biochemical and antioxidant constituents in different parts of turnip, against stress induced by PBM effluent, was assessed by estimating the contents of chlorophyll (a+b), carotenoids, protein, phenolics, flavonoids, ascorbic acid and malondialdehyde. Antioxidant activity was evaluated by measuring DPPH radical scavenging potential. The results of this study suggest that the impact of PBM effluent irrigation is dependent on concentration of effluent in irrigation mixture and is very clear on plant growth and antioxidant attributes. Maximum benefits were secured at 40% PBM effluent to irrigate turnip plants till maturity while higher concentrations were found useful for shorter period (25-50 d). PMID:23507497

  12. Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

    PubMed Central

    Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

    2013-01-01

    Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

  13. Evidence of root zone hypoxia in Brassica rapa L. grown in microgravity

    NASA Technical Reports Server (NTRS)

    Stout, S. C.; Porterfield, D. M.; Briarty, L. G.; Kuang, A.; Musgrave, M. E.

    2001-01-01

    A series of experiments was conducted aboard the U.S. space shuttle and the Mir space station to evaluate microgravity-induced root zone hypoxia in rapid-cycling Brassica (Brassica rapa L.), using both root and foliar indicators of low-oxygen stress to the root zone. Root systems from two groups of plants 15 and 30 d after planting, grown in a phenolic foam nutrient delivery system on the shuttle (STS-87), were harvested and fixed for microscopy or frozen for enzyme assays immediately postflight or following a ground-based control. Activities of fermentative enzymes were measured as indicators of root zone hypoxia and metabolism. Following 16 d of microgravity, ADH (alcohol dehydrogenase) activity was increased in the spaceflight roots 47% and 475% in the 15-d-old and 30-d-old plants, respectively, relative to the ground control. Cytochemical localization showed ADH activity in only the root tips of the space-grown plants. Shoots from plants that were grown from seed in flight in a particulate medium on the Mir station were harvested at 13 d after planting and quick-frozen and stored in flight in a gaseous nitrogen freezer or chemically fixed in flight for subsequent microscopy. When compared to material from a high-fidelity ground control, concentrations of shoot sucrose and total soluble carbohydrate were significantly greater in the spaceflight treatment according to enzymatic carbohydrate analysis. Stereological analysis of micrographs of sections from leaf and cotyledon tissue fixed in flight and compared with ground controls indicated no changes in the volume of protoplast, cell wall, and intercellular space in parenchyma cells. Within the protoplasm, the volume occupied by starch was threefold higher in the spaceflight than in the ground control, with a concomitant decrease in vacuolar volume in the spaceflight treatment. Both induction of fermentative enzyme activity in roots and accumulation of carbohydrates in foliage have been repeatedly shown to occur

  14. Physiological and genetic analysis of CO2-induced breakdown of self-incompatibility in Brassica rapa.

    PubMed

    Lao, Xintian; Suwabe, Keita; Niikura, Satoshi; Kakita, Mitsuru; Iwano, Megumi; Takayama, Seiji

    2014-03-01

    Self-incompatibility (SI) of the Brassicaceae family can be overcome by CO2 gas treatment. This method has been used for decades as an effective means to obtain a large amount of inbred seeds which can then be used for F1 hybrid seed production; however, the molecular mechanism by which CO2 alters the SI pathway has not been elucidated. In this study, to obtain new insights into the mechanism of CO2-induced SI breakdown, the focus was on two inbred lines of Brassica rapa (syn. campestris) with different CO2 sensitivity. Physiological examination using X-ray microanalysis suggested that SI breakdown in the CO2-sensitive line was accompanied by a significant accumulation of calcium at the pollen-stigma interface. Pre-treatment of pollen or pistil with CO2 gas before pollination showed no effect on the SI reaction, suggesting that some physiological process after pollination is necessary for SI to be overcome. Genetic analyses using F1 progeny of a CO2-sensitive × CO2-insensitive cross suggested that CO2 sensitivity is a semi-dominant trait in these lines. Analysis of F2 progeny suggested that CO2 sensitivity could be a quantitative trait, which is controlled by more than one gene. Quantitative trait locus (QTL) analyses identified two major loci, BrSIO1 and BrSIO2, which work additively in overcoming SI during CO2 treatment. No QTL was detected at the loci previously shown to affect SI stability, suggesting that CO2 sensitivity is determined by novel genes. The QTL data presented here should be useful for determining the responsible genes, and for the marker-assisted selection of desirable parental lines with stable but CO2-sensitive SI in F1 hybrid breeding. PMID:24376255

  15. Expression of δ-cyclins of Brassica rapa L. embryos by clinorotation

    NASA Astrophysics Data System (ADS)

    Artemenko, O. A.

    Cyclins is one of the important regulators of cell cycle. There are several types of cyclins exists. They are responding for different phases of cycle and have high homology in plant's and mammalian's cells. δ -cyclins are specific for plants and controlling the presynthetic phase events. These cyclins likes to mammalian D-cyclins and have similar functions. This class consist three types of cyclins -- δ 1, δ 2 and δ 3. Cyclin δ 1 is responding for events in cell, which take place before exiting from stage of quiet (G0). Cyclin δ 1 is responding for entering and outputting from G0, and cyclin δ 3 -- for events, which happen in cell after stage of quiet, by entering to S-phase (phase of DNA's synthesis). In present research was used δ 1- and δ 3-cyclins. For determination of δ -cyclins gene's expression level was excreted RNA from embryos: 3-days (spherical stage), 6-days (heart-shaped stage) and 9-days (generated stage) seedlings of Brassica rapa L. in control and under clinorotation. For definition the cyclins gene's expression level applied Northern Blot Analysis. Obtained data testify about difference in level of gene's expression of cyclin δ 1 between control and clinorotation variants. After three days by pollination the expression of this gene in embryos was observed in control only. By clinorotation the gene's expression was detected on 6 days later, but it level was lower than in control variant. On 9 days it was gently expressed by clinorotation, where as by control it was not detected absolutely. Cyclin δ 3 gene's expression was observed during all time of the experiment. These data also confirm known one about expression δ 1- cyclin, which expressed on beginning of cell cycle only. And δ 3 --cyclin that express during whole presinthetic phase of cell cycle (Sony et al., 1995, Murray, 1994, Inze et al, 1999, Umeda, 2000).

  16. Quantifying the Stress Responses of Brassica Rapa Genotypes, With Experimental Drought in Two Nitrogen Treatments

    NASA Astrophysics Data System (ADS)

    Hickerson, J. L.; Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B. E.; Weinig, C.

    2014-12-01

    In a greenhouse study designed to quantify and compare stress responses of four genotypes of Brassica rapa, broccolette (bro), cabbage (cab), turnip (tur), and oil, leaf water potential and net CO2 assimilations were measured. Individuals from each genotype, grown either with high or low nitrogen, were exposed to experimental drought of the same duration. One hypothesis was that the genotypes would differ significantly in their responses to periodic drought. The other hypothesis was that the nitrogen treatment versus no nitrogen treatment would play a significant role in the stress responses during drought. It would be expected that the nitrogen treated would have greater dry leaf mass. A LI-6400 XT portable photosynthesis system was used to obtain A/Ci curves (net CO2 assimilation rate versus substomatal CO2) for each treatment group. Predawn and midday water potentials were obtained throughout the hydrated and drought periods using a Model 670 pressure chamber. The dry leaf mass was significantly greater among the high nitrogen group versus the low nitrogen group for each genotype. Nitrogen and genotype were both determinants in variation of water potentials and net CO2 assimilation. Bro and cab genotypes with high nitrogen showed the highest net CO2 assimilation rates during hydration, but the assimilation rates dropped to the lowest during droughts. The water potentials for bro and cab were lower than values for tur and oil. Nitrogen treated genotypes had lower water potentials, but higher net CO2 assimilation rates. Bayesian ecophysiological modeling with the TREES model showed significant differences in trait expression, quantified in terms of differences in model parameter posteriors, among the four genotypes.

  17. Growth and (137)Cs uptake and accumulation among 56 Japanese cultivars of Brassica rapa, Brassica juncea and Brassica napus grown in a contaminated field in Fukushima: Effect of inoculation with a Bacillus pumilus strain.

    PubMed

    Djedidi, Salem; Kojima, Katsuhiro; Ohkama-Ohtsu, Naoko; Bellingrath-Kimura, Sonoko Dorothea; Yokoyama, Tadashi

    2016-06-01

    Fifty six local Japanese cultivars of Brassica rapa (40 cultivars), Brassica juncea (10 cultivars) and Brassica napus (6 cultivars) were assessed for variability in growth and (137)Cs uptake and accumulation in association with a Bacillus pumilus strain. Field trial was conducted at a contaminated farmland in Nihonmatsu city, in Fukushima prefecture. Inoculation resulted in different responses of the cultivars in terms of growth and radiocesium uptake and accumulation. B. pumilus induced a significant increase in shoot dry weight in 12 cultivars that reached up to 40% in one B. rapa and three B. juncea cultivars. Differences in radiocesium uptake were observed between the cultivars of each Brassica species. Generally, inoculation resulted in a significant increase in (137)Cs uptake in 22 cultivars, while in seven cultivars it was significantly decreased. Regardless of plant cultivar and bacterial inoculation, the transfer of (137)Cs to the plant shoots (TF) varied by a factor of up to 5 and it ranged from to 0.011 to 0.054. Five inoculated cultivars, showed enhanced shoot dry weights and decreased (137)Cs accumulations, among which two B. rapa cultivars named Bitamina and Nozawana had a significantly decreased (137)Cs accumulation in their shoots. Such cultivars could be utilized to minimize the entry of radiocesium into the food chain; however, verifying the consistency of their radiocesium accumulation in other soils is strongly required. Moreover, the variations in growth and radiocesium accumulation, as influenced by Bacillus inoculation, could help selecting well grown inoculated Brassica cultivars with low radiocesium accumulation in their shoots. PMID:26986237

  18. Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables.

    PubMed

    Zhang, Xiaohui; Liu, Tongjin; Li, Xixiang; Duan, Mengmeng; Wang, Jinglei; Qiu, Yang; Wang, Haiping; Song, Jiangping; Shen, Di

    2016-01-01

    Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops. PMID:26727246

  19. Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables

    PubMed Central

    Zhang, Xiaohui; Liu, Tongjin; Li, Xixiang; Duan, Mengmeng; Wang, Jinglei; Qiu, Yang; Wang, Haiping; Song, Jiangping; Shen, Di

    2016-01-01

    Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops. PMID:26727246

  20. Atmospheric H2S and SO2 as sulfur source for Brassica juncea and Brassica rapa: impact on the glucosinolate composition

    PubMed Central

    Aghajanzadeh, Tahereh; Kopriva, Stanislav; Hawkesford, Malcolm J.; Koprivova, Anna; De Kok, Luit J.

    2015-01-01

    The impact of sulfate deprivation and atmospheric H2S and SO2 nutrition on the content and composition of glucosinolates was studied in Brassica juncea and B. rapa. Both species contained a number of aliphatic, aromatic and indolic glucosinolates. The total glucosinolate content was more than 5.5-fold higher in B. juncea than in B. rapa, which could solely be attributed to the presence of high levels of sinigrin, which was absent in the latter species. Sulfate deprivation resulted in a strong decrease in the content and an altered composition of the glucosinolates of both species. Despite the differences in patterns in foliarly uptake and metabolism, their exposure hardly affected the glucosinolate composition of the shoot, both at sulfate-sufficient and sulfate-deprived conditions. This indicated that the glucosinolate composition in the shoot was hardly affected by differences in sulfur source (viz., sulfate, sulfite and sulfide). Upon sulfate deprivation, where foliarly absorbed H2S and SO2 were the sole sulfur source for growth, the glucosinolate composition of roots differed from sulfate-sufficient B. juncea and B. rapa, notably the fraction of the indolic glucosinolates was lower than that observed in sulfur-sufficient roots. PMID:26579170

  1. Genetic Variation and Divergence of Genes Involved in Leaf Adaxial-Abaxial Polarity Establishment in Brassica rapa.

    PubMed

    Liang, Jianli; Liu, Bo; Wu, Jian; Cheng, Feng; Wang, Xiaowu

    2016-01-01

    Alterations in leaf adaxial-abaxial (ad-ab) polarity are one of the main factors that influence leaf curvature. In Chinese cabbage, leaf incurvature is an essential prerequisite to the formation of a leafy head. Identifying ad-ab patterning genes and investigating their genetic variation may facilitate elucidation of the mechanisms underlying leaf incurvature during head formation. Comparative genomic analysis of 45 leaf ad-ab patterning genes in Brassica rapa based on 26 homologs of Arabidopsis thaliana indicated that these genes underwent expansion and were retained after whole genome triplication (WGT). We also assessed the nucleotide diversity and selection footprints of these 45 genes in a collection of 94 Brassica rapa accessions that were composed of heading and non-heading morphotypes. Six of the 45 genes showed significant negative Tajima's D indices and nucleotide diversity reduction in heading accessions compared to those in non-heading accessions, indicating that they underwent purifying selection. Further testing of the BrARF3.1 gene, which was one of the selection signals from a larger collection, confirmed that purifying selection did occur. Our results provide genetic evidence that ad-ab patterning genes are involved in leaf incurvature, which is associated with formation of a leafy head, as well as promote an understanding of the genetic mechanism underlying leafy head formation in Chinese cabbage. PMID:26904064

  2. Growth inhibition in Chinese cabbage (Brassica rapa var. chinensis) growth exposed to di-n-butyl phthalate.

    PubMed

    Liao, Chien-Sen; Yen, Jui-Hung; Wang, Yei-Shung

    2009-04-30

    The toxicity and effects of di-n-butyl phthalate (DBP), an endocrine disruptor, on the growth of Chinese cabbage (Brassica rapa var. chinensis) were studied. Etiolation occurred on leaves of Chinese cabbage plant treated with 50mg/L of DBP for 42 d. DBP even below 1mg/L had a significant effect on the concentration of chlorophyll in Chinese cabbage and the biomass showed a severe decrease under treatment with more than 30 mg/L of DBP. At a concentration below 1mg/L of DBP, no significant difference in accumulation was found, but treatments with concentration exceeding 10, 30, 50 and 100mg/L all resulted in significant accumulation of DBP. Six protein spots extracted from leaf tissue of DBP-treated Chinese cabbage displaying a differential expression are shown in 2-DE maps. According to proteome level studies, three protein spots were found to increase and were identified, respectively, as acyl-[acyl-carrier-protein] desaturase (acyl-ACP desaturase), root phototropism protein 3 (RPT3) and ferredoxin-nitrite reductase (Fd-NiR). The other three protein spots were found to decrease and were identified respectively as dihydroflavonol-4-reductase (DFR), aminoacyl-tRNA synthetase (aaRS) and ATP synthase subunit beta. The key finding is that the other closely related plant, Bok choy (Brassica rapa subsp. chinensis), the subspecies of Chinese cabbage, respond differently to the same chemicals. PMID:18678443

  3. Genetic Variation and Divergence of Genes Involved in Leaf Adaxial-Abaxial Polarity Establishment in Brassica rapa

    PubMed Central

    Liang, Jianli; Liu, Bo; Wu, Jian; Cheng, Feng; Wang, Xiaowu

    2016-01-01

    Alterations in leaf adaxial-abaxial (ad-ab) polarity are one of the main factors that influence leaf curvature. In Chinese cabbage, leaf incurvature is an essential prerequisite to the formation of a leafy head. Identifying ad-ab patterning genes and investigating their genetic variation may facilitate elucidation of the mechanisms underlying leaf incurvature during head formation. Comparative genomic analysis of 45 leaf ad-ab patterning genes in Brassica rapa based on 26 homologs of Arabidopsis thaliana indicated that these genes underwent expansion and were retained after whole genome triplication (WGT). We also assessed the nucleotide diversity and selection footprints of these 45 genes in a collection of 94 Brassica rapa accessions that were composed of heading and non-heading morphotypes. Six of the 45 genes showed significant negative Tajima's D indices and nucleotide diversity reduction in heading accessions compared to those in non-heading accessions, indicating that they underwent purifying selection. Further testing of the BrARF3.1 gene, which was one of the selection signals from a larger collection, confirmed that purifying selection did occur. Our results provide genetic evidence that ad-ab patterning genes are involved in leaf incurvature, which is associated with formation of a leafy head, as well as promote an understanding of the genetic mechanism underlying leafy head formation in Chinese cabbage. PMID:26904064

  4. Stable Bacillus thuringiensis (Bt) toxin content in interspecific F1 and backcross populations of wild Brassica rapa after Bt gene transfer.

    PubMed

    Zhu, B; Lawrence, J R; Warwick, S I; Mason, P; Braun, L; Halfhill, M D; Stewart, C N

    2004-01-01

    Stable expression of a transgene may lead to increased fitness for wild plants after acquiring the transgene via crop-weed hybridization. Here, we investigate the stability of Bt toxin content in wild Brassica rapa acquiring the Bt gene from Bt Brassica napus. The Bt toxin content in nine Bt-expressing B. napus lines was 0.80-1.70 micro g/g leaf tissue throughout the growing season. These nine lines were crossed with three accessions of wild B. rapa and the Bt gene was successfully transferred to interspecific hybrids (F1) and successive backcross generations (BC1 to BC4). The Bt toxin level in F1 and BC progenies containing the Bt gene remained at 0.90-3.10 micro g/g leaf tissue. This study indicates that the Bt gene can persist and be stably expressed in wild B. rapa. PMID:14653804

  5. Conservation and Expression Patterns Divergence of Ascorbic Acid d-mannose/l-galactose Pathway Genes in Brassica rapa.

    PubMed

    Duan, Weike; Ren, Jun; Li, Yan; Liu, Tongkun; Song, Xiaoming; Chen, Zhongwen; Huang, Zhinan; Hou, Xilin; Li, Ying

    2016-01-01

    Ascorbic acid (AsA) participates in diverse biological processes, is regulated by multiple factors and is a potent antioxidant and cellular reductant. The D-Mannose/L-Galactose pathway is a major plant AsA biosynthetic pathway that is highly connected within biosynthetic networks, and generally conserved across plants. Previous work has shown that, although most genes of this pathway are expressed under standard growth conditions in Brassica rapa, some paralogs of these genes are not. We hypothesize that regulatory evolution in duplicate AsA pathway genes has occurred as an adaptation to environmental stressors, and that gene retention has been influenced by polyploidation events in Brassicas. To test these hypotheses, we explored the conservation of these genes in Brassicas and their expression patterns divergence in B. rapa. Similar retention and a high degree of gene sequence similarity were identified in B. rapa (A genome), B. oleracea (C genome) and B. napus (AC genome). However, the number of genes that encode the same type of enzymes varied among the three plant species. With the exception of GMP, which has nine genes, there were one to four genes that encoded the other enzymes. Moreover, we found that expression patterns divergence widely exists among these genes. (i) VTC2 and VTC5 are paralogous genes, but only VTC5 is influenced by FLC. (ii) Under light treatment, PMI1 co-regulates the AsA pool size with other D-Man/L-Gal pathway genes, whereas PMI2 is regulated only by darkness. (iii) Under NaCl, Cu(2+), MeJA and wounding stresses, most of the paralogs exhibit different expression patterns. Additionally, GME and GPP are the key regulatory enzymes that limit AsA biosynthesis in response to these treatments. In conclusion, our data support that the conservative and divergent expression patterns of D-Man/L-Gal pathway genes not only avoid AsA biosynthesis network instability but also allow B. rapa to better adapt to complex environments. PMID:27313597

  6. Conservation and Expression Patterns Divergence of Ascorbic Acid d-mannose/l-galactose Pathway Genes in Brassica rapa

    PubMed Central

    Duan, Weike; Ren, Jun; Li, Yan; Liu, Tongkun; Song, Xiaoming; Chen, Zhongwen; Huang, Zhinan; Hou, Xilin; Li, Ying

    2016-01-01

    Ascorbic acid (AsA) participates in diverse biological processes, is regulated by multiple factors and is a potent antioxidant and cellular reductant. The D-Mannose/L-Galactose pathway is a major plant AsA biosynthetic pathway that is highly connected within biosynthetic networks, and generally conserved across plants. Previous work has shown that, although most genes of this pathway are expressed under standard growth conditions in Brassica rapa, some paralogs of these genes are not. We hypothesize that regulatory evolution in duplicate AsA pathway genes has occurred as an adaptation to environmental stressors, and that gene retention has been influenced by polyploidation events in Brassicas. To test these hypotheses, we explored the conservation of these genes in Brassicas and their expression patterns divergence in B. rapa. Similar retention and a high degree of gene sequence similarity were identified in B. rapa (A genome), B. oleracea (C genome) and B. napus (AC genome). However, the number of genes that encode the same type of enzymes varied among the three plant species. With the exception of GMP, which has nine genes, there were one to four genes that encoded the other enzymes. Moreover, we found that expression patterns divergence widely exists among these genes. (i) VTC2 and VTC5 are paralogous genes, but only VTC5 is influenced by FLC. (ii) Under light treatment, PMI1 co-regulates the AsA pool size with other D-Man/L-Gal pathway genes, whereas PMI2 is regulated only by darkness. (iii) Under NaCl, Cu2+, MeJA and wounding stresses, most of the paralogs exhibit different expression patterns. Additionally, GME and GPP are the key regulatory enzymes that limit AsA biosynthesis in response to these treatments. In conclusion, our data support that the conservative and divergent expression patterns of D-Man/L-Gal pathway genes not only avoid AsA biosynthesis network instability but also allow B. rapa to better adapt to complex environments. PMID:27313597

  7. A Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of TIFY Family Genes in Brassica rapa

    PubMed Central

    Saha, Gopal; Park, Jong-In; Kayum, Md. Abdul; Nou, Ill-Sup

    2016-01-01

    The TIFY family is a plant-specific group of proteins with a diversity of functions and includes four subfamilies, viz. ZML, TIFY, PPD, and JASMONATE ZIM-domain (JAZ) proteins. TIFY family members, particularly JAZ subfamily proteins, play roles in biological processes such as development and stress and hormone responses in Arabidopsis, rice, chickpea, and grape. However, there is no information about this family in any Brassica crop. This study identifies 36 TIFY genes in Brassica rapa, an economically important crop species in the Brassicaceae. An extensive in silico analysis of phylogenetic grouping, protein motif organization and intron-exon distribution confirmed that there are four subfamilies of BrTIFY proteins. Out of 36 BrTIFY genes, we identified 21 in the JAZ subfamily, seven in the TIFY subfamily, six in ZML and two in PPD. Extensive expression profiling of 21 BrTIFY JAZs in various tissues, especially in floral organs and at different flower growth stages revealed constitutive expression patterns, which suggest that BrTIFY JAZ genes are important during growth and development of B. rapa flowers. A protein interaction network analysis also pointed to association of these proteins with fertility and defense processes of B. rapa. Using a low temperature-treated whole-genome microarray data set, most of the JAZ genes were found to have variable transcript abundance between the contrasting inbred lines Chiifu and Kenshin of B. rapa. Subsequently, the expression of all 21 BrTIFY JAZs in response to cold stress was characterized in the same two lines via qPCR, demonstrating that nine genes were up-regulated. Importantly, the BrTIFY JAZs showed strong and differential expression upon JA treatment, pointing to their probable involvement in JA-mediated growth regulatory functions, especially during flower development and stress responses. Additionally, BrTIFY JAZs were induced in response to salt, drought, Fusarium, ABA, and SA treatments, and six genes (BrTIFY3

  8. A Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of TIFY Family Genes in Brassica rapa.

    PubMed

    Saha, Gopal; Park, Jong-In; Kayum, Md Abdul; Nou, Ill-Sup

    2016-01-01

    The TIFY family is a plant-specific group of proteins with a diversity of functions and includes four subfamilies, viz. ZML, TIFY, PPD, and JASMONATE ZIM-domain (JAZ) proteins. TIFY family members, particularly JAZ subfamily proteins, play roles in biological processes such as development and stress and hormone responses in Arabidopsis, rice, chickpea, and grape. However, there is no information about this family in any Brassica crop. This study identifies 36 TIFY genes in Brassica rapa, an economically important crop species in the Brassicaceae. An extensive in silico analysis of phylogenetic grouping, protein motif organization and intron-exon distribution confirmed that there are four subfamilies of BrTIFY proteins. Out of 36 BrTIFY genes, we identified 21 in the JAZ subfamily, seven in the TIFY subfamily, six in ZML and two in PPD. Extensive expression profiling of 21 BrTIFY JAZs in various tissues, especially in floral organs and at different flower growth stages revealed constitutive expression patterns, which suggest that BrTIFY JAZ genes are important during growth and development of B. rapa flowers. A protein interaction network analysis also pointed to association of these proteins with fertility and defense processes of B. rapa. Using a low temperature-treated whole-genome microarray data set, most of the JAZ genes were found to have variable transcript abundance between the contrasting inbred lines Chiifu and Kenshin of B. rapa. Subsequently, the expression of all 21 BrTIFY JAZs in response to cold stress was characterized in the same two lines via qPCR, demonstrating that nine genes were up-regulated. Importantly, the BrTIFY JAZs showed strong and differential expression upon JA treatment, pointing to their probable involvement in JA-mediated growth regulatory functions, especially during flower development and stress responses. Additionally, BrTIFY JAZs were induced in response to salt, drought, Fusarium, ABA, and SA treatments, and six genes (BrTIFY3

  9. Seeds of a possible natural hybrid between herbicide-resistant Brassica napus and Brassica rapa detected on a riverbank in Japan.

    PubMed

    Aono, Mitsuko; Wakiyama, Seiji; Nagatsu, Masato; Kaneko, Yukio; Nishizawa, Toru; Nakajima, Nobuyoshi; Tamaoki, Masanori; Kubo, Akihiro; Saji, Hikaru

    2011-01-01

    Transgenic herbicide-resistant varieties of Brassica napus, or oilseed rape, from which canola oil is obtained, are imported into Japan, where this plant is not commercially cultivated to a large extent. This study aimed to examine the distribution of herbicide-resistant B. napus and transgene flow to escaped populations of its closely related species, B. rapa and B. juncea. Samples were collected from 12 areas near major ports through which oilseed rape imports into Japan passed--Kashima, Chiba, Yokohama, Shimizu, Nagoya, Yokkaichi, Sakai-Senboku, Kobe, Uno, Mizushima, Kita-Kyushu, and Hakata--and the presence of glyphosate- and/or glufosinate-resistant B. napus was confirmed in all areas except Yokohama, Sakai-Senboku, Uno, and Kita-Kyushu. The Yokkaichi area was the focus because several herbicide-resistant B. napus plants were detected not only on the roadside where oilseed rape spilled during transportation but also on the riverbanks, where escaped populations of B. rapa and B. juncea grew. Samples of B. napus that were tolerant to both herbicides were detected in four continuous years (2005-2008) in this area, suggesting the possibility of intraspecific transgene flow within the escaped B. napus populations. Moreover, in 2008, seeds of a possible natural hybrid between herbicide-tolerant B. napus (2n = 38) and B. rapa (2n = 20) were detected; some seedlings derived from the seeds collected at a Yokkaichi site showed glyphosate resistance and had 2n = 29 chromosomes. This observation strongly suggests the occurrence of hybridization between herbicide-resistant B. napus and escaped B. rapa and the probability of introgression of a herbicide-resistance gene into related escaped species. PMID:22179196

  10. Identification and characterization of microRNAs in oilseed rape (Brassica napus) responsive to infection with the pathogenic fungus Verticillium longisporum using Brassica AA (Brassica rapa) and CC (Brassica oleracea) as reference genomes.

    PubMed

    Shen, Dan; Suhrkamp, Ina; Wang, Yu; Liu, Shenyi; Menkhaus, Jan; Verreet, Joseph-Alexander; Fan, Longjiang; Cai, Daguang

    2014-11-01

    Verticillium longisporum, a soil-borne pathogenic fungus, causes vascular disease in oilseed rape (Brassica napus). We proposed that plant microRNAs (miRNAs) are involved in the plant-V. longisporum interaction. To identify oilseed rape miRNAs, we deep-sequenced two small RNA libraries made from V. longisporum infected/noninfected roots and employed Brassica rapa and Brassica oleracea genomes as references for miRNA prediction and characterization. We identified 893 B. napus miRNAs representing 360 conserved and 533 novel miRNAs, and mapped 429 and 464 miRNAs to the AA and CC genomes, respectively. Microsynteny analysis with the conserved miRNAs and their flanking protein coding sequences revealed 137 AA-CC genome syntenic miRNA pairs and 61 AA and 42 CC genome-unique miRNAs. Sixty-two miRNAs were responsive to the V. longisporum infection. We present data for specific interactions and simultaneously reciprocal changes in the expression levels of the miRNAs and their targets in the infected roots. We demonstrate that miRNAs are involved in the plant-fungus interaction and that miRNA168-Argonaute 1 (AGO1) expression modulation might act as a key regulatory module in a compatible plant-V. longisporum interaction. Our results suggest that V. longisporum may have evolved a virulence mechanism by interference with plant miRNAs to reprogram plant gene expression and achieve infection. PMID:25132374

  11. Genomic and Post-Translational Modification Analysis of Leucine-Rich-Repeat Receptor-Like Kinases in Brassica rapa

    PubMed Central

    Dhandapani, Vignesh; Yu, Xiaona; Choi, Su Ryun; Oh, Man-Ho; Lim, Yong Pyo

    2015-01-01

    Among several receptor-like kinases (RLKs), leucine-rich-repeat receptor-like kinases (LRR-RLKs) are a major group of genes that play crucial roles in growth, development and stress responses in plant systems. Given that they have several functional roles, it is important to investigate their roles in Brassica rapa. In the present study, 303 LRR-RLKs were identified in the genome of B. rapa and comparative phylogenetic analysis of 1213 combined LRR-RLKs of B. rapa, Arabidopsis thaliana, Oryza sativa and Populus trichocarpa helped us to categorize the gene family into 15 subfamilies based on their sequence and structural similarities. The chromosome localizations of 293 genes allowed the prediction of duplicates, and motif conservation and intron/exon patterns showed differences among the B. rapa LRR-RLK (BrLRR-RLK) genes. Additionally, computational function annotation and expression analysis was used to predict their possible functional roles in the plant system. Biochemical results for 11 selected genes showed variations in phosphorylation activity. Interestingly, BrBAK1 showed strong auto-phosphorylation and trans-phosphorylation on its tyrosine and threonine residues compared with AtBAK1 in previous studies. The AtBAK1 receptor kinase is involved in plant growth and development, plant innate immunity, and programmed cell death, and our results suggest that BrBAK1 might also be involved in the same functions. Another interesting result was that BrBAK1, BrBRI1, BrPEPR1 and BrPEPR2 showed activity with both anti-phosphotyrosine and anti-phosphothreonine antibodies, indicating that they might have dual-specificity kinase activity. This study provides comprehensive results for the BrLRR-RLKs, revealing expansion of the gene family through gene duplications, structural similarities and variations among the genes, and potential functional roles according to gene ontology, transcriptome profiling and biochemical analysis. PMID:26588465

  12. Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed in Brassica rapa.

    PubMed

    Zhang, Jifang; Liu, Zhiyuan; Liang, Jianli; Wu, Jian; Cheng, Feng; Wang, Xiaowu

    2015-10-01

    The glucosinolate biosynthetic gene AOP2 encodes an enzyme that plays a crucial role in catalysing the conversion of beneficial glucosinolates into anti-nutritional ones. In Brassica rapa, three copies of BrAOP2 have been identified, but their function in establishing the glucosinolate content of B. rapa is poorly understood. Here, we used phylogenetic and gene structure analyses to show that BrAOP2 proteins have evolved via a duplication process retaining two highly conserved domains at the N-terminal and C-terminal regions, while the middle part has experienced structural divergence. Heterologous expression and in vitro enzyme assays and Arabidopsis mutant complementation studies showed that all three BrAOP2 genes encode functional BrAOP2 proteins that convert the precursor methylsulfinyl alkyl glucosinolate to the alkenyl form. Site-directed mutagenesis showed that His356, Asp310, and Arg376 residues are required for the catalytic activity of one of the BrAOP2 proteins (BrAOP2.1). Promoter-β-glucuronidase lines revealed that the BrAOP2.3 gene displayed an overlapping but distinct tissue- and cell-specific expression profile compared with that of the BrAOP2.1 and BrAOP2.2 genes. Quantitative real-time reverse transcription-PCR assays demonstrated that BrAOP2.1 showed a slightly different pattern of expression in below-ground tissue at the seedling stage and in the silique at the reproductive stage compared with BrAOP2.2 and BrAOP2.3 genes in B. rapa. Taken together, our results revealed that all three BrAOP2 paralogues are active in B. rapa but have functionally diverged. PMID:26188204

  13. Three genes encoding AOP2, a protein involved in aliphatic glucosinolate biosynthesis, are differentially expressed in Brassica rapa

    PubMed Central

    Zhang, Jifang; Liu, Zhiyuan; Liang, Jianli; Wu, Jian; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The glucosinolate biosynthetic gene AOP2 encodes an enzyme that plays a crucial role in catalysing the conversion of beneficial glucosinolates into anti-nutritional ones. In Brassica rapa, three copies of BrAOP2 have been identified, but their function in establishing the glucosinolate content of B. rapa is poorly understood. Here, we used phylogenetic and gene structure analyses to show that BrAOP2 proteins have evolved via a duplication process retaining two highly conserved domains at the N-terminal and C-terminal regions, while the middle part has experienced structural divergence. Heterologous expression and in vitro enzyme assays and Arabidopsis mutant complementation studies showed that all three BrAOP2 genes encode functional BrAOP2 proteins that convert the precursor methylsulfinyl alkyl glucosinolate to the alkenyl form. Site-directed mutagenesis showed that His356, Asp310, and Arg376 residues are required for the catalytic activity of one of the BrAOP2 proteins (BrAOP2.1). Promoter–β-glucuronidase lines revealed that the BrAOP2.3 gene displayed an overlapping but distinct tissue- and cell-specific expression profile compared with that of the BrAOP2.1 and BrAOP2.2 genes. Quantitative real-time reverse transcription-PCR assays demonstrated that BrAOP2.1 showed a slightly different pattern of expression in below-ground tissue at the seedling stage and in the silique at the reproductive stage compared with BrAOP2.2 and BrAOP2.3 genes in B. rapa. Taken together, our results revealed that all three BrAOP2 paralogues are active in B. rapa but have functionally diverged. PMID:26188204

  14. Development of InDel markers for Brassica rapa based on whole-genome re-sequencing.

    PubMed

    Liu, Bo; Wang, Yan; Zhai, Wen; Deng, Jie; Wang, Hui; Cui, Yang; Cheng, Feng; Wang, Xiaowu; Wu, Jian

    2013-01-01

    Genome-wide detection of short insertion/deletion length polymorphisms (InDels, <5 bp) in Brassica rapa (named the A genome) was performed by comparing whole-genome re-sequencing data from two B. rapa accessions, L144 and Z16, to the reference genome sequence of Chiifu-401-42. In total, we identified 108,558 InDel polymorphisms between Chiifu-401-42 and L144, 26,795 InDels between Z16 and Chiifu-401-42, and 26,693 InDels between L144 and Z16. From these, 639 InDel polymorphisms of 3-5 bp in length between L144 and Z16 were selected for experimental validation; 491 (77%) yielded single PCR fragments and showed polymorphisms, 7 (1%) did not amplify a product, and 141 (22%) showed no polymorphism. For further validation of these intra-specific InDel polymorphisms, 503 candidates, randomly selected from the 639 InDels, were screened across seven accessions representing different B. rapa cultivar groups. Of these assayed markers, 387 (77%) were polymorphic, 111 (22%) were not polymorphic and 5 (1%) did not amplify a PCR product. Furthermore, we randomly selected 518 InDel markers to validate their polymorphism in B. napus (the AC genome) and B. juncea (the AB genome), of which more than 90% amplified a PCR product; 132 (25%) showed polymorphism between the two B. napus accessions and 41 (8%) between the two B. juncea accessions. This set of novel PCR-based InDel markers will be a valuable resource for genetic studies and breeding programs in B. rapa. PMID:22972202

  15. Genomic and Post-Translational Modification Analysis of Leucine-Rich-Repeat Receptor-Like Kinases in Brassica rapa.

    PubMed

    Rameneni, Jana Jeevan; Lee, Yeon; Dhandapani, Vignesh; Yu, Xiaona; Choi, Su Ryun; Oh, Man-Ho; Lim, Yong Pyo

    2015-01-01

    Among several receptor-like kinases (RLKs), leucine-rich-repeat receptor-like kinases (LRR-RLKs) are a major group of genes that play crucial roles in growth, development and stress responses in plant systems. Given that they have several functional roles, it is important to investigate their roles in Brassica rapa. In the present study, 303 LRR-RLKs were identified in the genome of B. rapa and comparative phylogenetic analysis of 1213 combined LRR-RLKs of B. rapa, Arabidopsis thaliana, Oryza sativa and Populus trichocarpa helped us to categorize the gene family into 15 subfamilies based on their sequence and structural similarities. The chromosome localizations of 293 genes allowed the prediction of duplicates, and motif conservation and intron/exon patterns showed differences among the B. rapa LRR-RLK (BrLRR-RLK) genes. Additionally, computational function annotation and expression analysis was used to predict their possible functional roles in the plant system. Biochemical results for 11 selected genes showed variations in phosphorylation activity. Interestingly, BrBAK1 showed strong auto-phosphorylation and trans-phosphorylation on its tyrosine and threonine residues compared with AtBAK1 in previous studies. The AtBAK1 receptor kinase is involved in plant growth and development, plant innate immunity, and programmed cell death, and our results suggest that BrBAK1 might also be involved in the same functions. Another interesting result was that BrBAK1, BrBRI1, BrPEPR1 and BrPEPR2 showed activity with both anti-phosphotyrosine and anti-phosphothreonine antibodies, indicating that they might have dual-specificity kinase activity. This study provides comprehensive results for the BrLRR-RLKs, revealing expansion of the gene family through gene duplications, structural similarities and variations among the genes, and potential functional roles according to gene ontology, transcriptome profiling and biochemical analysis. PMID:26588465

  16. Evaluation of the biophysical limitations on photosynthesis of four varietals of Brassica rapa

    NASA Astrophysics Data System (ADS)

    Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B.; Weinig, C.

    2014-12-01

    Evaluating performance of agricultural varietals can support the identification of genotypes that will increase yield and can inform management practices. The biophysical limitations of photosynthesis are amongst the key factors that necessitate evaluation. This study evaluated how four biophysical limitations on photosynthesis, stomatal response to vapor pressure deficit, maximum carboxylation rate by Rubisco (Ac), rate of photosynthetic electron transport (Aj) and triose phosphate use (At) vary between four Brassica rapa genotypes. Leaf gas exchange data was used in an ecophysiological process model to conduct this evaluation. The Terrestrial Regional Ecosystem Exchange Simulator (TREES) integrates the carbon uptake and utilization rate limiting factors for plant growth. A Bayesian framework integrated in TREES here used net A as the target to estimate the four limiting factors for each genotype. As a first step the Bayesian framework was used for outlier detection, with data points outside the 95% confidence interval of model estimation eliminated. Next parameter estimation facilitated the evaluation of how the limiting factors on A different between genotypes. Parameters evaluated included maximum carboxylation rate (Vcmax), quantum yield (ϕJ), the ratio between Vc-max and electron transport rate (J), and trios phosphate utilization (TPU). Finally, as trios phosphate utilization has been shown to not play major role in the limiting A in many plants, the inclusion of At in models was evaluated using deviance information criteria (DIC). The outlier detection resulted in a narrowing in the estimated parameter distributions allowing for greater differentiation of genotypes. Results show genotypes vary in the how limitations shape assimilation. The range in Vc-max , a key parameter in Ac, was 203.2 - 223.9 umol m-2 s-1 while the range in ϕJ, a key parameter in AJ, was 0.463 - 0.497 umol m-2 s-1. The added complexity of the TPU limitation did not improve model

  17. Structural changes in the main root of brassica rapa l. seedlings under clinorotation

    NASA Astrophysics Data System (ADS)

    Kalinina, Y.

    In order to understand the level of the influence of gravity upon root growth and development the complex investigations has to be carried out. The aim of our work was the research of formation of root growth zones in altered gravity. With this purpose the root anatomy of 6-day old Brassica rapa L. seedlings grown on the Hogland's medium at illumination 12000 luxes and temperature 24-25°C on a slowly rotating horizontal clinostat and at 1 g was investigated using light microscopy. It has been shown that clinorotation causes a decrease of the length of root growth zones: meristematic zone - on 38 %, transition zone (distal elongation zone) - on 50 %, and elongation zone - on 64 %. The greatest differences between control and clinostat variants are revealed in the length of both the layers of periblem in the meristematic zone and epidermis in the distal elongation zone. The reliable difference between cell sizes of the all investigated zones in the control and experiment was not found. Only in a cortex of transition zone was marked the decreasing of cell length on 16 % in subepidermal layer and on 20 % in the other layer of a cortex. In the same time, the reduction of cell number in protoderm on 41 % and in the both periblem outer layer on 50 % and the inner layer on 47 % of the meristematic zone was revealed. The lack of significant difference in sizes of meristematic cells along with the simultaneous decrease of cell number allowed us to conclude that proliferation activity of meristem is depressed under clinorotation. The information about the most gravisensitive processes and strategies of adaptation to microgravity is a basis of our understanding of plants' growth and development under the long-term influence of this factor in space flight. Thus, the obtained results are the addition to our knowledge in root development in the absence of gravity but further investigations are going on and still more are required. Electron microscopic examinations are the next

  18. Differential Gene Expression in Brassica rapa Roots After Reorientation and Clinorotation.

    NASA Astrophysics Data System (ADS)

    Edge, Andrea; Hasenstein, Karl H.

    Seedlings align their growth axes parallel to the gravity vector. Any growth adjustment affects genes. We examined these changes in Brassica rapa roots that were reoriented and clinorotated. Gene expression levels related to the actin cytoskeleton (ACT7 and ADK1) and auxin transport (IAA5, PIN1, PIN3, AGR1, ARG1) were assessed in roots grown for 42 hours and then either reoriented to 90° for 15 min, 1, 2 and 3 hours or clinorotated vertically or horizontally for 42 hrs at 2 rpm. After these treatments, roots from 20 seedlings were divided into three sections, the root tip, elongation zone, and maturation zone. The samples from corresponding treatments were combined for RNA extraction, reverse transcription and analysis by quantitative PCR. The results show that gene expression changes in response to duration of reorientation and orientation during clinorotation. All genes, except PIN1 and AGR1 were upregulated in the tip after 2 hours of reorientation. Expression of genes also varied between the root sections except for PIN1, which was uniformly expressed. ADK1 was the only gene that showed consistent down-regulation in all three root regions in vertically and horizontally clinorotated roots (ca 30% of controls). In contrast, ADK1 was upregulated (more than 150 fold) in the tip of roots that were reoriented for 2 hours but little upregulation after one hour (less than 2 fold compared to controls). Our results indicate that gene expression during the gravitropic response changes over time with the tip region being the most dynamic tissue in the root. The large upregulation of ADK1 at 2 h after reorientation may be related to the persistence of the gravitropic response. Because of the variability of the expression profiles, analyses that are based on the entire root miss tissue specific changes in gene expression. Differences in gene expression after vertical and horizontal clinorotation indicates that the graviresponse system is sensitive not just to the magnitude

  19. Evolution, Expression Differentiation and Interaction Specificity of Heterotrimeric G-Protein Subunit Gene Family in the Mesohexaploid Brassica rapa

    PubMed Central

    Arya, Gulab C.; Kumar, Roshan; Bisht, Naveen C.

    2014-01-01

    Heterotrimeric G-proteins, comprising of Gα, Gβ, and Gγ subunits, are important signal transducers which regulate many aspects of fundamental growth and developmental processes in all eukaryotes. Initial studies in model plants Arabidopsis and rice suggest that the repertoire of plant G-protein is much simpler than that observed in metazoans. In order to assess the consequence of whole genome triplication events within Brassicaceae family, we investigated the multiplicity of G-protein subunit genes in mesohexaploid Brassica rapa, a globally important vegetable and oilseed crop. We identified one Gα (BraA.Gα1), three Gβ (BraA.Gβ1, BraA.Gβ2, and BraA.Gβ3), and five Gγ (BraA.Gγ1, BraA.Gγ2, BraA.Gγ3, BraA.Gγ4, and BraA.Gγ5) genes from B. rapa, with a possibility of 15 Gαβγ heterotrimer combinations. Our analysis suggested that the process of genome triplication coupled with gene-loss (gene-fractionation) phenomenon have shaped the quantitative and sequence diversity of G-protein subunit genes in the extant B. rapa genome. Detailed expression analysis using qRT-PCR assays revealed that the G-protein genes have retained ubiquitous but distinct expression profiles across plant development. The expression of multiple G-protein genes was differentially regulated during seed-maturation and germination stages, and in response to various phytohormone treatments and stress conditions. Yeast-based interaction analysis showed that G-protein subunits interacted in most of the possible combinations, with some degree of subunit-specific interaction specificity, to control the functional selectivity of G-protein heterotrimer in different cell and tissue-types or in response to different environmental conditions. Taken together, this research identifies a highly diverse G-protein signaling network known to date from B. rapa, and provides a clue about the possible complexity of G-protein signaling networks present across globally important Brassica species. PMID

  20. Evolution, expression differentiation and interaction specificity of heterotrimeric G-protein subunit gene family in the mesohexaploid Brassica rapa.

    PubMed

    Arya, Gulab C; Kumar, Roshan; Bisht, Naveen C

    2014-01-01

    Heterotrimeric G-proteins, comprising of Gα, Gβ, and Gγ subunits, are important signal transducers which regulate many aspects of fundamental growth and developmental processes in all eukaryotes. Initial studies in model plants Arabidopsis and rice suggest that the repertoire of plant G-protein is much simpler than that observed in metazoans. In order to assess the consequence of whole genome triplication events within Brassicaceae family, we investigated the multiplicity of G-protein subunit genes in mesohexaploid Brassica rapa, a globally important vegetable and oilseed crop. We identified one Gα (BraA.Gα1), three Gβ (BraA.Gβ1, BraA.Gβ2, and BraA.Gβ3), and five Gγ (BraA.Gγ1, BraA.Gγ2, BraA.Gγ3, BraA.Gγ4, and BraA.Gγ5) genes from B. rapa, with a possibility of 15 Gαβγ heterotrimer combinations. Our analysis suggested that the process of genome triplication coupled with gene-loss (gene-fractionation) phenomenon have shaped the quantitative and sequence diversity of G-protein subunit genes in the extant B. rapa genome. Detailed expression analysis using qRT-PCR assays revealed that the G-protein genes have retained ubiquitous but distinct expression profiles across plant development. The expression of multiple G-protein genes was differentially regulated during seed-maturation and germination stages, and in response to various phytohormone treatments and stress conditions. Yeast-based interaction analysis showed that G-protein subunits interacted in most of the possible combinations, with some degree of subunit-specific interaction specificity, to control the functional selectivity of G-protein heterotrimer in different cell and tissue-types or in response to different environmental conditions. Taken together, this research identifies a highly diverse G-protein signaling network known to date from B. rapa, and provides a clue about the possible complexity of G-protein signaling networks present across globally important Brassica species. PMID

  1. Genome-Wide Survey and Expression Analysis of the Putative Non-Specific Lipid Transfer Proteins in Brassica rapa L

    PubMed Central

    Li, Jun; Gao, Guizhen; Xu, Kun; Chen, Biyun; Yan, Guixin; Li, Feng; Qiao, Jiangwei; Zhang, Tianyao; Wu, Xiaoming

    2014-01-01

    Background Plant non-specific lipid transfer proteins (nsLtps) are small, basic proteins encoded by multigene families and have reported functions in many physiological processes such as mediating phospholipid transfer, defense reactions against phytopathogens, the adaptation of plants to various environmental conditions, and sexual reproduction. To date, no genome-wide overview of the Brassica rapa nsLtp (BrnsLtp) gene family has been performed. Therefore, as the first step and as a helpful strategy to elucidate the functions of BrnsLtps, a genome-wide study for this gene family is necessary. Methodology/Principal Finding In this study, a total of 63 putative BrnsLtp genes were identified through a comprehensive in silico analysis of the whole genome of B. rapa. Based on the sequence similarities, these BrnsLtps was grouped into nine types (I, II, III, IV, V, VI, VIII, IX, and XI). There is no type VII nsLtps in B. rapa, and a new type, XI nsLtps, was identified in B. rapa. Furthermore, nine type II AtLtps have no homologous genes in B. rapa. Gene duplication analysis demonstrated that the conserved collinear block of each BrnsLtp is highly identical to those in Arabidopsis and that both segmental duplications and tandem duplications seem to play equal roles in the diversification of this gene family. Expression analysis indicated that 29 out of the 63 BrnsLtps showed specific expression patterns. After careful comparison and analysis, we hypothesize that some of the type I BrnsLtps may function like Arabidopsis pathogenesis-related-14 (PR-14) proteins to protect the plant from phytopathogen attack. Eleven BrnsLtps with inflorescence-specific expression may play important roles in sexual reproduction. Additionally, BrnsLtpI.3 may have functions similar to Arabidopsis LTP1. Conclusions/Significance The genome-wide identification, bioinformatic analysis and expression analysis of BrnsLtp genes should facilitate research of this gene family and polyploidy evolution

  2. Growth, productivity, and competitiveness of introgressed weedy Brassica rapa hybrids selected for the presence of Bt cry1Ac and gfp transgenes.

    PubMed

    Halfhill, Matthew D; Sutherland, Jamie P; Moon, Hong Seok; Poppy, Guy M; Warwick, Suzanne I; Weissinger, Arthur K; Rufty, Thomas W; Raymer, Paul L; Stewart, C Neal

    2005-09-01

    Concerns exist that transgenic crop x weed hybrid populations will be more vigorous and competitive with crops compared with the parental weed species. Hydroponic, glasshouse, and field experiments were performed to evaluate the effects of introgression of Bacillus thuringiensis (Bt) cry1Ac and green fluorescent protein (GFP) transgenes on hybrid productivity and competitiveness in four experimental Brassica rapa x transgenic Brassica napus hybrid generations (F1, BC1F1, BC2F1 and BC2F2). The average vegetative growth and nitrogen (N) use efficiency of transgenic hybrid generations grown under high N hydroponic conditions were lower than that of the weed parent (Brassica rapa, AA, 2n = 20), but similar to the transgenic crop parent, oilseed rape (Brassica napus, AACC, 2n = 38). No generational differences were detected under low N conditions. In two noncompetitive glasshouse experiments, both transgenic and nontransgenic BC2F2 hybrids had on average less vegetative growth and seed production than B. rapa. In two high intraspecific competition field experiments with varied herbivore pressure, BC2F2 hybrids produced less vegetative dry weight than B. rapa. The competitive ability of transgenic and nontransgenic BC2F2 hybrids against a neighbouring crop species were quantified in competition experiments that assayed wheat (Triticum aestivum) yield reductions under agronomic field conditions. The hybrids were the least competitive with wheat compared with parental Brassica competitors, although differences between transgenic and nontransgenic hybrids varied with location. Hybridization, with or without transgene introgression, resulted in less productive and competitive populations. PMID:16101783

  3. Metabolic Profiling in Chinese Cabbage (Brassica rapa L. subsp. pekinensis) Cultivars Reveals that Glucosinolate Content Is Correlated with Carotenoid Content.

    PubMed

    Baek, Seung-A; Jung, Young-Ho; Lim, Sun-Hyung; Park, Sang Un; Kim, Jae Kwang

    2016-06-01

    A total of 38 bioactive compounds, including glucosinolates, carotenoids, tocopherols, sterols, and policosanols, were characterized from nine varieties of Chinese cabbage (Brassica rapa L. subsp. pekinensis) to determine their phytochemical diversity and analyze their abundance relationships. The metabolite profiles were evaluated with principal component analysis (PCA), Pearson correlation analysis, and hierarchical clustering analysis (HCA). PCA and HCA identified two distinct varieties of Chinese cabbage (Cheonsangcheonha and Waldongcheonha) with higher levels of glucosinolates and carotenoids. Pairwise comparisons of the 38 metabolites were calculated using Pearson correlation coefficients. The HCA, which used the correlation coefficients, clustered metabolites that are derived from closely related biochemical pathways. Significant correlations were discovered between chlorophyll and carotenoids. Additionally, aliphatic glucosinolate and carotenoid levels were positively correlated. The Cheonsangcheonha and Waldongcheonha varieties appear to be good candidates for breeding because they have high glucosinolate and carotenoid levels. PMID:27172980

  4. Analysis of global gene expression profiles to identify differentially expressed genes critical for embryo development in Brassica rapa.

    PubMed

    Zhang, Yu; Peng, Lifang; Wu, Ya; Shen, Yanyue; Wu, Xiaoming; Wang, Jianbo

    2014-11-01

    Embryo development represents a crucial developmental period in the life cycle of flowering plants. To gain insights into the genetic programs that control embryo development in Brassica rapa L., RNA sequencing technology was used to perform transcriptome profiling analysis of B. rapa developing embryos. The results generated 42,906,229 sequence reads aligned with 32,941 genes. In total, 27,760, 28,871, 28,384, and 25,653 genes were identified from embryos at globular, heart, early cotyledon, and mature developmental stages, respectively, and analysis between stages revealed a subset of stage-specific genes. We next investigated 9,884 differentially expressed genes with more than fivefold changes in expression and false discovery rate ≤ 0.001 from three adjacent-stage comparisons; 1,514, 3,831, and 6,633 genes were detected between globular and heart stage embryo libraries, heart stage and early cotyledon stage, and early cotyledon and mature stage, respectively. Large numbers of genes related to cellular process, metabolism process, response to stimulus, and biological process were expressed during the early and middle stages of embryo development. Fatty acid biosynthesis, biosynthesis of secondary metabolites, and photosynthesis-related genes were expressed predominantly in embryos at the middle stage. Genes for lipid metabolism and storage proteins were highly expressed in the middle and late stages of embryo development. We also identified 911 transcription factor genes that show differential expression across embryo developmental stages. These results increase our understanding of the complex molecular and cellular events during embryo development in B. rapa and provide a foundation for future studies on other oilseed crops. PMID:25214014

  5. Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns.

    PubMed

    Duan, Weike; Huang, Zhinan; Song, Xiaoming; Liu, Tongkun; Liu, Hailong; Hou, Xilin; Li, Ying

    2016-01-01

    Pectins are fundamental polysaccharides in the plant primary cell wall. Polygalacturonases (PGs) and pectin methylesterases (PMEs), major components of the pectin remodeling and disassembly network, are involved in cell separation processes during many stages of plant development. A comprehensive study of these genes in plants could shed light on the evolution patterns of their structural development. In this study, we conducted whole-genome annotation, molecular evolution and gene expression analyses of PGs and PMEs in Brassica rapa and 8 other plant species. A total of 100 PGs and 110 PMEs were identified in B. rapa; they primarily diverged from 12-18 MYA and PMEs were retained more than PGs. Along with another 305 PGs and 348 PMEs in the 8 species, two different expansion or evolution types were discovered: a new branch of class A PGs appeared after the split of gymnosperms and angiosperms, which led to the rapid expansion of PGs; the pro domain was obtained or lost in the proPMEs through comprehensive analyses among PME genes. In addition, the PGs and PMEs exhibit diverged expression patterns. These findings will lead to novel insight regarding functional divergence and conservation in the gene families and provide more support for molecular evolution analyses. PMID:27112365

  6. Construction of random sheared fosmid library from Chinese cabbage and its use for Brassica rapa genome sequencing project.

    PubMed

    Park, Tae-Ho; Park, Beom-Seok; Kim, Jin-A; Hong, Joon Ki; Jin, Mina; Seol, Young-Joo; Mun, Jeong-Hwan

    2011-01-01

    As a part of the Multinational Genome Sequencing Project of Brassica rapa, linkage group R9 and R3 were sequenced using a bacterial artificial chromosome (BAC) by BAC strategy. The current physical contigs are expected to cover approximately 90% euchromatins of both chromosomes. As the project progresses, BAC selection for sequence extension becomes more limited because BAC libraries are restriction enzyme-specific. To support the project, a random sheared fosmid library was constructed. The library consists of 97536 clones with average insert size of approximately 40 kb corresponding to seven genome equivalents, assuming a Chinese cabbage genome size of 550 Mb. The library was screened with primers designed at the end of sequences of nine points of scaffold gaps where BAC clones cannot be selected to extend the physical contigs. The selected positive clones were end-sequenced to check the overlap between the fosmid clones and the adjacent BAC clones. Nine fosmid clones were selected and fully sequenced. The sequences revealed two completed gap filling and seven sequence extensions, which can be used for further selection of BAC clones confirming that the fosmid library will facilitate the sequence completion of B. rapa. PMID:21338952

  7. Responses of wheat (Triticum aestivum) and turnip (Brassica rapa) to the combined exposure of carbaryl and ultraviolet radiation.

    PubMed

    Lima, Maria P R; Soares, Amadeu M V M; Loureiro, Susana

    2015-07-01

    The increase of ultraviolet (UV) radiation reaching the Earth's surface as a result of increased ozone layer depletion has affected crop production systems and, in combination with pesticides used in agricultural activities, can lead to greater risks to the environment. The impact of UV radiation and carbaryl singly and in combination on Triticum aestivum (wheat) and Brassica rapa (turnip) was studied. The combined exposure was analyzed using the MixTox tool and was based on the conceptual model of independent action, where possible deviations to synergism or antagonism and dose-ratio or dose-level response pattern were also considered. Compared with the control, carbaryl and UV radiation individually led to reductions in growth, fresh and dry weight, and water content for both species. Combined treatment of UV and carbaryl was more deleterious compared with single exposure. For T. aestivum length, no interaction between the 2 stressors was found (independent action), and a dose-level deviation was the best description for the weight parameters. For B. rapa, dose-ratio deviations from the conceptual model were found when length and dry weight were analyzed, and a higher than expected effect on the fresh weight (synergism) occurred with combined exposure. PMID:25754078

  8. Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns

    PubMed Central

    Duan, Weike; Huang, Zhinan; Song, Xiaoming; Liu, Tongkun; Liu, Hailong; Hou, Xilin; Li, Ying

    2016-01-01

    Pectins are fundamental polysaccharides in the plant primary cell wall. Polygalacturonases (PGs) and pectin methylesterases (PMEs), major components of the pectin remodeling and disassembly network, are involved in cell separation processes during many stages of plant development. A comprehensive study of these genes in plants could shed light on the evolution patterns of their structural development. In this study, we conducted whole-genome annotation, molecular evolution and gene expression analyses of PGs and PMEs in Brassica rapa and 8 other plant species. A total of 100 PGs and 110 PMEs were identified in B. rapa; they primarily diverged from 12–18 MYA and PMEs were retained more than PGs. Along with another 305 PGs and 348 PMEs in the 8 species, two different expansion or evolution types were discovered: a new branch of class A PGs appeared after the split of gymnosperms and angiosperms, which led to the rapid expansion of PGs; the pro domain was obtained or lost in the proPMEs through comprehensive analyses among PME genes. In addition, the PGs and PMEs exhibit diverged expression patterns. These findings will lead to novel insight regarding functional divergence and conservation in the gene families and provide more support for molecular evolution analyses. PMID:27112365

  9. Cotyledon-Generated Auxin Is Required for Shade-Induced Hypocotyl Growth in Brassica rapa1[C][W][OPEN

    PubMed Central

    Procko, Carl; Crenshaw, Charisse Michelle; Ljung, Karin; Noel, Joseph Patrick; Chory, Joanne

    2014-01-01

    Plant architecture is optimized for the local light environment. In response to foliar shade or neighbor proximity (low red to far-red light), some plant species exhibit shade-avoiding phenotypes, including increased stem and hypocotyl growth, which increases the likelihood of outgrowing competitor plants. If shade persists, early flowering and the reallocation of growth resources to stem elongation ultimately affect the yield of harvestable tissues in crop species. Previous studies have shown that hypocotyl growth in low red to far-red shade is largely dependent on the photoreceptor phytochrome B and the phytohormone auxin. However, where shade is perceived in the plant and how auxin regulates growth spatially are less well understood. Using the oilseed and vegetable crop species Brassica rapa, we show that the perception of low red to far-red shade by the cotyledons triggers hypocotyl cell elongation and auxin target gene expression. Furthermore, we find that following shade perception, elevated auxin levels occur in a basipetal gradient away from the cotyledons and that this is coincident with a gradient of auxin target gene induction. These results show that cotyledon-generated auxin regulates hypocotyl elongation. In addition, we find in mature B. rapa plants that simulated shade does not affect seed oil composition but may affect seed yield. This suggests that in field settings where mutual shading between plants may occur, a balance between plant density and seed yield per plant needs to be achieved for maximum oil yield, while oil composition might remain constant. PMID:24891610

  10. DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory

    PubMed Central

    Slankster, Eryn E.; Chase, Jillian M.; Jones, Lauren A.; Wendell, Douglas L.

    2012-01-01

    We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tandem repeat (VNTR)-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a non-genic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology. PMID:22675329

  11. DNA-Based Genetic Markers for Rapid Cycling Brassica Rapa (Fast Plants Type) Designed for the Teaching Laboratory.

    PubMed

    Slankster, Eryn E; Chase, Jillian M; Jones, Lauren A; Wendell, Douglas L

    2012-01-01

    We have developed DNA-based genetic markers for rapid cycling Brassica rapa (RCBr), also known as Fast Plants. Although markers for B. rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP) based markers and 14 variable number tandem repeat (VNTR)-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a non-genic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology. PMID:22675329

  12. Transcriptome analysis of newly classified bZIP transcription factors of Brassica rapa in cold stress response.

    PubMed

    Hwang, Indeok; Jung, Hee-Jeong; Park, Jong-In; Yang, Tae-Jin; Nou, Ill-Sup

    2014-09-01

    Plant bZIP transcription factors play crucial roles in biological processes. In this study, 136 putative bZIP transcription members were identified in Brassica rapa. The bZIP family can be divided into nine groups according to the specific amino acid rich domain in B. rapa and Arabidopsis thaliana. To screen the cold stress responsive BrbZIP genes, we evaluated whether the transcription patterns of the BrbZIP genes were enhanced by cold treatment in the inbred lines, Chiifu and Kenshin, by microarray data analysis and qRT-PCR. The expression level of six genes increased significantly in Kenshin, but these genes were unchanged in Chiifu. These findings suggest that the six genes that encoded proteins containing N-rich regions might be involved in cold stress response. The results presented herein provide valuable information regarding the molecular basis of the bZIP transcription factors and their potential function in regulation growth and development, particularly in cold stress response. PMID:25075938

  13. Genome-Wide Survey and Expression Profile Analysis of the Mitogen-Activated Protein Kinase (MAPK) Gene Family in Brassica rapa

    PubMed Central

    Yu, Hao; Qu, Cunmin; Tang, Zhanglin; Li, Jiana; Chai, Yourong; Liang, Ying

    2015-01-01

    Mitogen-activated protein kinase (MAPK) cascades are fundamental signal transduction modules in plants, controlling cell division, development, hormone signaling, and biotic and abiotic stress responses. Although MAPKs have been investigated in several plant species, a comprehensive analysis of the MAPK gene family has hitherto not been performed in Brassica rapa. In this study, we identified 32 MAPKs in the B. rapa genome by conducting BLASTP and syntenic block analyses, and screening for the essential signature motif (TDY or TEY) of plant MAPK proteins. Of the 32 BraMAPK genes retrieved from the Brassica Database, 13 exhibited exon splicing errors, excessive splicing of the 5' sequence, excessive retention of the 5' sequence, and sequencing errors of the 3' end. Phylogenetic trees of the 32 corrected MAPKs from B. rapa and of MAPKs from other plants generated by the neighbor-joining and maximum likelihood methods suggested that BraMAPKs could be divided into four groups (groups A, B, C, and D). Gene number expansion was observed for BraMAPK genes in groups A and D, which may have been caused by the tandem duplication and genome triplication of the ancestral genome of the Brassica progenitor. Except for five members of the BraMAPK10 subfamily, the identified BraMAPKs were expressed in most of the tissues examined, including callus, root, stem, leaf, flower, and silique. Quantitative real-time PCR demonstrated that at least six and five BraMAPKs were induced or repressed by various abiotic stresses and hormone treatments, respectively, suggesting their potential roles in the abiotic stress response and various hormone signal transduction pathways in B. rapa. This study provides valuable insight into the putative physiological and biochemical functions of MAPK genes in B. rapa. PMID:26173020

  14. Genome-Wide Survey and Expression Profile Analysis of the Mitogen-Activated Protein Kinase (MAPK) Gene Family in Brassica rapa.

    PubMed

    Lu, Kun; Guo, Wenjin; Lu, Junxing; Yu, Hao; Qu, Cunmin; Tang, Zhanglin; Li, Jiana; Chai, Yourong; Liang, Ying

    2015-01-01

    Mitogen-activated protein kinase (MAPK) cascades are fundamental signal transduction modules in plants, controlling cell division, development, hormone signaling, and biotic and abiotic stress responses. Although MAPKs have been investigated in several plant species, a comprehensive analysis of the MAPK gene family has hitherto not been performed in Brassica rapa. In this study, we identified 32 MAPKs in the B. rapa genome by conducting BLASTP and syntenic block analyses, and screening for the essential signature motif (TDY or TEY) of plant MAPK proteins. Of the 32 BraMAPK genes retrieved from the Brassica Database, 13 exhibited exon splicing errors, excessive splicing of the 5' sequence, excessive retention of the 5' sequence, and sequencing errors of the 3' end. Phylogenetic trees of the 32 corrected MAPKs from B. rapa and of MAPKs from other plants generated by the neighbor-joining and maximum likelihood methods suggested that BraMAPKs could be divided into four groups (groups A, B, C, and D). Gene number expansion was observed for BraMAPK genes in groups A and D, which may have been caused by the tandem duplication and genome triplication of the ancestral genome of the Brassica progenitor. Except for five members of the BraMAPK10 subfamily, the identified BraMAPKs were expressed in most of the tissues examined, including callus, root, stem, leaf, flower, and silique. Quantitative real-time PCR demonstrated that at least six and five BraMAPKs were induced or repressed by various abiotic stresses and hormone treatments, respectively, suggesting their potential roles in the abiotic stress response and various hormone signal transduction pathways in B. rapa. This study provides valuable insight into the putative physiological and biochemical functions of MAPK genes in B. rapa. PMID:26173020

  15. Selection during crop diversification involves correlated evolution of the circadian clock and ecophysiological traits in Brassica rapa.

    PubMed

    Yarkhunova, Yulia; Edwards, Christine E; Ewers, Brent E; Baker, Robert L; Aston, Timothy Llewellyn; McClung, C Robertson; Lou, Ping; Weinig, Cynthia

    2016-04-01

    Crop selection often leads to dramatic morphological diversification, in which allocation to the harvestable component increases. Shifts in allocation are predicted to impact (as well as rely on) physiological traits; yet, little is known about the evolution of gas exchange and related anatomical features during crop diversification. In Brassica rapa, we tested for physiological differentiation among three crop morphotypes (leaf, turnip, and oilseed) and for correlated evolution of circadian, gas exchange, and phenological traits. We also examined internal and surficial leaf anatomical features and biochemical limits to photosynthesis. Crop types differed in gas exchange; oilseed varieties had higher net carbon assimilation and stomatal conductance relative to vegetable types. Phylogenetically independent contrasts indicated correlated evolution between circadian traits and both gas exchange and biomass accumulation; shifts to shorter circadian period (closer to 24 h) between phylogenetic nodes are associated with higher stomatal conductance, lower photosynthetic rate (when CO2 supply is factored out), and lower biomass accumulation. Crop type differences in gas exchange are also associated with stomatal density, epidermal thickness, numbers of palisade layers, and biochemical limits to photosynthesis. Brassica crop diversification involves correlated evolution of circadian and physiological traits, which is potentially relevant to understanding mechanistic targets for crop improvement. PMID:26618783

  16. Antioxidant response and carboxylate metabolism in Brassica rapa exposed to different external Zn, Ca, and Mg supply.

    PubMed

    Blasco, Begoña; Graham, Neil S; Broadley, Martin R

    2015-03-15

    Zinc (Zn), calcium (Ca), and magnesium (Mg) malnutrition are common deficiencies in many developed and developing countries, resulting in a widespread health problem. Biofortification of food crops is an agricultural strategy that can be used to increase the levels of these elements in the edible portions of crops. Deficiency or toxicity of these cations in soils reduces plant growth, crop yield, and the quality of plant foodstuff. The aim of this study was to investigate the effect of external Zn, Ca, and Mg supply on accumulation and distribution of this elements as well as antioxidant response and organic acid composition of Brassica rapa ssp. trilocularis line R-o-18. Plants were grown at low Zn (0.05 μM Zn) and high Zn (500 μM Zn), low Ca (0.4 mM) and high Ca (40 mM), and low Mg (0.2 mM), and high Mg (20 mM) to simulate deficiency and toxicity conditions. Larger shoot biomass reductions were observed under high Zn, Ca and Mg treatments, and superoxide dismutase (SOD), ascorbate peroxidase (APX), H2O2, malondialdehyde (MDA), and total ascorbate (AA) showed a marked increase in these treatments. Therefore, Brassica plants might be more sensitive to excess of these elements in the nutrient solution. The translocation factor (TF) and distribution coefficient (DC) values of Zn, Ca, and Mg indicated higher translocation and accumulation in deficient conditions. High biosynthesis and citrate content in Brassica plants may be associated mainly with a high-nutrient solution extraction ability of these plants. These results provide background data, which will be used to characterize TILLING mutants to study the effects of mutations in genes involved in regulating Zn, Ca, and Mg distribution and accumulation in plants. PMID:25544655

  17. Demonstrated Ways to Use Rapid Cycling "Brassica Rapa" in Ecology Instruction and Research

    ERIC Educational Resources Information Center

    Kelly, Martin G.

    2004-01-01

    The National Science Foundation has a long supported the use of "Wisconsin Fast Plants" (rapid cycling "B. rapa") in the teaching of Biology (K-12). I believe that the opportunity is at hand for biologists to significantly extend past efforts made by our colleagues at the K-12 level to higher education. Biology faculty can realize the many…

  18. A large-scale introgression of genomic components of Brassica rapa into B. napus by the bridge of hexaploid derived from hybridization between B. napus and B. oleracea.

    PubMed

    Li, Qinfei; Mei, Jiaqin; Zhang, Yongjing; Li, Jiana; Ge, Xianhong; Li, Zaiyun; Qian, Wei

    2013-08-01

    Brassica rapa (AA) has been used to widen the genetic basis of B. napus (AACC), which is a new but important oilseed crop worldwide. In the present study, we have proposed a strategy to develop new type B. napus carrying genomic components of B. rapa by crossing B. rapa with hexaploid (AACCCC) derived from B. napus and B. oleracea (CC). The hexaploid exhibited large flowers and high frequency of normal chromosome segregation, resulting in good seed set (average of 4.48 and 12.53 seeds per pod by self and open pollination, respectively) and high pollen fertility (average of 87.05 %). It was easy to develop new type B. napus by crossing the hexaploid with 142 lines of B. rapa from three ecotype groups, with the average crossability of 9.24 seeds per pod. The genetic variation of new type B. napus was diverse from that of current B. napus, especially in the A subgenome, revealed by genome-specific simple sequence repeat markers. Our data suggest that the strategy proposed here is a large-scale and highly efficient method to introgress genomic components of B. rapa into B. napus. PMID:23699961

  19. A scanner system for high-resolution quantification of variation in root growth dynamics of Brassica rapa genotypes.

    PubMed

    Adu, Michael O; Chatot, Antoine; Wiesel, Lea; Bennett, Malcolm J; Broadley, Martin R; White, Philip J; Dupuy, Lionel X

    2014-05-01

    The potential exists to breed for root system architectures that optimize resource acquisition. However, this requires the ability to screen root system development quantitatively, with high resolution, in as natural an environment as possible, with high throughput. This paper describes the construction of a low-cost, high-resolution root phenotyping platform, requiring no sophisticated equipment and adaptable to most laboratory and glasshouse environments, and its application to quantify environmental and temporal variation in root traits between genotypes of Brassica rapa L. Plants were supplied with a complete nutrient solution through the wick of a germination paper. Images of root systems were acquired without manual intervention, over extended periods, using multiple scanners controlled by customized software. Mixed-effects models were used to describe the sources of variation in root traits contributing to root system architecture estimated from digital images. It was calculated that between one and 43 replicates would be required to detect a significant difference (95% CI 50% difference between traits). Broad-sense heritability was highest for shoot biomass traits (>0.60), intermediate (0.25-0.60) for the length and diameter of primary roots and lateral root branching density on the primary root, and lower (<0.25) for other root traits. Models demonstrate that root traits show temporal variations of various types. The phenotyping platform described here can be used to quantify environmental and temporal variation in traits contributing to root system architecture in B. rapa and can be extended to screen the large populations required for breeding for efficient resource acquisition. PMID:24604732

  20. A Systems Genetics Approach Identifies Gene Regulatory Networks Associated with Fatty Acid Composition in Brassica rapa Seed.

    PubMed

    Basnet, Ram Kumar; Del Carpio, Dunia Pino; Xiao, Dong; Bucher, Johan; Jin, Mina; Boyle, Kerry; Fobert, Pierre; Visser, Richard G F; Maliepaard, Chris; Bonnema, Guusje

    2016-01-01

    Fatty acids in seeds affect seed germination and seedling vigor, and fatty acid composition determines the quality of seed oil. In this study, quantitative trait locus (QTL) mapping of fatty acid and transcript abundance was integrated with gene network analysis to unravel the genetic regulation of seed fatty acid composition in a Brassica rapa doubled haploid population from a cross between a yellow sarson oil type and a black-seeded pak choi. The distribution of major QTLs for fatty acids showed a relationship with the fatty acid types: linkage group A03 for monounsaturated fatty acids, A04 for saturated fatty acids, and A05 for polyunsaturated fatty acids. Using a genetical genomics approach, expression quantitative trait locus (eQTL) hotspots were found at major fatty acid QTLs on linkage groups A03, A04, A05, and A09. An eQTL-guided gene coexpression network of lipid metabolism-related genes showed major hubs at the genes BrPLA2-ALPHA, BrWD-40, a number of seed storage protein genes, and the transcription factor BrMD-2, suggesting essential roles for these genes in lipid metabolism. Three subnetworks were extracted for the economically important and most abundant fatty acids erucic, oleic, linoleic, and linolenic acids. Network analysis, combined with comparison of the genome positions of cis- or trans-eQTLs with fatty acid QTLs, allowed the identification of candidate genes for genetic regulation of these fatty acids. The generated insights in the genetic architecture of fatty acid composition and the underlying complex gene regulatory networks in B. rapa seeds are discussed. PMID:26518343

  1. Impact of biologically synthesized silver nanoparticles on the growth and physiological responses in Brassica rapa ssp. pekinensis.

    PubMed

    Baskar, Venkidasamy; Venkatesh, Jelli; Park, Se Won

    2015-11-01

    Silver nanoparticles (AgNPs) were extensively used in various fields, particularly in medicine as an antimicrobial agent. The unavoidable and extensive usage of AgNPs in turn accumulates in the environment. Plants are the essential base of ecosystem and are ready to disturb by environmental pollutants. Therefore, in the present study, we have planned to evaluate the impact of biologically synthesized AgNPs on the essential food crop Chinese cabbage (Brassica rapa ssp. pekinensis). The effects of AgNP-induced plant morphological and physiological changes were investigated in different concentrations (100, 250, and 500 mg/L). The results of morphological features showed that AgNPs at lower concentrations (100 mg/L) exhibit growth-stimulating activity, whereas at higher concentrations (250 and 500 mg/L), particularly, 500 mg/L exhibited growth-suppressing activities which are in terms of reduced root, shoot growth, and fresh biomass. The increased reactive oxygen species (ROS) generation, malondialdehyde production, anthocyanin biosynthesis, and decreased chlorophyll content were also more obviously present at higher concentrations of AgNPs. The concentration-dependent DNA damage was observed in the AgNP-treated plants. The molecular responses of AgNPs indicate that most of the genes related to secondary metabolism (glucosinolates, anthocyanin) and antioxidant activities were induced at higher concentrations of AgNP treatment. The dose-dependent phytotoxicity effects of AgNPs were also observed. Taken together, the highest concentration of AgNPs (500 mg/L) could induce growth-suppressing activities via the induction of ROS generation and other molecular changes in B. rapa seedlings. PMID:26154034

  2. Regulation of bolting and identification of the α-tubulin gene family in Brassica rapa L. ssp pekinensis.

    PubMed

    Zhang, Y W; Jin, D; Xu, C; Zhang, L; Guo, M H; Fang, Z Y

    2016-01-01

    Microtubules are important components of eukaryotic cells, and they play vital roles in cell morphogenesis, carrying of signaling molecules, transport of materials, and establishing the cell polarity. During bolting of biennial plants, cell division and elongation are involved, and cell elongation inevitably involves the microtubules arrangement and expression of related genes. So we deduce that it is of great significance to figure out the mechanism of bolting and flowering in which TUA genes are involved. In the present study, bioinformatic methods were used to predict and identify the α-tubulin gene family (BrTUAs) in Brassica rapa L. ssp pekinensis (Chinese cabbage) through the alignment of AtTUA gene sequence from Arabidopsis thaliana with the B. rapa genome database (http://brassicadb.org/brad/) using the basic local alignment search tool. The change in the structure and functions of BrTUAs during the process of evolution, cis-acting elements in the promoter sequences of BrTUAs, and the expression of the identified genes was also analyzed. Twelve members of the α-tubulin gene family were identified from Chinese cabbage. The gene length, intron, exon, and promoter regions were determined to have changed significantly during the genome evolution. Only five of the 12 members were encoded completely and were observed to differ in their spatial and temporal expression. The five BrTUA promoter sequences contained different numbers of cis-elements responsive to light and low-temperature response, cis-elements responsive among which hormonal responses were significantly different. We also report that the BrTUAs were involved in the regulation of the bolting in Chinese cabbage, and propose that this process could be controlled by regulating the expression of BrTUAs. PMID:26909938

  3. Loss/retention and evolution of NBS-encoding genes upon whole genome triplication of Brassica rapa.

    PubMed

    Wu, Ping; Shao, Zhu-Qing; Wu, Xun-Zong; Wang, Qiang; Wang, Bin; Chen, Jian-Qun; Hang, Yue-Yu; Xue, Jia-Yu

    2014-04-25

    A genome triplication took place in the ancestor of Brassiceae species after the split of the Arabidopsis lineage. The postfragmentation and shuffling of the genome turned the ancestral hexaploid back to diploids and caused the radiation of Brassiceae species. The course of speciation was accompanied by the loss of duplicate genes and also influenced the evolution of retained genes. Of all the genes, those encoding NBS domains are typical R genes that confer resistance to invading pathogens. In this study, using the genome of Arabidopsis thaliana as a reference, we examined the loss/retention of orthologous NBS-encoding loci in the tripled Brassica rapa genome and discovered differential loss/retention frequencies. Further analysis indicated that loci of different retention ratios showed different evolutionary patterns. The loci of classesII and III (maintaining two and three syntenic loci, respectively, multi-loci) show sharper expansions by tandem duplications, have faster evolutionary rates and have more potential to be associated with novel gene functions. On the other hand, the loci that are retained at the minimal rate (keeping only one locus, class I, single locus) showed opposite patterns. Phylogenetic analysis indicated that recombination and translocation events were common among multi-loci in B. rapa, and differential evolutionary patterns between multi- and single-loci are likely the consequence of recombination. Investigations towards other gene families demonstrated different evolutionary characteristics between different gene families. The evolution of genes is more likely determined by the property of each gene family, and the whole genome triplication provided only a specific condition. PMID:24576745

  4. Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in Brassica rapa.

    PubMed

    Dong, Xiangshu; Yi, Hankuil; Lee, Jeongyeo; Nou, Ill-Sup; Han, Ching-Tack; Hur, Yoonkang

    2015-01-01

    Genome-wide dissection of the heat stress response (HSR) is necessary to overcome problems in crop production caused by global warming. To identify HSR genes, we profiled gene expression in two Chinese cabbage inbred lines with different thermotolerances, Chiifu and Kenshin. Many genes exhibited >2-fold changes in expression upon exposure to 0.5- 4 h at 45°C (high temperature, HT): 5.2% (2,142 genes) in Chiifu and 3.7% (1,535 genes) in Kenshin. The most enriched GO (Gene Ontology) items included 'response to heat', 'response to reactive oxygen species (ROS)', 'response to temperature stimulus', 'response to abiotic stimulus', and 'MAPKKK cascade'. In both lines, the genes most highly induced by HT encoded small heat shock proteins (Hsps) and heat shock factor (Hsf)-like proteins such as HsfB2A (Bra029292), whereas high-molecular weight Hsps were constitutively expressed. Other upstream HSR components were also up-regulated: ROS-scavenging genes like glutathione peroxidase 2 (BrGPX2, Bra022853), protein kinases, and phosphatases. Among heat stress (HS) marker genes in Arabidopsis, only exportin 1A (XPO1A) (Bra008580, Bra006382) can be applied to B. rapa for basal thermotolerance (BT) and short-term acquired thermotolerance (SAT) gene. CYP707A3 (Bra025083, Bra021965), which is involved in the dehydration response in Arabidopsis, was associated with membrane leakage in both lines following HS. Although many transcription factors (TF) genes, including DREB2A (Bra005852), were involved in HS tolerance in both lines, Bra024224 (MYB41) and Bra021735 (a bZIP/AIR1 [Anthocyanin-Impaired-Response-1]) were specific to Kenshin. Several candidate TFs involved in thermotolerance were confirmed as HSR genes by real-time PCR, and these assignments were further supported by promoter analysis. Although some of our findings are similar to those obtained using other plant species, clear differences in Brassica rapa reveal a distinct HSR in this species. Our data could also provide a

  5. Global Gene-Expression Analysis to Identify Differentially Expressed Genes Critical for the Heat Stress Response in Brassica rapa

    PubMed Central

    Dong, Xiangshu; Yi, Hankuil; Lee, Jeongyeo; Nou, Ill-Sup; Han, Ching-Tack; Hur, Yoonkang

    2015-01-01

    Genome-wide dissection of the heat stress response (HSR) is necessary to overcome problems in crop production caused by global warming. To identify HSR genes, we profiled gene expression in two Chinese cabbage inbred lines with different thermotolerances, Chiifu and Kenshin. Many genes exhibited >2-fold changes in expression upon exposure to 0.5– 4 h at 45°C (high temperature, HT): 5.2% (2,142 genes) in Chiifu and 3.7% (1,535 genes) in Kenshin. The most enriched GO (Gene Ontology) items included ‘response to heat’, ‘response to reactive oxygen species (ROS)’, ‘response to temperature stimulus’, ‘response to abiotic stimulus’, and ‘MAPKKK cascade’. In both lines, the genes most highly induced by HT encoded small heat shock proteins (Hsps) and heat shock factor (Hsf)-like proteins such as HsfB2A (Bra029292), whereas high-molecular weight Hsps were constitutively expressed. Other upstream HSR components were also up-regulated: ROS-scavenging genes like glutathione peroxidase 2 (BrGPX2, Bra022853), protein kinases, and phosphatases. Among heat stress (HS) marker genes in Arabidopsis, only exportin 1A (XPO1A) (Bra008580, Bra006382) can be applied to B. rapa for basal thermotolerance (BT) and short-term acquired thermotolerance (SAT) gene. CYP707A3 (Bra025083, Bra021965), which is involved in the dehydration response in Arabidopsis, was associated with membrane leakage in both lines following HS. Although many transcription factors (TF) genes, including DREB2A (Bra005852), were involved in HS tolerance in both lines, Bra024224 (MYB41) and Bra021735 (a bZIP/AIR1 [Anthocyanin-Impaired-Response-1]) were specific to Kenshin. Several candidate TFs involved in thermotolerance were confirmed as HSR genes by real-time PCR, and these assignments were further supported by promoter analysis. Although some of our findings are similar to those obtained using other plant species, clear differences in Brassica rapa reveal a distinct HSR in this species. Our data

  6. Multiple copies of eukaryotic translation initiation factors in Brassica rapa facilitate redundancy, enabling diversification through variation in splicing and broad-spectrum virus resistance.

    PubMed

    Nellist, Charlotte F; Qian, Wei; Jenner, Carol E; Moore, Jonathan D; Zhang, Shujiang; Wang, Xiaowu; Briggs, William H; Barker, Guy C; Sun, Rifei; Walsh, John A

    2014-01-01

    Recessive strain-specific resistance to a number of plant viruses in the Potyvirus genus has been found to be based on mutations in the eukaryotic translation initiation factor 4E (eIF4E) and its isoform, eIF(iso)4E. We identified three copies of eIF(iso)4E in a number of Brassica rapa lines. Here we report broad-spectrum resistance to the potyvirus Turnip mosaic virus (TuMV) due to a natural mechanism based on the mis-splicing of the eIF(iso)4E allele in some TuMV-resistant B. rapa var. pekinensis lines. Of the splice variants, the most common results in a stop codon in intron 1 and a much truncated, non-functional protein. The existence of multiple copies has enabled redundancy in the host plant's translational machinery, resulting in diversification and emergence of the resistance. Deployment of the resistance is complicated by the presence of multiple copies of the gene. Our data suggest that in the B. rapa subspecies trilocularis, TuMV appears to be able to use copies of eIF(iso)4E at two loci. Transformation of different copies of eIF(iso)4E from a resistant B. rapa line into an eIF(iso)4E knockout line of Arabidopsis thaliana proved misleading because it showed that, when expressed ectopically, TuMV could use multiple copies which was not the case in the resistant B. rapa line. The inability of TuMV to access multiple copies of eIF(iso)4E in B. rapa and the broad spectrum of the resistance suggest it may be durable. PMID:24274163

  7. Polyphyletic origin of Brassica juncea with B. rapa and B. nigra (Brassicaceae) participating as cytoplasm donor parents in independent hybridization events.

    PubMed

    Kaur, Puneet; Banga, Shashi; Kumar, Nitin; Gupta, Shilpa; Akhatar, Javed; Banga, Surinder S

    2014-07-16

    • Premise of the study: Brassica juncea is a major source of edible oil in the Indian subcontinent and northern China. It is also used as a root and leaf vegetable in China and as a condiment in Europe and America. There is a long-standing view that B. juncea originated from multiple hybridization events between B. rapa and B. nigra and that hybridizations were always unidirectional with B. rapa as the cytoplasmic donor. These conclusions were, however, centered primarily on nuclear markers.• Methods: Two hundred forty-six accessions of B. juncea, B. rapa, and B. nigra were genotyped using chloroplast and nuclear simple sequence repeat (SSR) markers.• Key results: A structure analysis assigned B. juncea germplasm (122) into three major groups based on plasmotype variation. The bulk of Indian B. juncea genotypes were grouped along with Chinese and Australian accessions. This plasmotype was absent in sampled accessions of B. rapa (97), B. nigra (27), and other wild crucifers (10). The second group of B. juncea included East European genotypes and four accessions from India. It showed unambiguous homology with the predominant B. nigra plasmotype. The neighbor joining tree produced seven subgroups, arranged into two broad lineages. The first lineage included Indian, Australian, and Chinese B. juncea genotypes; it was associated with wild species belonging to the "rapa" lineage. Nuclear SSR marker-based analyses were largely supportive of results from chloroplast SSR analyses.• Conclusions: Based on these results, we provide the first report that B. juncea originated several times with both B. rapa and B. nigra as cytoplasmic donors in separate hybridization events. PMID:25030348

  8. Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools.

    PubMed

    Franks, Steven J; Kane, Nolan C; O'Hara, Niamh B; Tittes, Silas; Rest, Joshua S

    2016-08-01

    There is increasing evidence that evolution can occur rapidly in response to selection. Recent advances in sequencing suggest the possibility of documenting genetic changes as they occur in populations, thus uncovering the genetic basis of evolution, particularly if samples are available from both before and after selection. Here, we had a unique opportunity to directly assess genetic changes in natural populations following an evolutionary response to a fluctuation in climate. We analysed genome-wide differences between ancestors and descendants of natural populations of Brassica rapa plants from two locations that rapidly evolved changes in multiple phenotypic traits, including flowering time, following a multiyear late-season drought in California. These ancestor-descendant comparisons revealed evolutionary shifts in allele frequencies in many genes. Some genes showing evolutionary shifts have functions related to drought stress and flowering time, consistent with an adaptive response to selection. Loci differentiated between ancestors and descendants (FST outliers) were generally different from those showing signatures of selection based on site frequency spectrum analysis (Tajima's D), indicating that the loci that evolved in response to the recent drought and those under historical selection were generally distinct. Very few genes showed similar evolutionary responses between two geographically distinct populations, suggesting independent genetic trajectories of evolution yielding parallel phenotypic changes. The results show that selection can result in rapid genome-wide evolutionary shifts in allele frequencies in natural populations, and highlight the usefulness of combining resurrection experiments in natural populations with genomics for studying the genetic basis of adaptive evolution. PMID:27072809

  9. Promoting Effects of a Single Rhodopseudomonas palustris Inoculant on Plant Growth by Brassica rapa chinensis under Low Fertilizer Input

    PubMed Central

    Wong, Wai-Tak; Tseng, Ching-Han; Hsu, Shu-Hua; Lur, Huu-Sheng; Mo, Chia-Wei; Huang, Chu-Ning; Hsu, Shu-Chiung; Lee, Kung-Ta; Liu, Chi-Te

    2014-01-01

    Several Rhodopseudomonas palustris strains have been isolated from rice paddy fields in Taiwan by combining the Winogradsky column method and molecular marker detection. These isolates were initially screened by employing seed germination and seedling vigor assays to evaluate their potential as inoculants. To fulfill the demand in the present farming system for reducing the application of chemical fertilizers, we assessed the plant growth-promoting effects of the R. palustris YSC3, YSC4, and PS3 inoculants on Brassica rapa chinensis (Chinese cabbage) cultivated under a half quantity of fertilizer. The results obtained showed that supplementation with approximately 4.0×106 CFU g−1 soil of the PS3 inoculant at half the amount of fertilizer consistently produced the same plant growth potential as 100% fertility, and also increased the nitrogen use efficiency of the applied fertilizer nutrients. Furthermore, we noted that the plant growth-promotion rate elicited by PS3 was markedly higher with old seeds than with new seeds, suggesting it has the potential to boost the development of seedlings that were germinated from carry-over seeds of poor quality. These beneficial traits suggest that the PS3 isolate may serve as a potential PGPR inoculant for integrated nutrient management in agriculture. PMID:25130882

  10. Genotype-environment interactions affecting preflowering physiological and morphological traits of Brassica rapa grown in two watering regimes.

    PubMed

    El-Soda, Mohamed; Boer, Martin P; Bagheri, Hedayat; Hanhart, Corrie J; Koornneef, Maarten; Aarts, Mark G M

    2014-02-01

    Plant growth and productivity are greatly affected by drought, which is likely to become more threatening with the predicted global temperature increase. Understanding the genetic architecture of complex quantitative traits and their interaction with water availability may lead to improved crop adaptation to a wide range of environments. Here, the genetic basis of 20 physiological and morphological traits is explored by describing plant performance and growth in a Brassica rapa recombinant inbred line (RIL) population grown on a sandy substrate supplemented with nutrient solution, under control and drought conditions. Altogether, 54 quantitative trait loci (QTL) were identified, of which many colocated in 11 QTL clusters. Seventeen QTL showed significant QTL-environment interaction (Q×E), indicating genetic variation for phenotypic plasticity. Of the measured traits, only hypocotyl length did not show significant genotype-environment interaction (G×E) in both environments in all experiments. Correlation analysis showed that, in the control environment, stomatal conductance was positively correlated with total leaf dry weight (DW) and aboveground DW, whereas in the drought environment, stomatal conductance showed a significant negative correlation with total leaf DW and aboveground DW. This correlation was explained by antagonistic fitness effects in the drought environment, controlled by a QTL cluster on chromosome A7. These results demonstrate that Q×E is an important component of the genetic variance and can play a great role in improving drought tolerance in future breeding programmes. PMID:24474811

  11. Analysis of carotenoid accumulation and expression of carotenoid biosynthesis genes in different organs of Chinese cabbage (Brassica rapa subsp. pekinensis)

    PubMed Central

    Tuan, Pham Anh; Kim, Jae Kwang; Lee, Jeongyeo; Park, Woo Tae; Kwon, Do Yeon; Kim, Yeon Bok; Kim, Haeng Hoon; Kim, Hye Ran; Park, Sang Un

    2012-01-01

    The relationship between carotenoid accumulation and expression of carotenoid biosynthesis genes was investigated in the flowers, stems, young leaves, old leaves, and roots of Chinese cabbage (Brassica rapa subsp. pekinensis). Quantitative real-time PCR analysis showed that the mRNA levels of BrPSY, BrPDS, BrZDS, BrLCYB, BrLCYE, BrCHXB, and BrZEP leading to the production of carotenoids were highest in the flowers or the leaves and lowest in the roots of Chinese cabbage. In contrast, the mRNA expression of BrNCED, a gene involved in abscisic acid (ABA) biosynthesis, was highest in the roots. High-performance liquid chromatography revealed that carotenoids, namely, lutein and β-carotene, were distributed predominantly in the flowers and leaves, with very little in the underground organ, the roots. Specifically, old leaves contained 120.3 μg/g lutein and 103.93 μg/g β-carotene, which is the most potent dietary precursor of vitamin A. Moreover, we found a relatively large amount of cis isomers of β-carotene, namely, 9-cis β-carotene and 13-cis β-carotene, in Chinese cabbage. These results provide insight into carotenoid biosynthetic mechanisms in Chinese cabbage and may be helpful in the metabolic engineering of carotenoid biosynthesis in plants.

  12. Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress in Brassica rapa L. (Inbred Line “Chiifu”)

    PubMed Central

    Kwon, Soon-Wook

    2016-01-01

    Through a comparative shotgun quantitative proteomics analysis in Brassica rapa (inbred line Chiifu), total of 3,009 nonredundant proteins were identified with a false discovery rate of 0.01 in 3-week-old plants subjected to dehydration treatment for 0, 24, and 48 h, plants subjected to drought stress. Ribulose-bisphosphate carboxylases, chlorophyll a/b-binding protein, and light harvesting complex in photosystem II were highly abundant proteins in the leaves and accounted for 9%, 2%, and 4%, respectively, of the total identified proteins. Comparative analysis of the treatments enabled detection of 440 differentially expressed proteins during dehydration. The results of clustering analysis, gene ontology (GO) enrichment analysis, and analysis of composite expression profiles of functional categories for the differentially expressed proteins indicated that drought stress reduced the levels of proteins associated with photosynthesis and increased the levels of proteins involved in catabolic processes and stress responses. We observed enhanced expression of many proteins involved in osmotic stress responses and proteins with antioxidant activities. Based on previously reported molecular functions, we propose that the following five differentially expressed proteins could provide target genes for engineering drought resistance in plants: annexin, phospholipase D delta, sDNA-binding transcriptional regulator, auxin-responsive GH3 family protein, and TRAF-like family protein. PMID:27419125

  13. Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress in Brassica rapa L. (Inbred Line "Chiifu").

    PubMed

    Kwon, Soon-Wook; Kim, Mijeong; Kim, Hijin; Lee, Joohyun

    2016-01-01

    Through a comparative shotgun quantitative proteomics analysis in Brassica rapa (inbred line Chiifu), total of 3,009 nonredundant proteins were identified with a false discovery rate of 0.01 in 3-week-old plants subjected to dehydration treatment for 0, 24, and 48 h, plants subjected to drought stress. Ribulose-bisphosphate carboxylases, chlorophyll a/b-binding protein, and light harvesting complex in photosystem II were highly abundant proteins in the leaves and accounted for 9%, 2%, and 4%, respectively, of the total identified proteins. Comparative analysis of the treatments enabled detection of 440 differentially expressed proteins during dehydration. The results of clustering analysis, gene ontology (GO) enrichment analysis, and analysis of composite expression profiles of functional categories for the differentially expressed proteins indicated that drought stress reduced the levels of proteins associated with photosynthesis and increased the levels of proteins involved in catabolic processes and stress responses. We observed enhanced expression of many proteins involved in osmotic stress responses and proteins with antioxidant activities. Based on previously reported molecular functions, we propose that the following five differentially expressed proteins could provide target genes for engineering drought resistance in plants: annexin, phospholipase D delta, sDNA-binding transcriptional regulator, auxin-responsive GH3 family protein, and TRAF-like family protein. PMID:27419125

  14. Genome-wide analysis of the SBP-box gene family in Chinese cabbage (Brassica rapa subsp. pekinensis).

    PubMed

    Tan, Hua-Wei; Song, Xiao-Ming; Duan, Wei-Ke; Wang, Yan; Hou, Xi-Lin

    2015-11-01

    The SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box gene family contains highly conserved plant-specific transcription factors that play an important role in plant development, especially in flowering. Chinese cabbage (Brassica rapa subsp. pekinensis) is a leafy vegetable grown worldwide and is used as a model crop for research in genome duplication. The present study aimed to characterize the SBP-box transcription factor genes in Chinese cabbage. Twenty-nine SBP-box genes were identified in the Chinese cabbage genome and classified into six groups. We identified 23 orthologous and 5 co-orthologous SBP-box gene pairs between Chinese cabbage and Arabidopsis. An interaction network among these genes was constructed. Sixteen SBP-box genes were expressed more abundantly in flowers than in other tissues, suggesting their involvement in flowering. We show that the MiR156/157 family members may regulate the coding regions or 3'-UTR regions of Chinese cabbage SBP-box genes. As SBP-box genes were found to potentially participate in some plant development pathways, quantitative real-time PCR analysis was performed and showed that Chinese cabbage SBP-box genes were also sensitive to the exogenous hormones methyl jasmonic acid and salicylic acid. The SBP-box genes have undergone gene duplication and loss, evolving a more refined regulation for diverse stimulation in plant tissues. Our comprehensive genome-wide analysis provides insights into the SBP-box gene family of Chinese cabbage. PMID:26599708

  15. Genome-wide identification, classification, and analysis of heat shock transcription factor family in Chinese cabbage (Brassica rapa pekinensis).

    PubMed

    Huang, X Y; Tao, P; Li, B Y; Wang, W H; Yue, Z C; Lei, J L; Zhong, X M

    2015-01-01

    Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important vegetable crops grown worldwide, and various methods exist for selection, propagation, and cultivation. The entire Chinese cabbage genome has been sequenced, and the heat shock transcription factor family (Hsfs) has been found to play a central role in plant growth and development and in the response to biotic and abiotic stress conditions, particularly in acquired thermotolerance. We analyzed heat tolerance mechanisms in Chinese cabbage. In this study, 30 Hsfs were identified from the Chinese cabbage genome database. The classification, phylogenetic reconstruction, chromosome distribution, conserved motifs, expression analysis, and interaction networks of the Hsfs were predicted and analyzed. Thirty BrHsfs were classified into 3 major classes (class A, B, and C) according to their structural characteristics and phylogenetic comparisons, and class A was further subdivided into 8 subclasses. Distribution mapping results showed that Hsf genes were located on 10 Chinese cabbage chromosomes. The expression profile indicated that Hsfs play differential roles in 5 organs in Chinese cabbage, and likely participate in the development of underground parts and regulation of reproductive growth. An orthologous gene interaction network was constructed, and included MBF1C, ROF1, TBP2, CDC2, and HSP70 5 genes, which are closely related to heat stress. Our results contribute to the understanding of the complexity of Hsfs in Chinese cabbage and provide a basis for further functional gene research. PMID:25867366

  16. Promoting effects of a single Rhodopseudomonas palustris inoculant on plant growth by Brassica rapa chinensis under low fertilizer input.

    PubMed

    Wong, Wai-Tak; Tseng, Ching-Han; Hsu, Shu-Hua; Lur, Huu-Sheng; Mo, Chia-Wei; Huang, Chu-Ning; Hsu, Shu-Chiung; Lee, Kung-Ta; Liu, Chi-Te

    2014-09-17

    Several Rhodopseudomonas palustris strains have been isolated from rice paddy fields in Taiwan by combining the Winogradsky column method and molecular marker detection. These isolates were initially screened by employing seed germination and seedling vigor assays to evaluate their potential as inoculants. To fulfill the demand in the present farming system for reducing the application of chemical fertilizers, we assessed the plant growth-promoting effects of the R. palustris YSC3, YSC4, and PS3 inoculants on Brassica rapa chinensis (Chinese cabbage) cultivated under a half quantity of fertilizer. The results obtained showed that supplementation with approximately 4.0×10(6) CFU g(-1) soil of the PS3 inoculant at half the amount of fertilizer consistently produced the same plant growth potential as 100% fertility, and also increased the nitrogen use efficiency of the applied fertilizer nutrients. Furthermore, we noted that the plant growth-promotion rate elicited by PS3 was markedly higher with old seeds than with new seeds, suggesting it has the potential to boost the development of seedlings that were germinated from carry-over seeds of poor quality. These beneficial traits suggest that the PS3 isolate may serve as a potential PGPR inoculant for integrated nutrient management in agriculture. PMID:25130882

  17. Metabolite profiling of mizuna ( Brassica rapa L. var. Nipponsinica) to evaluate the effects of organic matter amendments.

    PubMed

    Watanabe, Ayano; Okazaki, Keiki; Watanabe, Toshihiro; Osaki, Mitsuru; Shinano, Takuro

    2013-02-01

    Organic matter amendment is an essential agricultural protocol to improve soil function and carbon sequestration. However, the effect of organic matter amendments on crop quality has not been well-defined. This study applied gas chromatography-mass spectrometry to investigate the metabolite profiling of mizuna ( Brassica rapa L. var. Nipponsinica) with different organic matter amendments with respect to quality and quantity. Principal component analysis showed that 33.4, 15.6, and 6.6% of the total variance was attributable to the plant N concentration, fast-release organic fertilizer (fish cake), chicken droppings), and rapeseed cake), and manure application (fresh and dried), respectively. The peak areas of 18 and 15 compounds were significantly altered under organic fertilizer and manure amendment, respectively, compared with pure chemical fertilizer amendment. The compounds altered with manure amendment were similar to those reported in previous studies using other species. This study is the first to show clear metabolic alterations in plants through the amendment of fast-release organic fertilizer. Mizuna is a unique plant species that responds to both organic fertilizer and manure. These observations are useful to clarify the effect of organic matter amendment and quality control in farming systems using organic matter. PMID:23244647

  18. Glucotoxicity Induced Oxidative Stress and Inflammation In Vivo and In Vitro in Psammomys obesus: Involvement of Aqueous Extract of Brassica rapa rapifera

    PubMed Central

    Berdja, Sihem; Smail, Leila; Saka, Boualem; Neggazi, Samia; Haffaf, El-mehdi; Benazzoug, Yasmina; Kacimi, Ghouti; Boudarene, Lynda; Aouichat Bouguerra, Souhila

    2016-01-01

    Context. Brassica rapa is considered as natural source of antioxidants and is used to treat diabetes. Objective. Our study carried the impact of glucotoxicity induced in vivo and in vitro in vascular smooth muscle cells (VSMCs) in Psammomys and the therapeutic effect of Brassica rapa (AEBr). Materials and Methods. We administered a hyperglucidic diet (30% sucrose) for 9 months and a treatment for 20 days with AEBr at 100 mg/kg. VSMCs were submitted to D-Glucose (0.6%) for 48 hours and treated with AEBr (2100 μg/mL) for 24 hours. We measured, in blood metabolic parameters, the redox statues and inflammatory markers in adipose tissue. Histological study was effectuated in liver. In VSMCs, we measured markers of glucotoxicity (IRS1p Serine, AKT) inflammation (NO, MCP1, TNFα, and NF-κB) and oxidative stress (oxidants and antioxydants markers). Cell viability and apoptosis were estimated by the morphological study. Results. AEBr corrects the metabolic parameters and inflammatory and oxidative markers in blood and homogenate tissue and reduces lipid droplets in liver. It induces, in VSMCs, a significant decrease of IRS1p serine, cyt c, NO, MCP1, TNFα, NF-κB, protein, and lipid oxidation and increases cell viability, AKT, ERK1/2, catalase, and SOD activity. Conclusion. Brassica enhanced the antidiabetic, anti-inflammatory, and antioxidant defense leading to the protection of cardiovascular diseases. PMID:27047569

  19. Glucotoxicity Induced Oxidative Stress and Inflammation In Vivo and In Vitro in Psammomys obesus: Involvement of Aqueous Extract of Brassica rapa rapifera.

    PubMed

    Berdja, Sihem; Smail, Leila; Saka, Boualem; Neggazi, Samia; Haffaf, El-Mehdi; Benazzoug, Yasmina; Kacimi, Ghouti; Boudarene, Lynda; Aouichat Bouguerra, Souhila

    2016-01-01

    Context. Brassica rapa is considered as natural source of antioxidants and is used to treat diabetes. Objective. Our study carried the impact of glucotoxicity induced in vivo and in vitro in vascular smooth muscle cells (VSMCs) in Psammomys and the therapeutic effect of Brassica rapa (AEBr). Materials and Methods. We administered a hyperglucidic diet (30% sucrose) for 9 months and a treatment for 20 days with AEBr at 100 mg/kg. VSMCs were submitted to D-Glucose (0.6%) for 48 hours and treated with AEBr (2100 μg/mL) for 24 hours. We measured, in blood metabolic parameters, the redox statues and inflammatory markers in adipose tissue. Histological study was effectuated in liver. In VSMCs, we measured markers of glucotoxicity (IRS1p Serine, AKT) inflammation (NO, MCP1, TNFα, and NF-κB) and oxidative stress (oxidants and antioxydants markers). Cell viability and apoptosis were estimated by the morphological study. Results. AEBr corrects the metabolic parameters and inflammatory and oxidative markers in blood and homogenate tissue and reduces lipid droplets in liver. It induces, in VSMCs, a significant decrease of IRS1p serine, cyt c, NO, MCP1, TNFα, NF-κB, protein, and lipid oxidation and increases cell viability, AKT, ERK1/2, catalase, and SOD activity. Conclusion. Brassica enhanced the antidiabetic, anti-inflammatory, and antioxidant defense leading to the protection of cardiovascular diseases. PMID:27047569

  20. Relationship of Enhanced Butyrate Production by Colonic Butyrate-Producing Bacteria to Immunomodulatory Effects in Normal Mice Fed an Insoluble Fraction of Brassica rapa L.

    PubMed

    Tanaka, Sachi; Yamamoto, Kana; Yamada, Kazuki; Furuya, Kanon; Uyeno, Yutaka

    2016-05-01

    This study was performed to determine the effects of feeding a fiber-rich fraction of Brassica vegetables on the immune response through changes in enteric bacteria and short-chain fatty acid (SCFA) production in normal mice. The boiled-water-insoluble fraction of Brassica rapa L. (nozawana), which consists mainly of dietary fiber, was chosen as a test material. A total of 31 male C57BL/6J mice were divided into two groups and housed in a specific-pathogen-free facility. The animals were fed either a control diet or the control diet plus the insoluble B. rapa L. fraction for 2 weeks and sacrificed to determine microbiological and SCFA profiles in lower-gut samples and immunological molecules. rRNA-based quantification indicated that the relative population of Bacteroidetes was markedly lower in the colon samples of the insoluble B. rapa L. fraction-fed group than that in the controls. Populations of the Eubacterium rectale group and Faecalibacterium prausnitzii, both of which are representative butyrate-producing bacteria, doubled after 2 weeks of fraction intake, accompanying a marginal increase in the proportion of colonic butyrate. In addition, feeding with the fraction significantly increased levels of the anti-inflammatory cytokine interleukin-10 (IL-10) and tended to increase splenic regulatory T cell numbers but significantly reduced the population of cells expressing activation markers. We demonstrated that inclusion of the boiled-water-insoluble fraction of B. rapa L. can alter the composition of the gut microbiota to decrease the numbers of Bacteroidetes and to increase the numbers of butyrate-producing bacteria, either of which may be involved in the observed shift in the production of splenic IL-10. PMID:26921420

  1. Effect of enhanced UV-B radiation on pollen quantity, quality, and seed yield in Brassica rapa (Brassicaceae)

    SciTech Connect

    Demchik, S.M.; Day, T.A.

    1996-05-01

    Three experiments examined the influence of ultraviolet-B radiation (UV-B; 280-320 nm) exposure on reproduction in Brassica rapa (Brassicacaeae). Plants were grown in a greenhouse under three biologically effective UV-B levels that stimulated either an ambient stratospheric ozone level (control), 16% ({open_quotes}low enhanced{close_quotes}), or 32% ({open_quotes}high enhanced{close_quotes}) ozone depletion levels at Morgantown, WV, USA in mid-March. In the first experiment,pollen production and viability per flower were reduced by {approx}50% under both enhanced UV-B levels relative to ambient controls. While plants under high-enhanced UV-B produced over 40% more flowers than plants under the two lower UV-B treatments, whole-plant production of viable pollen was reduced under low-enhanced UV-B to 34% of ambient controls. In the second experiment, the influence of source-plant UV-B exposure on in vitro pollen from plants was examined and whether source-plant UV-B exposure influenced in vitro pollen germination and viability. Pollen from plants under both enhanced-UV-B was reduced from 65 to 18%. Viability of the pollen from plants grown under both enhanced UV-B treatments was reduced to a much lesser extent: only from {approx}43 to 22%. Thus, ambient source-plant pollen was more sensitive to enhanced UV-B levels to fertilize plants growing under ambient-UV-B levels, and assessed subsequent seed production and germination. Seed abortion rates were higher in plants pollinated with pollen from the enhanced UV-B treatments, than from ambient UV-B. Despite this, seed yield (number and mass) per plant was similar, regardless of the UV-B exposure of their pollen source. Our findings demonstrate that enhanced UV-B levels associated with springtime ozone depletion events have the capacity to substantially reduce viable pollen production, and could ultimately reduce reproductive success of B. rapa. 37 refs., 4 figs., 2 tabs.

  2. Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in Brassica rapa L.

    PubMed

    Kawanabe, Takahiro; Osabe, Kenji; Itabashi, Etsuko; Okazaki, Keiichi; Dennis, Elizabeth S; Fujimoto, Ryo

    2016-07-20

    Epigenetic regulation is crucial for the development of plants and for adaptation to a changing environment. Recently, genome-wide profiles of histone modifications have been determined by a combination of chromatin immunoprecipitation (ChIP) and genomic tiling arrays (ChIP on chip) or ChIP and high-throughput sequencing (ChIP-seq) in species including Arabidopsis thaliana, rice and maize. Validation of ChIP analysis by PCR or qPCR using positive and negative regions of histone modification is necessary. In contrast, information about histone modifications is limited in Chinese cabbage, Brassica rapa. The aim of this study was to develop positive and negative control primer sets for H3K4me3 (trimethylation of the 4(th) lysine of H3), H3K9me2, H3K27me3 and H3K36me3 in B. rapa. The expression and histone modification of four FLC paralogs in B. rapa, before and after vernalization, were examined using the method developed here. After vernalization, expression of all four BrFLC genes was reduced, and accumulation of H3K27me3 was observed in three of them. As with A. thaliana, the vernalization response and stability of FLC repression correlated with the accumulation of H3K27me3. These results suggest that the epigenetic state during vernalization is important for high bolting resistance in B. rapa. The positive and negative control primer sets developed here revealed positive and negative histone modifications in B. rapa that can be used as a control for future studies. PMID:27074983

  3. The effects of chloroform, ethyl acetate and methanolic extracts of Brassica rapa L. on cell-mediated immune response in mice

    PubMed Central

    Jafarian-Dehkordi, A.; Zolfaghari, B.; Mirdamadi, M.

    2013-01-01

    Turnips with a long history of usage, are helpful in preventing breast and prostate cancer, inflammation and body`s immune system dysfunction. In this study, we investigated the effects of chloroform, ethyl acetate and methanolic extracts of Brassica rapa L. on cell-mediated immune response in mice. Chloroform, ethyl acetate and methanolic extracts of B. rapa glands were prepared by maceration method. To study the effects of B. rapa on acquired immunity, groups of Balb/c mice (n=8) were used. Sheep red blood cell (SRBC) was injected (s.c., 1×108cells/ml, 0.02 ml) and 5 days later, different extracts (10, 100 and 500 mg/kg), betamethasone (4 mg/kg) and Levamisol (4 mg/kg) as a positive control and normal saline as a negative control were given i.p. After 1 h SRBC was injected to footpad (s.c., 1×108cells/ml, 0.02 ml) and footpad swelling was measured up to 72 h. To investigate the effects of B. rapa on innate immunity the same procedure was used, but animals only received one injection of SRBC 1 h after i.p. injection of test compounds. Our findings showed that SRBC induced an increase in paw swelling with maximum response at 6-8 and 2-4 h for innate and acquired immunity, respectively. Betamethasone inhibited and levamisol increased paw thickness in both models. In both innate and acquired immunity models, chloroform, ethyl acetate and methanolic extracts of B. rapa glands significantly and dose-dependently reduced paw thickness. Ethyl acetate extract showed better effect. As glucosinolates are better extracted by ethyl acetate, it may be concluded that they are contributed in the more pronounced effects of ethyl acetate extract. PMID:24019825

  4. Foraging behavior of honey bees (hymenoptera: Apidae) on Brassica nigra and B. rapa grown under simulated ambient and enhanced UV-B radiation

    SciTech Connect

    Collins, S.A.; Robinson, G.E.; Conner, J.K.

    1997-01-01

    Two species of mustard, Brassica nigra and B. rapa, were grown under simulated ambient and enhanced ultraviolet-B (UV-B) radiation and exposed to pollinators, Apis mellifera L. Observations were made to determine whether UV-B-induced changes in these plants affected pollinator behavior. Total duration of the foraging trip, number of flowers visited, foraging time per flower, search time per flower, total amount of pollen collected, and pollen collected per flower were measured. There were no significant differences between UV-B treatments in any of the behaviors measured or in any of the pollen measurements. These results suggest that increases in the amount of solar UV-B reaching the earth`s surface may not have a negative effect on the relationship between these members of the genus Brassica and their honey bee pollinators. 28 refs., 2 figs., 1 tab.

  5. ANALYSIS OF GENOMIC DNA METHYLATION AND GENE EXPRESSION IN CHINESE CABBAGE (Brassica rapa L. ssp. pekinensis) AFTER CONTINUOUS SEEDLING BREEDING.

    PubMed

    Tao, L; Wang, X L; Guo, M H; Zhang, Y W

    2015-08-01

    Vernalization plays a key role in the bolting and flowering of Chinese cabbage (Brassica rapa L. ssp. pekinensis). Plants can switch from vegetative to reproductive growth and then bolt and flower under low temperature induction. The economic benefits of Chinese cabbage will decline significantly when the bolting happens before the vegetative body fully grows due to a lack of the edible value. It was found that continuous seedling breeding reduced the heading of Chinese cabbage and led to bolt and flower more easily. In the present study, two inbred lines, termed A161 and A105, were used as experiment materials. These two lines were subjected to vernalization and formed four types: seeds-seedling breeding once, seedling breeding twice, seedling breeding thrice and normal type. Differences in plant phenotype were compared. DNA methylation analysis was performed based on MSAP method. The differential fragments were cloned and analyzed by qPCR. Results showed that plants after seedling breeding thrice had a loosen heading leaves, elongated center axis and were easier to bolt and flower. It is suggested that continuous seedling breeding had a weaker winterness. It was observed that genome methylation level decreased with increasing generation. Four differential genes were identified, short for BraAPC1, BraEMP3, BraUBC26, and BraAL5. Fluorescent qPCR analysis showed that expression of four genes varied at different reproduction modes and different vernalization time. It is indicated that these genes might be involve in the development and regulation of bolting and flowering of plants. Herein, the molecular mechanism that continuous seedling breeding caused weaker winterness was analyzed preliminarily. It plays an important guiding significance for Chinese cabbage breeding. PMID:26601490

  6. Genome-wide identification, classification, and expression analysis of sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis).

    PubMed

    Tao, P; Guo, W L; Li, B Y; Wang, W H; Yue, Z C; Lei, J L; Zhong, X M

    2015-01-01

    Small heat shock proteins (sHSPs) are essential for the plant's normal development and stress responses, especially the heat stress response. The information regarding sHSP genes in Chinese cabbage (Brassica rapa ssp pekinensis) is sparse, hence we performed a genome-wide analysis to identify sHSP genes in this species. We identified 26 non-redundant sHSP genes distributed on all chromosomes, except chromosome A7, with one additional sHSP gene identified from an expressed sequence tag library. Chinese cabbage was found to contain more sHSP genes than Arabidopsis. The 27 sHSP genes were classified into 11 subfamilies. We identified 22 groups of sHSP syntenic orthologous genes between Chinese cabbage and Arabidopsis. In addition, eight groups of paralogous genes were uncovered in Chinese cabbage. Protein structures of the 27 Chinese cabbage sHSPs were modeled using Phyre2, which revealed that all of them contain several conserved β strands across different subfamilies. In general, gene structure was conserved within each subfamily between Chinese cabbage and Arabidopsis, except for peroxisome sHSP. Analysis of promoter motifs showed that most sHSP genes contain heat shock elements or variants. We also found that biased gene loss has occurred during the evolution of the sHSP subfamily in Chinese cabbage. Expression analysis indicated that the greatest transcript abundance of most Chinese cabbage sHSP genes was found in siliques and early cotyledon embryos. Thus, genome-wide identification and characterization of sHSP genes is a first and important step in the investigation of sHSPs in Chinese cabbage. PMID:26505345

  7. A new combined green method for 2-Chlorophenol removal using cross-linked Brassica rapa peroxidase in silicone oil.

    PubMed

    Tandjaoui, Nassima; Abouseoud, Mahmoud; Couvert, Annabelle; Amrane, Abdeltif; Tassist, Amina

    2016-04-01

    This study proposes a new technique to treat waste air containing 2-Chlorophenol (2-CP), namely an integrated process coupling absorption of the compound in an organic liquid phase and its enzymatic degradation. Silicone oil (47V20) was used as an organic absorbent to allow the volatile organic compound (VOC) transfer from the gas phase to the liquid phase followed by its degradation by means of Cross-linked Brassica rapa peroxidase (BRP) contained in the organic phase. An evaluation of silicone oil (47V20) absorption capacity towards 2-CP was first accomplished by determining its partition coefficient (H) in this solvent. The air-oil partition coefficient of 2-CP was found equal to 0.136 Pa m(3) mol(-1), which is five times lower than the air-water value (0.619 Pam(3) mol(-1)). The absorbed 2-CP was then subject to enzymatic degradation by cross-linked BRP aggregates (BRP-CLEAs). The degradation step was affected by four parameters (contact time; 2-CP, hydrogen peroxide and enzyme concentrations), which were optimized in order to obtain the highest conversion yield. A maximal conversion yield of 69% and a rate of 1.58 mg L(-1) min(-1)were obtained for 100 min duration time when 2-CP and hydrogen peroxide concentrations were respectively 80 mg L(-1) and 6 mM in the presence of 2.66 UI mL(-1) BRP-CLEAs. The reusability of BRP-CLEAs in silicone oil was assessed, showing promising results since 59% of their initial efficiency remained after three batches. PMID:26802263

  8. Effects of endocrine disruptor di-n-butyl phthalate on the growth of Bok choy (Brassica rapa subsp. chinensis).

    PubMed

    Liao, Chien-Sen; Yen, Jui-Hung; Wang, Yei-Shung

    2006-12-01

    The effects of the endocrine disrupter, di-n-butyl phthalate (DBP), on the growth of leaf vegetable Bok choy (Brassica rapa subsp. chinensis, white stem Bok choy) were investigated. The results showed that leaves of Bok choy became white in color with the occurrence of chlorosis and necrosis upon treating with 30 mg l(-1) DBP for 42 days. Transmission electron microscopic images revealed that changes in the chloroplast structures accompanied the chlorosis. In addition, a decrease in biomass and chlorophyll, and accumulation of DBP, were found in DBP-treated Bok choy. The growth and morphology of Bok choy showed a significant dose-response relationship upon treatment with DBP in a hydroponic culture medium. The proteome of the leaf tissue was analyzed using two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). Six protein spots were identified in 2-DE that showed reproducible differences in expression between the normal control and the DBP-treated sample. Based on proteome level studies two protein spots increased and were identified as superoxide dismutase (SOD) and peroxidase 21 precursor. These proteins are believed to increase in expression in response to free radical exposure as a detoxification mechanism. The other four protein spots that disappeared on treatment with DBP were identified as heat shock cognate protein 80, protein disulfide isomerase precursor, apocytochrome f precursor, and RNA polymerase beta subunit. The first two play an important role in polypeptide folding, the third is associated with electron transport, and the last has a critical function in DNA transcription. This study indicated that DBP affects the proteome formation as well as the physiology and the morphology of Bok choy during growth. The decrease in those four proteins might be related to the growth and development of a plant. PMID:16824579

  9. Brassica rapa Has Three Genes That Encode Proteins Associated with Different Neutral Lipids in Plastids of Specific Tissues1

    PubMed Central

    Kim, Hyun Uk; Wu, Sherry S.H.; Ratnayake, Chandra; Huang, Anthony H.C.

    2001-01-01

    Plastid lipid-associated protein (PAP), a predominant structural protein associated with carotenoids and other non-green neutral lipids in plastids, was shown to be encoded by a single nuclear gene in several species. Here we report three PAP genes in the diploid Brassica rapa; the three PAPs are associated with different lipids in specific tissues. Pap1 and Pap2 are more similar to each other (84% amino acid sequence identity) than to Pap3 (46% and 44%, respectively) in the encoded mature proteins. Pap1 transcript was most abundant in the maturing anthers (tapetum) and in lesser amounts in leaves, fruit coats, seeds, and sepals; Pap2 transcript was abundant only in the petals; and Pap3 transcript had a wide distribution, but at minimal levels in numerous organs. Immunoblotting after sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that most organs had several nanograms of PAP1 or PAP2 per milligram of total protein, the highest amounts being in the anthers (10.9 μg mg−1 PAP1) and petals (6.6 μg mg−1 PAP2), and that they had much less PAP3 (<0.02 μg mg−1). In these organs PAP was localized in isolated plastid fractions. Plants were subjected to abiotic stresses; drought and ozone reduced the levels of the three Pap transcripts, whereas mechanical wounding and altering the light intensity enhanced their levels. We conclude that the PAP gene family consists of several members whose proteins are associated with different lipids and whose expressions are controlled by distinct mechanisms. Earlier reports of the expression of one Pap gene in various organs in a species need to be re-examined. PMID:11351096

  10. Photophysiology of the Elongated Internode (ein) Mutant of Brassica rapa: ein Mutant Lacks a Detectable Phytochrome B-Like Polypeptide.

    PubMed

    Devlin, P F; Rood, S B; Somers, D E; Quail, P H; Whitelam, G C

    1992-11-01

    Several phytochrome-controlled processes have been examined in etiolated and light-grown seedlings of a normal genotype and the elongated internode (ein/ein) mutant of rapid-cycling Brassica rapa. Although etiolated ein seedlings displayed normal sensitivity to prolonged far-red light with respect to inhibition of hypocotyl elongation, expansion of cotyledons, and synthesis of anthocyanin, they displayed reduced sensitivity to prolonged red light for all three of these deetiolation responses. In contrast to normal seedlings, light-grown ein seedlings did not show a growth promotion in response to end-of-day far-red irradiation. Additionally, whereas the first internode of light-grown normal seedlings showed a marked increase in elongation in response to reduced ratio of red to far-red light, ein seedlings showed only a small elongation response. When blots of protein extracts from etiolated and light-treated ein and normal seedlings were probed with monoclonal antibody to phytochrome A, an immunostaining band at about 120 kD was observed for both extracts. The immunostaining intensity of this band was substantially reduced for extracts of light-treated normal and ein seedlings. A mixture of three monoclonal antibodies directed against phytochrome B from Arabidopsis thaliana immunostained a band at about 120 kD for extracts of etiolated and light-treated normal seedlings. This band was undetectable in extracts of ein seedlings. We propose that ein is a photoreceptor mutant that is deficient in a light-stable phytochrome B-like species. PMID:16653143

  11. Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution.

    PubMed

    Chen, Xun; Ge, Xianhong; Wang, Jing; Tan, Chen; King, Graham J; Liu, Kede

    2015-01-01

    Brassica rapa includes some of the most important vegetables worldwide as well as oilseed crops. The complete annotated genome sequence confirmed its paleohexaploid origins and provides opportunities for exploring the detailed process of polyploid genome evolution. We generated a genome-wide DNA methylation profile for B. rapa using a modified reduced representation bisulfite sequencing (RRBS) method. This sampling represented 2.24% of all CG loci (2.5 × 10(5)), 2.16% CHG (2.7 × 10(5)), and 1.68% CHH loci (1.05 × 10(5)) (where H = A, T, or C). Our sampling of DNA methylation in B. rapa indicated that 52.4% of CG sites were present as (5m)CG, with 31.8% of CHG and 8.3% of CHH. It was found that genic regions of single copy genes had significantly higher methylation compared to those of two or three copy genes. Differences in degree of genic DNA methylation were observed in a hierarchical relationship corresponding to the relative age of the three ancestral subgenomes, primarily accounted by single-copy genes. RNA-seq analysis revealed that overall the level of transcription was negatively correlated with mean gene methylation content and depended on copy number or was associated with the different subgenomes. These results provide new insights into the role epigenetic variation plays in polyploid genome evolution, and suggest an alternative mechanism for duplicate gene loss. PMID:26500672

  12. Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution

    PubMed Central

    Chen, Xun; Ge, Xianhong; Wang, Jing; Tan, Chen; King, Graham J.; Liu, Kede

    2015-01-01

    Brassica rapa includes some of the most important vegetables worldwide as well as oilseed crops. The complete annotated genome sequence confirmed its paleohexaploid origins and provides opportunities for exploring the detailed process of polyploid genome evolution. We generated a genome-wide DNA methylation profile for B. rapa using a modified reduced representation bisulfite sequencing (RRBS) method. This sampling represented 2.24% of all CG loci (2.5 × 105), 2.16% CHG (2.7 × 105), and 1.68% CHH loci (1.05 × 105) (where H = A, T, or C). Our sampling of DNA methylation in B. rapa indicated that 52.4% of CG sites were present as 5mCG, with 31.8% of CHG and 8.3% of CHH. It was found that genic regions of single copy genes had significantly higher methylation compared to those of two or three copy genes. Differences in degree of genic DNA methylation were observed in a hierarchical relationship corresponding to the relative age of the three ancestral subgenomes, primarily accounted by single-copy genes. RNA-seq analysis revealed that overall the level of transcription was negatively correlated with mean gene methylation content and depended on copy number or was associated with the different subgenomes. These results provide new insights into the role epigenetic variation plays in polyploid genome evolution, and suggest an alternative mechanism for duplicate gene loss. PMID:26500672

  13. Teaching Human Genetics with Mustard: Rapid Cycling Brassica rapa (Fast Plants Type) as a Model for Human Genetics in the Classroom Laboratory

    PubMed Central

    Pickard, Dawn

    2007-01-01

    We have developed experiments and materials to model human genetics using rapid cycling Brassica rapa, also known as Fast Plants. Because of their self-incompatibility for pollination and the genetic diversity within strains, B. rapa can serve as a relevant model for human genetics in teaching laboratory experiments. The experiment presented here is a paternity exclusion project in which a child is born with a known mother but two possible alleged fathers. Students use DNA markers (microsatellites) to perform paternity exclusion on these subjects. Realistic DNA marker analysis can be challenging to implement within the limitations of an instructional lab, but we have optimized the experimental methods to work in a teaching lab environment and to maximize the “hands-on” experience for the students. The genetic individuality of each B. rapa plant, revealed by analysis of polymorphic microsatellite markers, means that each time students perform this project, they obtain unique results that foster independent thinking in the process of data interpretation. PMID:17548880

  14. Effect of Diffusion on Discoloration of Congo Red by Alginate Entrapped Turnip (Brassica rapa) Peroxidase

    PubMed Central

    Ahmedi, Afaf; Abouseoud, Mahmoud; Abdeltif, Amrane; Annabelle, Couvert

    2015-01-01

    Enzymatic discoloration of the diazo dye, Congo red (CR), by immobilized plant peroxidase from turnip “Brassica rapa” is investigated. Partially purified turnip peroxidase (TP) was immobilized by entrapment in spherical particles of calcium alginate and was assayed for the discoloration of aqueous CR solution. Experimental data revealed that pH, reaction time, temperature, colorant, and H2O2 concentration play a significant role in dye degradation. Maximum CR removal was found at pH 2.0, constant temperature of 40°C in the presence of 10 mM H2O2, and 180 mg/L of CR. More than 94% of CR was removed by alginate immobilized TP after 1 h of incubation in a batch process under optimal conditions. About 74% removal efficiency was retained after four recycles. Diffusional limitations in alginate beads such as effectiveness factor η, Thiele modulus Φ, and effective diffusion coefficients (De) of Congo red were predicted assuming a first-order biodegradation kinetic. Results showed that intraparticle diffusion resistance has a significant effect on the CR biodegradation rate. PMID:25734011

  15. Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome.

    PubMed Central

    Jackson, S A; Cheng, Z; Wang, M L; Goodman, H M; Jiang, J

    2000-01-01

    Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A set of six bacterial artificial chromosomes (BACs) representing a 431-kb contiguous region of chromosome 2 of A. thaliana was mapped on both chromosomes and DNA fibers of B. rapa. This DNA fragment has a single location in the A. thaliana genome, but hybridized to four to six B. rapa chromosomes, indicating multiple duplications in the B. rapa genome. The sizes of the fiber-FISH signals from the same BACs were not longer in B. rapa than those in A. thaliana, suggesting that this genomic region is duplicated but not expanded in the B. rapa genome. The comparative fiber-FISH mapping results support that chromosomal duplications, rather than regional expansion due to accumulation of repetitive sequences in the intergenic regions, played the major role in the evolution of the B. rapa genome. PMID:11014828

  16. Identification, expression, and comparative genomic analysis of the IPT and CKX gene families in Chinese cabbage (Brassica rapa ssp. pekinensis)

    PubMed Central

    2013-01-01

    Background Cytokinins (CKs) have significant roles in various aspects of plant growth and development, and they are also involved in plant stress adaptations. The fine-tuning of the controlled CK levels in individual tissues, cells, and organelles is properly maintained by isopentenyl transferases (IPTs) and cytokinin oxidase/dehydrogenases (CKXs). Chinese cabbage is one of the most economically important vegetable crops worldwide. The whole genome sequencing of Brassica rapa enables us to perform the genome-wide identification and functional analysis of the IPT and CKX gene families. Results In this study, a total of 13 BrIPT genes and 12 BrCKX genes were identified. The gene structures, conserved domains and phylogenetic relationships were analyzed. The isoelectric point, subcellular localization and glycosylation sites of the proteins were predicted. Segmental duplicates were found in both BrIPT and BrCKX gene families. We also analyzed evolutionary patterns and divergence of the IPT and CKX genes in the Cruciferae family. The transcription levels of BrIPT and BrCKX genes were analyzed to obtain an initial picture of the functions of these genes. Abiotic stress elements related to adverse environmental stimuli were found in the promoter regions of BrIPT and BrCKX genes and they were confirmed to respond to drought and high salinity conditions. The effects of 6-BA and ABA on the expressions of BrIPT and BrCKX genes were also investigated. Conclusions The expansion of BrIPT and BrCKX genes after speciation from Arabidopsis thaliana is mainly attributed to segmental duplication events during the whole genome triplication (WGT) and substantial duplicated genes are lost during the long evolutionary history. Genes produced by segmental duplication events have changed their expression patterns or may adopted new functions and thus are obtained. BrIPT and BrCKX genes respond well to drought and high salinity stresses, and their transcripts are affected by exogenous

  17. Glyphosate-drift but not herbivory alters the rate of transgene flow from single and stacked trait transgenic canola (Brassica napus) to nontransgenic B. napus and B. rapa.

    PubMed

    Londo, Jason P; Bollman, Michael A; Sagers, Cynthia L; Lee, E Henry; Watrud, Lidia S

    2011-08-01

    • Transgenic plants can offer agricultural benefits, but the escape of transgenes is an environmental concern. In this study we tested the hypothesis that glyphosate drift and herbivory selective pressures can change the rate of transgene flow between the crop Brassica napus (canola), and weedy species and contribute to the potential for increased transgene escape risk and persistence outside of cultivation. • We constructed plant communities containing single transgenic B. napus genotypes expressing glyphosate herbicide resistance (CP4 EPSPS), lepidopteran insect resistance (Cry1Ac), or both traits ('stacked'), plus nontransgenic B. napus, Brassica rapa and Brassica nigra. Two different selective pressures, a sublethal glyphosate dose and lepidopteran herbivores (Plutella xylostella), were applied and rates of transgene flow and transgenic seed production were measured. • Selective treatments differed in the degree in which they affected gene flow and production of transgenic hybrid seed. Most notably, glyphosate-drift increased the incidence of transgenic seeds on nontransgenic B. napus by altering flowering phenology and reproductive function. • The findings of this study indicate that transgenic traits may be transmitted to wild populations and may increase in frequency in weedy populations through the direct and indirect effects of selection pressures on gene flow. PMID:21443650

  18. Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing.

    PubMed

    Yu, Fengqun; Zhang, Xingguo; Huang, Zhen; Chu, Mingguang; Song, Tao; Falk, Kevin C; Deora, Abhinandan; Chen, Qilin; Zhang, Yan; McGregor, Linda; Gossen, Bruce D; McDonald, Mary Ruth; Peng, Gary

    2016-01-01

    Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar "Flower Nabana". In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker

  19. Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing

    PubMed Central

    Yu, Fengqun; Zhang, Xingguo; Huang, Zhen; Chu, Mingguang; Song, Tao; Falk, Kevin C.; Deora, Abhinandan; Chen, Qilin; Zhang, Yan; McGregor, Linda; Gossen, Bruce D.; McDonald, Mary Ruth; Peng, Gary

    2016-01-01

    Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar “Flower Nabana”. In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker

  20. A Large Insertion in bHLH Transcription Factor BrTT8 Resulting in Yellow Seed Coat in Brassica rapa

    PubMed Central

    Li, Xia; Chen, Li; Hong, Meiyan; Zhang, Yan; Zu, Feng; Wen, Jing; Yi, Bin; Ma, Chaozhi; Shen, Jinxiong; Tu, Jinxing; Fu, Tingdong

    2012-01-01

    Yellow seed is a desirable quality trait of the Brassica oilseed species. Previously, several seed coat color genes have been mapped in the Brassica species, but the molecular mechanism is still unknown. In the present investigation, map-based cloning method was used to identify a seed coat color gene, located on A9 in B. rapa. Blast analysis with the Arabidopsis genome showed that there were 22 Arabidopsis genes in this region including at4g09820 to at4g10620. Functional complementation test exhibited a phenotype reversion in the Arabidopsis thaliana tt8-1 mutant and yellow-seeded plant. These results suggested that the candidate gene was a homolog of TRANSPARENT TESTA8 (TT8) locus. BrTT8 regulated the accumulation of proanthocyanidins (PAs) in the seed coat. Sequence analysis of two alleles revealed a large insertion of a new class of transposable elements, Helitron in yellow sarson. In addition, no mRNA expression of BrTT8 was detected in the yellow-seeded line. It indicated that the natural transposon might have caused the loss in function of BrTT8. BrTT8 encodes a basic/helix-loop-helix (bHLH) protein that shares a high degree of similarity with other bHLH proteins in the Brassica. Further expression analysis also revealed that BrTT8 was involved in controlling the late biosynthetic genes (LBGs) of the flavonoid pathway. Our present findings provided with further studies could assist in understanding the molecular mechanism involved in seed coat color formation in Brassica species, which is an important oil yielding quality trait. PMID:22984469

  1. Developing stable progenies of ×Brassicoraphanus, an intergeneric allopolyploid between Brassica rapa and Raphanus sativus, through induced mutation using microspore culture.

    PubMed

    Lee, Soo-Seong; Lee, Sun-Ae; Yang, Jungmin; Kim, Jongkee

    2011-03-01

    Induced mutations were used to improve the low seed fertility of an intergeneric allopolyploid, 'Baemoochae,' ×Brassicoraphanus, synthesized following hybridization between Brassica rapa and Raphanus sativus. The mutagen N-methyl-N-nitroso-urethane (NMU) was added to microspore cultures. Four lines of nine in the Mi(2) generation showed very high fertility under controlled pollination. The progeny lines (Mi(3)) confirmed this result under open pollination, and excellent uniformity was observed in plants grown in the field, as well as in their AFLP profile. On attaining high fertility and uniformity, one of the lines was released to farmers as a new leafy vegetable crop. The original nine lines shared very similar AFLP banding patterns, without any large differences between the high and low seed fertility lines. Thus, mutation induction accelerated genetic stabilization of a newly synthesized allopolyploid, ×Brassicoraphanus. PMID:21113703

  2. Construction of a genetic map based on high-throughput SNP genotyping and genetic mapping of a TuMV resistance locus in Brassica rapa.

    PubMed

    Chung, Hee; Jeong, Young-Min; Mun, Jeong-Hwan; Lee, Soo-Seong; Chung, Won-Hyong; Yu, Hee-Ju

    2014-04-01

    Brassica rapa is a member of the Brassicaceae family and includes vegetables and oil crops that are cultivated worldwide. The introduction of durable resistance against turnip mosaic virus (TuMV) into agronomically important cultivars has been a significant challenge for genetic and horticultural breeding studies of B. rapa. Based on our previous genome-wide analysis of DNA polymorphisms between the TuMV-resistant doubled haploid (DH) line VC40 and the TuMV-susceptible DH line SR5, we constructed a core genetic map of the VCS-13M DH population, which is composed of 83 individuals derived from microspore cultures of a F1 cross between VC40 and SR5, by analyzing the segregation of 314 sequence-characterized genetic markers. The genetic markers correspond to 221 SNPs and 31 InDels of genes as well as 62 SSRs, covering 1,115.9 cM with an average distance of 3.6 cM between the adjacent marker loci. The alignment and orientation of the constructed map showed good agreement with the draft genome sequence of Chiifu, thus providing an efficient strategy to map genic sequences. Using the genetic map, a novel dominant TuMV resistance locus (TuMV-R) in the VCS-13M DH population was identified as a 0.34 Mb region in the short arm of chromosome A6 in which four CC-NBS-LRR resistance genes and two pathogenesis-related-1 genes reside. The genetic map developed in this study can play an important role in the genetic study of TuMV resistance and the molecular breeding of B. rapa. PMID:24326528

  3. Mapping and candidate-gene screening of the novel Turnip mosaic virus resistance gene retr02 in Chinese cabbage (Brassica rapa L.).

    PubMed

    Qian, Wei; Zhang, Shujiang; Zhang, Shifan; Li, Fei; Zhang, Hui; Wu, Jian; Wang, Xiaowu; Walsh, John A; Sun, Rifei

    2013-01-01

    The extreme resistance to Turnip mosaic virus observed in the Chinese cabbage (Brassica rapa) line, BP8407, is monogenic and recessive. Bulked segregant analysis was carried out to identify simple sequence repeat and Indel markers linked to this recessive resistance gene, termed recessive Turnip mosaic virus resistance 02 (retr02). Mapping of PCR-specific Indel markers on 239 individuals of a BP8407 × Ji Zao Chun F(2) population, located this resistance gene to a 0.9-cM interval between two Indel markers (BrID10694 and BrID101309) and in scaffold000060 or scaffold000104 on chromosome A04 of the B. rapa genome. Eleven eukaryotic initiation factor 4E (eIF4E) and 14 eukaryotic initiation factor 4G (eIF4G) genes are predicted in the B. rapa genome. A candidate gene, Bra035393 on scaffold000104, was predicted within the mapped resistance locus. The gene encodes the eIF(iso)4E protein. Bra035393 was sequenced in BP8407 and Ji Zao Chun. A polymorphism (A/G) was found in exon 3 between BP8407 and Ji Zao Chun. This gene was analysed in four resistant and three susceptible lines. A correlation was observed between the amino acid substitution (Gly/Asp) in the eIF(iso)4E protein and resistance/susceptibility. eIF(iso)4E has been shown previously to interact with the TuMV genome-linked protein, VPg. PMID:22996569

  4. Combinations of a host resistance gene and the CI gene of turnip mosaic virus differentially regulate symptom expression in Brassica rapa cultivars.

    PubMed

    Fujiwara, Ayaka; Inukai, Tsuyoshi; Kim, Bo Min; Masuta, Chikara

    2011-09-01

    In the pathosystem of Brassica rapa and turnip mosaic virus (TuMV), the type of symptoms expressed by susceptible plants are determined by the gene combinations between the host cultivar and virus strain. In this study, we found that the resistance reaction and symptoms such as systemic lethal necrosis, leaf malformation and mosaic were differentially determined, depending on the combinations of the genotypes for a host locus or two closely linked host loci and the viral CI gene. Systemic necrosis caused by TuMV-UK1 on some B. rapa subsp. pekinensis cultivars is induced in conjunction with a recessive gene, rnt1-2 (resistance and necrosis to tumv 1-2), which is allelic or closely linked to TuMV resistance gene Rnt1-1 on chromosome R6. rnt1-2 is incompletely recessive to rnt1-3, which does not cause any necrotic responses. The genotype rnt1-2/rnt1-3 caused a mild necrosis along leaf veins of severely malformed leaves. A spontaneous mutant, TuMV-UK1 (UK1m), with the amino acid substitution V1827E in CI, broke Rnt1-1 resistance and altered the systemic necrosis and leaf malformation induced by rnt1-2. This single amino acid in the CI protein of UK1 was also associated with severe mosaic and abnormal leaf development, perhaps interacting with unknown host factors. To clarify the relationship between Rnt1-1 and TuRB01b, which was previously reported as a TuMV-UK1 resistance gene on chromosome R6, the B. rapa cultivar Tropical Delight carrying TuRB01b was inoculated with UK1m or the infectious UK1 clone with the CI V1827E mutation. Because Tropical Delight showed resistance to both mutants, Rnt1-1 might be different from TuRB01b. PMID:21625976

  5. Toxic effects of heavy metals (Cd, Cr and Pb) on seed germination and growth and DPPH-scavenging activity in Brassica rapa var. turnip.

    PubMed

    Siddiqui, Maryam Mehmood; Abbasi, Bilal Haider; Ahmad, Nisar; Ali, Mohammad; Mahmood, Tariq

    2014-04-01

    Toxicity of heavy metal is a wide spread environmental problem affecting all life forms including plants. In the present study the toxic effects of heavy metals, cadmium (Cd), chromium (Cr) and lead (Pb) on seed germination rate (%), germination index (G-index) and growth (mm) of Brassica rapa var. turnip have been investigated. The seeds were soaked either in distilled water (control) or in aqueous solutions of Cd, Cr and Pb (1 g/l, 2.5 g/l and 5 g/l) at 4°C in dark for 24 hours. Prior to inoculation onto MS0 medium, the soaked seeds were either washed with sterile distilled water or inoculated without washing on solidified MS0 medium at 25 ± 2°C with 16/8-hour photoperiod in a growth chamber to germinate in vitro. Such stress conditions revealed that by increasing the concentration of heavy metals, the germination rate (%), G-index value and growth (mm) decreased significantly, suggesting their toxic effect on B. rapa var. turnip. This study further revealed that experiment with seed washing resulted in less toxicity of selected heavy metals on germination and growth of B. rapa var. turnip, as compared to experiment without washing. However, the resulting toxicity order of the selected heavy metals remained the same (Cd > Cr > Pb). Significant decrease has been observed in seed viability and germination potential and finally heavy metals completely ceased further growth and development of plants. The 2, 2-diphenyl-1-picrylhydrazyl (DPPH)-scavenging activity revealed that significantly higher activity was observed in control plants without heavy metals treatment. Furthermore, the Cd-treated plants showed decreased antioxidant activity. Cr and Pb were less toxic as compared to Cd (control > Pb > Cr > Cd). This study revealed that selected heavy metals not only affected plant development but also disturbed plant metabolic pathways. PMID:22872632

  6. The influence of various biochars on the bioaccessibility and bioaccumulation of PAHs and potentially toxic elements to turnips (Brassica rapa L.).

    PubMed

    Khan, Sardar; Waqas, Muhammad; Ding, Fenghua; Shamshad, Isha; Arp, Hans Peter H; Li, Gang

    2015-12-30

    The influence of amending a contaminated soil with different dry-pyrolyzed biochars on the bioaccessibility and biouptake of polycyclic aromatic hydrocarbons (PAH) and potentially toxic elements (PTE) in turnip (Brassica rapa L.,) was investigated. This is the first study to examine the influence of biochar amendments on turnips grown in a contaminated soil. The biochars came from different local feedstocks, including sewage sludge biochar (SSBC), soybean straw biochar (SBBC), rice straw biochar (RSBC) and peanut shell biochar (PNBC). The biochars were applied to soil at 2% and 5% amendments, and the resulting influence on various soil and porewater properties were quantified. The bioaccessible concentrations of PAHs in soil and their bioaccumulation in B. rapa L. significantly (P < 0.05) decreased in the biochar amended soils. Biochar additions significantly (P ≤ 0.05) reduced the bioaccumulation of PTEs (As, Cd, Cu, Pb and Zn) in B. rapa L, though not as much as for PAHs. The most effective biochar at reducing both PAHs and PTEs was PNBC (P ≤ 0.05). Amendments of 5% biochar were more effective at reducing contaminant bioaccessibility than amendments at 2% (P < 0.05). Crop yield, however, increased the most for the 2% biochar amendments, in particular for SSBC (with a 49% increase in crop yield compared to the non-amended soil). Therefore, which biochar would be the most advantageous in this system would require a cost-benefit analysis between increasing crop yield (best achieved with 2% SSBC amendments) and decreasing the PAH and PTE uptake (best achieved with 5% PNBC amendments). PMID:26188867

  7. Synthesis of a Brassica trigenomic allohexaploid (B. carinata × B. rapa) de novo and its stability in subsequent generations.

    PubMed

    Tian, Entang; Jiang, Yingfen; Chen, Lunlin; Zou, Jun; Liu, Fei; Meng, Jinling

    2010-11-01

    Allopolyploidy plays an important role in plant evolution and confers obvious advantages on crop growth and breeding compared to low ploidy levels. The present investigation was aimed at synthesising the first known chromosomally stable hexaploid Brassica with the genome constitution AABBCC. More than 2,000 putative hexaploid plants were obtained through large-scale hybridisation from various combinations of crosses between different cultivars of Brassica carinata (BBCC) and B. rapa (AA). The majority of plants after two generations of selfing within selected hexaploid plants (H(2)) were aneuploid, and only 80 plants (4.6%) had the expected hexaploid chromosome number (2n = 54). The hexaploid ratio increased to an average of 23.0 and 26.3% in the H(3) and H(4) generations, respectively, and was accompanied by an increase in pollen fertility. The appearance of aneuploid plants in each generation could be detected having various chromosomal abnormalities at meiosis. The frequency of hexaploid plants varied significantly among different cultivar combinations, from 0 to 56% in the H(4) generation, and it showed a positive correlation with pollen fertility. The frequency of SSR allelic fragments lost or novel alleles gained was significantly lower in H(4) than in H(2) and H(3), which reflects increasing genome stability in H(4). The A and C genomes were significantly less stable than the B genome, which may mainly result from frequent homoeologous pairing and rearrangements between the A and C genomes. Methods to establish a stable hexaploid Brassica crop by intercrossing these lines followed by intensive selection are also discussed. PMID:20607208

  8. Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea

    PubMed Central

    2013-01-01

    Background The Brassica B genome is known to carry several important traits, yet there has been limited analyses of its underlying genome structure, especially in comparison to the closely related A and C genomes. A bacterial artificial chromosome (BAC) library of Brassica nigra was developed and screened with 17 genes from a 222 kb region of A. thaliana that had been well characterised in both the Brassica A and C genomes. Results Fingerprinting of 483 apparently non-redundant clones defined physical contigs for the corresponding regions in B. nigra. The target region is duplicated in A. thaliana and six homologous contigs were found in B. nigra resulting from the whole genome triplication event shared by the Brassiceae tribe. BACs representative of each region were sequenced to elucidate the level of microscale rearrangements across the Brassica species divide. Conclusions Although the B genome species separated from the A/C lineage some 6 Mya, comparisons between the three paleopolyploid Brassica genomes revealed extensive conservation of gene content and sequence identity. The level of fractionation or gene loss varied across genomes and genomic regions; however, the greatest loss of genes was observed to be common to all three genomes. One large-scale chromosomal rearrangement differentiated the B genome suggesting such events could contribute to the lack of recombination observed between B genome species and those of the closely related A/C lineage. PMID:23586706

  9. Molecular characterization of BrMYB28 and BrMYB29 paralogous transcription factors involved in the regulation of aliphatic glucosinolate profiles in Brassica rapa ssp. pekinensis.

    PubMed

    Baskar, Venkidasamy; Park, Se Won

    2015-07-01

    Glucosinolates (GSL) are one of the major secondary metabolites of the Brassicaceae family. In the present study, we aim at characterizing the multiple paralogs of aliphatic GSL regulators, such as BrMYB28 and BrMYB29 genes in Brassica rapa ssp. pekinensis, by quantitative real-time PCR (qRT-PCR) analysis in different tissues and at various developmental stages. An overlapping gene expression pattern between the BrMYBs as well as their downstream genes (DSGs) was found at different developmental stages. Among the BrMYB28 and BrMYB29 paralogous genes, the BrMYB28.3 and BrMYB29.1 genes were dominantly expressed in most of the developmental stages, compared to the other paralogs of the BrMYB genes. Furthermore, the differential expression pattern of the BrMYBs was observed under various stress treatments. Interestingly, BrMYB28.2 showed the least expression in most developmental stages, while its expression was remarkably high in different stress conditions. More specifically, the BrMYB28.2, BrMYB28.3, and BrMYB29.1 genes were highly responsive to various abiotic and biotic stresses, further indicating their possible role in stress tolerance. Moreover, the in silico cis motif analysis in the upstream regulatory regions of BrMYBs showed the presence of various putative stress-specific motifs, which further indicated their responsiveness to biotic and abiotic stresses. These observations suggest that the dominantly expressed BrMYBs, both in different developmental stages and under various stress treatments (BrMYB28.3 and BrMYB29.1), may be potential candidate genes for altering the GSL level through genetic modification studies in B. rapa ssp. pekinensis. PMID:26043798

  10. Genome-Wide Transcriptome Analysis of Two Contrasting Brassica rapa Doubled Haploid Lines under Cold-Stresses Using Br135K Oligomeric Chip

    PubMed Central

    Park, Jong-In; Thamilarasan, Senthil Kumar; Lee, Sang Sook; Kim, Yeon-Ki; Lim, Yong-Pyo; Nou, Ill-Sup; Hur, Yoonkang

    2014-01-01

    Genome wide transcription analysis in response to stresses is important to provide a basis of effective engineering strategies to improve stress tolerance in crop plants. We assembled a Brassica rapa oligomeric microarray (Br135K microarray) using sequence information from 41,173 unigenes and analyzed the transcription profiles of two contrasting doubled haploid (DH) lines, Chiifu and Kenshin, under cold-treatments. The two DH lines showed great differences in electrolyte leakage below −4°C, but similar patterns from 4°C to −2°C. Cold-treatments induced 885 and 858 genes in Chiifu and Kenshin, respectively. Overall, 134, and 56 genes showed an intrinsic difference in expression in Chiifu and Kenshin, respectively. Among 5,349 genes that showed no hit found (NHF) in public databases, 61 and 24 were specifically expressed in Chiifu and Kenshin, respectively. Many transcription factor genes (TFs) also showed various characteristics of expression. BrMYB12, BrMYBL2, BrbHLHs, BrbHLH038, a C2H2, a WRKY, BrDREB19 and a integrase-type TF were induced in a Chiifu-specific fashion, while a bHLH (Bra001826/AT3G21330), bHLH, cycling Dof factor and two Dof type TFs were Kenshin specific. Similar to previous studies, a large number of genes were differently induced or regulated among the two genotypes, but many genes, including NHFs, were specifically or intrinsically expressed with genotype specificity. Expression patterns of known-cold responsive genes in plants resulted in discrepancy to membrane leakage in the two DH lines, indicating that timing of gene expression is more important to conferring freezing tolerance rather than expression levels. Otherwise, the tolerance will be related to the levels of transcripts before cold-treatment or regulated by other mechanisms. Overall, these results indicate common signaling pathways and various transcriptional regulatory mechanisms are working together during cold-treatment of B. rapa. Our newly developed Br135K oligomeric

  11. Changes in the Relative Abundance and Movement of Insect Pollinators During the Flowering Cycle of Brassica rapa Crops: Implications for Gene Flow

    PubMed Central

    Mesa, Laura A.; Howlett, Bradley G.; Grant, Jan E.; Didham, Raphael K.

    2013-01-01

    The potential movement of transgenes from genetically modified crops to non-genetically modified crops via insect-mediated pollen dispersal has been highlighted as one of the areas of greatest concern in regards to genetically modified crops. Pollen movement depends sensitively on spatial and temporal variation in the movement of insect pollinators between crop fields. This study tested the degree of variation in the diversity and relative abundance of flower-visiting insects entering versus leaving pak choi, Brassica rapa var. chinensis L. (Brassicales: Brassicaceae), crops throughout different stages of the flowering cycle. The relative abundance of flower-visiting insects varied significantly with Brassica crop phenology. Greater numbers of flower-visiting insects were captured inside rather than outside the crop fields, with the highest capture rates of flower-visitors coinciding with the peak of flowering in both spring-flowering and summer-flowering crops. Moreover, the ratio of flower-visiting insects entering versus leaving crop fields also varied considerably with changing crop phenology. Despite high variation in relative capture rates, the data strongly indicate non-random patterns of variation in insect movement in relation to crop phenology, with early-season aggregation of flower-visiting insects entering and remaining in the crop, and then mass emigration of flower-visiting insects leaving the crop late in the flowering season. Although pollen movement late in the flowering cycle might contribute relatively little to total seed set (and hence crop production), the findings here suggest that extensive late-season pollinator redistribution in the landscape could contribute disproportionately to long-distance gene movement between crops. PMID:23937538

  12. Changes in the relative abundance and movement of insect pollinators during the flowering cycle of Brassica rapa crops: implications for gene flow.

    PubMed

    Mesa, Laura A; Howlett, Bradley G; Grant, Jan E; Didham, Raphael K

    2013-01-01

    The potential movement of transgenes from genetically modified crops to non-genetically modified crops via insect-mediated pollen dispersal has been highlighted as one of the areas of greatest concern in regards to genetically modified crops. Pollen movement depends sensitively on spatial and temporal variation in the movement of insect pollinators between crop fields. This study tested the degree of variation in the diversity and relative abundance of flower-visiting insects entering versus leaving pak choi, Brassica rapa var. chinensis L. (Brassicales: Brassicaceae), crops throughout different stages of the flowering cycle. The relative abundance of flower-visiting insects varied significantly with Brassica crop phenology. Greater numbers of flower-visiting insects were captured inside rather than outside the crop fields, with the highest capture rates of flower-visitors coinciding with the peak of flowering in both spring-flowering and summer-flowering crops. Moreover, the ratio of flower-visiting insects entering versus leaving crop fields also varied considerably with changing crop phenology. Despite high variation in relative capture rates, the data strongly indicate non-random patterns of variation in insect movement in relation to crop phenology, with early-season aggregation of flower-visiting insects entering and remaining in the crop, and then mass emigration of flower-visiting insects leaving the crop late in the flowering season. Although pollen movement late in the flowering cycle might contribute relatively little to total seed set (and hence crop production), the findings here suggest that extensive late-season pollinator redistribution in the landscape could contribute disproportionately to long-distance gene movement between crops. PMID:23937538

  13. Fast Plants for Finer Science--An Introduction to the Biology of Rapid-Cycling Brassica Campestris (rapa) L.

    ERIC Educational Resources Information Center

    Tomkins, Stephen P.; Williams, Paul H.

    1990-01-01

    Rapid-cycling brassicas can be used in the classroom to teach concepts such as plant growth, tropisms, floral reproduction, pollination, embryonic development, and plant genetics. Directions on how to obtain them for classroom use and how they may be grown are included. Practical physiology and genetics exercises are listed. (KR)

  14. Production and genetic analysis of resynthesized Brassica napus from a B. rapa landrace from the Qinghai-Tibet Plateau and B. alboglabra.

    PubMed

    Liu, H D; Zhao, Z G; Du, D Z; Deng, C R; Fu, G

    2016-01-01

    This study aimed to reveal the genetic and epigenetic variations involved in a resynthesized Brassica napus (AACC) generated from a hybridization between a B. rapa (AA) landrace and B. alboglabra (CC). Amplified fragment length polymorphism (AFLP), methylation-sensitive amplified polymorphism, and the cDNA-AFLP technique were performed to detect changes between different generations at the genome, methylation, and transcription levels. We obtained 30 lines of resynthesized B. napus with a mean 1000-seed weight of over 7.50 g. All of the lines were self-compatible, probably because both parents were self-compatible. At the genome level, the S0 generation had the lowest frequency of variations (0.18%) and the S3 generation had the highest (6.07%). The main variation pattern was the elimination of amplified restriction fragments on the CC genome from the S0 to the S4 generations. At the methylation level, we found three loci that exhibited altered methylation patterns on the parental A genome; the variance rate was 1.35%. At the transcription level, we detected 43.77% reverse mutations and 37.56% deletion mutations that mainly occurred on the A and C genomes, respectively, in the S3 generation. Our results highlight the genetic variations that occur during the diploidization of resynthesized B. napus. PMID:26909899

  15. Anthocyanin Accumulation, Antioxidant Ability and Stability, and a Transcriptional Analysis of Anthocyanin Biosynthesis in Purple Heading Chinese Cabbage (Brassica rapa L. ssp. pekinensis).

    PubMed

    He, Qiong; Zhang, Zhanfeng; Zhang, Lugang

    2016-01-13

    Heading Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a significant dietary vegetable for its edible heading leaves in Asia countries. The new purple anthocyanin-rich pure line (11S91) was successfully bred, and the anthocyanins were mainly distributed in 2-3 cell layers beneath the leaf epidermis, whereas siliques and stems accumulated only a cell layer of anthocyanins. The anthocyanins of 11S91 were more stable at pHs below 3.0 and temperatures below 45 °C. The total antioxidant ability was highly positive correlated with the anthocyanin content in 11S91. Thirty-two anthocyanins were separated and identified, and 70% of them were glycosylated and acylated cyanidins. The four major anthocyanins present were cyanidin-3-sophoroside(p-coumaroyl)-5-glucoside(malonyl), cyanidin-3-sophoroside(ferulyl)-5-glucoside(malonyl), cyanidin-3-sophoroside(sinapyl-p-coumaroyl)-5-glucoside(malonyl), and cyanidin-3-sophoroside-(sinapyl-ferulyl)-5-glucoside(malonyl). According to the expression of biosynthetic genes and the component profile of anthocyanins in 11S91 and its parents, regulatory genes BrMYB2 and BrTT8 probably activate the anthocyanin biosynthesis but other factors may govern the primary anthocyanins and the distribution. PMID:26709726

  16. Co-Expression of Monodehydroascorbate Reductase and Dehydroascorbate Reductase from Brassica rapa Effectively Confers Tolerance to Freezing-Induced Oxidative Stress

    PubMed Central

    Shin, Sun-Young; Kim, Myung-Hee; Kim, Yul-Ho; Park, Hyang-Mi; Yoon, Ho-Sung

    2013-01-01

    Plants are exposed to various environmental stresses and have therefore developed antioxidant enzymes and molecules to protect their cellular components against toxicity derived from reactive oxygen species (ROS). Ascorbate is a very important antioxidant molecule in plants, and monodehydroascorbate reductase (MDHAR; EC 1.6.5.4) and dehydroascorbate reductase (DHAR; EC 1.8.5.1) are essential to regeneration of ascorbate for maintenance of ROS scavenging ability. The MDHAR and DHAR genes from Brassica rapa were cloned, transgenic plants overexpressing either BrMDHAR and BrDHAR were established, and then, each transgenic plant was hybridized to examine the effects of co-expression of both genes conferring tolerance to freezing. Transgenic plants co-overexpressing BrMDHAR and BrDHAR showed activated expression of relative antioxidant enzymes, and enhanced levels of glutathione and phenolics under freezing condition. Then, these alteration caused by co-expression led to alleviated redox status and lipid peroxidation and consequently conferred improved tolerance against severe freezing stress compared to transgenic plants overexpressing single gene. The results of this study suggested that although each expression of BrMDHAR or BrDHAR was available to according tolerance to freezing, the simultaneous expression of two genes generated synergistic effects conferring improved tolerance more effectively even severe freezing. PMID:24170089

  17. Induced production of 1-methoxy-indol-3-ylmethyl glucosinolate by jasmonic acid and methyl jasmonate in sprouts and leaves of pak choi (Brassica rapa ssp. chinensis).

    PubMed

    Wiesner, Melanie; Hanschen, Franziska S; Schreiner, Monika; Glatt, Hansruedi; Zrenner, Rita

    2013-01-01

    Pak choi plants (Brassica rapa ssp. chinensis) were treated with different signaling molecules methyl jasmonate, jasmonic acid, linolenic acid, and methyl salicylate and were analyzed for specific changes in their glucosinolate profile. Glucosinolate levels were quantified using HPLC-DAD-UV, with focus on induction of indole glucosinolates and special emphasis on 1-methoxy-indol-3-ylmethyl glucosinolate. Furthermore, the effects of the different signaling molecules on indole glucosinolate accumulation were analyzed on the level of gene expression using semi-quantitative realtime RT-PCR of selected genes. The treatments with signaling molecules were performed on sprouts and mature leaves to determine ontogenetic differences in glucosinolate accumulation and related gene expression. The highest increase of indole glucosinolate levels, with considerable enhancement of the 1-methoxy-indol-3-ylmethyl glucosinolate content, was achieved with treatments of sprouts and mature leaves with methyl jasmonate and jasmonic acid. This increase was accompanied by increased expression of genes putatively involved in the indole glucosinolate biosynthetic pathway. The high levels of indole glucosinolates enabled the plant to preferentially produce the respective breakdown products after tissue damage. Thus, pak choi plants treated with methyl jasmonate or jasmonic acid, are a valuable tool to analyze the specific protection functions of 1-methoxy-indole-3-carbinole in the plants defense strategy in the future. PMID:23873294

  18. Impact of herbivore-induced plant volatiles on parasitoid foraging success: a spatial simulation of the Cotesia rubecula, Pieris rapae, and Brassica oleracea system.

    PubMed

    Puente, Molly; Magori, Krisztian; Kennedy, George G; Gould, Fred

    2008-07-01

    Many parasitoids are known to use herbivore-induced plant volatiles as cues to locate hosts. However, data are lacking on how much of an advantage a parasitoid can gain from following these plant cues and which factors can limit the value of these cues to the parasitoid. In this study, we simulate the Cotesia rubecula-Pieris rapae-Brassica oleracea system, and ask how many more hosts can a parasitoid attack in a single day of foraging by following plant signals versus randomly foraging. We vary herbivore density, plant response time, parasitoid flight distance, and available host stages to see under which conditions parasitoids benefit from herbivore-induced plant cues. In most of the parameter combinations studied, parasitoids that responded to cues attacked more hosts than those that foraged randomly. Parasitoids following plant cues attacked up to ten times more hosts when they were able to successfully attack herbivores older than first instar; however, if parasitoids were limited to first instar hosts, those following plant cues were at a disadvantage when plants took longer than a day to respond to herbivory. At low herbivore densities, only parasitoids with a larger foraging radius could take advantage of plant cues. Although preference for herbivore-induced volatiles was not always beneficial for a parasitoid, under the most likely natural conditions, the model predicts that C. rubecula gains fitness from following plant cues. PMID:18438615

  19. The Gene Encoding Dihydroflavonol 4-Reductase Is a Candidate for the anthocyaninless Locus of Rapid Cycling Brassica rapa (Fast Plants Type)

    PubMed Central

    Wendell, Douglas L.; Vaziri, Anoumid; Shergill, Gurbaksh

    2016-01-01

    Rapid cycling Brassica rapa, also known as Wisconsin Fast Plants, are a widely used organism in both K-12 and college science education. They are an excellent system for genetics laboratory instruction because it is very easy to conduct genetic crosses with this organism, there are numerous seed stocks with variation in both Mendelian and quantitative traits, they have a short generation time, and there is a wealth of educational materials for instructors using them. Their main deficiency for genetics education is that none of the genetic variation in RCBr has yet been characterized at the molecular level. Here we present the first molecular characterization of a gene responsible for a trait in Fast Plants. The trait under study is purple/nonpurple variation due to the anthocyaninless locus, which is one of the Mendelian traits most frequently used for genetics education with this organism. We present evidence that the DFR gene, which encodes dihyroflavonol 4-reductase, is the candidate gene for the anthocyaninless (ANL) locus in RCBr. DFR shows complete linkage with ANL in genetic crosses with a total of 948 informative chromosomes, and strains with the recessive nonpurple phenotype have a transposon-related insertion in the DFR which is predicted to disrupt gene function. PMID:27548675

  20. The Gene Encoding Dihydroflavonol 4-Reductase Is a Candidate for the anthocyaninless Locus of Rapid Cycling Brassica rapa (Fast Plants Type).

    PubMed

    Wendell, Douglas L; Vaziri, Anoumid; Shergill, Gurbaksh

    2016-01-01

    Rapid cycling Brassica rapa, also known as Wisconsin Fast Plants, are a widely used organism in both K-12 and college science education. They are an excellent system for genetics laboratory instruction because it is very easy to conduct genetic crosses with this organism, there are numerous seed stocks with variation in both Mendelian and quantitative traits, they have a short generation time, and there is a wealth of educational materials for instructors using them. Their main deficiency for genetics education is that none of the genetic variation in RCBr has yet been characterized at the molecular level. Here we present the first molecular characterization of a gene responsible for a trait in Fast Plants. The trait under study is purple/nonpurple variation due to the anthocyaninless locus, which is one of the Mendelian traits most frequently used for genetics education with this organism. We present evidence that the DFR gene, which encodes dihyroflavonol 4-reductase, is the candidate gene for the anthocyaninless (ANL) locus in RCBr. DFR shows complete linkage with ANL in genetic crosses with a total of 948 informative chromosomes, and strains with the recessive nonpurple phenotype have a transposon-related insertion in the DFR which is predicted to disrupt gene function. PMID:27548675

  1. Glucosinolate Accumulation and Related Gene Expression in Pak Choi (Brassica rapa L. ssp. chinensis var. communis [N. Tsen & S.H. Lee] Hanelt) in Response to Insecticide Application.

    PubMed

    Zhu, Biao; Yang, Jing; He, Yong; Zang, Yunxiang; Zhu, Zhujun

    2015-11-11

    Glucosinolates and their breakdown products are well-known for their cancer-chemoprotective functions and biocidal activities against pathogens and generalist herbivores. Insecticides are commonly used in the production of pak choi (Brassica rapa L. ssp. chinensis var. communis [N. Tsen & S.H. Lee] Hanelt). We studied the effects of four commonly used insecticides, namely, β-cypermethrin, acephate, pymetrozine, and imidacloprid, on glucosinolate metabolism in pak choi. All insecticides significantly increased both the transcription of glucosinolate biosynthetic genes and the aliphatic and total glucosinolate accumulations in pak choi. β-Cypermethrin and acephate caused gradual and continuous up-regulation of gene expression from 0.5 to 24 h after treatment, whereas pymetrozine and imidacloprid did so more rapidly, reaching a peak at 1 h and returning to normal at 3 h. Our findings indicate that the four insecticides affect glucosinolate metabolism in pak choi plants to various degrees and suggest that glucosinolates may be involved in plant insecticide metabolism. PMID:26485123

  2. Genome-Wide Identification and Analysis of the VQ Motif-Containing Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)

    PubMed Central

    Zhang, Gaoyuan; Wang, Fengde; Li, Jingjuan; Ding, Qian; Zhang, Yihui; Li, Huayin; Zhang, Jiannong; Gao, Jianwei

    2015-01-01

    Previous studies have showed that the VQ motif–containing proteins in Arabidopsis thaliana and Oryza sativa play an important role in plant growth, development, and stress responses. However, little is known about the functions of the VQ genes in Brassica rapa (Chinese cabbage). In this study, we performed genome-wide identification, characterization, and expression analysis of the VQ genes in Chinese cabbage, especially under adverse environment. We identified 57 VQ genes and classified them into seven subgroups (I–VII), which were dispersedly distributed on chromosomes 1 to 10. The expansion of these genes mainly contributed to segmental and tandem duplication. Fifty-four VQ genes contained no introns and 50 VQ proteins were less than 300 amino acids in length. Quantitative real-time PCR showed that the VQ genes were differentially expressed in various tissues and during different abiotic stresses and plant hormone treatments. This study provides a comprehensive overview of Chinese cabbage VQ genes and will benefit the molecular breeding for resistance to stresses and disease, as well as further studies on the biological functions of the VQ proteins. PMID:26633387

  3. Regulated changes in the acetylation of α-tubulin on lys(40) during growth and organ development in fast plants, Brassica rapa L.

    PubMed

    Nakagawa, Umihito; Kamemura, Kazuo; Imamura, Aya

    2013-01-01

    Recently, we confirmed the widespread occurrence of α-tubulin acetylation on Lys(40) in angiosperms. In the present study, we found that α-tubulin acetylation is regulated in a growth stage- and organ development-dependent manner in the rapid cycling Brassica rapa, also known as Fast Plants. Organ distribution analysis showed that the proportion of acetylated α-tubulin is high in the cotyledons of young plants and in the true leaves and flowers of mature plants. A correlation between the increase in the levels of α-tubulin acetylation and the maturation of true leaves was observed. In the mature leaves, the acetylated α-tubulin showed an uneven distribution pattern, and the cells in the region of the leaf margins contained a high proportion of acetylated α-tubulin. These results indicate that α-tubulin acetylation is dynamically regulated in plant organs during development, and that it might play an important role in microtubule functioning throughout the angiosperm's life cycle. PMID:24200785

  4. Beyond Punnett squares: Student word association and explanations of phenotypic variation through an integrative quantitative genetics unit investigating anthocyanin inheritance and expression in Brassica rapa Fast plants.

    PubMed

    Batzli, Janet M; Smith, Amber R; Williams, Paul H; McGee, Seth A; Dósa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory course focused on the inheritance and expression of a quantitative trait in varying environments. We utilized Brassica rapa Fast Plants as a model organism to study variation in the phenotype anthocyanin pigment intensity. As an initial curriculum assessment, we used free word association to examine students' cognitive structures before and after the unit and explanations in students' final research posters with particular focus on variation (Pv = Gv + Ev). Comparison of pre- and postunit word frequency revealed a shift in words and a pattern of co-occurring concepts indicative of change in cognitive structure, with particular focus on "variation" as a proposed threshold concept and primary goal for students' explanations. Given review of 53 posters, we found ∼50% of students capable of intermediate to high-level explanations combining both Gv and Ev influence on expression of anthocyanin intensity (Pv). While far from "plug and play," this conceptually rich, inquiry-based unit holds promise for effective integration of quantitative and Mendelian genetics. PMID:25185225

  5. Analysis of genetic diversity of Brassica rapa var. chinensis using ISSR markers and development of SCAR marker specific for Fragrant Bok Choy, a product of geographic indication.

    PubMed

    Shen, X L; Zhang, Y M; Xue, J Y; Li, M M; Lin, Y B; Sun, X Q; Hang, Y Y

    2016-01-01

    Non-heading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] is a popular vegetable and is also used as a medicinal plant in traditional Chinese medicine. Fragrant Bok Choy is a unique accession of non-heading Chinese cabbage and a product of geographic indication certified by the Ministry of Agriculture of China, which is noted for its rich aromatic flavor. However, transitional and overlapping morphological traits can make it difficult to distinguish this accession from other non-heading Chinese cabbages. This study aimed to develop a molecular method for efficient identification of Fragrant Bok Choy. Genetic diversity analysis, based on inter-simple sequence repeat molecular markers, was conducted for 11 non-heading Chinese cabbage accessions grown in the Yangtze River Delta region. Genetic similarity coefficients between the 11 accessions ranged from 0.5455 to 0.8961, and the genetic distance ranged from 0.0755 to 0.4475. Cluster analysis divided the 11 accessions into two major groups. The primer ISSR-840 amplified a fragment specific for Fragrant Bok Choy. A pair of specific sequence-characterized amplified region (SCAR) primers based on this fragment amplified a target band in Fragrant Bok Choy individuals, but no band was detected in individuals of other accessions. In conclusion, this study has developed an efficient strategy for authentication of Fragrant Bok Choy. The SCAR marker described here will facilitate the conservation and utilization of this unique non-heading Chinese cabbage germplasm resource. PMID:27173238

  6. Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in Brassica rapa Fast Plants

    PubMed Central

    Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dósa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question “What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev),” we developed a 4-wk unit for an inquiry-based laboratory course focused on the inheritance and expression of a quantitative trait in varying environments. We utilized Brassica rapa Fast Plants as a model organism to study variation in the phenotype anthocyanin pigment intensity. As an initial curriculum assessment, we used free word association to examine students’ cognitive structures before and after the unit and explanations in students’ final research posters with particular focus on variation (Pv = Gv + Ev). Comparison of pre- and postunit word frequency revealed a shift in words and a pattern of co-occurring concepts indicative of change in cognitive structure, with particular focus on “variation” as a proposed threshold concept and primary goal for students’ explanations. Given review of 53 posters, we found ∼50% of students capable of intermediate to high-level explanations combining both Gv and Ev influence on expression of anthocyanin intensity (Pv). While far from “plug and play,” this conceptually rich, inquiry-based unit holds promise for effective integration of quantitative and Mendelian genetics. PMID:25185225

  7. Genome-Wide Identification and Analysis of the VQ Motif-Containing Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis).

    PubMed

    Zhang, Gaoyuan; Wang, Fengde; Li, Jingjuan; Ding, Qian; Zhang, Yihui; Li, Huayin; Zhang, Jiannong; Gao, Jianwei

    2015-01-01

    Previous studies have showed that the VQ motif-containing proteins in Arabidopsis thaliana and Oryza sativa play an important role in plant growth, development, and stress responses. However, little is known about the functions of the VQ genes in Brassica rapa (Chinese cabbage). In this study, we performed genome-wide identification, characterization, and expression analysis of the VQ genes in Chinese cabbage, especially under adverse environment. We identified 57 VQ genes and classified them into seven subgroups (I-VII), which were dispersedly distributed on chromosomes 1 to 10. The expansion of these genes mainly contributed to segmental and tandem duplication. Fifty-four VQ genes contained no introns and 50 VQ proteins were less than 300 amino acids in length. Quantitative real-time PCR showed that the VQ genes were differentially expressed in various tissues and during different abiotic stresses and plant hormone treatments. This study provides a comprehensive overview of Chinese cabbage VQ genes and will benefit the molecular breeding for resistance to stresses and disease, as well as further studies on the biological functions of the VQ proteins. PMID:26633387

  8. Induced Production of 1-Methoxy-indol-3-ylmethyl Glucosinolate by Jasmonic Acid and Methyl Jasmonate in Sprouts and Leaves of Pak Choi (Brassica rapa ssp. chinensis)

    PubMed Central

    Wiesner, Melanie; Hanschen, Franziska S.; Schreiner, Monika; Glatt, Hansruedi; Zrenner, Rita

    2013-01-01

    Pak choi plants (Brassica rapa ssp. chinensis) were treated with different signaling molecules methyl jasmonate, jasmonic acid, linolenic acid, and methyl salicylate and were analyzed for specific changes in their glucosinolate profile. Glucosinolate levels were quantified using HPLC-DAD-UV, with focus on induction of indole glucosinolates and special emphasis on 1-methoxy-indol-3-ylmethyl glucosinolate. Furthermore, the effects of the different signaling molecules on indole glucosinolate accumulation were analyzed on the level of gene expression using semi-quantitative realtime RT-PCR of selected genes. The treatments with signaling molecules were performed on sprouts and mature leaves to determine ontogenetic differences in glucosinolate accumulation and related gene expression. The highest increase of indole glucosinolate levels, with considerable enhancement of the 1-methoxy-indol-3-ylmethyl glucosinolate content, was achieved with treatments of sprouts and mature leaves with methyl jasmonate and jasmonic acid. This increase was accompanied by increased expression of genes putatively involved in the indole glucosinolate biosynthetic pathway. The high levels of indole glucosinolates enabled the plant to preferentially produce the respective breakdown products after tissue damage. Thus, pak choi plants treated with methyl jasmonate or jasmonic acid, are a valuable tool to analyze the specific protection functions of 1-methoxy-indole-3-carbinole in the plants defense strategy in the future. PMID:23873294

  9. Speciation of vanadium in Chinese cabbage (Brassica rapa L.) and soils in response to different levels of vanadium in soils and cabbage growth.

    PubMed

    Tian, Liyan; Yang, Jinyan; Alewell, Christine; Huang, Jen-How

    2014-09-01

    This study highlights the accumulation and speciation of vanadium in Chinese cabbage (Brassica rapa L.) in relation to the speciation of soil vanadium with pot experiments at 122-622mgVkg(-1) by spiking NH4VO3. Cabbage planting decreased the bioavailable and residual vanadium based on sequential extraction, leading to enrichment of oxalate-extractable vanadium in soils. The biomass production increased with increasing concentrations of soil vanadium from 122 to 372mgVkg(-1), probably due to the increasing nitrogen availability and low vanadium availability in our soils with a consequent low vanadium toxicity. Although the concentrations of root vanadium (14.4-24.9mgVkg(-1)) related positively with soil vanadium, the bio-dilution alleviated the increase of leaf vanadium (2.1-2.7mgVkg(-1)). The predominance of vanadium(IV) in leaves (∼60-80% of total vanadium) indicates bio-reduction of vanadium in Chinese cabbage, since the mobile vanadium in oxic soils was usually pentavalent. Approximately 15-20% of the leaf vanadium was associated with recalcitrant leaf tissues. The majority of leaf vanadium was water and ethanol extractable, which is considered mobile and may cause more toxic effects on Chinese cabbage. PMID:24997904

  10. Genetic analysis of morphological traits in a new, versatile, rapid-cycling Brassica rapa recombinant inbred line population

    PubMed Central

    Bagheri, Hedayat; El-Soda, Mohamed; van Oorschot, Inge; Hanhart, Corrie; Bonnema, Guusje; Jansen-van den Bosch, Tanja; Mank, Rolf; Keurentjes, Joost J. B.; Meng, Lin; Wu, Jian; Koornneef, Maarten; Aarts, Mark G. M.

    2012-01-01

    A recombinant inbred line (RIL) population was produced based on a wide cross between the rapid-cycling and self-compatible genotypes L58, a Caixin vegetable type, and R-o-18, a yellow sarson oil type. A linkage map based on 160 F7 lines was constructed using 100 Single nucleotide polymorphisms (SNPs), 130 AFLP®, 27 InDel, and 13 publicly available SSR markers. The map covers a total length of 1150 centiMorgan (cM) with an average resolution of 4.3 cM/marker. To demonstrate the versatility of this new population, 17 traits, related to plant architecture and seed characteristics, were subjected to quantitative trait loci (QTL) analysis. A total of 47 QTLs were detected, each explaining between 6 and 54% of the total phenotypic variance for the concerned trait. The genetic analysis shows that this population is a useful new tool for analyzing genetic variation for interesting traits in B. rapa, and for further exploitation of the recent availability of the B. rapa whole genome sequence for gene cloning and gene function analysis. PMID:22912644

  11. Bile duct lesions associated with turnip (Brassica rapa) photosensitization compared with those due to sporidesmin toxicosis in dairy cows.

    PubMed

    Collett, M G

    2014-09-01

    Cattle grazing turnips or other brassica forage crops occasionally develop hepatogenous photosensitization. In New Zealand, cases of bovine photosensitization associated with such crops frequently occur during late summer and fall, and this coincides with the facial eczema (sporidesmin toxicosis) "season." Clinical chemistry findings in acute photosensitization cases associated with both brassica and facial eczema include marked serum elevations in γ-glutamyl transferase and glutamate dehydrogenase activities. Distinctive bile duct lesions of "subacute" turnip photosensitization in 2 cows, comprising microscopic cholangiectasis with concentric periductal fibrosis of small bile ducts, and a spectrum of changes from bile duct necrosis progressing to obliterative sclerosis are described. These bile duct lesions are compared with those in 3 cases of "subacute" facial eczema in adult cows, where medium-sized and larger ducts tend to be involved and bile duct hyperplasia and portal fibrosis are more prominent, often leading to bridging between neighboring portal triads. PMID:24280939

  12. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa.

    PubMed

    Franks, Steven J; Perez-Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Jennifer J; Lalchan, Rebecca; Jordan, Kevin P; Litt, Amy

    2015-01-01

    Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of

  13. Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa

    PubMed Central

    Perez-Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Jennifer J.; Lalchan, Rebecca; Jordan, Kevin P.; Litt, Amy

    2015-01-01

    Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ∼30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of

  14. Compared with the intake of commercial vegetable juice, the intake of fresh fruit and komatsuna (Brassica rapa L. var. perviridis) juice mixture reduces serum cholesterol in middle-aged men: a randomized controlled pilot study

    PubMed Central

    2014-01-01

    Background Vegetables and fruits are rich in vitamins, minerals and, dietary fiber and contribute to the prevention and improvement of obesity and metabolic syndrome. However, inadequate intake of vegetable and fruit is a concern in Japan. We therefore produced a juice mixture of fresh fruit and komatsuna (Brassica rapa L. var. perviridis: B. rapa) with the aim to investigate the effects of this juice mixture on anthropometric data, blood parameters, and dietary intake differences. Methods This study was performed as a single blind and randomized controlled trial. Subjects were 16 men (mean age, 46.4 ± 7.1 years), and they were divided into two groups (control group and intervention group). The intervention group consumed the juice mixture of fresh fruit and B. rapa. The control group consumed commercial vegetable juice. Subjects consumed juice twice a day throughout the weekday, for 4 weeks. We prepared both juices with an equivalent energy balance. Results Weight and body mass index (BMI) of the control group after 4 weeks were significantly increased compared with baseline values. Serum total cholesterol (T-Chol) and low-density lipoprotein cholesterol (LDL-Chol) of the intervention group after 4 weeks were significantly reduced compared with baseline values. Furthermore, intake of total vegetables and fruits were significantly increased compared with baseline values in both groups. Conclusions Both vegetable juices contributed to improved intake of total vegetables and fruit. Compared with the intake of commercial vegetable juice, the intake of fresh fruit and B. rapa juice is highly effective in reducing serum cholesterol. Short-term intake of fresh fruit and B. rapa juice was shown to enhance cholesterol metabolism. PMID:24961537

  15. The role of conserved Cys residues in Brassica rapa auxin amidohydrolase: Cys139 is crucial for the enzyme activity and Cys320 regulates enzyme stability.

    PubMed

    Smolko, Ana; Šupljika, Filip; Martinčić, Jelena; Jajčanin-Jozić, Nina; Grabar-Branilović, Marina; Tomić, Sanja; Ludwig-Müller, Jutta; Piantanida, Ivo; Salopek-Sondi, Branka

    2016-04-01

    Brassica rapa auxin amidohydrolase (BrILL2) participates in the homeostasis of the plant hormones auxins by hydrolyzing the amino acid conjugates of auxins, thereby releasing the free active form of hormones. Herein, the potential role of the two conserved Cys residues of BrILL2 (at sequence positions 139 and 320) has been investigated by using interdisciplinary approaches and methods of molecular biology, biochemistry, biophysics and molecular modelling. The obtained results show that both Cys residues participate in the regulation of enzyme activity. Cys320 located in the satellite domain of the enzyme is mainly responsible for protein stability and regulation of enzyme activity through polymer formation, as has been revealed by enzyme kinetics and differential scanning calorimetry analysis of the BrILL2 wild type and mutants C320S and C139S. Cys139 positioned in the active site of the catalytic domain is involved in the coordination of one Mn(2+) ion of the bimetal center and is crucial for the enzymatic activity. Although the point mutation Cys139 to Ser causes the loss of enzyme activity, it does not affect the metal binding to the BrILL2 enzyme, as has been shown by isothermal titration calorimetry, circular dichroism spectropolarimetry and differential scanning calorimetry data. MD simulations (200 ns) revealed a different active site architecture of the BrILL2C139S mutant in comparison to the wild type enzyme. Additional possible reasons for the inactivity of the BrILL2C139S mutant have been discussed based on MD simulations and MM-PBSA free energy calculations of BrILL2 enzyme complexes (wt and C139S mutant) with IPA-Ala as a substrate. PMID:26959939

  16. Leaf and root glucosinolate profiles of Chinese cabbage (Brassica rapa ssp. pekinensis) as a systemic response to methyl jasmonate and salicylic acid elicitation.

    PubMed

    Zang, Yun-xiang; Ge, Jia-li; Huang, Ling-hui; Gao, Fei; Lv, Xi-shan; Zheng, Wei-wei; Hong, Seung-beom; Zhu, Zhu-jun

    2015-08-01

    Glucosinolates (GSs) are an important group of defensive phytochemicals mainly found in Brassicaceae. Plant hormones jasmonic acid (JA) and salicylic acid (SA) are major regulators of plant response to pathogen attack. However, there is little information about the interactive effect of both elicitors on inducing GS biosynthesis in Chinese cabbage (Brassica rapa ssp. pekinensis). In this study, we applied different concentrations of methyl jasmonate (MeJA) and/or SA onto the leaf and root of Chinese cabbage to investigate the time-course interactive profiles of GSs. Regardless of the site of the elicitation and the concentrations of the elicitors, the roots accumulated much more GSs and were more sensitive and more rapidly responsive to the elicitors than leaves. Irrespective of the elicitation site, MeJA had a greater inducing and longer lasting effect on GS accumulation than SA. All three components of indole GS (IGS) were detected along with aliphatic and aromatic GSs. However, IGS was a major component of total GSs that accumulated rapidly in both root and leaf tissues in response to MeJA and SA elicitation. Neoglucobrassicin (neoGBC) did not respond to SA but to MeJA in leaf tissue, while it responded to both SA and MeJA in root tissue. Conversion of glucobrassicin (GBC) to neoGBC occurred at a steady rate over 3 d of elicitation. Increased accumulation of 4-methoxy glucobrassicin (4-MGBC) occurred only in the root irrespective of the type of elicitors and the site of elicitation. Thus, accumulation of IGS is a major metabolic hallmark of SA- and MeJA-mediated systemic response systems. SA exerted an antagonistic effect on the MeJA-induced root GSs irrespective of the site of elicitation. However, SA showed synergistic and antagonistic effects on the MeJA-induced leaf GSs when roots and leaves are elicitated for 3 d, respectively. PMID:26238545

  17. Stress-responsive expression patterns and functional characterization of cold shock domain proteins in cabbage (Brassica rapa) under abiotic stress conditions.

    PubMed

    Choi, Min Ji; Park, Ye Rin; Park, Su Jung; Kang, Hunseung

    2015-11-01

    Although the functional roles of cold shock domain proteins (CSDPs) have been demonstrated during the growth, development, and stress adaptation of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and wheat (Triticum aestivum), the functions of CSDPs in other plants species, including cabbage (Brassica rapa), are largely unknown. To gain insight into the roles of CSDPs in cabbage under stress conditions, the genes encoding CSDPs in cabbage were isolated, and the functional roles of CSDPs in response to environmental stresses were analyzed. Real-time RT-PCR analysis revealed that the levels of BrCSDP transcripts increased during cold, salt, or drought stress, as well as upon ABA treatment. Among the five BrCSDP genes found in the cabbage genome, one CSDP (BRU12051), named BrCSDP3, was unique in that it is localized to the chloroplast as well as to the nucleus. Ectopic expression of BrCSDP3 in Arabidopsis resulted in accelerated seed germination and better seedling growth compared to the wild-type plants under high salt or dehydration stress conditions, and in response to ABA treatment. BrCSDP3 did not affect the splicing of intron-containing genes and processing of rRNAs in the chloroplast. BrCSDP3 had the ability to complement RNA chaperone-deficient Escherichia coli mutant cells under low temperatures as well as DNA- and RNA-melting abilities, suggesting that it possesses RNA chaperone activity. Taken together, these results suggest that BrCSDP3, harboring RNA chaperone activity, plays a role as a positive regulator in seed germination and seedling growth under stress conditions. PMID:26263516

  18. Leaf and root glucosinolate profiles of Chinese cabbage (Brassica rapa ssp. pekinensis) as a systemic response to methyl jasmonate and salicylic acid elicitation*

    PubMed Central

    Zang, Yun-xiang; Ge, Jia-li; Huang, Ling-hui; Gao, Fei; Lv, Xi-shan; Zheng, Wei-wei; Hong, Seung-beom; Zhu, Zhu-jun

    2015-01-01

    Glucosinolates (GSs) are an important group of defensive phytochemicals mainly found in Brassicaceae. Plant hormones jasmonic acid (JA) and salicylic acid (SA) are major regulators of plant response to pathogen attack. However, there is little information about the interactive effect of both elicitors on inducing GS biosynthesis in Chinese cabbage (Brassica rapa ssp. pekinensis). In this study, we applied different concentrations of methyl jasmonate (MeJA) and/or SA onto the leaf and root of Chinese cabbage to investigate the time-course interactive profiles of GSs. Regardless of the site of the elicitation and the concentrations of the elicitors, the roots accumulated much more GSs and were more sensitive and more rapidly responsive to the elicitors than leaves. Irrespective of the elicitation site, MeJA had a greater inducing and longer lasting effect on GS accumulation than SA. All three components of indole GS (IGS) were detected along with aliphatic and aromatic GSs. However, IGS was a major component of total GSs that accumulated rapidly in both root and leaf tissues in response to MeJA and SA elicitation. Neoglucobrassicin (neoGBC) did not respond to SA but to MeJA in leaf tissue, while it responded to both SA and MeJA in root tissue. Conversion of glucobrassicin (GBC) to neoGBC occurred at a steady rate over 3 d of elicitation. Increased accumulation of 4-methoxy glucobrassicin (4-MGBC) occurred only in the root irrespective of the type of elicitors and the site of elicitation. Thus, accumulation of IGS is a major metabolic hallmark of SA- and MeJA-mediated systemic response systems. SA exerted an antagonistic effect on the MeJA-induced root GSs irrespective of the site of elicitation. However, SA showed synergistic and antagonistic effects on the MeJA-induced leaf GSs when roots and leaves are elicitated for 3 d, respectively. PMID:26238545

  19. Uptake of arsenic species by turnip (Brassica rapa L.) and lettuce (Lactuca sativa L.) treated with roxarsone and its metabolites in chicken manure.

    PubMed

    Huang, Lian Xi; Yao, Li Xian; He, Zhao Huan; Zhou, Chang Min; Li, Guo Liang; Yang, Bao Mei; Li, Ying Fen

    2013-01-01

    Roxarsone is an organoarsenic feed additive that can be metabolised to other higher toxic arsenic (As) species in animal manure such as arsenate, arsenite, monomethylarsonic acid, dimethylarsinic acid, 3-amino-4-hydroxyphenylarsonic acid and other unknown As species. The accumulation, transport and distribution of As species in turnip (Brassica rapa L.) and lettuce (Lactuca sativa L.) amended with roxarsone and its metabolites in chicken manure were investigated. Results showed arsenite was the predominant As form, followed by arsenate in turnip and lettuce plants, and a low content of dimethylarsinic acid was detected only in lettuce roots. Compared with the control plants treated with chicken manure without roxarsone and its metabolites, the treatments containing roxarsone and its metabolites increased arsenite content by 2.0-3.2% in turnip shoots, by 6.6-6.7% in lettuce shoots, by 11-44% in turnip tubers and by 18-20% in lettuce roots at two growth stages. The enhanced proportion of arsenate content in turnip shoots, turnip tubers and lettuce roots was 4.3-14%, 20-35% and 70%, respectively, while dimethylarsinic acid content in lettuce roots increased 2.4 times. Results showed that the occurrence of dimethylarsinic acid in lettuce roots might be converted from the inorganic As species and the uptake of both inorganic and organic As compounds in turnip and lettuce plants would be enhanced by roxarsone and its metabolites in chicken manure. The pathway of roxarsone metabolites introduced into the human body via roxarsone → animal → manure → soil → crop was indicated. PMID:23859781

  20. Functional analysis of three BrMYB28 transcription factors controlling the biosynthesis of glucosinolates in Brassica rapa.

    PubMed

    Seo, Mi-Suk; Jin, Mina; Chun, Jin-Hyuk; Kim, Sun-Ju; Park, Beom-Seok; Shon, Seong-Han; Kim, Jung Sun

    2016-03-01

    Glucosinolates (GSLs) are secondary metabolites that have anticarcinogenic activity and play defense roles in plants of the Brassicaceae family. MYB28 is known as a transcription factor that regulates aliphatic GSL biosynthesis in Arabidopsis thaliana. Brassicaceae plants have three orthologous copies of AtMYB28 derived from recent genome triplication. These BrMYB28 genes have a high level of sequence homology, with 81-87% similarities in the coding DNA sequence compared to Arabidopsis. Overexpression of three paralogous BrMYB28 genes in transgenic Chinese cabbage increased the total GSL content in all T1 generation plants and in two inbred lines of homozygous T2 plants. The highest total GSL contents were detected in homozygous T2 lines overexpressing BrMYB28.1, which showed an approximate fivefold increase compared to that of nontransgenic plants. The homozygous T2 lines with overexpressed BrMYB28.1 also showed an increased content of aliphatic, indolic, and aromatic GSLs compared to that of nontransgenic plants. Furthermore, all of the three BrMYB28 genes were identified as negative regulators of BrAOP2 and positive regulators of BrGSL-OH in the homozygous T2 lines. These data indicate the regulatory mechanism of GSL biosynthesis in B. rapa is unlike that in A. thaliana. Our results will provide useful information for elucidating the regulatory mechanism of GSL biosynthesis in polyploid plants. PMID:26820138

  1. Oil Seed Brassica's

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oilseed Brassicas, also known by the trade name of rapeseed-mustard, comprise Brassica napus, B. juncea, B. carinata and three ecotypes of B. rapa. Their current global production exceeds 54 million tons, making them the second-most valuable source of vegetable oil in the world. Besides its pre-emin...

  2. Molecular chemistry of plant protein structure at a cellular level by synchrotron-based FTIR spectroscopy: Comparison of yellow ( Brassica rapa) and Brown ( Brassica napus) canola seed tissues

    NASA Astrophysics Data System (ADS)

    Yu, Peiqiang

    2008-05-01

    The objective of this study was to use synchrotron light sourced FTIR microspectroscopy as a novel approach to characterize protein molecular structure of plant tissue: compared yellow and brown Brassica canola seed within cellular dimensions. Differences in the molecular chemistry and the structural-chemical characteristics were identified between two type of plant tissues. The yellow canola seeds contained a relatively lower (P < 0.05) percentage of model-fitted α-helices (33 vs. 37), a higher (P < 0.05) relative percentage of model-fitted β-sheets (27 vs. 21) and a lower (P < 0.05) ratio of α-helices to β-sheets (1.3 vs. 1.9) than the brown seeds. These results may indicate that the protein value of the yellow canola seeds as food or feed was different from that of the brown canola seeds. The cluster analysis and principal component analysis did not show clear differences between the yellow and brown canola seed tissues in terms of protein amide I structures, indicating they are related to each other. Both yellow and brown canola seeds contain the same proteins but in different ratios.

  3. Transgenic Brassica rapa plants over-expressing eIF(iso)4E variants show broad-spectrum Turnip mosaic virus (TuMV) resistance.

    PubMed

    Kim, Jinhee; Kang, Won-Hee; Hwang, Jeena; Yang, Hee-Bum; Dosun, Kim; Oh, Chang-Sik; Kang, Byoung-Cheorl

    2014-08-01

    The protein-protein interaction between VPg (viral protein genome-linked) of potyviruses and eIF4E (eukaryotic initiation factor 4E) or eIF(iso)4E of their host plants is a critical step in determining viral virulence. In this study, we evaluated the approach of engineering broad-spectrum resistance in Chinese cabbage (Brassica rapa) to Turnip mosaic virus (TuMV), which is one of the most important potyviruses, by a systematic knowledge-based approach to interrupt the interaction between TuMV VPg and B. rapa eIF(iso)4E. The seven amino acids in the cap-binding pocket of eIF(iso)4E were selected on the basis of other previous results and comparison of protein models of cap-binding pockets, and mutated. Yeast two-hybrid assay and co-immunoprecipitation analysis demonstrated that W95L, K150L and W95L/K150E amino acid mutations of B. rapa eIF(iso)4E interrupted its interaction with TuMV VPg. All eIF(iso)4E mutants were able to complement an eIF4E-knockout yeast strain, indicating that the mutated eIF(iso)4E proteins retained their function as a translational initiation factor. To determine whether these mutations could confer resistance, eIF(iso)4E W95L, W95L/K150E and eIF(iso)4E wild-type were over-expressed in a susceptible Chinese cabbage cultivar. Evaluation of the TuMV resistance of T1 and T2 transformants demonstrated that the over-expression of the eIF(iso)4E mutant forms can confer resistance to multiple TuMV strains. These data demonstrate the utility of knowledge-based approaches for the engineering of broad-spectrum resistance in Chinese cabbage. PMID:24417952

  4. Characterization and expression profiling of MYB transcription factors against stresses and during male organ development in Chinese cabbage (Brassica rapa ssp. pekinensis).

    PubMed

    Saha, Gopal; Park, Jong-In; Ahmed, Nasar Uddin; Kayum, Md Abdul; Kang, Kwon-Kyoo; Nou, Ill-Sup

    2016-07-01

    MYB proteins comprise a large family of plant transcription factors that play regulatory roles in different biological processes such as plant development, metabolism, and defense responses. To gain insight into this gene superfamily and to elucidate its roles in stress resistance, we performed a comprehensive genome-wide identification, characterization, and expression analysis of MYB genes in Chinese cabbage (Brassica rapa ssp. pekinensis). We identified 475 Chinese cabbage MYB genes, among which most were from R2R3-MYB (256 genes) and MYB-related (202) subfamilies. Analysis of sequence characteristics, phylogenetic classification, and protein motif structures confirmed the existence of several categories (1R, 2R, 3R, 4R, and 5R) of Chinese cabbage MYB genes, which is comparable with MYB genes of other crops. An extensive in silico functional analysis, based on established functional properties of MYB genes from different crop species, revealed 11 and four functional clades within the Chinese cabbage R2R3-MYB and MYB-related subfamilies, respectively. In this study, we reported a MYB-like group within the MYB-related subfamily contains 77 MYB genes. Expression analysis using low temperature-treated whole-genome microarray data revealed variable transcript abundance of 1R/2R/3R/4R/5R-MYB genes in 11 clusters between two inbred lines of Chinese cabbage, Chiifu and Kenshin, which differ in cold tolerance. In further validation tests, we used qRT-PCR to examine the cold-responsive expression patterns of 27 BrMYB genes; surprisingly, the MYB-related genes were induced more highly than the R2R3-MYB genes. In addition, we identified 10 genes with corresponsive expression patterns from a set of salt-, drought-, ABA-, JA-, and SA-induced R2R3-MYB genes. We identified 11 R2R3-MYBs functioning in resistance against biotic stress, including 10 against Fusarium oxysporum f.sp. conglutinans and one against Pectobacterium carotovoram subsp. caratovorum. Furthermore, based on

  5. Differences in Cell Death Induction by Phytophthora Elicitins Are Determined by Signal Components Downstream of MAP Kinase Kinase in Different Species of Nicotiana and Cultivars of Brassica rapa and Raphanus sativus[w

    PubMed Central

    Takemoto, Daigo; Hardham, Adrienne R.; Jones, David A.

    2005-01-01

    Elicitins are small, secreted proteins produced by species of the plant-pathogenic oomycete Phytophthora. They induce hypersensitive cell death in most Nicotiana species and in some cultivars of Brassica rapa and Raphanus sativus. In this study, two true-breeding Fast Cycling B. rapa lines were established that showed severe necrosis (line 7-R) or no visible response (line 18-NR) after treatment with elicitin. Unexpectedly, microscopic examination revealed localized cell death in line 18-NR plants, and expression levels of various defense-marker genes were comparable in both lines. These results suggested that both “responsive” and “nonresponsive” plants responded to elicitin but differed in the extent of the cell death response. Expression of a constitutively active form of Arabidopsis (Arabidopsis thaliana) MAP kinase kinase 4 (AtMEK4DD) also induced rapid development of confluent cell death in line 7-R, whereas line 18-NR showed no visible cell death. Similarly, elicitin-responsive Nicotiana species and R. sativus cultivars showed significantly stronger cell death responses following expression of AtMEK4DD compared with nonresponsive species/cultivars. Line 7-R also showed higher sensitivity to toxin-containing culture filtrates produced by Alternaria brassicicola, and toxin sensitivity cosegregated with elicitin responsiveness, suggesting that the downstream responses induced by elicitin and Alternaria toxin share factors that control the extent of cell death. Interestingly, elicitin responsiveness was shown to correlate with greater susceptibility to A. brassicicola (a necrotroph) in B. rapa but less susceptibility to Phytophthora nicotianae (a hemibiotroph) in Nicotiana, suggesting a more extensive cell death response could cause opposite effects on the outcomes of biotrophic versus necrotrophic plant-pathogen interactions. PMID:15980203

  6. Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants

    PubMed Central

    Huang, Zhinan; Duan, Weike; Song, Xiaoming; Tang, Jun; Wu, Peng; Zhang, Bei; Hou, Xilin

    2016-01-01

    Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morphotypes of plants. We constructed comparative analyses of the retention, structure, expansion, and expression patterns of Aux/IAAs and ARFs in Brassica rapa and their evolution in eight other plant species, including algae, bryophytes, lycophytes, and angiosperms. All 33 of the ARFs, including 1 ARF-like (AL) (a type of ARF-like protein) and 53 Aux/IAAs, were identified in the B. rapa genome. The genes mainly diverged approximately 13 Ma. After the split, no Aux/IAA was completely lost, and they were more preferentially retained than ARFs. In land plants, compared with ARFs, which increased in stability, Aux/IAAs expanded more rapidly and were under more relaxed selective pressure. Moreover, BraIAAs were expressed in a more tissue-specific fashion than BraARFs and demonstrated functional diversification during gene duplication under different treatments, which enhanced the cooperative interaction of homologs to help plants adapt to complex environments. In addition, ALs existed widely and had a closer relationship with ARFs, suggesting that ALs might be the initial structure of ARFs. Our results suggest that the rapid expansion and preferential retention of Aux/IAAs are likely paralleled by the increasingly complex morphotypes in Brassicas and even in land plants. Meanwhile, the data support the hypothesis that the PB1 domain plays a key role in the origin of both Aux/IAAs and ARFs. PMID:26721260

  7. Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants.

    PubMed

    Huang, Zhinan; Duan, Weike; Song, Xiaoming; Tang, Jun; Wu, Peng; Zhang, Bei; Hou, Xilin

    2016-02-01

    Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morphotypes of plants. We constructed comparative analyses of the retention, structure, expansion, and expression patterns of Aux/IAAs and ARFs in Brassica rapa and their evolution in eight other plant species, including algae, bryophytes, lycophytes, and angiosperms. All 33 of the ARFs, including 1 ARF-like (AL) (a type of ARF-like protein) and 53 Aux/IAAs, were identified in the B. rapa genome. The genes mainly diverged approximately 13 Ma. After the split, no Aux/IAA was completely lost, and they were more preferentially retained than ARFs. In land plants, compared with ARFs, which increased in stability, Aux/IAAs expanded more rapidly and were under more relaxed selective pressure. Moreover, BraIAAs were expressed in a more tissue-specific fashion than BraARFs and demonstrated functional diversification during gene duplication under different treatments, which enhanced the cooperative interaction of homologs to help plants adapt to complex environments. In addition, ALs existed widely and had a closer relationship with ARFs, suggesting that ALs might be the initial structure of ARFs. Our results suggest that the rapid expansion and preferential retention of Aux/IAAs are likely paralleled by the increasingly complex morphotypes in Brassicas and even in land plants. Meanwhile, the data support the hypothesis that the PB1 domain plays a key role in the origin of both Aux/IAAs and ARFs. PMID:26721260

  8. RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapa and their use for genome-wide linkage mapping and specific-region fine mapping

    PubMed Central

    2013-01-01

    Background Brassica rapa (AA) contains very diverse forms which include oleiferous types and many vegetable types. Genome sequence of B. rapa line Chiifu (ssp. pekinensis), a leafy vegetable type, was published in 2011. Using this knowledge, it is important to develop genomic resources for the oleiferous types of B. rapa. This will allow more involved molecular mapping, in-depth study of molecular mechanisms underlying important agronomic traits and introgression of traits from B. rapa to major oilseed crops - B. juncea (AABB) and B. napus (AACC). The study explores the availability of SNPs in RNA-seq generated contigs of three oleiferous lines of B. rapa - Candle (ssp. oleifera, turnip rape), YSPB-24 and Tetra (ssp. trilocularis, Yellow sarson) and their use in genome-wide linkage mapping and specific-region fine mapping using a RIL population between Chiifu and Tetra. Results RNA-seq was carried out on the RNA isolated from young inflorescences containing unopened floral buds, floral axis and small leaves, using Illumina paired-end sequencing technology. Sequence assembly was carried out using the Velvet de-novo programme and the assembled contigs were organised against Chiifu gene models, available in the BRAD-CDS database. RNA-seq confirmed the presence of more than 17,000 single-copy gene models described in the BRAD database. The assembled contigs and the BRAD gene models were analyzed for the presence of SSRs and SNPs. While the number of SSRs was limited, more than 0.2 million SNPs were observed between Chiifu and the three oleiferous lines. Assays for SNPs were designed using KASPar technology and tested on a F7-RIL population derived from a Chiifu x Tetra cross. The design of the SNP assays were based on three considerations - the 50 bp flanking region of the SNPs should be strictly similar, the SNP should have a read-depth of ≥7 and no exon/intron junction should be present within the 101 bp target region. Using these criteria, a total of 640 markers

  9. Two plastid DNA lineages--Rapa/Oleracea and Nigra--within the tribe Brassiceae can be best explained by reciprocal crosses at hexaploidy: evidence from divergence times of the plastid genomes and R-block genes of the A and B genomes of Brassica juncea.

    PubMed

    Sharma, Sarita; Padmaja, K Lakshmi; Gupta, Vibha; Paritosh, Kumar; Pradhan, Akshay K; Pental, Deepak

    2014-01-01

    Brassica species (tribe Brassiceae) belonging to U's triangle--B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. juncea (AABB), B. napus (AACC) and B. carinata (BBCC)--originated via two polyploidization rounds: a U event producing the three allopolyploids, and a more ancient b genome-triplication event giving rise to the A-, B-, and C-genome diploid species. Molecular mapping studies, in situ hybridization, and genome sequencing of B. rapa support the genome triplication origin of tribe Brassiceae, and suggest that these three diploid species diversified from a common hexaploid ancestor. Analysis of plastid DNA has revealed two distinct lineages--Rapa/Oleracea and Nigra--that conflict with hexaploidization as a single event defining the tribe Brassiceae. We analysed an R-block region of A. thaliana present in six copies in B. juncea (AABB), three copies each on A- and B-genomes to study gene fractionation pattern and synonymous base substitution rates (Ks values). Divergence time of paralogues within the A and B genomes and homoeologues between the A and B genomes was estimated. Homoeologous R blocks of the A and B genomes exhibited high gene collinearity and a conserved gene fractionation pattern. The three progenitors of diploid Brassicas were estimated to have diverged approximately 12 mya. Divergence of B. rapa and B. nigra, calculated from plastid gene sequences, was estimated to have occurred approximately 12 mya, coinciding with the divergence of the three genomes participating in the b event. Divergence of B. juncea A and B genome homoeologues was estimated to have taken place around 7 mya. Based on divergence time estimates and the presence of distinct plastid lineages in tribe Brassiceae, it is concluded that at least two independent triplication events involving reciprocal crosses at the time of the b event have given rise to Rapa/Oleracea and Nigra lineages. PMID:24691069

  10. Comprehensive Analysis of Genic Male Sterility-Related Genes in Brassica rapa Using a Newly Developed Br300K Oligomeric Chip

    PubMed Central

    Dong, Xiangshu; Feng, Hui; Xu, Ming; Lee, Jeongyeo; Kim, Yeon Ki; Lim, Yong Pyo; Piao, Zhongyun; Park, Young Doo; Ma, Hong; Hur, Yoonkang

    2013-01-01

    To identify genes associated with genic male sterility (GMS) that could be useful for hybrid breeding in Chinese cabbage (Brassicarapa ssp. pekinensis), floral bud transcriptome analysis was carried out using a B. rapa microarray with 300,000 probes (Br300K). Among 47,548 clones deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region, a total of 10,622 genes were differentially expressed between fertile and sterile floral buds; 4,774 and 5,848 genes were up-regulated over 2-fold in fertile and sterile buds, respectively. However, the expression of 1,413 and 199 genes showed fertile and sterile bud-specific features, respectively. Genes expressed specifically in fertile buds, possibly GMS-related genes, included homologs of several Arabidopsis male sterility-related genes, genes associated with the cell wall and synthesis of its surface proteins, pollen wall and coat components, signaling components, and nutrient supplies. However, most early genes for pollen development, genes for primexine and callose formation, and genes for pollen maturation and anther dehiscence showed no difference in expression between fertile and sterile buds. Some of the known genes associated with Arabidopsis pollen development showed similar expression patterns to those seen in this study, while others did not. BrbHLH89 and BrMYP99 are putative GMS genes. Additionally, 17 novel genes identified only in B. rapa were specifically and highly expressed only in fertile buds, implying the possible involvement in male fertility. All data suggest that Chinese cabbage GMS might be controlled by genes acting in post-meiotic tapetal development that are different from those known to be associated with Arabidopsis male sterility. PMID:24039743

  11. Genome-Wide Identification, Phylogeny, Evolution and Expression Patterns of AP2/ERF Genes and Cytokinin Response Factors in Brassica rapa ssp. pekinensis

    PubMed Central

    Liu, Zhenning; Kong, Lijun; Zhang, Mei; Lv, Yanxia; Liu, Yapei; Zou, Minghau; Lu, Gang; Cao, Jiashu; Yu, Xiaolin

    2013-01-01

    The AP2/ERF transcription factor family is one of the largest families involved in growth and development, hormone responses, and biotic or abiotic stress responses in plants. In this study, 281 AP2/ERF transcription factor unigenes were identified in Chinese cabbage. These superfamily members were classified into three families (AP2, ERF, and RAV). The ERF family was subdivided into the DREB subfamily and the ERF subfamily with 13 groups (I– XI) based on sequence similarity. Duplication, evolution and divergence of the AP2/ERF genes in B. rapa and Arabidopsis thaliana were investigated and estimated. Cytokinin response factors (CRFs), as a subclade of the AP2/ERF family, are important transcription factors that define a branch point in the cytokinin two-component signal (TCS) transduction pathway. Up to 21 CRFs with a conserved CRF domain were retrieved and designated as BrCRFs. The amino acid sequences, conserved regions and motifs, phylogenetic relationships, and promoter regions of the 21 BrCRFs were analyzed in detail. The BrCRFs broadly expressed in various tissues and organs. The transcripts of BrCRFs were regulated by factors such as drought, high salinity, and exogenous 6-BA, NAA, and ABA, suggesting their involvement in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. These results provide new insight into the divergence, variation, and evolution of AP2/ERF genes at the genome-level in Chinese cabbage. PMID:24386201

  12. Genome-wide identification, phylogeny, evolution and expression patterns of AP2/ERF genes and cytokinin response factors in Brassica rapa ssp. pekinensis.

    PubMed

    Liu, Zhenning; Kong, Lijun; Zhang, Mei; Lv, Yanxia; Liu, Yapei; Zou, Minghau; Lu, Gang; Cao, Jiashu; Yu, Xiaolin

    2013-01-01

    The AP2/ERF transcription factor family is one of the largest families involved in growth and development, hormone responses, and biotic or abiotic stress responses in plants. In this study, 281 AP2/ERF transcription factor unigenes were identified in Chinese cabbage. These superfamily members were classified into three families (AP2, ERF, and RAV). The ERF family was subdivided into the DREB subfamily and the ERF subfamily with 13 groups (I- XI) based on sequence similarity. Duplication, evolution and divergence of the AP2/ERF genes in B. rapa and Arabidopsis thaliana were investigated and estimated. Cytokinin response factors (CRFs), as a subclade of the AP2/ERF family, are important transcription factors that define a branch point in the cytokinin two-component signal (TCS) transduction pathway. Up to 21 CRFs with a conserved CRF domain were retrieved and designated as BrCRFs. The amino acid sequences, conserved regions and motifs, phylogenetic relationships, and promoter regions of the 21 BrCRFs were analyzed in detail. The BrCRFs broadly expressed in various tissues and organs. The transcripts of BrCRFs were regulated by factors such as drought, high salinity, and exogenous 6-BA, NAA, and ABA, suggesting their involvement in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. These results provide new insight into the divergence, variation, and evolution of AP2/ERF genes at the genome-level in Chinese cabbage. PMID:24386201

  13. Molecular evolution, characterization, and expression analysis of SnRK2 gene family in Pak-choi (Brassica rapa ssp. chinensis)

    PubMed Central

    Huang, Zhinan; Tang, Jun; Duan, Weike; Wang, Zhen; Song, Xiaoming; Hou, Xilin

    2015-01-01

    The sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family members are plant-specific serine/threonine kinases that are involved in the plant response to abiotic stress and abscisic acid (ABA)-dependent plant development. Further understanding of the evolutionary history and expression characteristics of these genes will help to elucidate the mechanisms of the stress tolerance in Pak-choi, an important green leafy vegetable in China. Thus, we investigated the evolutionary patterns, footprints and conservation of SnRK2 genes in selected plants and later cloned and analyzed SnRK2 genes in Pak-choi. We found that this gene family was preferentially retained in Brassicas after the Brassica-Arabidopsis thaliana split. Next, we cloned and sequenced 13 SnRK2 from both cDNA and DNA libraries of stress-induced Pak-choi, which were under conditions of ABA, salinity, cold, heat, and osmotic treatments. Most of the BcSnRK2s have eight exons and could be divided into three groups. The subcellular localization predictions suggested that the putative BcSnRK2 proteins were enriched in the nucleus. The results of an analysis of the expression patterns of the BcSnRK2 genes showed that BcSnRK2 group III genes were robustly induced by ABA treatments. Most of the BcSnRK2 genes were activated by low temperature, and the BcSnRK2.6 genes responded to both ABA and low temperature. In fact, most of the BcSnRK2 genes showed positive or negative regulation under ABA and low temperature treatments, suggesting that they may be global regulators that function at the intersection of multiple signaling pathways to play important roles in Pak-choi stress responses. PMID:26557127

  14. Molecular evolution, characterization, and expression analysis of SnRK2 gene family in Pak-choi (Brassica rapa ssp. chinensis).

    PubMed

    Huang, Zhinan; Tang, Jun; Duan, Weike; Wang, Zhen; Song, Xiaoming; Hou, Xilin

    2015-01-01

    The sucrose non-fermenting 1-related protein kinase 2 (SnRK2) family members are plant-specific serine/threonine kinases that are involved in the plant response to abiotic stress and abscisic acid (ABA)-dependent plant development. Further understanding of the evolutionary history and expression characteristics of these genes will help to elucidate the mechanisms of the stress tolerance in Pak-choi, an important green leafy vegetable in China. Thus, we investigated the evolutionary patterns, footprints and conservation of SnRK2 genes in selected plants and later cloned and analyzed SnRK2 genes in Pak-choi. We found that this gene family was preferentially retained in Brassicas after the Brassica-Arabidopsis thaliana split. Next, we cloned and sequenced 13 SnRK2 from both cDNA and DNA libraries of stress-induced Pak-choi, which were under conditions of ABA, salinity, cold, heat, and osmotic treatments. Most of the BcSnRK2s have eight exons and could be divided into three groups. The subcellular localization predictions suggested that the putative BcSnRK2 proteins were enriched in the nucleus. The results of an analysis of the expression patterns of the BcSnRK2 genes showed that BcSnRK2 group III genes were robustly induced by ABA treatments. Most of the BcSnRK2 genes were activated by low temperature, and the BcSnRK2.6 genes responded to both ABA and low temperature. In fact, most of the BcSnRK2 genes showed positive or negative regulation under ABA and low temperature treatments, suggesting that they may be global regulators that function at the intersection of multiple signaling pathways to play important roles in Pak-choi stress responses. PMID:26557127

  15. BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species

    PubMed Central

    2014-01-01

    Background MITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops. Findings We have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences. Conclusions BrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a

  16. User Guidelines for the Brassica Database: BRAD.

    PubMed

    Wang, Xiaobo; Cheng, Feng; Wang, Xiaowu

    2016-01-01

    The genome sequence of Brassica rapa was first released in 2011. Since then, further Brassica genomes have been sequenced or are undergoing sequencing. It is therefore necessary to develop tools that help users to mine information from genomic data efficiently. This will greatly aid scientific exploration and breeding application, especially for those with low levels of bioinformatic training. Therefore, the Brassica database (BRAD) was built to collect, integrate, illustrate, and visualize Brassica genomic datasets. BRAD provides useful searching and data mining tools, and facilitates the search of gene annotation datasets, syntenic or non-syntenic orthologs, and flanking regions of functional genomic elements. It also includes genome-analysis tools such as BLAST and GBrowse. One of the important aims of BRAD is to build a bridge between Brassica crop genomes with the genome of the model species Arabidopsis thaliana, thus transferring the bulk of A. thaliana gene study information for use with newly sequenced Brassica crops. PMID:26519408

  17. First report of bacterial leaf blight on mustard greens (Brassica juncea) caused by pseudomonas cannabina pv. alisalensis in Mississippi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2010, a brassica leafy greens grower in Sunflower County, Mississippi, observed scattered outbreaks of a leaf blight disease on mustard greens (Brassica juncea) in a 180-hectare field. A severe outbreak of leaf blight occurred on mustard greens and turnip greens (Brassica rapa) in the same field...

  18. BRAD, the genetics and genomics database for Brassica plants

    PubMed Central

    2011-01-01

    Background Brassica species include both vegetable and oilseed crops, which are very important to the daily life of common human beings. Meanwhile, the Brassica species represent an excellent system for studying numerous aspects of plant biology, specifically for the analysis of genome evolution following polyploidy, so it is also very important for scientific research. Now, the genome of Brassica rapa has already been assembled, it is the time to do deep mining of the genome data. Description BRAD, the Brassica database, is a web-based resource focusing on genome scale genetic and genomic data for important Brassica crops. BRAD was built based on the first whole genome sequence and on further data analysis of the Brassica A genome species, Brassica rapa (Chiifu-401-42). It provides datasets, such as the complete genome sequence of B. rapa, which was de novo assembled from Illumina GA II short reads and from BAC clone sequences, predicted genes and associated annotations, non coding RNAs, transposable elements (TE), B. rapa genes' orthologous to those in A. thaliana, as well as genetic markers and linkage maps. BRAD offers useful searching and data mining tools, including search across annotation datasets, search for syntenic or non-syntenic orthologs, and to search the flanking regions of a certain target, as well as the tools of BLAST and Gbrowse. BRAD allows users to enter almost any kind of information, such as a B. rapa or A. thaliana gene ID, physical position or genetic marker. Conclusion BRAD, a new database which focuses on the genetics and genomics of the Brassica plants has been developed, it aims at helping scientists and breeders to fully and efficiently use the information of genome data of Brassica plants. BRAD will be continuously updated and can be accessed through http://brassicadb.org. PMID:21995777

  19. Glyphostate-drift but not herbivory alters the rate of transgene flow from single and stacked trait transgenic canola (Brassica napus L.) to non-transgenic B. napus and B. rapa

    EPA Science Inventory

    While transgenic plants can offer agricultural benefits, the escape of transgenes out of crop fields is a major environmental concern. Escape of transgenic herbicide resistance has occurred between transgenic Brassica napus (canola) and weedy species in numerous locations. In t...

  20. Characterization and expression patterns of small RNAs in synthesized Brassica hexaploids.

    PubMed

    Shen, Yanyue; Zhao, Qin; Zou, Jun; Wang, Wenliang; Gao, Yi; Meng, Jinling; Wang, Jianbo

    2014-06-01

    Polyploidy has played an important role in promoting plant evolution through genomic merging and doubling. We used high-throughput sequencing to compare miRNA expression profiles between Brassica hexaploid and its parents. A total of 613, 784 and 742 known miRNAs were identified in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. We detected 618 miRNAs were differentially expressed (log(2)Ratio ≥ 1, P ≤ 0.05) between Brassica hexaploid and its parents, and 425 miRNAs were non-additively expressed in Brassica hexaploid, which suggest a trend of non-additive miRNA regulation following hybridization and polyploidization. Remarkably, majority of the non-additively expressed miRNAs in the Brassica hexaploid are repressed, and there was a bias toward repression of B. rapa miRNAs, which is consistent with the progenitor-biased gene repression in the synthetic allopolyploids. In addition, we identified 653 novel mature miRNAs in Brassica hexaploid and its parents. Finally, we found that almost all the non-additive accumulation of siRNA clusters exhibited a low-parent pattern in Brassica hexaploid. Non-additive small RNA regulation is involved in a range of biological pathways, probably providing a driving force for variation and adaptation in allopolyploids. PMID:24584845

  1. Molybdenum Sequestration in Brassica Species. A Role for Anthocyanins?1

    PubMed Central

    Hale, Kerry L.; McGrath, Steve P.; Lombi, Enzo; Stack, Stephen M.; Terry, Norman; Pickering, Ingrid J.; George, Graham N.; Pilon-Smits, Elizabeth A.H.

    2001-01-01

    To elucidate plant mechanisms involved in molybdenum (Mo) sequestration and tolerance, Brassica spp. seedlings were supplied with molybdate, and the effects on plant physiology, morphology, and biochemistry were analyzed. When supplied with (colorless) molybdate Indian mustard (Brassica juncea) seedlings accumulated water-soluble blue crystals in their peripheral cell layers. Energy dispersive x-ray analysis showed that Mo accumulated predominantly in the vacuoles of the epidermal cells. Therefore, the blue crystals are likely to be a Mo compound. The x-ray absorption spectrum of the plant-accumulated Mo was different than that for molybdate, indicating complexation with a plant molecule. Because the blue compound was water soluble and showed a pH-dependent color change, possible involvement of anthocyanins was investigated. An anthocyanin-less mutant of Brassica rapa (“fast plants”) was compared with varieties containing normal or high anthocyanin levels. The anthocyanin-less mutant did not show accumulation of a blue compound when supplied with molybdate. In the anthocyanin-containing varieties, the blue compound colocalized with anthocyanins in the peripheral cell layers. Mo accumulation by the three B. rapa varieties was positively correlated with anthocyanin content. Addition of molybdate to purified B. rapa anthocyanin resulted in an in vitro color change from pink to blue. Therefore, Mo appears to be sequestered in vacuoles of the peripheral cell layers of Brassica spp. as a blue compound, probably a Mo-anthocyanin complex. PMID:11500539

  2. Molybdenum sequestration in Brassica species. A role for anthocyanins?

    PubMed

    Hale, K L; McGrath, S P; Lombi, E; Stack, S M; Terry, N; Pickering, I J; George, G N; Pilon-Smits, E A

    2001-08-01

    To elucidate plant mechanisms involved in molybdenum (Mo) sequestration and tolerance, Brassica spp. seedlings were supplied with molybdate, and the effects on plant physiology, morphology, and biochemistry were analyzed. When supplied with (colorless) molybdate Indian mustard (Brassica juncea) seedlings accumulated water-soluble blue crystals in their peripheral cell layers. Energy dispersive x-ray analysis showed that Mo accumulated predominantly in the vacuoles of the epidermal cells. Therefore, the blue crystals are likely to be a Mo compound. The x-ray absorption spectrum of the plant-accumulated Mo was different than that for molybdate, indicating complexation with a plant molecule. Because the blue compound was water soluble and showed a pH-dependent color change, possible involvement of anthocyanins was investigated. An anthocyanin-less mutant of Brassica rapa ("fast plants") was compared with varieties containing normal or high anthocyanin levels. The anthocyanin-less mutant did not show accumulation of a blue compound when supplied with molybdate. In the anthocyanin-containing varieties, the blue compound colocalized with anthocyanins in the peripheral cell layers. Mo accumulation by the three B. rapa varieties was positively correlated with anthocyanin content. Addition of molybdate to purified B. rapa anthocyanin resulted in an in vitro color change from pink to blue. Therefore, Mo appears to be sequestered in vacuoles of the peripheral cell layers of Brassica spp. as a blue compound, probably a Mo-anthocyanin complex. PMID:11500539

  3. Seed-borne viral dsRNA elements in three cultivated Raphanus and Brassica plants suggest three cryptoviruses.

    PubMed

    Li, Liqiang; Liu, Jianning; Zhang, Qiong; Fu, Runying; Zhu, Xiwu; Li, Chao; Chen, Jishuang

    2016-04-01

    Since the 1970s, several dsRNA viruses, including Radish yellow edge virus, Raphanus sativus virus 1, Raphanus sativus virus 2, and Raphanus sativus virus 3, have been identified and reported as infecting radish. In the present study, in conjunction with a survey of seed-borne viruses in cultivated Brassica and Raphanus using the dsRNA diagnostic method, we discovered 3 novel cryptoviruses that infect Brassica and Raphanus: Raphanus sativus partitivirus 1, which infects radish (Raphanus sativus); Sinapis alba cryptic virus 1, which infects Sinapis alba; and Brassica rapa cryptic virus 1 (BrCV1), which infects Brassica rapa. The genomic organization of these cryptoviruses was analyzed and characterized. BrCV1 might represent the first plant partitivirus found in Gammapartitivirus. Additionally, the evolutionary relationships among all of the partitiviruses reported in Raphanus and Brassica were analyzed. PMID:26974503

  4. Anthocyanins facilitate tungsten accumulation in Brassica

    SciTech Connect

    Hale, K.L.

    2002-11-01

    Accumulation of molybdenum in Brassica was recently found to be correlated with anthocyanin content, involving the formation of a blue complex. Here the role of anthocyanins in tungsten sequestration was investigated using three species of Brassica: B. rapa (cv. Fast plants), B. juncea (Indian mustard) and B. oleracea (red cabbage). Seedlings of B. rapa and B. juncea turned blue when supplied with colourless tungstate. The blue compound co-localized with anthocyanins in the peripheral cell layers, and the degree of blueness was correlated with anthocyanin content. The direct involvement of anthocyanins in the blue coloration was evident when purified anthocyanins showed a colour change from pink to blue in vitro upon addition of tungstate, over a wide pH range. Anthocyanin production was upregulated 3-fold by W in B. juncea, possibly reflecting a function for anthocyanins in W tolerance or sequestration. The presence of anthocyanins facilitated W accumulation in B. rapa: anthocyanin-containing seedlings accumulated 3-fold more W than an anthocyaninless mutant. There was no correlation between anthocyanin content and W tolerance under these conditions. The nature of the interaction between anthocyanins and tungstate was investigated. X-ray absorption spectroscopy showed no change in the local chemical environment of Wupon uptake of tungstate by the plant; HPLC analysis of purified anthocyanin with or without tungstate showed no peak shift after metal treatment.

  5. Flowering times in genetically modified Brassica hybrids in the absence of selection

    EPA Science Inventory

    Changes in days to flowering (DTF) were observed among reciprocal F1 progeny of Brassica napus ‘RaideRR’ with other B. napus and also with weedy B. rapa. Changes in DTF are presented as factors to consider in evaluating the potential of crop to weed gene flow in different geograp...

  6. A Search for Peppery Leaf Spot Resistance in Brassica Juncea Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The southeastern United States leads the country in the production of leafy crucifer greens, including turnip greens (Brassica rapa L.), mustard greens (B. Juncea L.), collard (B. oleracea L.) and kale (B. oleracea). Production of these vegetables is continuous throughout the four seasons in this r...

  7. Genome-wide identification of aquaporin encoding genes in Brassica oleracea and their phylogenetic sequence comparison to Brassica crops and Arabidopsis

    PubMed Central

    Diehn, Till A.; Pommerrenig, Benjamin; Bernhardt, Nadine; Hartmann, Anja; Bienert, Gerd P.

    2015-01-01

    Aquaporins (AQPs) are essential channel proteins that regulate plant water homeostasis and the uptake and distribution of uncharged solutes such as metalloids, urea, ammonia, and carbon dioxide. Despite their importance as crop plants, little is known about AQP gene and protein function in cabbage (Brassica oleracea) and other Brassica species. The recent releases of the genome sequences of B. oleracea and Brassica rapa allow comparative genomic studies in these species to investigate the evolution and features of Brassica genes and proteins. In this study, we identified all AQP genes in B. oleracea by a genome-wide survey. In total, 67 genes of four plant AQP subfamilies were identified. Their full-length gene sequences and locations on chromosomes and scaffolds were manually curated. The identification of six additional full-length AQP sequences in the B. rapa genome added to the recently published AQP protein family of this species. A phylogenetic analysis of AQPs of Arabidopsis thaliana, B. oleracea, B. rapa allowed us to follow AQP evolution in closely related species and to systematically classify and (re-) name these isoforms. Thirty-three groups of AQP-orthologous genes were identified between B. oleracea and Arabidopsis and their expression was analyzed in different organs. The two selectivity filters, gene structure and coding sequences were highly conserved within each AQP subfamily while sequence variations in some introns and untranslated regions were frequent. These data suggest a similar substrate selectivity and function of Brassica AQPs compared to Arabidopsis orthologs. The comparative analyses of all AQP subfamilies in three Brassicaceae species give initial insights into AQP evolution in these taxa. Based on the genome-wide AQP identification in B. oleracea and the sequence analysis and reprocessing of Brassica AQP information, our dataset provides a sequence resource for further investigations of the physiological and molecular functions of

  8. Genome-wide identification of aquaporin encoding genes in Brassica oleracea and their phylogenetic sequence comparison to Brassica crops and Arabidopsis.

    PubMed

    Diehn, Till A; Pommerrenig, Benjamin; Bernhardt, Nadine; Hartmann, Anja; Bienert, Gerd P

    2015-01-01

    Aquaporins (AQPs) are essential channel proteins that regulate plant water homeostasis and the uptake and distribution of uncharged solutes such as metalloids, urea, ammonia, and carbon dioxide. Despite their importance as crop plants, little is known about AQP gene and protein function in cabbage (Brassica oleracea) and other Brassica species. The recent releases of the genome sequences of B. oleracea and Brassica rapa allow comparative genomic studies in these species to investigate the evolution and features of Brassica genes and proteins. In this study, we identified all AQP genes in B. oleracea by a genome-wide survey. In total, 67 genes of four plant AQP subfamilies were identified. Their full-length gene sequences and locations on chromosomes and scaffolds were manually curated. The identification of six additional full-length AQP sequences in the B. rapa genome added to the recently published AQP protein family of this species. A phylogenetic analysis of AQPs of Arabidopsis thaliana, B. oleracea, B. rapa allowed us to follow AQP evolution in closely related species and to systematically classify and (re-) name these isoforms. Thirty-three groups of AQP-orthologous genes were identified between B. oleracea and Arabidopsis and their expression was analyzed in different organs. The two selectivity filters, gene structure and coding sequences were highly conserved within each AQP subfamily while sequence variations in some introns and untranslated regions were frequent. These data suggest a similar substrate selectivity and function of Brassica AQPs compared to Arabidopsis orthologs. The comparative analyses of all AQP subfamilies in three Brassicaceae species give initial insights into AQP evolution in these taxa. Based on the genome-wide AQP identification in B. oleracea and the sequence analysis and reprocessing of Brassica AQP information, our dataset provides a sequence resource for further investigations of the physiological and molecular functions of

  9. Screening different Brassica spp. germplasm for resistance to Rhizoctonia solani AG-2-1 and AG-8

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Poor stands of canola seedlings in Pacific Northwest (PNW) have been associated with Rhizoctonia solani AG-2-1 and AG-8. A total of eighty five genotypes of Brassica napus, B. rapa, B. carinata, B. juncea and Sinapsis alba were evaluated in the growth chamber for their resistance to both R. solani A...

  10. Exploiting comparative mapping among Brassica species to accelerate the physical delimitation of a genic male-sterile locus (BnRf) in Brassica napus.

    PubMed

    Xie, Yanzhou; Dong, Faming; Hong, Dengfeng; Wan, Lili; Liu, Pingwu; Yang, Guangsheng

    2012-07-01

    The recessive genic male sterility (RGMS) line 9012AB has been used as an important pollination control system for rapeseed hybrid production in China. Here, we report our study on physical mapping of one male-sterile locus (BnRf) in 9012AB by exploiting the comparative genomics among Brassica species. The genetic maps around BnRf from previous reports were integrated and enriched with markers from the Brassica A7 chromosome. Subsequent collinearity analysis of these markers contributed to the identification of a novel ancestral karyotype block F that possibly encompasses BnRf. Fourteen insertion/deletion markers were further developed from this conserved block and genotyped in three large backcross populations, leading to the construction of high-resolution local genetic maps where the BnRf locus was restricted to a less than 0.1-cM region. Moreover, it was observed that the target region in Brassica napus shares a high collinearity relationship with a region from the Brassica rapa A7 chromosome. A BnRf-cosegregated marker (AT3G23870) was then used to screen a B. napus bacterial artificial chromosome (BAC) library. From the resulting 16 positive BAC clones, one (JBnB089D05) was identified to most possibly contain the BnRf (c) allele. With the assistance of the genome sequence from the Brassica rapa homolog, the 13.8-kb DNA fragment covering both closest flanking markers from the BAC clone was isolated. Gene annotation based on the comparison of microcollinear regions among Brassica napus, B. rapa and Arabidopsis showed that five potential open reading frames reside in this fragment. These results provide a foundation for the characterization of the BnRf locus and allow a better understanding of the chromosome evolution around BnRf. PMID:22382487

  11. Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives.

    PubMed

    Rana, Debashis; van den Boogaart, Tom; O'Neill, Carmel M; Hynes, Llewelyn; Bent, Elisabeth; Macpherson, Lee; Park, Jee Young; Lim, Yong Pyo; Bancroft, Ian

    2004-12-01

    The cultivated Brassica species are the group of crops most closely related to Arabidopsis thaliana (Arabidopsis). They represent models for the application in crops of genomic information gained in Arabidopsis and provide an opportunity for the investigation of polyploid genome formation and evolution. The scientific literature contains contradictory evidence for the dynamics of the evolution of polyploid genomes. We aimed at overcoming the inherent complexity of Brassica genomes and clarify the effects of polyploidy on the evolution of genome microstructure in specific segments of the genome. To do this, we have constructed bacterial artificial chromosome (BAC) libraries from genomic DNA of B. rapa subspecies trilocularis (JBr) and B. napus var Tapidor (JBnB) to supplement an existing BAC library from B. oleracea. These allowed us to analyse both recent polyploidization (under 10,000 years in B. napus) and more ancient polyploidization events (ca. 20 Myr for B. rapa and B. oleracea relative to Arabidopsis), with an analysis of the events occurring on an intermediate time scale (over the ca. 4 Myr since the divergence of the B. rapa and B. oleracea lineages). Using the Arabidopsis genome sequence and clones from the JBr library, we have analysed aspects of gene conservation and microsynteny between six regions of the genome of B. rapa with the homoeologous regions of the genomes of B. oleracea and Arabidopsis. Extensive divergence of gene content was observed between the B. rapa paralogous segments and their homoeologous segments within the genome of Arabidopsis. A pattern of interspersed gene loss was identified that is similar, but not identical, to that observed in B. oleracea. The conserved genes show highly conserved collinearity with their orthologues across genomes, but a small number of species-specific rearrangements were identified. Thus the evolution of genome microstructure is an ongoing process. Brassica napus is a recently formed polyploid resulting

  12. Karyotype and identification of all homoeologous chromosomes of allopolyploid Brassica napus and its diploid progenitors.

    PubMed

    Xiong, Zhiyong; Pires, J Chris

    2011-01-01

    Investigating recombination of homoeologous chromosomes in allopolyploid species is central to understanding plant breeding and evolution. However, examining chromosome pairing in the allotetraploid Brassica napus has been hampered by the lack of chromosome-specific molecular probes. In this study, we establish the identification of all homoeologous chromosomes of allopolyploid B. napus by using robust molecular cytogenetic karyotypes developed for the progenitor species Brassica rapa (A genome) and Brassica oleracea (C genome). The identification of every chromosome among these three Brassica species utilized genetically mapped bacterial artificial chromosomes (BACs) from B. rapa as probes for fluorescent in situ hybridization (FISH). With this BAC-FISH data, a second karyotype was developed using two BACs that contained repetitive DNA sequences and the ubiquitous ribosomal and pericentromere repeats. Using this diagnostic probe mix and a BAC that contained a C-genome repeat in two successive hybridizations allowed for routine identification of the corresponding homoeologous chromosomes between the A and C genomes of B. napus. When applied to the B. napus cultivar Stellar, we detected one chromosomal rearrangement relative to the parental karyotypes. This robust novel chromosomal painting technique will have biological applications for the understanding of chromosome pairing, homoeologous recombination, and genome evolution in the genus Brassica and will facilitate new applied breeding technologies that rely upon identification of chromosomes. PMID:21041557

  13. Polymorphic minisatellites in the mitochondrial DNAs of Oryza and Brassica.

    PubMed

    Honma, Yujiro; Yoshida, Yu; Terachi, Toru; Toriyama, Kinya; Mikami, Tetsuo; Kubo, Tomohiko

    2011-08-01

    Polymorphic analyses of angiosperm mitochondrial DNA are rare in comparison with chloroplast DNA, because few target sequences in angiosperm mitochondrial DNA are known. Minisatellites, a tandem array of repeated sequences with a repeat unit of 10 to ~100 bp, are popular target sequences of animal mitochondria, but Beta vulgaris is the only known angiosperm species for which such an analysis has been conducted. From this lack of information, it was uncertain as to whether polymorphic minisatellites existed in other angiosperm species. Ten plant mitochondrial DNAs were found to contain minisatellite-like repeated sequences, most of which were located in intergenic regions but a few occurred in gene coding and intronic regions. Oryza and Brassica accessions were selected as models for the investigation of minisatellite polymorphism because substantial systematic information existed. PCR analysis of 42 Oryza accessions revealed length polymorphisms in four of the five minisatellites. The mitochondrial haplotypes of the 16 Oryza accessions with chromosomal complement (genome) types of CC, BBCC and CCDD were identical but were clearly distinguished from BB-genome accessions, a result consistent with the notion that the cytoplasmic donor parent of the amphidiploid species might be the CC-genome species. Twenty-nine accessions of six major cultivated species of Brassica were classified into five mitochondrial haplotypes based on two polymorphic minisatellites out of six loci. The haplotypes of Brassica juncea and Brassica carinata accessions were identical to Brassica rapa and Brassica nigra accessions, respectively. The haplotypes of Brassica napus accessions were heterogeneous and unique, results that were consistent with previous studies. PMID:21562713

  14. Leaf Colour as a Signal of Chemical Defence to Insect Herbivores in Wild Cabbage (Brassica oleracea)

    PubMed Central

    Wilkins, Lucas; Osorio, Daniel; Hartley, Susan E.

    2015-01-01

    Leaf colour has been proposed to signal levels of host defence to insect herbivores, but we lack data on herbivory, leaf colour and levels of defence for wild host populations necessary to test this hypothesis. Such a test requires measurements of leaf spectra as they would be sensed by herbivore visual systems, as well as simultaneous measurements of chemical defences and herbivore responses to leaf colour in natural host-herbivore populations. In a large-scale field survey of wild cabbage (Brassica oleracea) populations, we show that variation in leaf colour and brightness, measured according to herbivore spectral sensitivities, predicts both levels of chemical defences (glucosinolates) and abundance of specialist lepidopteran (Pieris rapae) and hemipteran (Brevicoryne brassicae) herbivores. In subsequent experiments, P. rapae larvae achieved faster growth and greater pupal mass when feeding on plants with bluer leaves, which contained lower levels of aliphatic glucosinolates. Glucosinolate-mediated effects on larval performance may thus contribute to the association between P. rapae herbivory and leaf colour observed in the field. However, preference tests found no evidence that adult butterflies selected host plants based on leaf coloration. In the field, B. brassicae abundance varied with leaf brightness but greenhouse experiments were unable to identify any effects of brightness on aphid preference or performance. Our findings suggest that although leaf colour reflects both levels of host defences and herbivore abundance in the field, the ability of herbivores to respond to colour signals may be limited, even in species where performance is correlated with leaf colour. PMID:26353086

  15. Characterization and expression analysis of dirigent family genes related to stresses in Brassica.

    PubMed

    Thamil Arasan, Senthil Kumar; Park, Jong-In; Ahmed, Nasar Uddin; Jung, Hee-Jeong; Hur, Yoonkang; Kang, Kwon-Kyoo; Lim, Yong-Pyo; Nou, Ill-Sup

    2013-06-01

    The dirigent (DIR) genes are playing a vital role in enhancing stress resistance in different crop plants. In this study, we collected 29 DIR like genes, two from a Brassica rapa cv. Osome full length cDNA library and 27 from the B. rapa database designated as B. rapa Dirigent (BrDIR) like genes. Sequence analysis and a comparison study of these genes confirmed that seven were dirigent and the remaining 22 were dirigent like genes. Expression analysis revealed an organ specific expression of these genes. BrDIR2 showed differential responses after Fusarium oxysporum f.sp. conglutinans infection in cabbage. Four Brassica oleracea dirigent like genes highly homologous to BrDIR2 also showed similar responses in cabbage plants infected with this fungus. Moreover, several BrDIR like genes showed significant responses after water, ABA and cold stress treatments in Chinese cabbage. Under water stress, most responsive genes showed the highest expression at 24 h, at which time the acid soluble lignin content of samples under the same stress condition were also highest, indicating a possible relationship between BrDIR like genes and lignin content. Taken together, our results indicate a protective role of BrDIR genes against biotic and abiotic stresses in Brassica. PMID:23562798

  16. Effect of Heavy Metals in Plants of the Genus Brassica

    PubMed Central

    Mourato, Miguel P.; Moreira, Inês N.; Leitão, Inês; Pinto, Filipa R.; Sales, Joana R.; Louro Martins, Luisa

    2015-01-01

    Several species from the Brassica genus are very important agricultural crops in different parts of the world and are also known to be heavy metal accumulators. There have been a large number of studies regarding the tolerance, uptake and defense mechanism in several of these species, notably Brassica juncea and B. napus, against the stress induced by heavy metals. Numerous studies have also been published about the capacity of these species to be used for phytoremediation purposes but with mixed results. This review will focus on the latest developments in the study of the uptake capacity, oxidative damage and biochemical and physiological tolerance and defense mechanisms to heavy metal toxicity on six economically important species: B. juncea, B. napus, B. oleracea, B. carinata, B. rapa and B. nigra. PMID:26247945

  17. Effect of Heavy Metals in Plants of the Genus Brassica.

    PubMed

    Mourato, Miguel P; Moreira, Inês N; Leitão, Inês; Pinto, Filipa R; Sales, Joana R; Martins, Luisa Louro

    2015-01-01

    Several species from the Brassica genus are very important agricultural crops in different parts of the world and are also known to be heavy metal accumulators. There have been a large number of studies regarding the tolerance, uptake and defense mechanism in several of these species, notably Brassica juncea and B. napus, against the stress induced by heavy metals. Numerous studies have also been published about the capacity of these species to be used for phytoremediation purposes but with mixed results. This review will focus on the latest developments in the study of the uptake capacity, oxidative damage and biochemical and physiological tolerance and defense mechanisms to heavy metal toxicity on six economically important species: B. juncea, B. napus, B. oleracea, B. carinata, B. rapa and B. nigra. PMID:26247945

  18. Herbivory and relative growth rates of Pieris rapae are correlated with host constitutive salicylic acid and flowering time.

    PubMed

    Lariviere, Andrew; Limeri, Lisa B; Meindl, George A; Traw, M Brian

    2015-04-01

    Treatment of plants with exogenous salicylic acid (SA) improves resistance to many bacterial pathogens, but can suppress resistance to insect herbivores. While plants vary naturally in constitutive SA, whether such differences are predictive of resistance to insect herbivores has not been studied previously. We examined the possible role of this endogenous SA in structuring the interactions between the cabbage white butterfly, Pieris rapae, and ten hosts in the mustard family (Brassicaceae). Because P. rapae has multiple generations that utilize different hosts across the year, we included five spring-flowering mustards and five summer-flowering mustards that co-occur in ruderal habitats in upstate New York. Under common garden conditions, the spring flowering mustards (Capsella bursa-pastoris, Draba verna, Cardamine impatiens, Barbarea vulgaris, and Arabidopsis thaliana) were significantly more resistant to P. rapae, supporting 42 % less herbivory (P = 0.015) and 64 % lower relative growth rates (P = 0.007), relative to the summer flowering mustards (Sisymbrium altissimum, Brassica nigra, Sinapis arvense, Lepidium campestre, and Arabis canadensis). Leaf total constitutive SA explained significant variation in larval herbivory (R (2)  = 75.3 %, P = 0.007) and relative growth rates (R (2)  = 59.4 %, P = 0.043). The three species with the lowest levels of constitutive SA (Capsella bursa-pastoris, Draba verna, and Cardamine impatiens) were the most resistant to larvae. Barbarea vulgaris and Arabis canadensis were notable exceptions, exhibiting high SA concentrations and intermediate resistance to P. rapae. These results suggest a curvilinear relationship between leaf constitutive SA and the herbivory by P. rapae, and they provide some insight into the ecology and possible management of this economically important crop pest. PMID:25893789

  19. Tracing the transcriptomic changes in synthetic Trigenomic allohexaploids of Brassica using an RNA-Seq approach.

    PubMed

    Zhao, Qin; Zou, Jun; Meng, Jinling; Mei, Shiyong; Wang, Jianbo

    2013-01-01

    Polyploidization has played an important role in plant evolution and speciation, and newly formed allopolyploids have experienced rapid transcriptomic changes. Here, we compared the transcriptomic differences between a synthetic Brassica allohexaploid and its parents using a high-throughput RNA-Seq method. A total of 35,644,409 sequence reads were generated, and 32,642 genes were aligned from the data. Totals of 29,260, 29,060, and 29,697 genes were identified in Brassicarapa, Brassicacarinata, and Brassica allohexaploid, respectively. We compared 7,397 differentially expressed genes (DEGs) between Brassica hexaploid and its parents, as well as 2,545 nonadditive genes of Brassica hexaploid. We hypothesized that the higher ploidy level as well as secondary polyploidy might have influenced these changes. The majority of the 3,184 DEGs between Brassica hexaploid and its paternal parent, B. rapa, were involved in the biosynthesis of secondary metabolites, plant-pathogen interactions, photosynthesis, and circadian rhythm. Among the 2,233 DEGs between Brassica hexaploid and its maternal parent, B. carinata, several played roles in plant-pathogen interactions, plant hormone signal transduction, ribosomes, limonene and pinene degradation, photosynthesis, and biosynthesis of secondary metabolites. There were more significant differences in gene expression between the allohexaploid and its paternal parent than between it and its maternal parent, possibly partly because of cytoplasmic and maternal effects. Specific functional categories were enriched among the 2,545 nonadditive genes of Brassica hexaploid compared with the additive genes; the categories included response to stimulus, immune system process, cellular process, metabolic process, rhythmic process, and pigmentation. Many transcription factor genes, methyltransferases, and methylation genes showed differential expression between Brassica hexaploid and its parents. Our results demonstrate that the Brassica

  20. A Complex Recombination Pattern in the Genome of Allotetraploid Brassica napus as Revealed by a High-Density Genetic Map

    PubMed Central

    Yi, Bin; Fan, Chuchuan; Edwards, David; Batley, Jacqueline; Zhou, Yongming

    2014-01-01

    Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus. PMID:25356735

  1. Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica.

    PubMed

    Xie, Lulu; Li, Fei; Zhang, Shifan; Zhang, Hui; Qian, Wei; Li, Peirong; Zhang, Shujiang; Sun, Rifei

    2016-01-01

    Introgression breeding is a widely used method for the genetic improvement of crop plants; however, the mechanism underlying candidate gene flow patterns during hybridization is poorly understood. In this study, we used a powerful pipeline to investigate a Chinese cabbage (Brassica rapa L. ssp. pekinensis) introgression line with the anthocyanin overaccumulation phenotype. Our purpose was to analyze the gene flow patterns during hybridization and elucidate the genetic factors responsible for the accumulation of this important pigment compound. We performed RNA-seq analysis by using two pipelines, one with and one without a reference sequence, to obtain transcriptome data. We identified 930 significantly differentially expressed genes (DEGs) between the purple-leaf introgression line and B. rapa green cultivar, namely, 389 up-regulated and 541 down-regulated DEGs that mapped to the B. rapa reference genome. Since only one anthocyanin pathway regulatory gene was identified, i.e., Bra037887 (bHLH), we mined unmapped reads, revealing 2031 de novo assembled unigenes, including c3563g1i2. Phylogenetic analysis suggested that c3563g1i2, which was transferred from the Brassica B genome of the donor parental line Brassica juncea, may represent an R2R3-MYB transcription factor that participates in the ternary transcriptional activation complex responsible for the anthocyanin overaccumulation phenotype of the B. rapa introgression line. We also identified genes involved in cold and light reaction pathways that were highly upregulated in the introgression line, as confirmed using quantitative real-time PCR analysis. The results of this study shed light on the mechanisms underlying the purple leaf trait in Brassica plants and may facilitate the use of introgressive hybridization for many traits of interest. PMID:27597857

  2. Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica

    PubMed Central

    Xie, Lulu; Li, Fei; Zhang, Shifan; Zhang, Hui; Qian, Wei; Li, Peirong; Zhang, Shujiang; Sun, Rifei

    2016-01-01

    Introgression breeding is a widely used method for the genetic improvement of crop plants; however, the mechanism underlying candidate gene flow patterns during hybridization is poorly understood. In this study, we used a powerful pipeline to investigate a Chinese cabbage (Brassica rapa L. ssp. pekinensis) introgression line with the anthocyanin overaccumulation phenotype. Our purpose was to analyze the gene flow patterns during hybridization and elucidate the genetic factors responsible for the accumulation of this important pigment compound. We performed RNA-seq analysis by using two pipelines, one with and one without a reference sequence, to obtain transcriptome data. We identified 930 significantly differentially expressed genes (DEGs) between the purple-leaf introgression line and B. rapa green cultivar, namely, 389 up-regulated and 541 down-regulated DEGs that mapped to the B. rapa reference genome. Since only one anthocyanin pathway regulatory gene was identified, i.e., Bra037887 (bHLH), we mined unmapped reads, revealing 2031 de novo assembled unigenes, including c3563g1i2. Phylogenetic analysis suggested that c3563g1i2, which was transferred from the Brassica B genome of the donor parental line Brassica juncea, may represent an R2R3-MYB transcription factor that participates in the ternary transcriptional activation complex responsible for the anthocyanin overaccumulation phenotype of the B. rapa introgression line. We also identified genes involved in cold and light reaction pathways that were highly upregulated in the introgression line, as confirmed using quantitative real-time PCR analysis. The results of this study shed light on the mechanisms underlying the purple leaf trait in Brassica plants and may facilitate the use of introgressive hybridization for many traits of interest. PMID:27597857

  3. Sequence and expression variation in SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1): homeolog evolution in Indian Brassicas.

    PubMed

    Sri, Tanu; Mayee, Pratiksha; Singh, Anandita

    2015-09-01

    Whole genome sequence analyses allow unravelling such evolutionary consequences of meso-triplication event in Brassicaceae (∼14-20 million years ago (MYA)) as differential gene fractionation and diversification in homeologous sub-genomes. This study presents a simple gene-centric approach involving microsynteny and natural genetic variation analysis for understanding SUPPRESSOR of OVEREXPRESSION of CONSTANS 1 (SOC1) homeolog evolution in Brassica. Analysis of microsynteny in Brassica rapa homeologous regions containing SOC1 revealed differential gene fractionation correlating to reported fractionation status of sub-genomes of origin, viz. least fractionated (LF), moderately fractionated 1 (MF1) and most fractionated (MF2), respectively. Screening 18 cultivars of 6 Brassica species led to the identification of 8 genomic and 27 transcript variants of SOC1, including splice-forms. Co-occurrence of both interrupted and intronless SOC1 genes was detected in few Brassica species. In silico analysis characterised Brassica SOC1 as MADS intervening, K-box, C-terminal (MIKC(C)) transcription factor, with highly conserved MADS and I domains relative to K-box and C-terminal domain. Phylogenetic analyses and multiple sequence alignments depicting shared pattern of silent/non-silent mutations assigned Brassica SOC1 homologs into groups based on shared diploid base genome. In addition, a sub-genome structure in uncharacterised Brassica genomes was inferred. Expression analysis of putative MF2 and LF (Brassica diploid base genome A (AA)) sub-genome-specific SOC1 homeologs of Brassica juncea revealed near identical expression pattern. However, MF2-specific homeolog exhibited significantly higher expression implying regulatory diversification. In conclusion, evidence for polyploidy-induced sequence and regulatory evolution in Brassica SOC1 is being presented wherein differential homeolog expression is implied in functional diversification. PMID:26276216

  4. Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica.

    PubMed

    Yang, J; Liu, G; Zhao, N; Chen, S; Liu, D; Ma, W; Hu, Z; Zhang, M

    2016-05-01

    The genus Brassica has many species that are important for oil, vegetable and other food products. Three mitochondrial genome types (mitotype) originated from its common ancestor. In this paper, a B. nigra mitochondrial main circle genome with 232,407 bp was generated through de novo assembly. Synteny analysis showed that the mitochondrial genomes of B. rapa and B. oleracea had a better syntenic relationship than B. nigra. Principal components analysis and development of a phylogenetic tree indicated maternal ancestors of three allotetraploid species in Us triangle of Brassica. Diversified mitotypes were found in allotetraploid B. napus, in which napus-type B. napus was derived from B. oleracea, while polima-type B. napus was inherited from B. rapa. In addition, the mitochondrial genome of napus-type B. napus was closer to botrytis-type than capitata-type B. oleracea. The sub-stoichiometric shifting of several mitochondrial genes suggested that mitochondrial genome rearrangement underwent evolutionary selection during domestication and/or plant breeding. Our findings clarify the role of diploid species in the maternal origin of allotetraploid species in Brassica and suggest the possibility of breeding selection of the mitochondrial genome. PMID:27079962

  5. High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing

    PubMed Central

    2012-01-01

    Background The complex genome of rapeseed (Brassica napus) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of B. napus representing eight different germplasm types to sequence genome-wide distributed restriction-site associated DNA (RAD) fragments for polymorphism detection and genotyping. Results More than 113,000 RAD clusters with more than 20,000 single nucleotide polymorphisms (SNPs) and 125 insertions/deletions were detected and characterized. About one third of the RAD clusters and polymorphisms mapped to the Brassica rapa reference sequence. An even distribution of RAD clusters and polymorphisms was observed across the B. rapa chromosomes, which suggests that there might be an equal distribution over the Brassica oleracea chromosomes, too. The representation of Gene Ontology (GO) terms for unigenes with RAD clusters and polymorphisms revealed no signature of selection with respect to the distribution of polymorphisms within genes belonging to a specific GO category. Conclusions Considering the decreasing costs for next-generation sequencing, the results of our study suggest that RAD sequencing is not only a simple and cost-effective method for high-density polymorphism detection but also an alternative to SNP genotyping from transcriptome sequencing or SNP arrays, even for species with complex genomes such as B. napus. PMID:22726880

  6. Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources

    PubMed Central

    Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/ PMID:26589635

  7. Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

    PubMed

    Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

    2015-01-01

    The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. PMID:26589635

  8. Changes in constructed Brassica communities treated with glyphosate drift.

    PubMed

    Watrud, Lidia S; King, George; Londo, Jason P; Colasanti, Ricardo; Smith, Bonnie M; Waschmann, Ronald S; Lee, E Henry

    2011-03-01

    We constructed a mixed-species community designed to simulate roadside and field edge plant communities and exposed it to glyphosate drift in order to test three hypotheses: (1) higher fitness in transgenic Brassica carrying the CP4 EPSPS transgene that confers resistance to glyphosate will result in significant changes in the plant community relative to control communities; (2) given repeated years of glyphosate drift selective pressure, the increased fitness of the transgenic Brassica with CP4 EPSPS will contribute to an increase in the proportion of transgenic progeny produced in plant communities; and (3) the increased fitness of Brassica carrying the CP4 EPSPS transgene will contribute to decreased levels of mycorrhizal infection and biomass in a host species (Trifolium incarnatum). Due to regulatory constraints that prevented the use of outdoor plots for our studies, in 2005 we established multispecies communities in five large cylindrical outdoor sunlit mesocosms (plastic greenhouses) designed for pollen confinement. Three of the community members were sexually compatible Brassica spp.: transgenic glyphosate-resistant canola (B. napus) cultivar (cv.) RaideRR, glyphosate-sensitive non-transgenic B. napus cv. Sponsor, and a weedy B. rapa (GRIN Accession 21735). Additional plant community members were the broadly distributed annual weeds Digitaria sanguinalis, Panicum capillare, and Lapsana communis. Once annually in 2006 and 2007, two mesocosms were sprayed with glyphosate at 10% of the field application rate to simulate glyphosate drift as a selective pressure. After two years, changes were observed in community composition, plant density, and biomass in both control and treatment mesocosms. In control mesocosms, the weed D. sanguinalis (crabgrass) began to dominate. In glyphosate drift-treated mesocosms, Brassica remained the dominant genus and the incidence of the CP4 EPSPS transgene increased in the community. Shoot biomass and mycorrhizal infection in

  9. Realizing the potential of rapid-cycling Brassica as a model system for use in plant biology research

    NASA Technical Reports Server (NTRS)

    Musgrave, M. E.

    2000-01-01

    Rapid-cycling Brassica populations were initially developed as a model for probing the genetic basis of plant disease. Paul Williams and co-workers selected accessions of the six main species for short time to flower and rapid seed maturation. Over multiple generations of breeding and selection, rapid-cycling populations of each of the six species were developed. Because of their close relationship with economically important Brassica species, rapid-cycling Brassica populations, especially those of B. rapa (RCBr) and B. oleracea, have seen wide application in plant and crop physiology investigations. Adding to the popularity of these small, short-lived plants for research applications is their extensive use in K-12 education and outreach.

  10. Selenium, putrescine, and cadmium influence health-promoting phytochemicals and molecular-level effects on turnip (Brassica rapa ssp. rapa).

    PubMed

    Thiruvengadam, Muthu; Chung, Ill-Min

    2015-04-15

    The effects of selenium, putrescine, and cadmium on the contents of glucosinolates, total phenolics, flavonoids, carotenoids, chlorophyll, anthocyanin, malondialdehyde, hydrogen peroxide, and antioxidant capacities as well as gene regulation of phenolics, flavonoids, carotenoids, and glucosinolates biosynthesis were investigated in turnip plants. Selenium dioxide (SeO2) treatment significantly induced the amount of gluconasturtiin, glucobrassicanapin, glucoallysin, glucobrassicin, 4-methoxyglucobrassicin, and 4-hydroxyglucobrassicin. Cadmium chloride (CdCl2)- and putrescine-treated plants had considerably enhanced gluconasturtiin and 4-hydroxyglucobrassicin levels, respectively. Total phenolic and flavonoid content as well as antioxidant capacities were significantly increased in SeO2-treated plants. Lutein was higher in control plants followed by, in decreasing order, SeO2-, putrescine-, and CdCl2-treated plants. The chlorophyll content was significantly decreased and anthocyanin, MDA, and H2O2 levels were significantly increased with CdCl2 treatment. Moreover, plants treated with selenium and cadmium showed significant induction of genes related to glucosinolate, phenolic, and carotenoid biosynthesis. These results demonstrated that SeO2 significantly increased the contents of health-promoting compounds and enhanced the antioxidant capacities of turnip plants. PMID:25466011

  11. Physiological, metabolic, and transcriptional effects of biologically-synthesized silver nanoparticles in turnip (Brassica rapa ssp. rapa L.).

    PubMed

    Thiruvengadam, Muthu; Gurunathan, Sangiliyandi; Chung, Ill-Min

    2015-07-01

    Silver nanoparticles (AgNPs) use has been increased in recent years, which has potentially antagonistic effects on living organisms, including microbes, human, and plants. The physiological and molecular responses of AgNPs have been reported for several plants; however, the detailed mechanism of action of AgNPs is not known in turnip. Accordingly, the aim of this study was determined to evaluate the impact of AgNPs exposure in turnip seedlings at concentrations up to 10.0 mg/l. The frequency of seed germination decreased with increasing AgNPs concentration. Moreover, while exposure to 1.0 mg/l AgNPs significantly increased plant fresh biomass. The plant growth, biomass, and chlorophyll content were decreased at 5.0 and 10.0 mg/l AgNPs. Anthocyanin, malondialdehyde, and hydrogen peroxide levels were significantly increased with higher concentrations of AgNPs. Furthermore, reactive oxygen species (ROS) production and DNA damage were significantly elevated in plants treated with higher concentrations of AgNPs. The DNA damage potential was confirmed in the experiment of DNA laddering, comet, and TUNEL assays. Consequently, the study confirms the phytotoxic, cytotoxic, and genotoxic potentials induced by AgNPs. Moreover, higher concentrations (5.0 and 10.0 mg/l) of AgNPs significantly induced expression of genes related to glucosinolates and phenolics biosynthesis as well as abiotic and biotic stresses whereas down-regulated the carotenoid gene expressions. To our knowledge, this is the first report to evaluate the physiological, metabolic, and transcriptional responses of turnip to biologically synthesized AgNPs. PMID:25471476

  12. Multiple Evolutionary Events Involved in Maintaining Homologs of Resistance to Powdery Mildew 8 in Brassica napus.

    PubMed

    Li, Qin; Li, Jing; Sun, Jin-Long; Ma, Xian-Feng; Wang, Ting-Ting; Berkey, Robert; Yang, Hui; Niu, Ying-Ze; Fan, Jing; Li, Yan; Xiao, Shunyuan; Wang, Wen-Ming

    2016-01-01

    The Resistance to Powdery Mildew 8 (RPW8) locus confers broad-spectrum resistance to powdery mildew in Arabidopsis thaliana. There are four Homologous to RPW8s (BrHRs) in Brassica rapa and three in Brassica oleracea (BoHRs). Brassica napus (Bn) is derived from diploidization of a hybrid between B. rapa and B. oleracea, thus should have seven homologs of RPW8 (BnHRs). It is unclear whether these genes are still maintained or lost in B. napus after diploidization and how they might have been evolved. Here, we reported the identification and sequence polymorphisms of BnHRs from a set of B. napus accessions. Our data indicated that while the BoHR copy from B. oleracea is highly conserved, the BrHR copy from B. rapa is relatively variable in the B. napus genome owing to multiple evolutionary events, such as gene loss, point mutation, insertion, deletion, and intragenic recombination. Given the overall high sequence homology of BnHR genes, it is not surprising that both intragenic recombination between two orthologs and two paralogs were detected in B. napus, which may explain the loss of BoHR genes in some B. napus accessions. When ectopically expressed in Arabidopsis, a C-terminally truncated version of BnHRa and BnHRb, as well as the full length BnHRd fused with YFP at their C-termini could trigger cell death in the absence of pathogens and enhanced resistance to powdery mildew disease. Moreover, subcellular localization analysis showed that both BnHRa-YFP and BnHRb-YFP were mainly localized to the extra-haustorial membrane encasing the haustorium of powdery mildew. Taken together, our data suggest that the duplicated BnHR genes might have been subjected to differential selection and at least some may play a role in defense and could serve as resistance resource in engineering disease-resistant plants. PMID:27493652

  13. Multiple Evolutionary Events Involved in Maintaining Homologs of Resistance to Powdery Mildew 8 in Brassica napus

    PubMed Central

    Li, Qin; Li, Jing; Sun, Jin-Long; Ma, Xian-Feng; Wang, Ting-Ting; Berkey, Robert; Yang, Hui; Niu, Ying-Ze; Fan, Jing; Li, Yan; Xiao, Shunyuan; Wang, Wen-Ming

    2016-01-01

    The Resistance to Powdery Mildew 8 (RPW8) locus confers broad-spectrum resistance to powdery mildew in Arabidopsis thaliana. There are four Homologous to RPW8s (BrHRs) in Brassica rapa and three in Brassica oleracea (BoHRs). Brassica napus (Bn) is derived from diploidization of a hybrid between B. rapa and B. oleracea, thus should have seven homologs of RPW8 (BnHRs). It is unclear whether these genes are still maintained or lost in B. napus after diploidization and how they might have been evolved. Here, we reported the identification and sequence polymorphisms of BnHRs from a set of B. napus accessions. Our data indicated that while the BoHR copy from B. oleracea is highly conserved, the BrHR copy from B. rapa is relatively variable in the B. napus genome owing to multiple evolutionary events, such as gene loss, point mutation, insertion, deletion, and intragenic recombination. Given the overall high sequence homology of BnHR genes, it is not surprising that both intragenic recombination between two orthologs and two paralogs were detected in B. napus, which may explain the loss of BoHR genes in some B. napus accessions. When ectopically expressed in Arabidopsis, a C-terminally truncated version of BnHRa and BnHRb, as well as the full length BnHRd fused with YFP at their C-termini could trigger cell death in the absence of pathogens and enhanced resistance to powdery mildew disease. Moreover, subcellular localization analysis showed that both BnHRa-YFP and BnHRb-YFP were mainly localized to the extra-haustorial membrane encasing the haustorium of powdery mildew. Taken together, our data suggest that the duplicated BnHR genes might have been subjected to differential selection and at least some may play a role in defense and could serve as resistance resource in engineering disease-resistant plants. PMID:27493652

  14. Inheritance and expression patterns of BN28, a low temperature induced gene in Brassica napus, throughout the Brassicaceae.

    PubMed

    Hawkins, G P; Nykiforuk, C L; Johnson-Flanagan, A M; Boothe, J G

    1996-08-01

    Molecular genetics is becoming an important tool in the breeding and selection of agronomically important traits. BN28 is a low temperature induced gene in Brassicaceae species. PCR and Southern blot analysis indicate that BN28 is polymorphic in the three diploid genomes: Brassica rapa (AA), Brassica nigra (BB), and Brassica oleracea (CC). Of the allotetraploids, Brassica napus (AACC) is the only species to have inherited homologous genes from both parental genomes. Brassica juncea (AABB) and Brassica carinata (BBCC) have inherited homologues from the AA and CC genomes, respectively, while Sinapsis arvensis (SS) contains a single homologue from the BB genome and Sinapsis alba (dd) appears to be different from all the diploid parents. All species show message induction when exposed to low temperature. However, differences in expression were noticed at the protein level, with silencing occurring in the BB genome at the level of translation. Results suggest that silencing is occurring in diploid species where duplication may not have occurred. Molecular characterization and inheritance of BN28 homologues in the Brassicaceae may play an important role in determining their quantitative function during exposure to low temperature. Key words : Brassicaceae, BN28, inheritance, polymorphism. PMID:18469930

  15. A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes.

    PubMed

    Dalton-Morgan, Jessica; Hayward, Alice; Alamery, Salman; Tollenaere, Reece; Mason, Annaliese S; Campbell, Emma; Patel, Dhwani; Lorenc, Michał T; Yi, Bin; Long, Yan; Meng, Jinling; Raman, Rosy; Raman, Harsh; Lawley, Cindy; Edwards, David; Batley, Jacqueline

    2014-12-01

    Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples. PMID:25147024

  16. A Brassica Exon Array for Whole-Transcript Gene Expression Profiling

    PubMed Central

    Love, Christopher G.; Graham, Neil S.; Ó Lochlainn, Seosamh; Bowen, Helen C.; May, Sean T.; White, Philip J.

    2010-01-01

    Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3′ exons. Plant whole-transcript (WT) GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E−5, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html. PMID:20862292

  17. Gene expression profiles associated with intersubgenomic heterosis in Brassica napus.

    PubMed

    Chen, Xin; Li, Maoteng; Shi, Jiaqin; Fu, Donghui; Qian, Wei; Zou, Jun; Zhang, Chunyu; Meng, Jinling

    2008-11-01

    In order to understand the genetic mechanism of heterosis that has been observed in hybrids between Brassica napus and partial new-type B. napus which had exotic genome components from relative species, this study focused on the difference in gene expression patterns among partial new-typed B. napus lines, B. napus cultivars and their hybrids using the cDNA amplified fragment length polymorphism technique (cDNA-AFLP) technique. First, three partial new-type B. napus lines were compared with their original parents. One new line contained the exotic genomic components from B. rapa, and the other two new lines were obtained by the introgression of genomic components from B. rapa and B. carinata. The experimental results showed that the introgression of A(r) and C(c) genome components from B. rapa and B. carinata led to considerable differences in the gene expression profiles of the partial new-type lines when compared with their parents. Secondly, the gene expression profiles of nine cross-combinations between three partial new-type lines and three B. napus cultivars were compared. Twenty transcript-derived fragments (TDFs) associated with intersubgenomic heterosis were randomly selected and converted into PCR-based molecular markers. Some of them were mapped in the confidence intervals of quantitative trait loci (QTLs) for yield and yield-related traits in three segregative populations of B. napus. These results suggested that a proportion of the heterosis-associated TDFs were really responsible for fluctuating seed yield in rapeseed. PMID:18754099

  18. Toxicity of zinc and copper to Brassica species: Implications for phytoremediation

    SciTech Connect

    Ebbs, S.D.; Kochian, L.V.

    1997-05-01

    The toxicity of Zn and Cu in three species from the genus Brassica was examined to determine if these plants showed sufficient tolerance and metal accumulation to be used to phytoremediate a site contaminated with these two heavy metals. Hydroponically grown 12-d-old plants of Brassica juncea, B. rapa, and B. napus were grown for an additional 14 d in the presence of either elevated Zn (6.5 mg L{sup {minus}1}), Cu (0.32 mg L{sup {minus}1}), or Zn+Cu to quantify the toxic effects of these metals on several different growth parameters. With few exceptions, both root and shoot dry weight for all three species decreased significantly in the presence of heavy metals. Cu inhibited lateral root elongation in B. rapa, B. napus, and, to a lesser extent, B. juncea, while Zn tended to decrease only lateral root diameter. Both metals reduced shoot Fe and Mn concentrations in all three Brassica spp. to levels associated with Fe and Mn deficiencies. These deficiencies, however, did not correlate with observed patterns of leaf chlorosis. Nonetheless, heavy metal-induced inhibition of Fe and Mn accumulation may have been a significant factor in reducing plant growth. In terms of heavy metal removal, the Brassica spp, were more effective at removing Zn from the nutrient solution than Cu. The extent of Zn and Cu removal was reduced in the presence of both metals, as compared to the single heavy metal treatments. The implications of these results for phytoremediation are discussed. 20 refs., 6 figs., 1 tab.

  19. Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

    PubMed

    Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

    2015-12-01

    Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers. PMID:26129767

  20. Brassica greens herbicide screening

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to screen herbicides for potential use in brassica greens. Plots were in a RBD with 4 replications. The study was direct seeded on May 19, 2009 with a seeding rate of 272,000 seeds/acre (‘Savanna’ mustard). Treatments included trifluralin PPI + DCPA pre-emergence ap...

  1. Diversity Array Technology Markers: Genetic Diversity Analyses and Linkage Map Construction in Rapeseed (Brassica napus L.)

    PubMed Central

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N.; Aslam, M.N.; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A.; Kilian, A.; Sharpe, Andrew G.; Schondelmaier, Joerg

    2012-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. PMID:22193366

  2. Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs.

    PubMed

    Graham, Neil S; Hammond, John P; Lysenko, Artem; Mayes, Sean; O Lochlainn, Seosamh; Blasco, Bego; Bowen, Helen C; Rawlings, Chris J; Rios, Juan J; Welham, Susan; Carion, Pierre W C; Dupuy, Lionel X; King, Graham J; White, Philip J; Broadley, Martin R

    2014-07-01

    Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca(2+) transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca(2+) transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization. PMID:25082855

  3. Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.).

    PubMed

    Raman, Harsh; Raman, Rosy; Nelson, Matthew N; Aslam, M N; Rajasekaran, Ravikesavan; Wratten, Neil; Cowling, Wallace A; Kilian, A; Sharpe, Andrew G; Schondelmaier, Joerg

    2012-01-01

    We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines 'Lynx-037DH' and 'Monty-028DH'. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed. PMID:22193366

  4. Oxygen dependency of germinating Brassica seeds.

    PubMed

    Park, Myoung Ryoul; Hasenstein, Karl H

    2016-02-01

    Establishing plants in space, Moon or Mars requires adaptation to altered conditions, including reduced pressure and composition of atmospheres. To determine the oxygen requirements for seed germination, we imbibed Brassica rapa seeds under varying oxygen concentrations and profiled the transcription patterns of genes related to early metabolism such as starch degradation, glycolysis, and fermentation. We also analyzed the activity of lactate dehydrogenase (LDH) and alcohol dehydrogenase (ADH), and measured starch degradation. Partial oxygen pressure (pO2) greater than 10% resulted in normal germination (i.e., protrusion of radicle about 18 hours after imbibition) but lower pO2 delayed and reduced germination. Imbibition in an oxygen-free atmosphere for three days resulted in no germination but subsequent transfer to air initiated germination in 75% of the seeds and the root growth rate was transiently greater than in roots germinated under ambient pO2. In hypoxic seeds soluble sugars degraded faster but the content of starch after 24 h was higher than at ambient oxygen. Transcription of genes related to starch degradation, α-amylase (AMY) and Sucrose Synthase (SUS), was higher under ambient O2 than under hypoxia. Glycolysis and fermentation pathway-related genes, glucose phosphate isomerase (GPI), 6-phosphofructokinase (PFK), fructose 1,6-bisphosphate aldolase (ALD), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), pyruvate decarboxylase (PDC), LDH, and ADH, were induced by low pO2. The activity of LDH and ADH was the highest in anoxic seeds. Germination under low O2 conditions initiated ethanolic fermentation. Therefore, sufficient oxygen availability is important for germination before photosynthesis provides necessary oxygen and the determination of an oxygen carrying capacity is important for uniform growth in space conditions. PMID:26948011

  5. Oxygen dependency of germinating Brassica seeds

    NASA Astrophysics Data System (ADS)

    Park, Myoung Ryoul; Hasenstein, Karl H.

    2016-02-01

    Establishing plants in space, Moon or Mars requires adaptation to altered conditions, including reduced pressure and composition of atmospheres. To determine the oxygen requirements for seed germination, we imbibed Brassica rapa seeds under varying oxygen concentrations and profiled the transcription patterns of genes related to early metabolism such as starch degradation, glycolysis, and fermentation. We also analyzed the activity of lactate dehydrogenase (LDH) and alcohol dehydrogenase (ADH), and measured starch degradation. Partial oxygen pressure (pO2) greater than 10% resulted in normal germination (i.e., protrusion of radicle about 18 hours after imbibition) but lower pO2 delayed and reduced germination. Imbibition in an oxygen-free atmosphere for three days resulted in no germination but subsequent transfer to air initiated germination in 75% of the seeds and the root growth rate was transiently greater than in roots germinated under ambient pO2. In hypoxic seeds soluble sugars degraded faster but the content of starch after 24 h was higher than at ambient oxygen. Transcription of genes related to starch degradation, α-amylase (AMY) and Sucrose Synthase (SUS), was higher under ambient O2 than under hypoxia. Glycolysis and fermentation pathway-related genes, glucose phosphate isomerase (GPI), 6-phosphofructokinase (PFK), fructose 1,6-bisphosphate aldolase (ALD), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), pyruvate decarboxylase (PDC), LDH, and ADH, were induced by low pO2. The activity of LDH and ADH was the highest in anoxic seeds. Germination under low O2 conditions initiated ethanolic fermentation. Therefore, sufficient oxygen availability is important for germination before photosynthesis provides necessary oxygen and the determination of an oxygen carrying capacity is important for uniform growth in space conditions.

  6. An Efficient Method for Adventitious Root Induction from Stem Segments of Brassica Species.

    PubMed

    Srikanth, Sandhya; Choong, Tsui Wei; Yan, An; He, Jie; Chen, Zhong

    2016-01-01

    Plant propagation via in vitro culture is a very laborious and time-consuming process. The growth cycle of some of the crop species is slow even in the field and the consistent commercial production is hard to maintain. Enhanced methods of reduced cost, materials and labor significantly impact the research and commercial production of field crops. In our studies, stem-segment explants of Brassica species were found to generate adventitious roots (AR) in aeroponic systems in less than a week. As such, the efficiency of rooting from stem explants of six cultivar varieties of Brassica spp was tested without using any plant hormones. New roots and shoots were developed from Brassica alboglabra (Kai Lan), B. oleracea var. acephala (purple kale), B. rapa L. ssp. chinensis L (Pai Tsai, Nai Bai C, and Nai Bai T) explants after 3 to 5 days of growing under 20 ± 2°C cool root zone temperature (C-RZT) and 4 to 7 days in 30 ± 2°C ambient root zone temperature (A-RZT). At the base of cut end, anticlinal and periclinal divisions of the cambial cells resulted in secondary xylem toward pith and secondary phloem toward cortex. The continuing mitotic activity of phloem parenchyma cells led to a ring of conspicuous white callus. Root initials formed from the callus which in turn developed into ARs. However, B. rapa var. nipposinica (Mizuna) explants were only able to root in C-RZT. All rooted explants were able to develop into whole plants, with higher biomass obtained from plants that grown in C-RZT. Moreover, explants from both RZTs produced higher biomass than plants grown from seeds (control plants). Rooting efficiency was affected by RZTs and explant cuttings of donor plants. Photosynthetic CO2 assimilation rate (Asat ) and stomatal conductance (gssat ) were significantly differentiated between plants derived from seeds and explants at both RZTs. All plants in A-RZT had highest transpiration rates. PMID:27446170

  7. An Efficient Method for Adventitious Root Induction from Stem Segments of Brassica Species

    PubMed Central

    Srikanth, Sandhya; Choong, Tsui Wei; Yan, An; He, Jie; Chen, Zhong

    2016-01-01

    Plant propagation via in vitro culture is a very laborious and time-consuming process. The growth cycle of some of the crop species is slow even in the field and the consistent commercial production is hard to maintain. Enhanced methods of reduced cost, materials and labor significantly impact the research and commercial production of field crops. In our studies, stem-segment explants of Brassica species were found to generate adventitious roots (AR) in aeroponic systems in less than a week. As such, the efficiency of rooting from stem explants of six cultivar varieties of Brassica spp was tested without using any plant hormones. New roots and shoots were developed from Brassica alboglabra (Kai Lan), B. oleracea var. acephala (purple kale), B. rapa L. ssp. chinensis L (Pai Tsai, Nai Bai C, and Nai Bai T) explants after 3 to 5 days of growing under 20 ± 2°C cool root zone temperature (C-RZT) and 4 to 7 days in 30 ± 2°C ambient root zone temperature (A-RZT). At the base of cut end, anticlinal and periclinal divisions of the cambial cells resulted in secondary xylem toward pith and secondary phloem toward cortex. The continuing mitotic activity of phloem parenchyma cells led to a ring of conspicuous white callus. Root initials formed from the callus which in turn developed into ARs. However, B. rapa var. nipposinica (Mizuna) explants were only able to root in C-RZT. All rooted explants were able to develop into whole plants, with higher biomass obtained from plants that grown in C-RZT. Moreover, explants from both RZTs produced higher biomass than plants grown from seeds (control plants). Rooting efficiency was affected by RZTs and explant cuttings of donor plants. Photosynthetic CO2 assimilation rate (Asat) and stomatal conductance (gssat) were significantly differentiated between plants derived from seeds and explants at both RZTs. All plants in A-RZT had highest transpiration rates. PMID:27446170

  8. BRASSICAS AND MUSTARDS”

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Brassica and mustard cover crops are known for their rapid fall growth, great biomass production and nutrient scavenging ability. However, they are attracting renewed interest primarily because of their pest management characteristics. Most Brassica species release chemical compounds that may be tox...

  9. Different genome-specific chromosome stabilities in synthetic Brassica allohexaploids revealed by wide crosses with Orychophragmus

    PubMed Central

    Ge, Xian-Hong; Wang, Jing; Li, Zai-Yun

    2009-01-01

    Background and Aims In sexual hybrids between cultivated Brassica species and another crucifer, Orychophragmus violaceus (2n = 24), parental genome separation during mitosis and meiosis is under genetic control but this phenomenon varies depending upon the Brassica species. To further investigate the mechanisms involved in parental genome separation, complex hybrids between synthetic Brassica allohexaploids (2n = 54, AABBCC) from three sources and O. violaceus were obtained and characterized. Methods Genomic in situ hybridization, amplified fragment length polymorphism (AFLP) and single-strand conformation polymorphism (SSCP) were used to explore chromosomal/genomic components and rRNA gene expression of the complex hybrids and their progenies. Key Results Complex hybrids with variable fertility exhibited phenotypes that were different from the female allohexaploids and expressed some traits from O. violaceus. These hybrids were mixoploids (2n = 34–46) and retained partial complements of allohexaploids, including whole chromosomes of the A and B genomes and some of the C genome but no intact O. violaceus chromosomes; AFLP bands specific for O. violaceus, novel for two parents and absent in hexaploids were detected. The complex hybrids produced progenies with chromosomes/genomic complements biased to B. juncea (2n = 36, AABB) and novel B. juncea lines with two genomes of different origins. The expression of rRNA genes from B. nigra was revealed in all allohexaploids and complex hybrids, showing that the hierarchy of nucleolar dominance (B. nigra, BB > B. rapa, AA > B. oleracea, CC) in Brassica allotetraploids was still valid in these plants. Conclusions The chromosomes of three genomes in these synthetic Brassica allohexaploids showed different genome-specific stabilities (B > A > C) under induction of alien chromosome elimination in crosses with O. violaceus, which was possibly affected by nucleolar dominance. PMID:19403626

  10. Consequences of gene flow between oilseed rape (Brassica napus) and its relatives.

    PubMed

    Liu, Yongbo; Wei, Wei; Ma, Keping; Li, Junsheng; Liang, Yuyong; Darmency, Henri

    2013-10-01

    Numerous studies have focused on the probability of occurrence of gene flow between transgenic crops and their wild relatives and the likelihood of transgene escape, which should be assessed before the commercial release of transgenic crops. This review paper focuses on this issue for oilseed rape, Brassica napus L., a species that produces huge numbers of pollen grains and seeds. We analyze separately the distinct steps of gene flow: (1) pollen and seeds as vectors of gene flow; (2) spontaneous hybridization; (3) hybrid behavior, fitness cost due to hybridization and mechanisms of introgression; (4) and fitness benefit due to transgenes (e.g. herbicide resistance and Bt toxin). Some physical, biological and molecular means of transgene containment are also described. Although hybrids and first generation progeny are difficult to identify in fields and non-crop habitats, the literature shows that transgenes could readily introgress into Brassica rapa, Brassica juncea and Brassica oleracea, while introgression is expected to be rare with Brassica nigra, Hirschfeldia incana and Raphanus raphanistrum. The hybrids grow well but produce less seed than their wild parent. The difference declines with increasing generations. However, there is large uncertainty about the evolution of chromosome numbers and recombination, and many parameters of life history traits of hybrids and progeny are not determined with satisfactory confidence to build generic models capable to really cover the wide diversity of situations. We show that more studies are needed to strengthen and organize biological knowledge, which is a necessary prerequisite for model simulations to assess the practical and evolutionary outputs of introgression, and to provide guidelines for gene flow management. PMID:23987810

  11. TRANSPARENT TESTA 12 genes from Brassica napus and parental species: cloning, evolution, and differential involvement in yellow seed trait.

    PubMed

    Chai, You-Rong; Lei, Bo; Huang, Hua-Lei; Li, Jia-Na; Yin, Jia-Ming; Tang, Zhang-Lin; Wang, Rui; Chen, Li

    2009-01-01

    Molecular dissection of the Brassica yellow seed trait has been the subject of intense investigation. Arabidopsis thaliana TRANSPARENT TESTA 12 (AtTT12) encodes a multidrug and toxic compound extrusion (MATE) transporter involved in seed coat pigmentation. Two, one, and one full-length TT12 genes were isolated from B. napus, B. oleracea, and B. rapa, respectively, and Southern hybridization confirmed these gene numbers, implying loss of some of the triplicated TT12 genes in Brassica. BnTT12-1, BnTT12-2, BoTT12, and BrTT12 are 2,714, 3,062, 4,760, and 2,716 bp, with the longest mRNAs of 1,749, 1,711, 1,739, and 1,752 bp, respectively. All genes contained alternative transcriptional start and polyadenylation sites. BrTT12 and BoTT12 are the progenitors of BnTT12-1 and BnTT12-2, respectively, validating B. napus as an amphidiploid. All Brassica TT12 proteins displayed high levels of identity (>99%) to each other and to AtTT12 (>92%). Brassica TT12 genes resembled AtTT12 in such basic features as MatE/NorM CDs, subcellular localization, transmembrane helices, and phosphorylation sites. Plant TT12 orthologs differ from other MATE proteins by two specific motifs. Like AtTT12, all Brassica TT12 genes are most highly expressed in developing seeds. However, a range of organ specificity was observed with BnTT12 genes being less organ-specific. TT12 expression is absent in B. rapa yellow-seeded line 06K124, but not downregulated in B. oleracea yellow-seeded line 06K165. In B. napus yellow-seeded line L2, BnTT12-2 expression is absent, whereas BnTT12-1 is expressed normally. Among Brassica species, TT12 genes are differentially related to the yellow seed trait. The molecular basis for the yellow seed trait, in Brassica, and the theoretical and practical implications of the highly variable intron 1 of these TT12 genes are discussed. PMID:19018571

  12. Fine mapping and characterization of the or gene in Chinese cabbage (Brassica rapa L. ssp pekinensis).

    PubMed

    Zou, C L; Zheng, Y; Wang, P; Zhang, X; Wang, Y-H; Liu, Z Y; Feng, H

    2016-01-01

    Orange inner leaves/heads is a qualitative trait in Chinese cabbage that is controlled by a single recessive gene. Orange head Chinese cabbage contain more carotenoids than its white head counterpart; hence, this trait is of interest to both researchers and consumers. In this study, we selected the orange head Chinese cabbage line 07A163 and the white head Chinese cabbage line Chiifu as test materials. We localized the target gene controlling the orange head trait to the A09 linkage group, with a physical distance of approximately 19.9 kb between the two markers, syau26 and syau28. This region contains six candidate genes, including Bra031539, which was predicted to encode CRTISO, a carotenoid isomerase specifically required for carotenoid biosynthesis. A comparison of the nucleic acid sequences of the two test materials revealed 88 and 7-bp deletions and 88 SNPs in the promoter region of Bra031539 in line 07A163, along with a 6-bp deletion in the first exon and early termination at the 3' end of this gene. BLAST analysis revealed that 22 amino acids were altered and 17 amino acids were lost in Bra031539 in the orange head line 07A163. We developed the BrPro1 molecular marker in the promoter region of Bra031539 that can be used for early identification of orange head materials, thereby accelerating the breeding process of orange head Chinese cabbage. PMID:27173304

  13. GENE FLOW STUDIES BETWEEN BRASSICA NAPUS AND B. RAPA IN CONSTRUCTED PLANT COMMUNITIES

    EPA Science Inventory

    The commercial production of genetically modified crops has led to a growing awareness of the difficulties of transgene confinement and of the potential environmental risks associated with the escape of transgenes into naturalized or native plant populations. A potential conseque...

  14. Effects of aqueous extract of turnip leaf (Brassica rapa) in alloxan-induced diabetic rats

    PubMed Central

    Hassanpour Fard, Mohammad; Naseh, Ghodratollah; Lotfi, Nassim; Hosseini, Seyed Mahmoud; Hosseini, Mehran

    2015-01-01

    Objectives: Turnip leaf has been used in folk medicine of Iran for the treatment of diabetes. However,so far no scientific study has been done to support its use in traditional medicine. The present study was carried out to evaluate the possible hypoglycemic efficacy of aqueous extract of turnip leaf (AETL) in diabetic rats. Materials and Methods: Alloxan-induced diabetic rats were orally treated with AETL at doses of 200 and 400 mg/kg body weight (bw) per day for 28 days. In order to evaluate the anti-diabetic activity, fasting blood glucose concentrations were determined on the 1st, 14th and 29th days. Moreover,at the end of the study, plasma concentrations of total cholesterol, triglyceride (TG), high density lipoprotein cholesterol (HDL-c), low density lipoprotein cholesterol (LDL-c), aspartate amino transfarase (AST), and alanine amino transferase (ALT) were measured by the use of standard kits and auto-analyzer. Results: Both doses of AETL significantly decreased (p<0.001) blood glucose and ALT levels in diabetic rats after 28 days of administration. AETL at both doses decreased (p<0.05) plasma total cholesterol and LDL-c in diabetic rats, but they significantly decreased (p<0.05) HDL-c and increased triglycerideand AST levels in a-dose dependent manner. Conclusion: The results showed that AETL has a dose- dependent decrease in the blood glucose in diabetic rats. However,we should not be unaware of adverse effects of AETL on lipid profiles and liver enzymes activity, especially decrease of HDL and increase of TG and AST. PMID:25949956

  15. Ultraviolet A-specific induction of anthocyanin biosynthesis in the swollen hypocotyls of turnip (Brassica rapa).

    PubMed

    Zhou, Bo; Li, Yuhua; Xu, Zhiru; Yan, Haifang; Homma, Shinichiro; Kawabata, Saneyuki

    2007-01-01

    Ultraviolet A (UV-A)-mediated regulation of anthocyanin biosynthesis was investigated in swollen hypocotyls of the red turnip 'Tsuda'. The shaded swollen hypocotyls which contained negligible anthocyanin were exposed to artificial light sources including low fluence UV-B, UV-A, blue, red, far-red, red plus UV-A, far-red plus UV-A, and blue plus red. Among these lights, only UV-A induced anthocyanin biosynthesis and co-irradiation of red or far-red with UV-A did not affect the extent of UV-A-induced anthocyanin accumulation. The expression of phenylalanine ammonia lyase (PAL; EC 4.3.1.5), chalcone synthase (CHS; EC 2.3.1.74), flavanone 3-hydroxylase (F3H; EC 1.14.11.9), dihydroflavonol 4-reductase (DFR; EC 1.1.1.219), and anthocyanidin synthase (ANS; EC 1.14.11.19) genes was increased with time during a 24 h exposure to UV-A. In contrast, irradiation with red, blue, UV-B, and a combination of blue with red failed to induce CHS expression. Microarray analysis showed that only a few genes, including CHS and F3H, were induced significantly by UV-A, while a separate set of many genes was induced by low fluence UV-B. The UV-A-specific induction of anthocyanin biosynthesis and the unique gene expression profile upon UV-A irradiation as compared with blue and UV-B demonstrated that the observed induction of anthocyanin biosynthesis in red turnips was mediated by a distinct UV-A-specific photoreceptor, but not by phytochromes, UV-A/blue photoreceptors, or UV-B photoreceptors. PMID:17426056

  16. Identification of Yellow Pigmentation Genes in Brassica rapa ssp. pekinensis Using Br300 Microarray

    PubMed Central

    Jung, Hee-Jeong; Manoharan, Ranjith Kumar; Park, Jong-In; Chung, Mi-Young; Lee, Jeongyeo; Lim, Yong-Pyo; Hur, Yoonkang; Nou, Ill-Sup

    2014-01-01

    The yellow color of inner leaves in Chinese cabbage depends on its lutein and carotene content. To identify responsible genes for yellow pigmentation in leaves, the transcriptome profiles of white (Kenshin) and yellow leaves (Wheessen) were examined using the Br300K oligomeric chip in Chinese cabbage. In yellow leaves, genes involved in carotene synthesis (BrPSY, BrPDS, BrCRTISO, and BrLCYE), lutein, and zeaxanthin synthesis (BrCYP97A3 and BrHYDB) were upregulated, while those associated with carotene degradation (BrNCED3, BrNCED4, and BrNCED6) were downregulated. These expression patterns might support that the content of both lutein and total carotenoid was much higher in the yellow leaves than that in the white leaves. These results indicate that the yellow leaves accumulate high levels of both lutein and β-carotene due to stimulation of synthesis and that the degradation rate is inhibited. A large number of responsible genes as novel genes were specifically expressed in yellow inner leaves, suggesting the possible involvement in pigment synthesis. Finally, we identified three transcription factors (BrA20/AN1-like, BrBIM1, and BrZFP8) that are specifically expressed and confirmed their relatedness in carotenoid synthesis from Arabidopsis plants. PMID:25629030

  17. Molecular characterization and transcriptome analysis of orange head Chinese cabbage (brassica rapa L. ssp.pekinensis)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Orange head leaves are a desirable quality trait for Chinese cabbage. Our previous fine mapping identified BrCRTISO as the Br-or candidate gene for the orange Chinese cabbage mutant. Here we examined the BrCRTISO gene from white and orange head Chinese cabbage. While BrCRTISO from the white control ...

  18. Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus.

    PubMed

    Shen, Enhui; Zou, Jun; Hubertus Behrens, Falk; Chen, Li; Ye, Chuyu; Dai, Shutao; Li, Ruiyan; Ni, Meng; Jiang, Xiaoxue; Qiu, Jie; Liu, Yang; Wang, Weidi; Zhu, Qian-Hao; Chalhoub, Boulos; Bancroft, Ian; Meng, Jinling; Cai, Daguang; Fan, Longjiang

    2015-12-01

    The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors' genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of B. napus MIRNAs. PMID:26357884

  19. Tuning growth cycles of Brassica crops via natural antisense transcripts of BrFLC.

    PubMed

    Li, Xiaorong; Zhang, Shaofeng; Bai, Jinjuan; He, Yuke

    2016-03-01

    Several oilseed and vegetable crops of Brassica are biennials that require a prolonged winter cold for flowering, a process called vernalization. FLOWERING LOCUS C (FLC) is a central repressor of flowering. Here, we report that the overexpression of natural antisense transcripts (NATs) of Brassica rapa FLC (BrFLC) greatly shortens plant growth cycles. In rapid-, medium- and slow-cycling crop types, there are four copies of the BrFLC genes, which show extensive variation in sequences and expression levels. In Bre, a biennial crop type that requires vernalization, five NATs derived from the BrFLC2 locus are rapidly induced under cold conditions, while all four BrFLC genes are gradually down-regulated. The transgenic Bre lines overexpressing a long NAT of BrFLC2 do not require vernalization, resulting in a gradient of shortened growth cycles. Among them, a subset of lines both flower and set seeds as early as Yellow sarson, an annual crop type in which all four BrFLC genes have non-sense mutations and are nonfunctional in flowering repression. Our results demonstrate that the growth cycles of biennial crops of Brassica can be altered by changing the expression levels of BrFLC2 NATs. Thus, BrFLC2 NATs and their transgenic lines are useful for the genetic manipulation of crop growth cycles. PMID:26250982

  20. Identification, evolution, and expression partitioning of miRNAs in allopolyploid Brassica napus

    PubMed Central

    Shen, Enhui; Zou, Jun; Hubertus Behrens, Falk; Chen, Li; Ye, Chuyu; Dai, Shutao; Li, Ruiyan; Ni, Meng; Jiang, Xiaoxue; Qiu, Jie; Liu, Yang; Wang, Weidi; Zhu, Qian-Hao; Chalhoub, Boulos; Bancroft, Ian; Meng, Jinling; Cai, Daguang; Fan, Longjiang

    2015-01-01

    The recently published genome of Brassica napus offers for the first time the opportunity to gain insights into the genomic organization and the evolution of miRNAs in oilseed rape. In this study, 12 small RNA libraries from two B. napus cultivars (Tapidor and Ningyou7) and their four double-haploid lines were sequenced, employing the newly sequenced B. napus genome, together with genomes of its progenitors Brassica rapa and Brassica oleracea. A total of 645 miRNAs including 280 conserved and 365 novel miRNAs were identified. Comparative analysis revealed a high level of genomic conservation of MIRNAs (75.9%) between the subgenomes of B. napus and its two progenitors’ genomes, and MIRNA lost/gain events (133) occurred in B. napus after its speciation. Furthermore, significant partitioning of miRNA expressions between the two subgenomes in B. napus was detected. The data of degradome sequencing, miRNA-mediated cleavage, and expression analyses support specific interactions between miRNAs and their targets in the modulation of diverse physiological processes in roots and leaves, as well as in biosynthesis of, for example, glucosinolates and lipids in oilseed rape. These data provide a first genome-wide view on the origin, evolution, and genomic organization of B. napus MIRNAs. PMID:26357884

  1. The Gastropod Menace: Slugs on Brassica Plants Affect Caterpillar Survival through Consumption and Interference with Parasitoid Attraction.

    PubMed

    Desurmont, Gaylord A; Zemanova, Miriam A; Turlings, Ted C J

    2016-03-01

    Terrestrial molluscs and insect herbivores play a major role as plant consumers in a number of ecosystems, but their direct and indirect interactions have hardly been explored. The omnivorous nature of slugs makes them potential disrupters of predator-prey relationships, as a direct threat to small insects and through indirect, plant-mediated effects. Here, we examined the effects of the presence of two species of slugs, Arion rufus (native) and A. vulgaris (invasive) on the survivorship of young Pieris brassicae caterpillars when feeding on Brassica rapa plants, and on plant attractiveness to the main natural enemy of P. brassicae, the parasitoid Cotesia glomerata. In two separate predation experiments, caterpillar mortality was significantly higher on plants co-infested with A. rufus or A. vulgaris. Moreover, caterpillar mortality correlated positively with slug mass and leaf consumption by A. vulgaris. At the third trophic level, plants infested with slugs and plants co-infested with slugs and caterpillars were far less attractive to parasitoids than plants damaged by caterpillars only, independently of slug species. Chemical analyses confirmed that volatile emissions, which provide foraging cues for parasitoids, were strongly reduced in co-infested plants. Our study shows that the presence of slugs has the potential to affect insect populations, directly via consumptive effects, and indirectly via changes in plant volatiles that result in a reduced attraction of natural enemies. The fitness cost for P. brassicae imposed by increased mortality in presence of slugs may be counterbalanced by the benefit of escaping its parasitoids. PMID:27002323

  2. Sub-lethal glyphosate exposure alters flowering phenology and causes transient male-sterility in Brassica spp

    PubMed Central

    2014-01-01

    Background Herbicide resistance in weedy plant populations can develop through different mechanisms such as gene flow of herbicide resistance transgenes from crop species into compatible weedy species or by natural evolution of herbicide resistance or tolerance following selection pressure. Results from our previous studies suggest that sub-lethal levels of the herbicide glyphosate can alter the pattern of gene flow between glyphosate resistant Canola®, Brassica napus, and glyphosate sensitive varieties of B. napus and B. rapa. The objectives of this study were to examine the phenological and developmental changes that occur in Brassica crop and weed species following sub-lethal doses of the herbicides glyphosate and glufosinate. We examined several vegetative and reproductive traits of potted plants under greenhouse conditions, treated with sub-lethal herbicide sprays. Results Our results indicate that exposure of Brassica spp. to a sub-lethal dose of glyphosate results in altering flowering phenology and reproductive function. Flowering of all sensitive species was significantly delayed and reproductive function, specifically male fertility, was suppressed. Higher dosage levels typically contributed to an increase in the magnitude of phenotypic changes. Conclusions These results demonstrate that Brassica spp. plants that are exposed to sub-lethal doses of glyphosate could be subject to very different pollination patterns and an altered pattern of gene flow that would result from changes in the overlap of flowering phenology between species. Implications include the potential for increased glyphosate resistance evolution and spread in weedy communities exposed to sub-lethal glyphosate. PMID:24655547

  3. Cloning of TTG1 gene and PCR identification of genomes A, B and C in Brassica species.

    PubMed

    Yan, Mingli; Liu, Xianjun; Guan, Chunyun; Liu, Lili; Xiang, Jianhua; Lu, Ying; Liu, Zhongsong

    2014-04-01

    Arabidopsis Transparent Testa Glabra 1 (TTG1) genes were cloned from three diploid Brassica species (B. rapa, B. nigra and B. oleracea) and two amphidiploids species (B. juncea and B. carinata) by homology cloning. TTG1 homologues identified in all the accessions of the investigated species had a coding sequence of 1,014 bp. One copy was obtained from each diploid species and two copies from each amphidiploid species. Combined analysis of the TTG1 sequences cloned in this study with those obtained from public databases demonstrated that three, forty-five and seven nucleotides were specific variations in TTG1 genes from genomes A, B and C, respectively. Primers designed with genome-specific nucleotide variations were able to distinguish among TTG1 genes originating from genomes A, B and C in Brassica. Therefore, the TTG1 gene could serve as a candidate marker gene to detect the pollen flow of Brassica and provide an alternative method for the detection of pollen drift and risk assessment of gene flow in Brassica species. PMID:24752509

  4. Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.).

    PubMed

    Lee, Jonghoon; Izzah, Nur Kholilatul; Choi, Beom-Soon; Joh, Ho Jun; Lee, Sang-Choon; Perumal, Sampath; Seo, Joodeok; Ahn, Kyounggu; Jo, Eun Ju; Choi, Gyung Ja; Nou, Ill-Sup; Yu, Yeisoo; Yang, Tae-Jin

    2016-02-01

    Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops. Many clubroot resistance genes and markers are available in Brassica rapa but less is known in Brassica oleracea. Here, we applied the genotyping-by-sequencing (GBS) technique to construct a high-resolution genetic map and identify clubroot resistance (CR) genes. A total of 43,821 SNPs were identified using GBS data for two parental lines, one resistant and one susceptible lines to clubroot, and 18,187 of them showed >5× coverage in the GBS data. Among those, 4,103 were credibly genotyped for all 78 F2 individual plants. These markers were clustered into nine linkage groups spanning 879.9 cM with an average interval of 1.15 cM. Quantitative trait loci (QTLs) survey based on three rounds of clubroot resistance tests using F2 : 3 progenies revealed two and single major QTLs for Race 2 and Race 9 of P. brassicae, respectively. The QTLs show similar locations to the previously reported CR loci for Race 4 in B. oleracea but are in different positions from any of the CR loci found in B. rapa. We utilized two reference genome sequences in this study. The high-resolution genetic map developed herein allowed us to reposition 37 and 2 misanchored scaffolds in the 02-12 and TO1000DH genome sequences, respectively. Our data also support additional positioning of two unanchored 3.3 Mb scaffolds into the 02-12 genome sequence. PMID:26622061

  5. Genetical and Comparative Genomics of Brassica under Altered Ca Supply Identifies Arabidopsis Ca-Transporter Orthologs[W][OPEN

    PubMed Central

    Graham, Neil S.; Hammond, John P.; Lysenko, Artem; Mayes, Sean; Ó Lochlainn, Seosamh; Blasco, Bego; Bowen, Helen C.; Rawlings, Chris J.; Rios, Juan J.; Welham, Susan; Carion, Pierre W.C.; Dupuy, Lionel X.; King, Graham J.; White, Philip J.; Broadley, Martin R.

    2014-01-01

    Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca2+ transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca2+ transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization. PMID:25082855

  6. Nutritional and Flavor Components of Brassica Xapa L. Grown on ISS

    NASA Technical Reports Server (NTRS)

    Musgrave, M. E.; Kuang, A.; Blasiak, J.; Tuominen, L. K.; Levine, L. H.; Morrow, R. C.

    2005-01-01

    Brassica rapa L. cv. 'Astroplants' were grown on the International Space Station during April - June 2002 in the Biomass Production System. Plants were manually pollinated and were maturing seeds when they were harvested for preservation in flight by fixation or freezing. Overall growth and development were comparable between flight and ground control plants. Chlorophyll and carbohydrate content of the leaves were the same in the two treatments. Although comparable numbers of seeds were produced inside the seed pods, the developing seeds from the spaceflight treatment had only half of the dry weight of the ground controls and had altered storage components. Glucosinolate content of the stem tissue was also determined. The concentration of 3-butenyl-glucosinolate was on average 75% greater in the spaceflight samples than in the ground control. The results demonstrate how the spaceflight environment influences nutritional and flavor characteristics of a potential crop for use in a Biological Life Support System.

  7. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.

    PubMed

    Chalhoub, Boulos; Denoeud, France; Liu, Shengyi; Parkin, Isobel A P; Tang, Haibao; Wang, Xiyin; Chiquet, Julien; Belcram, Harry; Tong, Chaobo; Samans, Birgit; Corréa, Margot; Da Silva, Corinne; Just, Jérémy; Falentin, Cyril; Koh, Chu Shin; Le Clainche, Isabelle; Bernard, Maria; Bento, Pascal; Noel, Benjamin; Labadie, Karine; Alberti, Adriana; Charles, Mathieu; Arnaud, Dominique; Guo, Hui; Daviaud, Christian; Alamery, Salman; Jabbari, Kamel; Zhao, Meixia; Edger, Patrick P; Chelaifa, Houda; Tack, David; Lassalle, Gilles; Mestiri, Imen; Schnel, Nicolas; Le Paslier, Marie-Christine; Fan, Guangyi; Renault, Victor; Bayer, Philippe E; Golicz, Agnieszka A; Manoli, Sahana; Lee, Tae-Ho; Thi, Vinh Ha Dinh; Chalabi, Smahane; Hu, Qiong; Fan, Chuchuan; Tollenaere, Reece; Lu, Yunhai; Battail, Christophe; Shen, Jinxiong; Sidebottom, Christine H D; Wang, Xinfa; Canaguier, Aurélie; Chauveau, Aurélie; Bérard, Aurélie; Deniot, Gwenaëlle; Guan, Mei; Liu, Zhongsong; Sun, Fengming; Lim, Yong Pyo; Lyons, Eric; Town, Christopher D; Bancroft, Ian; Wang, Xiaowu; Meng, Jinling; Ma, Jianxin; Pires, J Chris; King, Graham J; Brunel, Dominique; Delourme, Régine; Renard, Michel; Aury, Jean-Marc; Adams, Keith L; Batley, Jacqueline; Snowdon, Rod J; Tost, Jorg; Edwards, David; Zhou, Yongming; Hua, Wei; Sharpe, Andrew G; Paterson, Andrew H; Guan, Chunyun; Wincker, Patrick

    2014-08-22

    Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement. PMID:25146293

  8. Mapping loci controlling flowering time in Brassica oleracea.

    PubMed

    Camargo, L E; Osborn, T C

    1996-04-01

    The timing of the transition from vegetative to reproductive phase is a major determinant of the morphology and value of Brassica oleracea crops. Quantitative trait loci (QTLs) controlling flowering time in B. oleracea were mapped using restriction fragment length polymorphism (RFLP) loci and flowering data of F3 families derived from a cabbage by broccoli cross. Plants were grown in the field, and a total of 15 surveys were made throughout the experiment at 5-15 day intervals, in which plants were inspected for the presence of flower buds or open flowers. The flowering traits used for data analysis were the proportion of annual plants (PF) within each F3 family at the end of the experiment, and a flowering-time index (FT) that combined both qualitative (annual/biennial) and quantitative (days to flowering) information. Two QTLs on different linkage groups were found associated with both PF and FT and one additional QTL was found associated only with FT. When combined in a multi-locus model, all three QTLs explained 54.1% of the phenotypic variation in FT. Epistasis was found between two genomic regions associated with FT. Comparisons of map positions of QTLs in B. oleracea with those in B. napus and B. rapa provided no evidence for conservation of genomic regions associated with flowering time between these species. PMID:24166330

  9. Radiation effects on Brassica seeds and seedlings

    NASA Astrophysics Data System (ADS)

    Deoli, Naresh; Hasenstein, Karl H.

    2016-07-01

    Space radiation consists of high energy charged particles and affects biological systems, but because of its stochastic, non-directional nature is difficult to replicate on Earth. Radiation damages biological systems acutely at high doses or cumulatively at low doses through progressive changes in DNA organization. These damages lead to death or cause of mutations. While radiation biology typically focuses on mammalian or human systems, little is known as to how radiation affects plants. In addition, energetic ion beams are widely used to generate new mutants in plants considering their high-LET (Linear Energy Transfer) as compared to gamma rays and X-rays. Understanding the effect of ionizing radiation on plant provides a basis for studying effects of radiation on biological systems and will help mitigate (space) radiation damage in plants. We exposed dry and imbibed Brassica rapa seeds and seedling roots to proton beams of varying qualities and compared the theoretical penetration range of different energy levels with observable growth response. We used 1, 2 and 3 MeV protons in air at the varying fluences to investigate the effect of direct irradiation on the seeds (1012 - 1015 ions/cm2) and seedlings (1013 ions/cm2). The range of protons in the tissue was calculated using Monte-Carlo based SRIM (Stopping and Range of Ions in Matter) software. The simulation and biological results indicate that ions did not penetrate the tissue of dry or hydrated seeds at all used ion energies. Therefore the entire energy was transferred to the treated tissue. Irradiated seeds were germinated vertically under dim light and roots growth was observed for two days after imbibition. The LD50 of the germination was about 2×1014 ions/cm2 and about 5×1014 ions/cm2 for imbibed and dry seeds, respectively. Since seedlings are most sensitive to gravity, the change in gravitropic behavior is a convenient means to assess radiation damage on physiological responses other than direct tissue

  10. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids.

    PubMed

    Lukens, Lewis N; Pires, J Chris; Leon, Enrique; Vogelzang, Robert; Oslach, Lynne; Osborn, Thomas

    2006-01-01

    Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm, which may involve programmed genetic and epigenetic changes during the initial generations following genome fusion. To study the dynamics of genome change, we synthesized 49 isogenic Brassica napus allopolyploids and surveyed them with 76 restriction fragment length polymorphism (RFLP) probes and 30 simple sequence repeat (SSR) primer pairs. Here, we report on the types and distribution of genetic and epigenetic changes within the S(1) genotypes. We found that insertion/deletion (indel) events were rare, but not random. Of the 57,710 (54,383 RFLP and 3,327 SSR) parental fragments expected among the amphidiploids, we observed 56,676 or 99.9%. Three loci derived from Brassica rapa had indels, and one indel occurred repeatedly across 29% (14/49) of the lines. Loss of one parental fragment was due to the 400-bp reduction of a guanine-adenine dinucleotide repeat-rich sequence. In contrast to the 4% (3/76) RFLP probes that detected indels, 48% (35/73) detected changes in the CpG methylation status between parental genomes and the S1 lines. Some loci were far more likely than others to undergo epigenetic change, but the number of methylation changes within each synthetic polyploid was remarkably similar to others. Clear de novo methylation occurred at a much higher frequency than de novo demethylation within allopolyploid sequences derived from B. rapa. Our results suggest that there is little genetic change in the S(0) generation of resynthesized B. napus polyploids. In contrast, DNA methylation was altered extensively in a pattern that indicates tight regulation of epigenetic changes. PMID:16377753

  11. Evolution of mustard (Brassica juncea Coss) subspecies in China: evidence from the chalcone synthase gene.

    PubMed

    Chen, F B; Liu, H F; Yao, Q L; Fang, P

    2016-01-01

    To explore the phylogenetic relationship, genome donor, and evolutionary history of the polyploid mustard (Brassica juncea) from China, eighty-one sequences of the chalcone synthase gene (Chs) were analyzed in 43 individuals, including 34 B. juncea, 2 B. rapa, 1 B. nigra, 2 B. oleracea, 1 B. napus, 1 B. carinata, and 2 Raphanus sativus. A maximum likelihood analysis showed that sequences from B. juncea were separated into two well-supported groups in accordance with the A and B genomes, whereas the traditional phenotypic classification of B. juncea was not wholly supported by the molecular results. The SplitsTree analysis recognized four distinct groups of Brassicaceae, and the median-joining network analysis recognized four distinct haplotypes of Chs. The estimates of Tajima's D, Fu and Li's D, and Fu and Li's F statistic for the Chs gene in the B genome were negative, while those in the A genome were significant. The results indicated that 1) the Chs sequences revealed a high level of sequence variation in Chinese mustard, 2) both tree and reticulate evolutions existed, and artificial selection played an important role in the evolution of Chinese mustard, 3) the original parental species of Chinese mustard are B. rapa var. sinapis arvensis and B. nigra (derived from China), 4) nucleotide variation in the B genome was higher than that in the A genome, and 5) cultivated mustard evolved from wild mustard, and China is one of the primary origins of B. juncea. PMID:27173323

  12. Role of Relative Humidity in Processing and Storage of Seeds and Assessment of Variability in Storage Behaviour in Brassica spp. and Eruca sativa

    PubMed Central

    Suma, A.; Sreenivasan, Kalyani; Singh, A. K.; Radhamani, J.

    2013-01-01

    The role of relative humidity (RH) while processing and storing seeds of Brassica spp. and Eruca sativa was investigated by creating different levels of relative humidity, namely, 75%, 50%, 32%, and 11% using different saturated salt solutions and 1% RH using concentrated sulphuric acid. The variability in seed storage behaviour of different species of Brassica was also evaluated. The samples were stored at 40 ± 2°C in sealed containers and various physiological parameters were assessed at different intervals up to three months. The seed viability and seedling vigour parameters were considerably reduced in all accessions at high relative humidity irrespective of the species. Storage at intermediate relative humidities caused minimal decline in viability. All the accessions performed better at relative humidity level of 32% maintaining seed moisture content of 3%. On analyzing the variability in storage behaviour, B. rapa and B. juncea were better performers than B. napus and Eruca sativa. PMID:24489504

  13. Identification of a novel MLPK homologous gene MLPKn1 and its expression analysis in Brassica oleracea.

    PubMed

    Gao, Qiguo; Shi, Songmei; Liu, Yudong; Pu, Quanming; Liu, Xiaohuan; Zhang, Ying; Zhu, Liquan

    2016-09-01

    M locus protein kinase, one of the SRK-interacting proteins, is a necessary positive regulator for the self-incompatibility response in Brassica. In B. rapa, MLPK is expressed as two different transcripts, MLPKf1 and MLPKf2, and either isoform can complement the mlpk/mlpk mutation. The AtAPK1B gene has been considered to be the ortholog of BrMLPK, and AtAPK1B has no role in self-incompatibility (SI) response in A. thaliana SRK-SCR plants. Until now, what causes the MLPK and APK1B function difference during SI response in Brassica and A. thaliana SRKb-SCRb plants has remained unknown. Here, in addition to the reported MLPKf1/2, we identified the new MLPKf1 homologous gene MLPKn1 from B. oleracea. BoMLPKn1 and BoMLPKf1 shared nucleotide sequence identity as high as 84.3 %, and the most striking difference consisted in two fragment insertions in BoMLPKn1. BoMLPKn1 and BoMLPKf1 had a similar gene structure; both their deduced amino acid sequences contained a typical plant myristoylation consensus sequence and a Ser/Thr protein kinase domain. BoMLPKn1 was widely expressed in petal, sepal, anther, stigma and leaf. Genome-wide survey revealed that the B. oleracea genome contained three MLPK homologous genes: BoMLPKf1/2, BoMLPKn1 and Bol008343n. The B. rapa genome also contained three MLPK homologous genes, BrMLPKf1/2, BraMLPKn1 and Bra040929. Phylogenetic analysis revealed that BoMLPKf1/2 and BrMLPKf1/2 were phylogenetically more distant from AtAPK1A than Bol008343n, Bra040929, BraMLPKn1 and BoMLPKn1, Synteny analysis revealed that the B. oleracea chromosomal region containing BoMLPKn1 displayed high synteny with the A. thaliana chromosomal region containing APK1B, whereas the B. rapa chromosomal region containing BraMLPKn1 showed high synteny with the A. thaliana chromosomal region containing APK1B. Together, these results revealed that BoMLPKn1/BraMLPKn1, and not the formerly reported BoMLPKf1/2 (BrMLPKf1/2), was the orthologous genes of AtAPK1B, and no ortholog of Bo

  14. Genes encoding the alpha-carboxyltransferase subunit of acetyl-CoA carboxylase from Brassica napus and parental species: cloning, expression patterns, and evolution.

    PubMed

    Li, Zhi-Guo; Yin, Wei-Bo; Guo, Huan; Song, Li-Ying; Chen, Yu-Hong; Guan, Rong-Zhan; Wang, Jing-Qiao; Wang, Richard R-C; Hu, Zan-Min

    2010-05-01

    Heteromeric acetyl coenzyme A carboxylase (ACCase), a rate-limiting enzyme in fatty acid biosynthesis in dicots, is a multi-enzyme complex consisting of biotin carboxylase, biotin carboxyl carrier protein, and carboxyltransferase (alpha-CT and beta-CT). In the present study, four genes encoding alpha-CT were cloned from Brassica napus, and two were cloned from each of the two parental species, B. rapa and B. oleracea. Comparative and cluster analyses indicated that these genes were divided into two major groups. The major divergence between group-1 and group-2 occurred in the second intron. Group-2 alpha-CT genes represented the ancestral form in the genus Brassica. The divergence of group-1 and group-2 genes occurred in their common ancestor 12.96-17.78 million years ago (MYA), soon after the divergence of Arabidopsis thaliana and Brassica (15-20 MYA). This time of divergence is identical to that reported for the paralogous subgenomes of diploid Brassica species (13-17 MYA). Real-time reverse transcription PCR revealed that the expression patterns of the two groups of genes were similar in different organs, except in leaves. To better understand the regulation and evolution of alpha-CT genes, promoter regions from two sets of orthologous gene copies from B. napus, B. rapa, and B. oleracea were cloned and compared. The function of the promoter of gene Bnalpha-CT-1-1 in group-1 and gene Bnalpha-CT-2-1 in group-2 was examined by assaying beta-glucuronidase activity in transgenic A. thaliana. Our results will be helpful in elucidating the evolution and regulation of ACCase in oilseed rape. PMID:20616867

  15. Transcriptome Analysis of Canola (Brassica napus) under Salt Stress at the Germination Stage

    PubMed Central

    Long, Weihua; Zou, Xiling; Zhang, Xuekun

    2015-01-01

    Canola (Brassica napus) is one of the most important oil crops in the world. However, its yield has been constrained by salt stress. In this study, transcriptome profiles were explored using Digital Gene Expression (DGE) at 0, 3, 12 and 24 hours after H2O (control) and NaCl treatments on B. napus roots at the germination stage. Comparisons of gene-expression between the control and the treatment were conducted after tag-mapping to the sequenced Brassica rapa genome. The differentially expressed genes during the time course of salt stress were focused on, and 163 genes were identified to be differentially expressed at all the time points. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of the genes were involved in proline metabolism, inositol metabolism, carbohydrate metabolic processes and oxidation-reduction processes and may play vital roles in the salt-stress response at the germination stage. Thus, this study provides new candidate salt stress responding genes, which may function in novel putative nodes in the molecular pathways of salt stress resistance. PMID:25679513

  16. Inheritance of Race-Specific Resistance to Xanthomonas campestris pv. campestris in Brassica Genomes.

    PubMed

    Vicente, J G; Taylor, J D; Sharpe, A G; Parkin, I A P; Lydiate, D J; King, G J

    2002-10-01

    ABSTRACT The inheritance of resistance to three Xanthomonas campestris pv. campestris races was studied in crosses between resistant and susceptible lines of Brassica oleracea (C genome), B. carinata (BC genome), and B. napus (AC genome). Resistance to race 3 in the B. oleracea doubled haploid line BOH 85c and in PI 436606 was controlled by a single dominant locus (Xca3). Resistance to races 1 and 3 in the B. oleracea line Badger Inbred-16 was quantitative and recessive. Strong resistance to races 1 and 4 was controlled by a single dominant locus (Xca1) in the B. carinata line PI 199947. This resistance probably originates from the B genome. Resistance to race 4 in three B. napus lines, cv. Cobra, the rapid cycling line CrGC5, and the doubled haploid line N-o-1, was controlled by a single dominant locus (Xca4). A set of doubled haploid lines, selected from a population used previously to develop a restriction fragment length polymorphism map, was used to map this locus. Xca4 was positioned on linkage group N5 of the B. napus A genome, indicating that this resistance originated from B. rapa. Xca4 is the first major locus to be mapped that controls race-specific resistance to X. campestris pv. campestris in Brassica spp. PMID:18944224

  17. Characterization of Brassica nigra collections using simple sequence repeat markers reveals distinct groups associated with geographical location, and frequent mislabelling of species identity.

    PubMed

    Pradhan, Aneeta; Nelson, Matthew N; Plummer, Julie A; Cowling, Wallace A; Yan, Guijun

    2011-01-01

    Genetic diversity of 180 Brassica nigra (L.) Kochgenotypes from 60 different accessions was evaluated using 15 simple sequence repeat markers with known locations on the Brassica A, B, and C genomes. Two lines each from Brassica juncea (L.) Czern and Brassica carinata Braunwere also included as comparator species. A total of 218 high quality alleles were used to generate a genetic distance matrix, and clustering and multidimensional scaling analyses were used to investigate genetic relationships among the accessions. Accessions from the same country of origin tended to cluster together. Surprisingly, 13 accessions declared to be B. nigra had A- and B-genome alleles and morphology consistent with them being B. juncea, which was supported by their positioning near B. juncea in the cluster analysis. Two B. nigra accessions possessed alleles associated more closely with the A genome than the B genome, and these may be Brassica rapa L. accessions. One B. nigra accession had B- and C-genome alleles and morphology consistent with it being B. carinata. The remaining 44 accessions (73%) appeared to be truly B. nigra and formed morphologically and genetically distinct groups associated with country or region of origin, notably Ethiopia, Israel, India, and Europe. Most B. nigra accessions were highly heterozygous, consistent with their obligate outcrossing habit. This study demonstrated the value of using molecular markers with known genome locations (in this case, in the Brassica A, B, and C genomes) to confirm species identity in families such as Brassicaceae where species identification based solely on morphological characters is difficult. PMID:21217806

  18. Possibilities of direct introgression from Brassica napus to B. juncea and indirect introgression from B. napus to related Brassicaceae through B. juncea

    PubMed Central

    Tsuda, Mai; Ohsawa, Ryo; Tabei, Yutaka

    2014-01-01

    The impact of genetically modified canola (Brassica napus) on biodiversity has been examined since its initial stage of commercialization. Various research groups have extensively investigated crossability and introgression among species of Brassicaceae. B. rapa and B. juncea are ranked first and second as the recipients of cross-pollination and introgression from B. napus, respectively. Crossability between B. napus and B. rapa has been examined, specifically in terms of introgression from B. napus to B. rapa, which is mainly considered a weed in America and European countries. On the other hand, knowledge on introgression from B. napus to B. juncea is insufficient, although B. juncea is recognized as the main Brassicaceae weed species in Asia. It is therefore essential to gather information regarding the direct introgression of B. napus into B. juncea and indirect introgression of B. napus into other species of Brassicaceae through B. juncea to evaluate the influence of genetically modified canola on biodiversity. We review information on crossability and introgression between B. juncea and other related Brassicaseae in this report. PMID:24987292

  19. Possibilities of direct introgression from Brassica napus to B. juncea and indirect introgression from B. napus to related Brassicaceae through B. juncea.

    PubMed

    Tsuda, Mai; Ohsawa, Ryo; Tabei, Yutaka

    2014-05-01

    The impact of genetically modified canola (Brassica napus) on biodiversity has been examined since its initial stage of commercialization. Various research groups have extensively investigated crossability and introgression among species of Brassicaceae. B. rapa and B. juncea are ranked first and second as the recipients of cross-pollination and introgression from B. napus, respectively. Crossability between B. napus and B. rapa has been examined, specifically in terms of introgression from B. napus to B. rapa, which is mainly considered a weed in America and European countries. On the other hand, knowledge on introgression from B. napus to B. juncea is insufficient, although B. juncea is recognized as the main Brassicaceae weed species in Asia. It is therefore essential to gather information regarding the direct introgression of B. napus into B. juncea and indirect introgression of B. napus into other species of Brassicaceae through B. juncea to evaluate the influence of genetically modified canola on biodiversity. We review information on crossability and introgression between B. juncea and other related Brassicaseae in this report. PMID:24987292

  20. Silencing defense pathways in Arabidopsis by heterologous gene sequences from Brassica oleracea enhances the performance of a specialist and a generalist herbivorous insect.

    PubMed

    Zheng, Si-Jun; Zhang, Peng-Jun; van Loon, Joop J A; Dicke, Marcel

    2011-08-01

    The jasmonic acid (JA) signaling pathway and defensive secondary metabolites such as glucosinolates are generally considered to play central roles in the defense of brassicaceous plants against herbivorous insects. To determine the function of specific plant genes in plant-insect interactions, signaling or biosynthetic mutants are needed. However, mutants are not yet available for brassicaceous plants other than Arabidopsis thaliana, e.g., cabbage (Brassica oleracea). We employed virus-induced gene silencing (VIGS) by using tobacco rattle virus (TRV) to knock down the endogenous expression of lipoxygenase (LOX), an upstream enzyme of the JA pathway and thioglucoside glucohydrolase: myrosinase (TGG1/TGG2), a hydrolytic enzyme that catalyzes the release of defensive volatile products originating from glucosinolates, in Arabidopsis thaliana. This was done by using the heterologous gene sequences from B. oleracea. Silencing these genes in A. thaliana plants is efficient and specific. Only 18 nucleotides with 100% identity between the trigger (BoMYR) and the target (AtTGG1/2) sequence are sufficient to achieve gene silencing. LOX-silenced plants showed significantly reduced AtLOX2 transcript accumulation after Pieris rapae larval feeding. TGG-silenced plants exhibited significantly lower TGG1/TGG2 transcript levels only after shorter larval feeding. The inhibition of TGG1/TGG2 transcript accumulation via gene silencing may be overruled by longer larval feeding. Specialist P. rapae larvae developed significantly better on both types of silenced plants than on empty vector (EV) control plants, while generalist Mamestra brassicae larvae developed significantly better on the TGG1/TGG2 silenced plants than on EV control plants. This shows that not only the generalist herbivore but also the Brassicaceae-specialist P. rapae is negatively affected by the ability of brassicaceous plants to produce their specific secondary metabolites, i.e., glucosinolates. Our results

  1. Identification and expression analysis of chitinase genes related to biotic stress resistance in Brassica.

    PubMed

    Ahmed, Nasar Uddin; Park, Jong-In; Seo, Mi-Suk; Kumar, Thamilarasan Senthil; Lee, In-Ho; Park, Beom-Seok; Nou, Ill-Sup

    2012-04-01

    Brassica is a very important vegetable group because of its contribution to human nutrition and consequent economic benefits. However, biotic stress is a major concern for these crops and molecular biology techniques offer the most efficient of approaches to address this concern. Chitinase is an important biotic stress resistance-related gene. We identified three genes designated as Brassica chitinase like protein (BrCLP1), BrCLP2 and BrCLP3 from a full-length cDNA library of Brassica rapa cv. Osome. Sequence analysis of these genes confirmed that BrCLP1 was a class IV chitinase, and BrCLP2 and BrCLP3 were class VII chitinases. Also, these genes showed a high degree of homology with other biotic stress resistance-related plant chitinases. In expression analysis, organ-specific expression of all three genes was high except BrCLP1 in all the organs tested and BrCLP2 showed the highest expression compared to the other genes in flower buds. All these genes also showed expression during all developmental growth stages of Chinese cabbage. In addition, BrCLP1 was up-regulated with certain time of infection by Pectobacterium carotovorum subsp. carotovorum in Chinese cabbage plants during microarray expression analysis. On the other hand, expression of BrCLP2 and BrCLP3 were increased after 6 h post inoculation (hpi) but decreased from 12 hpi. All these data suggest that these three chitinase genes may be involved in plant resistance against biotic stresses. PMID:21720758

  2. Fine mapping of a male sterility gene MS-cd1 in Brassica oleracea.

    PubMed

    Zhang, Xinmei; Wu, Jian; Zhang, Hui; Ma, Yuan; Guo, Aiguang; Wang, Xiaowu

    2011-07-01

    A dominant male sterility (DGMS) line 79-399-3, developed from a spontaneous mutation in Brassica oleracea var. capitata, has been widely used in production of hybrid cultivars in China. In this line, male sterility is controlled by a dominant gene Ms-cd1. In the present study, fine mapping of Ms-cd1 was conducted by screening a segregating population Ms79-07 with 2,028 individuals developed by four times backcrossing using a male sterile Brassica oleracea var. italica line harboring Ms-cd1 as donor and Brassica oleracea var. alboglabra as the recipient. Bulked segregation analysis (BSA) was performed for the BC(4) population Ms79-07 using 26,417 SRAP primer SRAPs and 1,300 SSRs regarding of male sterility and fertility. A high-resolution map surrounding Ms-cd1 was constructed with 14 SRAPs and one SSR. The SSR marker 8C0909 was closely linked to the MS-cd1 gene with a distance of 2.06 cM. Fourteen SRAPs closely linked to the target gene were identified; the closest ones on each side were 0.18 cM and 2.16 cM from Ms-cd1. Three of these SRAPs were successfully converted to dominant SCAR markers with a distance to the Ms-cd1 gene of 0.18, 0.39 and 4.23 cM, respectively. BLAST analysis with these SCAR marker sequences identified a collinear genomic region about 600 kb in scaffold 000010 on chromosomeA10 in B. rapa and on chromosome 5 in A. thaliana. These results provide additional information for map-based cloning of the Ms-cd1 gene and will be helpful for marker-assisted selection (MAS). PMID:21538103

  3. Effect of temperature on cortical infection by Plasmodiophora brassicae and clubroot severity.

    PubMed

    Sharma, Kalpana; Gossen, Bruce D; McDonald, Mary Ruth

    2011-12-01

    A study was conducted to assess the effect of temperature on infection and development of Plasmodiophora brassicae in the root cortex of Shanghai pak choy (Brassica rapa subsp. chinensis) and on subsequent clubroot severity. Ten-day-old seedlings were grown individually, inoculated with resting spores, and maintained in growth cabinets at 10, 15, 20, 25, and 30?C. Seedlings were harvested at 2-day intervals, starting 8 days after inoculation (DAI) and continuing until 42 DAI. Roots were assessed at 4-day intervals for the incidence of cortical infection and stage of infection (young plasmodia, mature plasmodia, and resting spores), at 2-day intervals for symptom development and clubroot severity, and at 8-day intervals for the number of spores per gram of gall. Temperature affected every stage of clubroot development. Cortical infection was highest and symptoms were observed earliest at 25?C, intermediate at 20 and 30?C, and lowest and latest at 15?C. No cortical infection or symptoms were observed at 42 DAI in plants grown at 10?C. A substantial delay in the development of the pathogen was observed at 15?C. Resting spores were first observed at 38 DAI in plants at 15?C, 26 DAI at 20 and 30?C, and 22 DAI at 25?C. The yield of resting spores from galls was higher in galls that developed at 20 to 30?C than those that developed at 15?C over 42 days of assessment. These results support the observation in companion studies that cool temperatures result in slower development of clubroot symptoms in brassica crops, and demonstrate that the temperature has a consistent pattern of effect throughout the life cycle of the pathogen. PMID:21864086

  4. Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

    PubMed Central

    2014-01-01

    Background Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus. Results We generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event. Conclusions Differential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes. PMID:24916971

  5. The terrestrial Isopoda (Crustacea, Oniscidea) of Rapa Nui (Easter Island), with descriptions of two new species

    PubMed Central

    Taiti, Stefano; Wynne, J. Judson

    2015-01-01

    Abstract Nine species of terrestrial isopods are reported for the Polynesian island of Rapa Nui (Easter Island) based upon museum materials and recent collections from field sampling. Most of these animals are non-native species, but two are new to science: Styloniscus manuvaka sp. n. and Hawaiioscia rapui sp. n. Of these, the former is believed to be a Polynesian endemic as it has been recorded from Rapa Iti, Austral Islands, while the latter is identified as a Rapa Nui island endemic. Both of these new species are considered ‘disturbance relicts’ and appear restricted to the cave environment on Rapa Nui. A short key to all the oniscidean species presently recorded from Rapa Nui is provided. We also offered conservation and management recommendations for the two new isopod species. PMID:26261438

  6. The terrestrial Isopoda (Crustacea, Oniscidea) of Rapa Nui (Easter Island), with descriptions of two new species.

    PubMed

    Taiti, Stefano; Wynne, J Judson

    2015-01-01

    Nine species of terrestrial isopods are reported for the Polynesian island of Rapa Nui (Easter Island) based upon museum materials and recent collections from field sampling. Most of these animals are non-native species, but two are new to science: Styloniscusmanuvaka sp. n. and Hawaiiosciarapui sp. n. Of these, the former is believed to be a Polynesian endemic as it has been recorded from Rapa Iti, Austral Islands, while the latter is identified as a Rapa Nui island endemic. Both of these new species are considered 'disturbance relicts' and appear restricted to the cave environment on Rapa Nui. A short key to all the oniscidean species presently recorded from Rapa Nui is provided. We also offered conservation and management recommendations for the two new isopod species. PMID:26261438

  7. A mutant gene that increases gibberellin production in Brassica

    SciTech Connect

    Rood, S.B. ); Williams, P.H. ); Pearce, D.; Pharis, R.P. ); Murofushi, Noboru ); Mander, L.N. )

    1990-07-01

    A single gene mutant (elongated internode (ein/ein)) with accelerated shoot elongation was identified from a rapid cycling line of Brassica rapa. Relative to normal plants, mutant plants had slightly accelerated floral development, greater stem dry weights, and particularly, increased internode and inflorescence elongation. The application of the triazole plant growth retardant, paclobutrazol, inhibited shoot elongation, returning ein to a more normal phenotype. Conversely, exogenous gibberellin A{sub 3} (GA{sub 3}) can convert normal genotypes to a phenotype resembling ein. The content of endogenous GA{sub 1} and GA{sub 3} were estimated by gas chromatography-selected ion monitoring using ({sup 2}H)GA{sub 1} as a quantitative internal standard and at day 14 were 1.5- and 12.1-fold higher per stem, respectively, in ein than in normal plants, although GA concentrations were more similar. The endogenous levels of GA{sub 20} and GA{sub 1}, and the rate of GA{sub 19} metabolism were simultaneously analyzed. Levels of GA{sub 1} and GA{sub 20} were 4.6- and 12.9-fold higher, respectively, and conversions to GA{sub 20} and GA{sub 1} were 8.3 and 1.3 times faster in ein than normal plants. Confirming the enhanced rate of GA{sub 1} biosynthesis in ein, the conversion of ({sup 3}H)GA{sub 20} to ({sup 3}H) GA{sub 1} was also faster in ein than in the normal genotype. Thus, the ein allele results in accelerated GA{sub 1} biosynthesis and an elevated content of endogenous GAs, including the dihydroxylated GAs A{sub 1} and A{sub 3}.

  8. Heterosis as Investigated in Terms of Polyploidy and Genetic Diversity Using Designed Brassica juncea Amphiploid and Its Progenitor Diploid Species

    PubMed Central

    Bansal, Payal; Banga, Shashi; Banga, S. S.

    2012-01-01

    Fixed heterosis resulting from favorable interactions between the genes on their homoeologous genomes in an allopolyploid is considered analogous to classical heterosis accruing from interactions between homologous chromosomes in heterozygous plants of a diploid species. It has been hypothesized that fixed heterosis may be one of the causes of low classical heterosis in allopolyploids. We used Indian mustard (Brassica juncea, 2n = 36; AABB) as a model system to analyze this hypothesis due to ease of its resynthesis from its diploid progenitors, B. rapa (2n = 20; AA) and B. nigra (2n = 16; BB). Both forms of heterosis were investigated in terms of ploidy level, gene action and genetic diversity. To facilitate this, eleven B. juncea genotypes were resynthesized by hybridizing ten near inbred lines of B. rapa and nine of B. nigra. Three half diallel combinations involving resynthesized B. juncea (11×11) and the corresponding progenitor genotypes of B. rapa (10×10) and B. nigra (9×9) were evaluated. Genetic diversity was estimated based on DNA polymorphism generated by SSR primers. Heterosis and genetic diversity in parental diploid species appeared not to predict heterosis and genetic diversity at alloploid level. There was also no association between combining ability, genetic diversity and heterosis across ploidy. Though a large proportion (0.47) of combinations showed positive values, the average fixed heterosis was low for seed yield but high for biomass yield. The genetic diversity was a significant contributor to fixed heterosis for biomass yield, due possibly to adaptive advantage it may confer on de novo alloploids during evolution. Good general/specific combiners at diploid level did not necessarily produce good general/specific combiners at amphiploid level. It was also concluded that polyploidy impacts classical heterosis indirectly due to the negative association between fixed heterosis and classical heterosis. PMID:22363404

  9. Heterosis as investigated in terms of polyploidy and genetic diversity using designed Brassica juncea amphiploid and its progenitor diploid species.

    PubMed

    Bansal, Payal; Banga, Shashi; Banga, S S

    2012-01-01

    Fixed heterosis resulting from favorable interactions between the genes on their homoeologous genomes in an allopolyploid is considered analogous to classical heterosis accruing from interactions between homologous chromosomes in heterozygous plants of a diploid species. It has been hypothesized that fixed heterosis may be one of the causes of low classical heterosis in allopolyploids. We used Indian mustard (Brassica juncea, 2n = 36; AABB) as a model system to analyze this hypothesis due to ease of its resynthesis from its diploid progenitors, B. rapa (2n = 20; AA) and B. nigra (2n = 16; BB). Both forms of heterosis were investigated in terms of ploidy level, gene action and genetic diversity. To facilitate this, eleven B. juncea genotypes were resynthesized by hybridizing ten near inbred lines of B. rapa and nine of B. nigra. Three half diallel combinations involving resynthesized B. juncea (11×11) and the corresponding progenitor genotypes of B. rapa (10×10) and B. nigra (9×9) were evaluated. Genetic diversity was estimated based on DNA polymorphism generated by SSR primers. Heterosis and genetic diversity in parental diploid species appeared not to predict heterosis and genetic diversity at alloploid level. There was also no association between combining ability, genetic diversity and heterosis across ploidy. Though a large proportion (0.47) of combinations showed positive values, the average fixed heterosis was low for seed yield but high for biomass yield. The genetic diversity was a significant contributor to fixed heterosis for biomass yield, due possibly to adaptive advantage it may confer on de novo alloploids during evolution. Good general/specific combiners at diploid level did not necessarily produce good general/specific combiners at amphiploid level. It was also concluded that polyploidy impacts classical heterosis indirectly due to the negative association between fixed heterosis and classical heterosis. PMID:22363404

  10. Development of a population for substantial new type Brassica napus diversified at both A/C genomes.

    PubMed

    Xiao, Yong; Chen, Lunlin; Zou, Jun; Tian, Entang; Xia, Wei; Meng, Jinling

    2010-10-01

    Intersubgenomic heterosis in rapeseed has been revealed in previous studies by using traditional Brassica napus (A(n)A(n)C(n)C(n)) to cross partial new type B. napus with A(r)/C(c) introgression from the genomes of B. rapa and B. carinata, respectively. To further enlarge the genetic basis of B. napus and to facilitate a sustained heterosis breeding in rapeseed, it is crucial to create a population for substantial new type B. napus diversified at both A/C genomes. In this experiment, hundreds of artificial hexaploid plants (A(r)A(r)B(c)B(c)C(c)C(c)) involving hundreds of B. carinata/B. rapa combinations were first crossed with elite lines of partial new type B. napus. The pentaploid plants (AABCC) were open-pollinated in isolated conditions, and their offspring were successively self-pollinated and intensively selected for two generations. Thereafter, a population of substantial new type B. napus mainly with a genomic composition of A(r)A(r)C(c)C(c) harbouring genetic diversity from 25 original cultivars of B. rapa and 72 accessions of B. carinata was constructed. The population was cytologically verified to have the correct chromosome constitution of AACC and differed genetically from traditional B. napus, in terms of the genome components of A(r)/C(c) and B(c) as well as the novel genetic variations induced by the interspecific hybridisation process. Synchronously, rich phenotypic variation with plenty of novel valuable traits was observed in the population. The origin of the novel variations and the value of the population are discussed. PMID:20556596

  11. Patterns of Sequence Loss and Cytosine Methylation within a Population of Newly Resynthesized Brassica napus Allopolyploids1[W

    PubMed Central

    Lukens, Lewis N.; Pires, J. Chris; Leon, Enrique; Vogelzang, Robert; Oslach, Lynne; Osborn, Thomas

    2006-01-01

    Allopolyploid formation requires the adaptation of two nuclear genomes within a single cytoplasm, which may involve programmed genetic and epigenetic changes during the initial generations following genome fusion. To study the dynamics of genome change, we synthesized 49 isogenic Brassica napus allopolyploids and surveyed them with 76 restriction fragment length polymorphism (RFLP) probes and 30 simple sequence repeat (SSR) primer pairs. Here, we report on the types and distribution of genetic and epigenetic changes within the S1 genotypes. We found that insertion/deletion (indel) events were rare, but not random. Of the 57,710 (54,383 RFLP and 3,327 SSR) parental fragments expected among the amphidiploids, we observed 56,676 or 99.9%. Three loci derived from Brassica rapa had indels, and one indel occurred repeatedly across 29% (14/49) of the lines. Loss of one parental fragment was due to the 400-bp reduction of a guanine-adenine dinucleotide repeat-rich sequence. In contrast to the 4% (3/76) RFLP probes that detected indels, 48% (35/73) detected changes in the CpG methylation status between parental genomes and the S1 lines. Some loci were far more likely than others to undergo epigenetic change, but the number of methylation changes within each synthetic polyploid was remarkably similar to others. Clear de novo methylation occurred at a much higher frequency than de novo demethylation within allopolyploid sequences derived from B. rapa. Our results suggest that there is little genetic change in the S0 generation of resynthesized B. napus polyploids. In contrast, DNA methylation was altered extensively in a pattern that indicates tight regulation of epigenetic changes. PMID:16377753

  12. Long-term monitoring of feral genetically modified herbicide-tolerant Brassica napus populations around unloading Japanese ports

    PubMed Central

    Katsuta, Kensuke; Matsuo, Kazuhito; Yoshimura, Yasuyuki; Ohsawa, Ryo

    2015-01-01

    Genetically modified, herbicide-tolerant (GMHT) Brassica napus plants originating from seed spill have recently been found along roadsides leading from Japanese ports that unload oilseed rape. Such introductions have potential biodiversity effects (as defined by the Cartagena Protocol): these include replacement of native elements in the biota through competitive suppression or hybridization. We conducted surveys in the period 2006–2011 to assess such threats. We examined shifts in the population distribution and occurrence of GMHT plants in 1,029 volunteer introduced assemblages of B. napus, 1,169 of B. juncea, and 184 of B. rapa around 12 ports. GMHT B. napus was found around 10 of 12 ports, but its proportion in the populations varied greatly by year and location. Over the survey period, the distributions of a pure non-GMHT population around Tobata and a pure GMHT population around Hakata increased significantly. However, there was no common trend of population expansion or contraction around the 12 ports. Furthermore, we found no herbicide tolerant B. juncea and B. rapa plants derived from crosses with GMHT B. napus. Therefore, GMHT B. napus is not invading native vegetation surrounding its populations and not likely to cross with congeners in Japanese environment. PMID:26175624

  13. Long-term monitoring of feral genetically modified herbicide-tolerant Brassica napus populations around unloading Japanese ports.

    PubMed

    Katsuta, Kensuke; Matsuo, Kazuhito; Yoshimura, Yasuyuki; Ohsawa, Ryo

    2015-06-01

    Genetically modified, herbicide-tolerant (GMHT) Brassica napus plants originating from seed spill have recently been found along roadsides leading from Japanese ports that unload oilseed rape. Such introductions have potential biodiversity effects (as defined by the Cartagena Protocol): these include replacement of native elements in the biota through competitive suppression or hybridization. We conducted surveys in the period 2006-2011 to assess such threats. We examined shifts in the population distribution and occurrence of GMHT plants in 1,029 volunteer introduced assemblages of B. napus, 1,169 of B. juncea, and 184 of B. rapa around 12 ports. GMHT B. napus was found around 10 of 12 ports, but its proportion in the populations varied greatly by year and location. Over the survey period, the distributions of a pure non-GMHT population around Tobata and a pure GMHT population around Hakata increased significantly. However, there was no common trend of population expansion or contraction around the 12 ports. Furthermore, we found no herbicide tolerant B. juncea and B. rapa plants derived from crosses with GMHT B. napus. Therefore, GMHT B. napus is not invading native vegetation surrounding its populations and not likely to cross with congeners in Japanese environment. PMID:26175624

  14. Gene silencing of BnTT10 family genes causes retarded pigmentation and lignin reduction in the seed coat of Brassica napus.

    PubMed

    Zhang, Kai; Lu, Kun; Qu, Cunmin; Liang, Ying; Wang, Rui; Chai, Yourong; Li, Jiana

    2013-01-01

    Yellow-seed (i.e., yellow seed coat) is one of the most important agronomic traits of Brassica plants, which is correlated with seed oil and meal qualities. Previous studies on the Brassicaceae, including Arabidopsis and Brassica species, proposed that the seed-color trait is correlative to flavonoid and lignin biosynthesis, at the molecular level. In Arabidopsis thaliana, the oxidative polymerization of flavonoid and biosynthesis of lignin has been demonstrated to be catalyzed by laccase 15, a functional enzyme encoded by the AtTT10 gene. In this study, eight Brassica TT10 genes (three from B. napus, three from B. rapa and two from B. oleracea) were isolated and their roles in flavonoid oxidation/polymerization and lignin biosynthesis were investigated. Based on our phylogenetic analysis, these genes could be divided into two groups with obvious structural and functional differentiation. Expression studies showed that Brassica TT10 genes are active in developing seeds, but with differential expression patterns in yellow- and black-seeded near-isogenic lines. For functional analyses, three black-seeded B. napus cultivars were chosen for transgenic studies. Transgenic B. napus plants expressing antisense TT10 constructs exhibited retarded pigmentation in the seed coat. Chemical composition analysis revealed increased levels of soluble proanthocyanidins, and decreased extractable lignin in the seed coats of these transgenic plants compared with that of the controls. These findings indicate a role for the Brassica TT10 genes in proanthocyanidin polymerization and lignin biosynthesis, as well as seed coat pigmentation in B. napus. PMID:23613820

  15. Real-time analysis of sulfur-containing volatiles in Brassica plants infested with root-feeding Delia radicum larvae using proton-transfer reaction mass spectrometry

    PubMed Central

    van Dam, Nicole M.; Samudrala, Devasena; Harren, Frans J. M.; Cristescu, Simona M

    2012-01-01

    Background and aims Plants damaged by herbivores emit a variety of volatile organic compounds (VOCs). Here we used proton-transfer reaction mass spectrometry (PTR-MS) as a sensitive detection method for online analysis of herbivore-induced VOCs. Previously, it was found that Brassica nigra plants emit several sulfur-containing VOCs when attacked by cabbage root fly (Delia radicum) larvae with m/z 60 as a marker for the formation of allylisothiocyanate from the glucosinolate sinigrin. We tested the hypothesis that m/z 60 emission occurs only in plants with sinigrin in their roots. Additionally, we tested the hypothesis that methanethiol, dimethylsulfide and dimethyldisulfide are only emitted after larval infestation. Methodology Proton-transfer reaction mass spectrometry was used to track sulfur-containing VOCs from six different species of Brassica over time. The roots were either artificially damaged or infested with cabbage root fly larvae. Glucosinolate profiles of the roots were analysed using high-pressure liquid chromatography and compared with VOC emissions. Principal results Brassica nigra, B. juncea and B. napus primarily emitted m/z 60 directly after artificial damage or root fly infestation. Sulfide and methanethiol emissions from B. nigra and B. juncea also increased after larval damage but much later (6–12 h after damage). Brassica rapa, B. oleracea and B. carinata principally emitted methanethiol after artificial and after larval damage. Brassica oleracea and B. carinata showed some increase in m/z 60 emission after larval damage. Comparison with root glucosinolate profiles revealed that sinigrin cannot be the only precursor for m/z 60. Conclusions The principal compound emitted after root damage is determined by the plant species, and not by damage type or root glucosinolate composition. Once determined, the principal compounds may be used as markers for identifying damaged or infested plants. Further analyses of plant enzymes involved in the

  16. Analysis of plant leaf metabolites reveals no common response to insect herbivory by Pieris rapae in three related host-plant species

    PubMed Central

    Riach, A. C.; Perera, M. V. L.; Florance, H. V.; Penfield, S. D.; Hill, J. K.

    2015-01-01

    Studying the biochemical responses of different plant species to insect herbivory may help improve our understanding of the evolution of defensive metabolites found in host plants and their role in plant–herbivore interactions. Untargeted metabolic fingerprints measured as individual mass features were used to compare metabolite reactions in three Brassicales host-plant species (Cleome spinosa, Brassica oleracea, and Lunaria annua) to larval herbivore attack (Pieris rapae; Lepidoptera). Principal component analyses of metabolic fingerprints were able to distinguish among the three plant species and between uneaten control plants and plants that had been eaten. A large number of mass features (1186, 13% of mass features measured in control plants) were common to the three plant species. However, there were few similarities in the mass features that were induced (i.e. changed in abundance) following herbivory. Of the 87 and 68 induced mass features in B. oleracea and C. spinosa, respectively, there were only three that were induced in both plant species. By contrast, L. annua only had one mass feature induced by herbivory, and this was not induced in the other two plant species. The growth of the P. rapae larvae was poorer on the host plant L. annua than on B. oleracea and C. spinosa. The absence of common metabolites among the plants meant these induced responses could not be related to the performance of the herbivore. Thus, the response to herbivory by the same herbivore in these three host plants has evolved to be idiosyncratic in terms of the specific metabolites induced. PMID:25711707

  17. Seed bank dynamics govern persistence of Brassica hybrids in crop and natural habitats

    PubMed Central

    Hooftman, Danny A. P.; Bullock, James M.; Morley, Kathryn; Lamb, Caroline; Hodgson, David J.; Bell, Philippa; Thomas, Jane; Hails, Rosemary S.

    2015-01-01

    Background and Aims Gene flow from crops to their wild relatives has the potential to alter population growth rates and demography of hybrid populations, especially when a new crop has been genetically modified (GM). This study introduces a comprehensive approach to assess this potential for altered population fitness, and uses a combination of demographic data in two habitat types and mathematical (matrix) models that include crop rotations and outcrossing between parental species. Methods Full life-cycle demographic rates, including seed bank survival, of non-GM Brassica rapa × B. napus F1 hybrids and their parent species were estimated from experiments in both agricultural and semi-natural habitats. Altered fitness potential was modelled using periodic matrices including crop rotations and outcrossing between parent species. Key Results The demographic vital rates (i.e. for major stage transitions) of the hybrid population were intermediate between or lower than both parental species. The population growth rate (λ) of hybrids indicated decreases in both habitat types, and in a semi-natural habitat hybrids became extinct at two sites. Elasticity analyses indicated that seed bank survival was the greatest contributor to λ. In agricultural habitats, hybrid populations were projected to decline, but with persistence times up to 20 years. The seed bank survival rate was the main driver determining persistence. It was found that λ of the hybrids was largely determined by parental seed bank survival and subsequent replenishment of the hybrid population through outcrossing of B. rapa with B. napus. Conclusions Hybrid persistence was found to be highly dependent on the seed bank, suggesting that targeting hybrid seed survival could be an important management option in controlling hybrid persistence. For local risk mitigation, an increased focus on the wild parent is suggested. Management actions, such as control of B. rapa, could indirectly reduce hybrid

  18. Duplicate gene divergence by changes in microRNA binding sites in Arabidopsis and Brassica.

    PubMed

    Wang, Sishuo; Adams, Keith L

    2015-03-01

    Gene duplication provides large numbers of new genes that can lead to the evolution of new functions. Duplicated genes can diverge by changes in sequences, expression patterns, and functions. MicroRNAs play an important role in the regulation of gene expression in many eukaryotes. After duplication, two paralogs may diverge in their microRNA binding sites, which might impact their expression and function. Little is known about conservation and divergence of microRNA binding sites in duplicated genes in plants. We analyzed microRNA binding sites in duplicated genes in Arabidopsis thaliana and Brassica rapa. We found that duplicates are more often targeted by microRNAs than singletons. The vast majority of duplicated genes in A. thaliana with microRNA binding sites show divergence in those sites between paralogs. Analysis of microRNA binding sites in genes derived from the ancient whole-genome triplication in B. rapa also revealed extensive divergence. Paralog pairs with divergent microRNA binding sites show more divergence in expression patterns compared with paralog pairs with the same microRNA binding sites in Arabidopsis. Close to half of the cases of binding site divergence are caused by microRNAs that are specific to the Arabidopsis genus, indicating evolutionarily recent gain of binding sites after target gene duplication. We also show rapid evolution of microRNA binding sites in a jacalin gene family. Our analyses reveal a dynamic process of changes in microRNA binding sites after gene duplication in Arabidopsis and highlight the role of microRNA regulation in the divergence and contrasting evolutionary fates of duplicated genes. PMID:25644246

  19. Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq

    PubMed Central

    Zhang, Dawei; Pan, Qi; Cui, Cheng; Tan, Chen; Ge, Xianhong; Shao, Yujiao; Li, Zaiyun

    2015-01-01

    Polyploidy is popular for the speciation of angiosperms but the initial stage of allopolyploidization resulting from interspecific hybridization and genome duplication is associated with different extents of changes in genome structure and gene expressions. Herein, the transcriptomes detected by RNA-seq in resynthesized Brassica allotetraploids (Brassica juncea, AABB; B. napus, AACC; B. carinata, BBCC) from the pair-wise crosses of the same three diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC) were compared to reveal the patterns of gene expressions from progenitor genomes and the effects of different types of genome combinations and cytoplasm, upon the genome merger and duplication. From transcriptomic analyses for leaves and silique walls, extensive expression alterations were revealed in these resynthesized allotetraploids relative to their diploid progenitors, as well as during the transition from vegetative to reproductive development, for differential and transgressive gene expressions were variable in numbers and functions. Genes involved in glucosinolates and DNA methylation were transgressively up-regulated among most samples, suggesting that gene expression regulation was immediately established after allopolyploidization. The expression of ribosomal protein genes was also tissue-specific and showed a similar expression hierarchy of rRNA genes. The balance between the co-up and co-down regulation was observed between reciprocal B. napus with different types of the cytoplasm. Our results suggested that gene expression changes occurred after initial genome merger and such profound alterations might enhance the growth vigor and adaptability of Brassica allotetraploids. PMID:26583027

  20. Genome-specific differential gene expressions in resynthesized Brassica allotetraploids from pair-wise crosses of three cultivated diploids revealed by RNA-seq.

    PubMed

    Zhang, Dawei; Pan, Qi; Cui, Cheng; Tan, Chen; Ge, Xianhong; Shao, Yujiao; Li, Zaiyun

    2015-01-01

    Polyploidy is popular for the speciation of angiosperms but the initial stage of allopolyploidization resulting from interspecific hybridization and genome duplication is associated with different extents of changes in genome structure and gene expressions. Herein, the transcriptomes detected by RNA-seq in resynthesized Brassica allotetraploids (Brassica juncea, AABB; B. napus, AACC; B. carinata, BBCC) from the pair-wise crosses of the same three diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC) were compared to reveal the patterns of gene expressions from progenitor genomes and the effects of different types of genome combinations and cytoplasm, upon the genome merger and duplication. From transcriptomic analyses for leaves and silique walls, extensive expression alterations were revealed in these resynthesized allotetraploids relative to their diploid progenitors, as well as during the transition from vegetative to reproductive development, for differential and transgressive gene expressions were variable in numbers and functions. Genes involved in glucosinolates and DNA methylation were transgressively up-regulated among most samples, suggesting that gene expression regulation was immediately established after allopolyploidization. The expression of ribosomal protein genes was also tissue-specific and showed a similar expression hierarchy of rRNA genes. The balance between the co-up and co-down regulation was observed between reciprocal B. napus with different types of the cytoplasm. Our results suggested that gene expression changes occurred after initial genome merger and such profound alterations might enhance the growth vigor and adaptability of Brassica allotetraploids. PMID:26583027

  1. Three Homologous Genes Encoding sn-Glycerol-3-Phosphate Acyltransferase 4 Exhibit Different Expression Patterns and Functional Divergence in Brassica napus1[C][W][OA

    PubMed Central

    Chen, Xue; Truksa, Martin; Snyder, Crystal L.; El-Mezawy, Aliaa; Shah, Saleh; Weselake, Randall J.

    2011-01-01

    Brassica napus is an allotetraploid (AACC) formed from the fusion of two diploid progenitors, Brassica rapa (AA) and Brassica oleracea (CC). Polyploidy and genome-wide rearrangement during the evolution process have resulted in genes that are present as multiple homologs in the B. napus genome. In this study, three B. napus homologous genes encoding endoplasmic reticulum-bound sn-glycerol-3-phosphate acyltransferase 4 (GPAT4) were identified and characterized. Although the three GPAT4 homologs share a high sequence similarity, they exhibit different expression patterns and altered epigenetic features. Heterologous expression in yeast further revealed that the three BnGPAT4 homologs encoded functional GPAT enzymes but with different levels of polypeptide accumulation. Complementation of the Arabidopsis (Arabidopsis thaliana) gpat4 gpat8 double mutant line with individual BnGPAT4 homologs suggested their physiological roles in cuticle formation. Analysis of gpat4 RNA interference lines of B. napus revealed that the BnGPAT4 deficiency resulted in reduced cutin content and altered stomatal structures in leaves. Our results revealed that the BnGPAT4 homologs have evolved into functionally divergent forms and play important roles in cutin synthesis and stomatal development. PMID:21173024

  2. Yeast cell wall extract induces disease resistance against bacterial and fungal pathogens in Arabidopsis thaliana and Brassica crop.

    PubMed

    Narusaka, Mari; Minami, Taichi; Iwabuchi, Chikako; Hamasaki, Takashi; Takasaki, Satoko; Kawamura, Kimito; Narusaka, Yoshihiro

    2015-01-01

    Housaku Monogatari (HM) is a plant activator prepared from a yeast cell wall extract. We examined the efficacy of HM application and observed that HM treatment increased the resistance of Arabidopsis thaliana and Brassica rapa leaves to bacterial and fungal infections. HM reduced the severity of bacterial leaf spot and anthracnose on A. thaliana and Brassica crop leaves with protective effects. In addition, gene expression analysis of A. thaliana plants after treatment with HM indicated increased expression of several plant defense-related genes. HM treatment appears to induce early activation of jasmonate/ethylene and late activation of salicylic acid (SA) pathways. Analysis using signaling mutants revealed that HM required SA accumulation and SA signaling to facilitate resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola and the fungal pathogen Colletotrichum higginsianum. In addition, HM-induced resistance conferred chitin-independent disease resistance to bacterial pathogens in A. thaliana. These results suggest that HM contains multiple microbe-associated molecular patterns that activate defense responses in plants. These findings suggest that the application of HM is a useful tool that may facilitate new disease control methods. PMID:25565273

  3. Cytoplasmic and Genomic Effects on Meiotic Pairing in Brassica Hybrids and Allotetraploids from Pair Crosses of Three Cultivated Diploids

    PubMed Central

    Cui, Cheng; Ge, Xianhong; Gautam, Mayank; Kang, Lei; Li, Zaiyun

    2012-01-01

    Interspecific hybridization and allopolyploidization contribute to the origin of many important crops. Synthetic Brassica is a widely used model for the study of genetic recombination and “fixed heterosis” in allopolyploids. To investigate the effects of the cytoplasm and genome combinations on meiotic recombination, we produced digenomic diploid and triploid hybrids and trigenomic triploid hybrids from the reciprocal crosses of three Brassica diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC). The chromosomes in the resultant hybrids were doubled to obtain three allotetraploids (B. juncea, AA.BB; B. napus, AA.CC; B. carinata, BB.CC). Intra- and intergenomic chromosome pairings in these hybrids were quantified using genomic in situ hybridization and BAC-FISH. The level of intra- and intergenomic pairings varied significantly, depending on the genome combinations and the cytoplasmic background and/or their interaction. The extent of intragenomic pairing was less than that of intergenomic pairing within each genome. The extent of pairing variations within the B genome was less than that within the A and C genomes, each of which had a similar extent of pairing. Synthetic allotetraploids exhibited nondiploidized meiotic behavior, and their chromosomal instabilities were correlated with the relationship of the genomes and cytoplasmic background. Our results highlight the specific roles of the cytoplasm and genome to the chromosomal behaviors of hybrids and allopolyploids. PMID:22505621

  4. Cytoplasmic and genomic effects on meiotic pairing in Brassica hybrids and allotetraploids from pair crosses of three cultivated diploids.

    PubMed

    Cui, Cheng; Ge, Xianhong; Gautam, Mayank; Kang, Lei; Li, Zaiyun

    2012-07-01

    Interspecific hybridization and allopolyploidization contribute to the origin of many important crops. Synthetic Brassica is a widely used model for the study of genetic recombination and "fixed heterosis" in allopolyploids. To investigate the effects of the cytoplasm and genome combinations on meiotic recombination, we produced digenomic diploid and triploid hybrids and trigenomic triploid hybrids from the reciprocal crosses of three Brassica diploids (B. rapa, AA; B. nigra, BB; B. oleracea, CC). The chromosomes in the resultant hybrids were doubled to obtain three allotetraploids (B. juncea, AA.BB; B. napus, AA.CC; B. carinata, BB.CC). Intra- and intergenomic chromosome pairings in these hybrids were quantified using genomic in situ hybridization and BAC-FISH. The level of intra- and intergenomic pairings varied significantly, depending on the genome combinations and the cytoplasmic background and/or their interaction. The extent of intragenomic pairing was less than that of intergenomic pairing within each genome. The extent of pairing variations within the B genome was less than that within the A and C genomes, each of which had a similar extent of pairing. Synthetic allotetraploids exhibited nondiploidized meiotic behavior, and their chromosomal instabilities were correlated with the relationship of the genomes and cytoplasmic background. Our results highlight the specific roles of the cytoplasm and genome to the chromosomal behaviors of hybrids and allopolyploids. PMID:22505621

  5. Yeast Cell Wall Extract Induces Disease Resistance against Bacterial and Fungal Pathogens in Arabidopsis thaliana and Brassica Crop

    PubMed Central

    Narusaka, Mari; Minami, Taichi; Iwabuchi, Chikako; Hamasaki, Takashi; Takasaki, Satoko; Kawamura, Kimito; Narusaka, Yoshihiro

    2015-01-01

    Housaku Monogatari (HM) is a plant activator prepared from a yeast cell wall extract. We examined the efficacy of HM application and observed that HM treatment increased the resistance of Arabidopsis thaliana and Brassica rapa leaves to bacterial and fungal infections. HM reduced the severity of bacterial leaf spot and anthracnose on A. thaliana and Brassica crop leaves with protective effects. In addition, gene expression analysis of A. thaliana plants after treatment with HM indicated increased expression of several plant defense-related genes. HM treatment appears to induce early activation of jasmonate/ethylene and late activation of salicylic acid (SA) pathways. Analysis using signaling mutants revealed that HM required SA accumulation and SA signaling to facilitate resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola and the fungal pathogen Colletotrichum higginsianum. In addition, HM-induced resistance conferred chitin-independent disease resistance to bacterial pathogens in A. thaliana. These results suggest that HM contains multiple microbe-associated molecular patterns that activate defense responses in plants. These findings suggest that the application of HM is a useful tool that may facilitate new disease control methods. PMID:25565273

  6. Brassica oleracea and B. napus.

    PubMed

    Sparrow, Penny A C Hundleby Née; Irwin, Judith A

    2015-01-01

    With the accelerating advances in genetics and genomics research in Arabidopsis and Brassica, transformation technologies are now routinely being exploited to elucidate gene function as well as contributing to the development of novel enhanced crops. When a researcher's desired goal is simply to modify or introduce candidate genes into a Brassica, the availability of easy-to-follow protocols and knowledge of readily transformable genotypes becomes a valuable resource. In this chapter we outline a basic A. tumefaciens-mediated transformation method, using 4-day-old cotyledonary explants, that has been successfully applied to a range of different B. oleracea and B. napus genotypes. For demonstration purposes, we focus primarily on the diploid species B. oleracea using a model doubled haploid genotype, AG DH1012. After only 3-4 weeks on kanamycin selection the first transgenic shoots can be isolated. Transformation efficiencies are typically in the region of 15-25 % (based on 15-25 PCR-positive independent shoots from 100 inoculated explants). Most explants will produce multiple shoots (1-3+ per explant) and so the total number of transgenic shoots produced will exceed 15-25 per 100 explant experiment. The protocol is also applicable to B. napus and modifications specific to this species are highlighted accordingly. For researchers wishing to use their own plant genotype, tissue culture phenotypes that are conducive to efficient transformation are also highlighted within this chapter. PMID:25300849

  7. HYBRIDIZATION STUDY BETWEEN GENETICALLY MODIFIED BRASSICA NAPUS AND NON-GENETICALLY MODIFIED B. NAPUS AND B. RAPA

    EPA Science Inventory

    Gene exchange between cultivated crops and wild species has gained significance in recent years because of concerns regarding the potential for gene flow between genetically modified (GM) crops and their domesticated and wild relatives. As part of our ecological effects of gene ...

  8. A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa)

    PubMed Central

    2011-01-01

    Background Non-coding small RNAs play critical roles in various cellular processes in a wide spectrum of eukaryotic organisms. Their responses to abiotic stress have become a popular topic of economic and scientific importance in biological research. Several studies in recent years have reported a small number of non-coding small RNAs that map to chloroplast genomes. However, it remains uncertain whether small RNAs are generated from chloroplast genome and how they respond to environmental stress, such as high temperature. Chinese cabbage is an important vegetable crop, and heat stress usually causes great losses in yields and quality. Under heat stress, the leaves become etiolated due to the disruption and disassembly of chloroplasts. In an attempt to determine the heat-responsive small RNAs in chloroplast genome of Chinese cabbage, we carried out deep sequencing, using heat-treated samples, and analysed the proportion of small RNAs that were matched to chloroplast genome. Results Deep sequencing provided evidence that a novel subset of small RNAs were derived from the chloroplast genome of Chinese cabbage. The chloroplast small RNAs (csRNAs) include those derived from mRNA, rRNA, tRNA and intergenic RNA. The rRNA-derived csRNAs were preferentially located at the 3'-ends of the rRNAs, while the tRNA-derived csRNAs were mainly located at 5'-termini of the tRNAs. After heat treatment, the abundance of csRNAs decreased in seedlings, except those of 24 nt in length. The novel heat-responsive csRNAs and their locations in the chloroplast were verified by Northern blotting. The regulation of some csRNAs to the putative target genes were identified by real-time PCR. Our results reveal that high temperature suppresses the production of some csRNAs, which have potential roles in transcriptional or post-transcriptional regulation. Conclusions In addition to nucleus, the chloroplast is another important organelle that generates a number of small RNAs. Many members of csRNA families are highly sensitive to heat stress. Some csRNAs respond to heat stress by silencing target genes. We suggest that proper temperature is important for production of chloroplast small RNAs, which are associated with plant resistance to abiotic stress. PMID:21639890

  9. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

    PubMed Central

    Ding, Qian; Li, Jingjuan; Wang, Fengde; Zhang, Yihui; Li, Huayin; Zhang, Jiannong; Gao, Jianwei

    2015-01-01

    Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage. PMID:26504770

  10. [Ecotoxicological effects of tetracycline on the seedling development of Chinese white cabbage (Brassica rapa L. chinensis group.) in soil].

    PubMed

    Lin, Lin; An, Jing; Zhou, Qi-Xing

    2011-08-01

    The ecotoxicological effects of tetracycline (TC) on the early growth and seedlings development of Chinese white cabbage were investigated using the pot-culture method. The results showed that the stem elongation of the cabbages was promoted, while the root elongation and fresh weight of the cabbages were inhibited by 1-100 mg/kg TC. After a 28-day exposure, the inhibition rate of root elongation was up to 36.0% and that of fresh weight was up to 34.6% stressed by 100 mg/kg TC. With the exposure time of TC prolonged, the content of chlorophyll in leaves of the cabbage seedlings stressed by 100 mg/kg TC was significantly lower than that treated by other concentrations of TC, with the inhibition rate of chlorophyll was 21.7% - 29.0%. After a 7-day exposure to TC, the content of soluble protein (SP) and malondialdehyde (MDA) in the cabbage seedlings changed insignificantly. With the exposure time of TC prolonged, the content of SP in the cabbage seedlings decreased significantly, while the content of MDA increased significantly. Moreover, the activity of SOD, POD and CAT in Chinese white cabbage seedlings was inhibited by 1-100 mg/kg TC. The inhibition rates of SOD, POD and CAT activity exposed to 100 mg/kg TC were 33.9% - 45.3%, 33.8% - 67.7% and 29.6% - 57.7%, respectively. It suggested that TC has ecotoxicological effects on Chinese white cabbage seedlings with a chronic exposure. PMID:22619974

  11. Infection of Plasmodiophora brassicae in Chinese cabbage.

    PubMed

    Ji, R; Zhao, L; Xing, M; Shen, X; Bi, Q; Peng, S; Feng, H

    2014-01-01

    Brassica crops infected by Plasmodiophora brassicae can produce root galls (clubroots) and be prevented from growing normally. To understand the series of changes that occur in the host root during root gall production, the resistance character of 21 Chinese cabbage lines were identified and then resistant and susceptible lines were used for infection observation. Hydroponic technology system was used for plants growing, and the infection process of P. brassicae in the roots of resistant and susceptible Chinese cabbage was examined based on morphology and microscopic characteristics using micoscope. In susceptible Chinese cabbage, the root hair infection stage occurred over approximately 7 days after inoculation, the cortical infection happened over approximatly 14 days after inoculation, and clubroots formed in approximately 30 days after inoculation. However, in resistant Chinese cabbage, the pathogen could be prevented and maintained in the root hair infection stage. This research provides a foundation for the subsequent studies of cabbage resistance of P. brassicae. PMID:25526218

  12. How Different Genetically Manipulated Brassica Genotypes Affect Life Table Parameters of Plutella xylostella (Lepidoptera: Plutellidae).

    PubMed

    Nikooei, Mehrnoosh; Fathipour, Yaghoub; Jalali Javaran, Mokhtar; Soufbaf, Mahmoud

    2015-04-01

    The fitness of Plutella xylostella L. on different genetically manipulated Brassica plants, including canola's progenitor (Brassica rapa L.), two cultivated canola cultivars (Opera and RGS003), one hybrid (Hyula401), one gamma-ray mutant-RGS003, and one transgenic (PF) genotype was compared using two-sex and female-based life table parameters. All experiments were conducted in a growth chamber at 25±1°C, 65±5% relative humidity, and a photoperiod of 16:8 (L:D) h. There were significant differences in duration of different life stages of P. xylostella on different plant genotypes. The shortest (13.92 d) and longest (24.61 d) total developmental time were on Opera and PF, respectively. The intrinsic rate of increase of P. xylostella ranged between 0.236 (Opera) and 0.071 day(-1) (PF). The highest (60.79 offspring) and lowest (7.88 offspring) net reproductive rates were observed on Opera and PF, respectively. Comparison of intrinsic rate of increase, net reproductive rates, finite rate of increase, mean generation time, fecundity, and survivorship of P. xylostella on the plant genotypes suggested that this pest performed well on cultivars (RGS003 and Opera) and performed poorly on the other manipulated genotypes especially on mutant-RGS003 and PF. Glucosinolate levels were significantly higher in damaged plants than undamaged ones and the lowest and highest concentrations of glucosinolates were found in transgenic genotype and canola's progenitor, respectively. Interestingly, our results showed that performance and fitness of this pest was better on canola's progenitor and cultivated plants, which had high levels of glucosinolate. PMID:26470162

  13. Identification of genomic regions involved in resistance against Sclerotinia sclerotiorum from wild Brassica oleracea.

    PubMed

    Mei, Jiaqin; Ding, Yijuan; Lu, Kun; Wei, Dayong; Liu, Yao; Disi, Joseph Onwusemu; Li, Jiana; Liu, Liezhao; Liu, Shengyi; McKay, John; Qian, Wei

    2013-02-01

    The lack of resistant source has greatly restrained resistance breeding of rapeseed (Brassica napus, AACC) against Sclerotinia sclerotiorum which causes severe yield losses in rapeseed production all over the world. Recently, several wild Brassica oleracea accessions (CC) with high level of resistance have been identified (Mei et al. in Euphytica 177:393-400, 2011), bringing a new hope to improve Sclerotinia resistance of rapeseed. To map quantitative trait loci (QTL) for Sclerotinia resistance from wild B. oleracea, an F2 population consisting of 149 genotypes, with several clones of each genotypes, was developed from one F1 individual derived from the cross between a resistant accession of wild B. oleracea (B. incana) and a susceptible accession of cultivated B. oleracea var. alboglabra. The F2 population was evaluated for Sclerotinia reaction in 2009 and 2010 under controlled condition. Significant differences among genotypes and high heritability for leaf and stem reaction indicated that genetic components accounted for a large portion of the phenotypic variance. A total of 12 QTL for leaf resistance and six QTL for stem resistance were identified in 2 years, each explaining 2.2-28.4 % of the phenotypic variation. The combined effect of alleles from wild B. oleracea reduced the relative susceptibility by 22.5 % in leaves and 15 % in stems on average over 2 years. A 12.8-cM genetic region on chromosome C09 of B. oleracea consisting of two major QTL intervals for both leaf and stem resistance was assigned into a 2.7-Mb genomic region on chromosome A09 of B. rapa, harboring about 30 putative resistance-related genes. Significant negative corrections were found between flowering time and relative susceptibility of leaf and stem. The association of flowering time with Sclerotinia resistance is discussed. PMID:23096003

  14. Chitinase-mediated inhibitory activity of Brassica transgenic on growth of Alternaria brassicae.

    PubMed

    Mondal, Kalyan K; Chatterjee, Subhas Chandra; Viswakarma, Navin; Bhattacharya, Ram Charan; Grover, Anita

    2003-09-01

    Chitinase, capable of degrading the cell walls of invading phytopathogenic fungi, plays an important role in plant defense response, particularly when this enzyme is overexpressed through genetic engineering. In the present study, Brassica plant (Brassica juncea L.) was transformed with chitinase gene tagged with an overexpressing promoter 35 S CaMV. The putative transgenics were assayed for their inhibitory activity against Alternaria brassicae, the inducer of Alternaria leaf spot of Brassica both in vitro and under polyhouse conditions. In in vitro fungal growth inhibition assays, chitinase inhibited the fungal colony size by 12-56% over the non-trangenic control. The bioassay under artificial epiphytotic conditions revealed the delay in the onset of disease as well as reduced lesion number and size in 35S-chitinase Brassica as compared to the untransformed control plants. PMID:14570264

  15. Collembola of Rapa Nui (Easter Island) with descriptions of five endemic cave-restricted species.

    PubMed

    Bernard, Ernest C; Soto-Adames, Felipe N; Wynne, J Judson

    2015-01-01

    Eight species of Collembola are reported from recent collections made in caves on the Polynesian island of Rapa Nui (Easter Island). Five of these species are new to science and apparently endemic to the island: Coecobrya aitorererere n. sp., Cyphoderus manuneru n. sp., Entomobrya manuhoko n. sp., Pseudosinella hahoteana n. sp. and Seira manukio n. sp. The Hawaiian species Lepidocyrtus olena Christiansen & Bellinger and the cosmopolitan species Folsomia candida Willem also were collected from one or more caves. Coecobrya kennethi Jordana & Baquero, recently described from Rapa Nui and identified as endemic, was collected in sympatric association with C. aitorererere n.sp. With the exception of F. candida, all species are endemic to Rapa Nui or greater Polynesia and appear to be restricted to the cave environment on Rapa Nui. A key is provided to separate Collembola species reported from Rapa Nui. We provide recommendations to aid in the conservation and management of these new Collembola, as well as the other presumed cave-restricted arthropods. PMID:25947805

  16. Flower vs. Leaf Feeding by Pieris brassicae: Glucosinolate-Rich Flower Tissues are Preferred and Sustain Higher Growth Rate

    PubMed Central

    Smallegange, R. C.; Blatt, S. E.; Harvey, J. A.; Agerbirk, N.; Dicke, M.

    2007-01-01

    lower. Our results show that feeding on flower tissues, containing higher concentrations of glucosinolates, provides P. brassicae with a nutritional benefit in terms of higher growth rate. This preference appears to be in contrast to published negative effects of volatile glucosinolate breakdown products on the closely related Pieris rapae. PMID:17828429

  17. Ozone affects growth and development of Pieris brassicae on the wild host plant Brassica nigra.

    PubMed

    Khaling, Eliezer; Papazian, Stefano; Poelman, Erik H; Holopainen, Jarmo K; Albrectsen, Benedicte R; Blande, James D

    2015-04-01

    When plants are exposed to ozone they exhibit changes in both primary and secondary metabolism, which may affect their interactions with herbivorous insects. Here we investigated the performance and preferences of the specialist herbivore Pieris brassicae on the wild plant Brassica nigra under elevated ozone conditions. The direct and indirect effects of ozone on the plant-herbivore system were studied. In both cases ozone exposure had a negative effect on P. brassicae development. However, in dual-choice tests larvae preferentially consumed plant material previously fumigated with the highest concentration tested, showing a lack of correlation between larval preference and performance on ozone exposed plants. Metabolomic analysis of leaf material subjected to combinations of ozone and herbivore-feeding, and focussing on known defence metabolites, indicated that P. brassicae behaviour and performance were associated with ozone-induced alterations to glucosinolate and phenolic pools. PMID:25645061

  18. Complete mitochondrial genome sequence of black mustard (Brassica nigra; BB) and comparison with Brassica oleracea (CC) and Brassica carinata (BBCC).

    PubMed

    Yamagishi, Hiroshi; Tanaka, Yoshiyuki; Terachi, Toru

    2014-11-01

    Crop species of Brassica (Brassicaceae) consist of three monogenomic species and three amphidiploid species resulting from interspecific hybridizations among them. Until now, mitochondrial genome sequences were available for only five of these species. We sequenced the mitochondrial genome of the sixth species, Brassica nigra (nuclear genome constitution BB), and compared it with those of Brassica oleracea (CC) and Brassica carinata (BBCC). The genome was assembled into a 232 145 bp circular sequence that is slightly larger than that of B. oleracea (219 952 bp). The genome of B. nigra contained 33 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. The cox2-2 gene present in B. oleracea was absent in B. nigra. Although the nucleotide sequences of 52 genes were identical between B. nigra and B. carinata, the second exon of rps3 showed differences including an insertion/deletion (indel) and nucleotide substitutions. A PCR test to detect the indel revealed intraspecific variation in rps3, and in one line of B. nigra it amplified a DNA fragment of the size expected for B. carinata. In addition, the B. carinata lines tested here produced DNA fragments of the size expected for B. nigra. The results indicate that at least two mitotypes of B. nigra were present in the maternal parents of B. carinata. PMID:25767903

  19. Histone H3 methylation patterns in Brassica nigra, Brassica juncea, and Brassica carinata species.

    PubMed

    Braszewska-Zalewska, Agnieszka; Dziurlikowska, Alina; Maluszynska, Jolanta

    2012-01-01

    Core histones are subjected to various post-translational modifications, and one of them, most intensively studied in plants, is the methylation of histone H3. In the majority of analyzed plant species, dimethylation of H3 at lysine 9 (H3K9me2) is detected in heterochromatin domains, whereas methylation of H3 at lysine 4 (H3K4me2) is detected in euchromatin domains. The distribution of H3K9me2 in the interphase nucleus seems to be correlated with genome size, chromatin organization, but also with tissue specificity. In this paper, we present the analysis of the pattern and level of histone H3 methylation for two allotetraploid and one diploid Brassica species. We have found that the pattern of H3K9me2 in interphase nuclei from root meristematic tissue is comparable within the analyzed species and includes both heterochromatin and euchromatin, but the level of modification differs not only among species but even among nuclei in the same phase of the cell cycle within one species. Moreover, the differences in the level of H3K9me2 are not directly coupled with DNA content in the nuclei and are probably tissue specific. PMID:22195975

  20. BraLTP1, a Lipid Transfer Protein Gene Involved in Epicuticular Wax Deposition, Cell Proliferation and Flower Development in Brassica napus

    PubMed Central

    Liu, Fang; Xiong, Xiaojuan; Wu, Lei; Fu, Donghui; Hayward, Alice; Zeng, Xinhua; Cao, Yinglong; Wu, Yuhua; Li, Yunjing; Wu, Gang

    2014-01-01

    Plant non-specific lipid transfer proteins (nsLTPs) constitute large multigene families that possess complex physiological functions, many of which remain unclear. This study isolated and characterized the function of a lipid transfer protein gene, BraLTP1 from Brassica rapa, in the important oilseed crops Brassica napus. BraLTP1 encodes a predicted secretory protein, in the little known VI Class of nsLTP families. Overexpression of BnaLTP1 in B. napus caused abnormal green coloration and reduced wax deposition on leaves and detailed wax analysis revealed 17–80% reduction in various major wax components, which resulted in significant water-loss relative to wild type. BnaLTP1 overexpressing leaves exhibited morphological disfiguration and abaxially curled leaf edges, and leaf cross-sections revealed cell overproliferation that was correlated to increased cytokinin levels (tZ, tZR, iP, and iPR) in leaves and high expression of the cytokinin biosynthsis gene IPT3. BnaLTP1-overexpressing plants also displayed morphological disfiguration of flowers, with early-onset and elongated carpel development and outwardly curled stamen. This was consistent with altered expression of a a number of ABC model genes related to flower development. Together, these results suggest that BraLTP1 is a new nsLTP gene involved in wax production or deposition, with additional direct or indirect effects on cell division and flower development. PMID:25314222

  1. Anaerobic metabolism in Brassica seedlings

    NASA Astrophysics Data System (ADS)

    Park, Myoung-Ryoul; Hasenstein, Karl H.

    Germination typically depends on oxidative respiration. The lack of convection under space conditions may create hypoxic or conditions during seed germination. We investigated the effect of reduced oxygen on seed germination and metabolism to understand how metabolic constraints affect seed growth and responsiveness to reorientation. Germination was completely inhibited when seeds were imbibed in the absence of oxygen; germination occurred at 5% oxygen and higher levels. Adding oxygen after 72 h resulted in immediate germination (protrusion of the radicle). Hypoxia typically activates alcohol dehydrogenase (ADH, EC 1.1.1.1) and lactate dehydrogenase (LDH, EC 1.1.1.27) which produce ethanol and/or L-lactate, respectively. We report on the expression of ADH1 and LDH1, and changes in total soluble sugars, starch, pH, and L-lactate in seedlings grown at 28°C in 0, 2.5, 5, 10% and ambient (21%) oxygen conditions as controls. The highest consumption (lowest level) of sugars was seen at 0% oxygen but the lowest level of starch occurred 24 h after imbibition under ambient condition. Expression levels of ADH1 in ambient oxygen condition increased within 24 h but increased threefold under hypoxic conditions; LDH1 increased up to 8-fold under hypoxia compared to controls but ADH1 and LDH1 were less expressed as the oxygen levels increased. The intracellular pH of seeds decreased as the content of L-lactate increased for all oxygen concentrations. These results indicate that germination of Brassica is sensitive to oxygen levels and that oxygen availability during germination is an important factor for metabolic activities. (Supported by NASA grant NNX10AP91G)

  2. Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus

    PubMed Central

    2013-01-01

    Background The fertile and sterile plants were derived from the self-pollinated offspring of the F1 hybrid between the novel restorer line NR1 and the Nsa CMS line in Brassica napus. To elucidate gene expression and regulation caused by the A and C subgenomes of B. napus, as well as the alien chromosome and cytoplasm from Sinapis arvensis during the development of young floral buds, we performed a genome-wide high-throughput transcriptomic sequencing for young floral buds of sterile and fertile plants. Results In this study, equal amounts of total RNAs taken from young floral buds of sterile and fertile plants were sequenced using the Illumina/Solexa platform. After filtered out low quality data, a total of 2,760,574 and 2,714,441 clean tags were remained in the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. All distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. In total, 3231 genes of B. rapa and 3371 genes of B. oleracea were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further to understand the biological functions of those differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and their expression levels were confirmed by quantitative RT-PCR, and fourteen of them showed consistent expression patterns with the digital gene expression (DGE) data. Conclusions A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility

  3. BcMF9, a novel polygalacturonase gene, is required for both Brassica campestris intine and exine formation

    PubMed Central

    Huang, Li; Ye, Yiqun; Zhang, Yuchao; Zhang, Aihong; Liu, Tingting; Cao, Jiashu

    2009-01-01

    Background and Aims The polygalacturonase (PG) gene family has been found to be enriched in pollen of several species; however, little is currently known about the function of the PG gene in pollen development. To investigate the exact role that the PG gene has played in pollen development and about this family in general, one putative PG gene, Brassica campestris Male Fertility 9 (BcMF9), was isolated from Chinese cabbage (Brassica campestris ssp. chinensis, syn. B. rapa ssp. chinensis) and characterized. Methods RT-PCR, northern blotting and in situ hybridization were used to analyse the expression pattern of BcMF9, and antisense RNA technology was applied to study the function of this gene. Key Results BcMF9 is expressed in particular in the tapetum and microspore during the late stages of pollen development. Antisense RNA transgenic plants that displayed decreased expression of BcMF9 showed pollen morphological defects that resulted in reduced pollen germination efficiency. Transmission electron microscopy revealed that the homogeneous pectic exintine layer of pollen facing the exterior was over-developed and predominantly occupied the intine, reversing the normal proportional distribution of the internal endintine layer and the external exintine in transgenic pollen. Inhibition of BcMF9 also resulted in break-up of the previously formed tectum and baculae from the beginning of the binucleate stage, as a result of premature degradation of tapetum. Conclusions Several lines of evidence, including patterns of BcMF9 expression and phenotypic defects, suggest a sporophytic role in exine patterning, and a gametophytic mode of action of BcMF9 in intine formation. BcMF9 might act as a co-ordinator in the late stages of tapetum degeneration, and subsequently in the regulation of wall material secretion and, in turn, exine formation. BcMF9 might also play a role in intine formation, possibly via regulation of the dynamic metabolism of pectin. PMID:19815569

  4. Quantitative Trait Loci for Thermal Time to Flowering and Photoperiod Responsiveness Discovered in Summer Annual-Type Brassica napus L

    PubMed Central

    Nelson, Matthew N.; Rajasekaran, Ravikesavan; Smith, Alison; Chen, Sheng; Beeck, Cameron P.; Siddique, Kadambot H. M.; Cowling, Wallace A.

    2014-01-01

    Time of flowering is a key adaptive trait in plants and is conditioned by the interaction of genes and environmental cues including length of photoperiod, ambient temperature and vernalisation. Here we investigated the photoperiod responsiveness of summer annual-types of Brassica napus (rapeseed, canola). A population of 131 doubled haploid lines derived from a cross between European and Australian parents was evaluated for days to flowering, thermal time to flowering (measured in degree-days) and the number of leaf nodes at flowering in a compact and efficient glasshouse-based experiment with replicated short and long day treatments. All three traits were under strong genetic control with heritability estimates ranging from 0.85–0.93. There was a very strong photoperiod effect with flowering in the population accelerated by 765 degree-days in the long day versus short day treatments. However, there was a strong genetic correlation of line effects (0.91) between the long and short day treatments and relatively low genotype x treatment interaction indicating that photoperiod had a similar effect across the population. Bivariate analysis of thermal time to flowering in short and long days revealed three main effect quantitative trait loci (QTLs) that accounted for 57.7% of the variation in the population and no significant interaction QTLs. These results provided insight into the contrasting adaptations of Australian and European varieties. Both parents responded to photoperiod and their alleles shifted the population to earlier flowering under long days. In addition, segregation of QTLs in the population caused wide transgressive segregation in thermal time to flowering. Potential candidate flowering time homologues located near QTLs were identified with the aid of the Brassica rapa reference genome sequence. We discuss how these results will help to guide the breeding of summer annual types of B. napus adapted to new and changing environments. PMID:25061822

  5. The fusion of genomes leads to more options: A comparative investigation on the desulfo-glucosinolate sulfotransferases of Brassica napus and homologous proteins of Arabidopsis thaliana.

    PubMed

    Hirschmann, Felix; Papenbrock, Jutta

    2015-06-01

    Sulfotransferases (SOTs) (EC 2.8.2.-) play a crucial role in the glucosinolate (Gl) biosynthesis, by catalyzing the final step of the core glucosinolate formation. In Arabidopsis thaliana the three desulfo (ds)-Gl SOTs AtSOT16, AtSOT17 and AtSOT18 were previously characterized, showing different affinities to ds-Gls. But can the knowledge about these SOTs be generally transferred to other Gl-synthesizing plants? It was investigated how many SOTs are present in the economically relevant crop plant Brassica napus L., and if it is possible to predict their characteristics by sequence analysis. The recently sequenced B. napus is a hybrid of Brassica rapa and Brassica oleracea. By database research, 71 putative functional BnSOT family members were identified and at least eleven of those are putative ds-Gl SOTs. Besides the homologs of AtSOT16 - 18, phylogenetic analyses revealed new subfamilies of ds-Gl SOTs, which are not present in A. thaliana. Three of the B. napus ds-Gl SOT proteins were expressed and purified, and characterized by determining the substrate affinities to different ds-Gls. Two of them, BnSOT16-a and BnSOT16-b, showed a significantly higher affinity to an indolic ds-Gl, similarly to AtSOT16. Additionally, BnSOT17-a was characterized and showed a higher affinity to long chained aliphatic Gls, similarly to AtSOT17. Identification of homologs to AtSOT18 was less reliable, because putative SOT18 sequences are more heterogeneous and confirmation of similar characteristics was not possible. PMID:25827495

  6. A triallelic genetic male sterility locus in Brassica napus: an integrative strategy for its physical mapping and possible local chromosome evolution around it

    PubMed Central

    Lu, Wei; Liu, Jun; Xin, Qiang; Wan, Lili; Hong, Dengfeng; Yang, Guangsheng

    2013-01-01

    Background and Aims Spontaneous male sterility is an advantageous trait for both constructing efficient pollination control systems and for understanding the developmental process of the male reproductive unit in many crops. A triallelic genetic male-sterile locus (BnMs5) has been identified in Brassica napus; however, its complicated genome structure has greatly hampered the isolation of this locus. The aim of this study was to physically map BnMs5 through an integrated map-based cloning strategy and analyse the local chromosomal evolution around BnMs5. Methods A large F2 population was used to integrate the existing genetic maps around BnMs5. A map-based cloning strategy in combination with comparative mapping among B. napus, Arabidopsis, Brassica rapa and Brassica oleracea was employed to facilitate the identification of a target bacterial artificial chromosome (BAC) clone covering the BnMs5 locus. The genomic sequences from the Brassica species were analysed to reveal the regional chromosomal evolution around BnMs5. Key Results BnMs5 was finally delimited to a 0·3-cM genetic fragment from an integrated local genetic map, and was anchored on the B. napus A8 chromosome. Screening of a B. napus BAC clone library and identification of the positive clones validated that JBnB034L06 was the target BAC clone. The closest flanking markers restrict BnMs5 to a 21-kb region on JBnB034L06 containing six predicted functional genes. Good collinearity relationship around BnMs5 between several Brassica species was observed, while violent chromosomal evolutionary events including insertions/deletions, duplications and single nucleotide mutations were also found to have extensively occurred during their divergence. Conclusions This work represents major progress towards the molecular cloning of BnMs5, as well as presenting a powerful, integrative method to mapping loci in plants with complex genomic architecture, such as the amphidiploid B. napus. PMID:23243189

  7. Multiple NUCLEAR FACTOR Y transcription factors respond to abiotic stress in Brassica napus L.

    PubMed

    Xu, Li; Lin, Zhongyuan; Tao, Qing; Liang, Mingxiang; Zhao, Gengmao; Yin, Xiangzhen; Fu, Ruixin

    2014-01-01

    Members of the plant NUCLEAR FACTOR Y (NF-Y) family are composed of the NF-YA, NF-YB, and NF-YC subunits. In Brassica napus (canola), each of these subunits forms a multimember subfamily. Plant NF-Ys were reported to be involved in several abiotic stresses. In this study, we demonstrated that multiple members of thirty three BnNF-Ys responded rapidly to salinity, drought, or ABA treatments. Transcripts of five BnNF-YAs, seven BnNF-YBs, and two BnNF-YCs were up-regulated by salinity stress, whereas the expression of thirteen BnNF-YAs, ten BnNF-YBs, and four BnNF-YCs were induced by drought stress. Under NaCl treatments, the expression of one BnNF-YA10 and four NF-YBs (BnNF-YB3, BnNF-YB7, BnNF-YB10, and BnNF-YB14) were greatly increased. Under PEG treatments, the expression levels of four NF-YAs (BnNF-YA9, BnNF-YA10, BnNF-YA11, and BnNF-YA12) and five NF-YBs (BnNF-YB1, BnNF-YB8, BnNF-YB10, BnNF-YB13, and BnNF-YB14) were greatly induced. The expression profiles of 20 of the 27 salinity- or drought-induced BnNF-Ys were also affected by ABA treatment. The expression levels of six NF-YAs (BnNF-YA1, BnNF-YA7, BnNF-YA8, BnNF-YA9, BnNF-YA10, and BnNF-YA12) and seven BnNF-YB members (BnNF-YB2, BnNF-YB3, BnNF-YB7, BnNF-YB10, BnNF-YB11, BnNF-YB13, and BnNF-YB14) and two NF-YC members (BnNF-YC2 and BnNF-YC3) were greatly up-regulated by ABA treatments. Only a few BnNF-Ys were inhibited by the above three treatments. Several NF-Y subfamily members exhibited collinear expression patterns. The promoters of all stress-responsive BnNF-Ys harbored at least two types of stress-related cis-elements, such as ABRE, DRE, MYB, or MYC. The cis-element organization of BnNF-Ys was similar to that of Arabidopsis thaliana, and the promoter regions exhibited higher levels of nucleotide sequence identity with Brassica rapa than with Brassica oleracea. This work represents an entry point for investigating the roles of canola NF-Y proteins during abiotic stress responses and provides insight into

  8. Production and genetic analysis of partial hybrids from intertribal sexual crosses between Brassica napus and Isatis indigotica and progenies.

    PubMed

    Tu, Y Q; Sun, J; Ge, X H; Li, Z Y

    2010-02-01

    With the dye and medicinal plant Isatis indigotica (2n = 14) as pollen parent, intertribal sexual hybrids with Brassica napus (2n = 38, AACC) were obtained and characterized. Among a lot of F1 plants produced, only five hybrids (H1-H5) were distinguished morphologically from female B. napus parents by showing low fertility and some characters of I. indigotica, and also by having different chromosome numbers. H1-H4 had similar but variable chromosome numbers in their somatic and meiotic cells (2n = 25-30), and H5 had 2n = 19, the same number as the haploid of B. napus. GISH analysis of the cells from H1 and H5 detected one I. indigotica chromosome and one or two chromosome terminal fragments. New B. napus types with phenotypic and genomic alterations were produced by H1 after pollination by B. napus and selfing for several generations, and by H5 after selfing. A progeny plant (2n = 20) was derived from H1 after pollination by I. indigotica twice and had a phenotype similar to a certain type of B. rapa, showing that hybrid H1 likely retained all chromosomes of the A genome and lost some of the C genome in parental B. napus. The reasons for the formation of the partial hybrids with unexpected chromosomal complements and for the chromosome elimination are discussed. PMID:20140033

  9. Genome-Wide Identification and Characterization of bZIP Transcription Factors in Brassica oleracea under Cold Stress.

    PubMed

    Hwang, Indeok; Manoharan, Ranjith Kumar; Kang, Jong-Goo; Chung, Mi-Young; Kim, Young-Wook; Nou, Ill-Sup

    2016-01-01

    Cabbages (Brassica oleracea L.) are an important vegetable crop around world, and cold temperature is among the most significant abiotic stresses causing agricultural losses, especially in cabbage crops. Plant bZIP transcription factors play diverse roles in biotic/abiotic stress responses. In this study, 119 putative BolbZIP transcription factors were identified using amino acid sequences from several bZIP domain consensus sequences. The BolbZIP members were classified into 63 categories based on amino acid sequence similarity and were also compared with BrbZIP and AtbZIP transcription factors. Based on this BolbZIP identification and classification, cold stress-responsive BolbZIP genes were screened in inbred lines, BN106 and BN107, using RNA sequencing data and qRT-PCR. The expression level of the 3 genes, Bol008071, Bol033132, and Bol042729, was significantly increased in BN107 under cold conditions and was unchanged in BN106. The upregulation of these genes in BN107, a cold-susceptible inbred line, suggests that they might be significant components in the cold response. Among three identified genes, Bol033132 has 97% sequence similarity to Bra020735, which was identified in a screen for cold-related genes in B. rapa and a protein containing N-rich regions in LCRs. The results obtained in this study provide valuable information for understanding the potential function of BolbZIP transcription factors in cold stress responses. PMID:27314020

  10. Genome-Wide Identification and Characterization of bZIP Transcription Factors in Brassica oleracea under Cold Stress

    PubMed Central

    Hwang, Indeok; Manoharan, Ranjith Kumar; Kang, Jong-Goo; Chung, Mi-Young; Kim, Young-Wook; Nou, Ill-Sup

    2016-01-01

    Cabbages (Brassica oleracea L.) are an important vegetable crop around world, and cold temperature is among the most significant abiotic stresses causing agricultural losses, especially in cabbage crops. Plant bZIP transcription factors play diverse roles in biotic/abiotic stress responses. In this study, 119 putative BolbZIP transcription factors were identified using amino acid sequences from several bZIP domain consensus sequences. The BolbZIP members were classified into 63 categories based on amino acid sequence similarity and were also compared with BrbZIP and AtbZIP transcription factors. Based on this BolbZIP identification and classification, cold stress-responsive BolbZIP genes were screened in inbred lines, BN106 and BN107, using RNA sequencing data and qRT-PCR. The expression level of the 3 genes, Bol008071, Bol033132, and Bol042729, was significantly increased in BN107 under cold conditions and was unchanged in BN106. The upregulation of these genes in BN107, a cold-susceptible inbred line, suggests that they might be significant components in the cold response. Among three identified genes, Bol033132 has 97% sequence similarity to Bra020735, which was identified in a screen for cold-related genes in B. rapa and a protein containing N-rich regions in LCRs. The results obtained in this study provide valuable information for understanding the potential function of BolbZIP transcription factors in cold stress responses. PMID:27314020

  11. Comparative mapping of Raphanus sativus genome using Brassica markers and quantitative trait loci analysis for the Fusarium wilt resistance trait.

    PubMed

    Yu, Xiaona; Choi, Su Ryun; Ramchiary, Nirala; Miao, Xinyang; Lee, Su Hee; Sun, Hae Jeong; Kim, Sunggil; Ahn, Chun Hee; Lim, Yong Pyo

    2013-10-01

    Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum is a serious disease in cruciferous plants, including the radish (Raphanus sativus). To identify quantitative trait loci (QTL) or gene(s) conferring resistance to FW, we constructed a genetic map of R. sativus using an F2 mapping population derived by crossing the inbred lines '835' (susceptible) and 'B2' (resistant). A total of 220 markers distributed in 9 linkage groups (LGs) were mapped in the Raphanus genome, covering a distance of 1,041.5 cM with an average distance between adjacent markers of 4.7 cM. Comparative analysis of the R. sativus genome with that of Arabidopsis thaliana and Brassica rapa revealed 21 and 22 conserved syntenic regions, respectively. QTL mapping detected a total of 8 loci conferring FW resistance that were distributed on 4 LGs, namely, 2, 3, 6, and 7 of the Raphanus genome. Of the detected QTL, 3 QTLs (2 on LG 3 and 1 on LG 7) were constitutively detected throughout the 2-year experiment. QTL analysis of LG 3, flanked by ACMP0609 and cnu_mBRPGM0085, showed a comparatively higher logarithm of the odds (LOD) value and percentage of phenotypic variation. Synteny analysis using the linked markers to this QTL showed homology to A. thaliana chromosome 3, which contains disease-resistance gene clusters, suggesting conservation of resistance genes between them. PMID:23864230

  12. Changes in the Proteome of Xylem Sap in Brassica oleracea in Response to Fusarium oxysporum Stress.

    PubMed

    Pu, Zijing; Ino, Yoko; Kimura, Yayoi; Tago, Asumi; Shimizu, Motoki; Natsume, Satoshi; Sano, Yoshitaka; Fujimoto, Ryo; Kaneko, Kentaro; Shea, Daniel J; Fukai, Eigo; Fuji, Shin-Ichi; Hirano, Hisashi; Okazaki, Keiichi

    2016-01-01

    Fusarium oxysporum f.sp. conlutinans (Foc) is a serious root-invading and xylem-colonizing fungus that causes yellowing in Brassica oleracea. To comprehensively understand the interaction between F. oxysporum and B. oleracea, composition of the xylem sap proteome of the non-infected and Foc-infected plants was investigated in both resistant and susceptible cultivars using liquid chromatography-tandem mass spectrometry (LC-MS/MS) after in-solution digestion of xylem sap proteins. Whole genome sequencing of Foc was carried out and generated a predicted Foc protein database. The predicted Foc protein database was then combined with the public B. oleracea and B. rapa protein databases downloaded from Uniprot and used for protein identification. About 200 plant proteins were identified in the xylem sap of susceptible and resistant plants. Comparison between the non-infected and Foc-infected samples revealed that Foc infection causes changes to the protein composition in B. oleracea xylem sap where repressed proteins accounted for a greater proportion than those of induced in both the susceptible and resistant reactions. The analysis on the proteins with concentration change > = 2-fold indicated a large portion of up- and down-regulated proteins were those acting on carbohydrates. Proteins with leucine-rich repeats and legume lectin domains were mainly induced in both resistant and susceptible system, so was the case of thaumatins. Twenty-five Foc proteins were identified in the infected xylem sap and 10 of them were cysteine-containing secreted small proteins that are good candidates for virulence and/or avirulence effectors. The findings of differential response of protein contents in the xylem sap between the non-infected and Foc-infected samples as well as the Foc candidate effectors secreted in xylem provide valuable insights into B. oleracea-Foc interactions. PMID:26870056

  13. Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus.

    PubMed

    Körber, Niklas; Bus, Anja; Li, Jinquan; Parkin, Isobel A P; Wittkop, Benjamin; Snowdon, Rod J; Stich, Benjamin

    2016-01-01

    In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations. PMID:27066036

  14. Glyphosate drift promotes changes in fitness and transgene gene flow in canola (Brassica napus) and hybrids

    PubMed Central

    Londo, Jason P.; Bautista, Nonnatus S.; Sagers, Cynthia L.; Lee, E. Henry; Watrud, Lidia S.

    2010-01-01

    Background and Aims With the advent of transgenic crops, genetically modified, herbicide-resistant Brassica napus has become a model system for examining the risks and potential ecological consequences of escape of transgenes from cultivation into wild compatible species. Escaped transgenic feral B. napus and hybrids with compatible weedy species have been identified outside of agriculture and without the apparent selection for herbicide resistance. However, herbicide (glyphosate) exposure can extend beyond crop field boundaries, and a drift-level of herbicide could function as a selective agent contributing to increased persistence of transgenes in the environment. Methods The effects of a drift level (0·1 × the field application rate) of glyphosate herbicide and varied levels of plant competition were examined on plant fitness-associated traits and gene flow in a simulated field plot, common garden experiment. Plants included transgenic, glyphosate-resistant B. napus, its weedy ancestor B. rapa, and hybrid and advanced generations derived from them. Key Results The results of this experiment demonstrate reductions in reproductive fitness for non-transgenic genotypes and a contrasting increase in plant fitness for transgenic genotypes as a result of glyphosate-drift treatments. Results also suggest that a drift level of glyphosate spray may influence the movement of transgenes among transgenic crops and weeds and alter the processes of hybridization and introgression in non-agronomic habitats by impacting flowering phenology and pollen availability within the community. Conclusions The results of this study demonstrate the potential for persistence of glyphosate resistance transgenes in weedy plant communities due to the effect of glyphosate spray drift on plant fitness. Additionally, glyphosate drift has the potential to change the gene-flow dynamics between compatible transgenic crops and weeds, simultaneously reducing direct introgression into weedy species

  15. Changes in the Proteome of Xylem Sap in Brassica oleracea in Response to Fusarium oxysporum Stress

    PubMed Central

    Pu, Zijing; Ino, Yoko; Kimura, Yayoi; Tago, Asumi; Shimizu, Motoki; Natsume, Satoshi; Sano, Yoshitaka; Fujimoto, Ryo; Kaneko, Kentaro; Shea, Daniel J.; Fukai, Eigo; Fuji, Shin-Ichi; Hirano, Hisashi; Okazaki, Keiichi

    2016-01-01

    Fusarium oxysporum f.sp. conlutinans (Foc) is a serious root-invading and xylem-colonizing fungus that causes yellowing in Brassica oleracea. To comprehensively understand the interaction between F. oxysporum and B. oleracea, composition of the xylem sap proteome of the non-infected and Foc-infected plants was investigated in both resistant and susceptible cultivars using liquid chromatography-tandem mass spectrometry (LC-MS/MS) after in-solution digestion of xylem sap proteins. Whole genome sequencing of Foc was carried out and generated a predicted Foc protein database. The predicted Foc protein database was then combined with the public B. oleracea and B. rapa protein databases downloaded from Uniprot and used for protein identification. About 200 plant proteins were identified in the xylem sap of susceptible and resistant plants. Comparison between the non-infected and Foc-infected samples revealed that Foc infection causes changes to the protein composition in B. oleracea xylem sap where repressed proteins accounted for a greater proportion than those of induced in both the susceptible and resistant reactions. The analysis on the proteins with concentration change > = 2-fold indicated a large portion of up- and down-regulated proteins were those acting on carbohydrates. Proteins with leucine-rich repeats and legume lectin domains were mainly induced in both resistant and susceptible system, so was the case of thaumatins. Twenty-five Foc proteins were identified in the infected xylem sap and 10 of them were cysteine-containing secreted small proteins that are good candidates for virulence and/or avirulence effectors. The findings of differential response of protein contents in the xylem sap between the non-infected and Foc-infected samples as well as the Foc candidate effectors secreted in xylem provide valuable insights into B. oleracea-Foc interactions. PMID:26870056

  16. Agronomic and Seed Quality Traits Dissected by Genome-Wide Association Mapping in Brassica napus

    PubMed Central

    Körber, Niklas; Bus, Anja; Li, Jinquan; Parkin, Isobel A. P.; Wittkop, Benjamin; Snowdon, Rod J.; Stich, Benjamin

    2016-01-01

    In Brassica napus breeding, traits related to commercial success are of highest importance for plant breeders. However, such traits can only be assessed in an advanced developmental stage. Molecular markers genetically linked to such traits have the potential to accelerate the breeding process of B. napus by marker-assisted selection. Therefore, the objectives of this study were to identify (i) genome regions associated with the examined agronomic and seed quality traits, (ii) the interrelationship of population structure and the detected associations, and (iii) candidate genes for the revealed associations. The diversity set used in this study consisted of 405 B. napus inbred lines which were genotyped using a 6K single nucleotide polymorphism (SNP) array and phenotyped for agronomic and seed quality traits in field trials. In a genome-wide association study, we detected a total of 112 associations between SNPs and the seed quality traits as well as 46 SNP-trait associations for the agronomic traits with a P < 1.28e-05 (Bonferroni correction of α = 0.05) for the inbreds of the spring and winter trial. For the seed quality traits, a single SNP-sulfur concentration in seeds (SUL) association explained up to 67.3% of the phenotypic variance, whereas for the agronomic traits, a single SNP-blossom color (BLC) association explained up to 30.2% of the phenotypic variance. In a basic local alignment search tool (BLAST) search within a distance of 2.5 Mbp around these SNP-trait associations, 62 hits of potential candidate genes with a BLAST-score of ≥100 and a sequence identity of ≥70% to A. thaliana or B. rapa could be found for the agronomic SNP-trait associations and 187 hits of potential candidate genes for the seed quality SNP-trait associations. PMID:27066036

  17. De Novo Assembly and Developmental Transcriptome Analysis of the Small White Butterfly Pieris rapae.

    PubMed

    Qi, Lixing; Fang, Qi; Zhao, Lei; Xia, Hao; Zhou, Yuxun; Xiao, Junhua; Li, Kai; Ye, Gongyin

    2016-01-01

    The small white butterfly Pieris rapae is one of the most destructive pests of Brassicaceae. Yet little is understood about its genes involved in development. To facilitate research on P. rapae, we sequenced the transcriptome of P. rapae during six developmental stages, including the egg, three larval stages, the pupa, and the adult. In total, 240 million high-quality reads were obtained. De novo assembly generated 96,069 unigenes with an average length of 1353 nt. Of these, 31,629 unigenes had homologs as determined by a blastx search against the NR database with a cut-off e-value of 10-5. Clusters of Orthologous Groups of proteins (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to functionally annotate those genes. Then, 849 genes involved in seven canonical development signaling pathway were identified, including dozens of key genes such as Hippo, Notch, and JAK2. A total of 21,883 differentially expressed (cut-off of 2-fold) unigenes were detected across the developmental stages, most of which were found between the egg and first larval stages. Interestingly, only 34 differentially expressed unigenes, most of which are cuticle protein related genes, were detected with a cut-off of 210-fold. Furthermore, we identified 32 heat shock protein (Hsp) genes that were expressed with complete open reading frames. Based on phylogenetic trees of the Hsp genes, we found that Hsp genes with close evolutionary relationships had similar expression pattern. Additionally, partial pattern recognition receptors genes were found to be developmental regulated. This study provides comprehensive sequence resources for P. rapae and numerous differential expressed genes, and these findings will lay the foundation for future functional genomics studies on this species. PMID:27428371

  18. RAPA: a novel in vitro method to evaluate anti-bacterial skin cleansing products.

    PubMed

    Ansari, S A; Gafur, R B; Jones, K; Espada, L A; Polefka, T G

    2010-04-01

    Development of efficacious anti-bacterial skin cleansing products has been limited by the availability of a pre-clinical (in vitro) method to predict clinical efficacy adequately. We report a simple and rapid method, designated as rapid agar plate assay (RAPA), that uses the bacteriological agar surface as a surrogate substrate for skin and combines elements of two widely used in vivo (clinical) methods (Agar Patch and Cup Scrub). To simulate the washing of the human hand or forearm skin with the test product, trypticase soy agar plates were directly washed with the test product and rinsed under running tap water. After air-drying the washed plates, test bacteria (Staphylococcus aureus or Escherichia coli) were applied and the plates were incubated at 37 degrees C for 18-24 h. Using S. aureus as the test organism, anti-bacterial bar soap containing triclocarbanilide showed a strong linear relationship (R(2) = 0.97) between bacterial dose and their per cent reduction. A similar dose-response relationship (R(2) = 0.96) was observed for anti-bacterial liquid hand soap against E. coli. RAPA was able to distinguish between anti-bacterial products based on the nature and level of actives in them. In limited comparative tests, results obtained by RAPA were comparable with the results obtained by clinical agar patch and clinical cup scrub methods. In conclusion, RAPA provides a simple, rugged and reproducible in vitro method for testing the relative efficacy of anti-bacterial skin cleansing products with a likelihood of comparable clinical efficacy. Further testing is warranted to improve the clinical predictability of this method. PMID:19818085

  19. Mayolenes: labile defensive lipids from the glandular hairs of a caterpillar (Pieris rapae).

    PubMed

    Smedley, Scott R; Schroeder, Frank C; Weibel, Douglas B; Meinwald, Jerrold; Lafleur, Katie A; Renwick, J Alan; Rutowski, Ronald; Eisner, Thomas

    2002-05-14

    Larvae of the European cabbage butterfly, Pieris rapae (Pieridae), are beset with glandular hairs, bearing droplets of a clear oily secretion at their tip. The fluid consists primarily of a series of chemically labile, unsaturated lipids, the mayolenes, which are derived from 11-hydroxylinolenic acid. In bioassays with the ant Crematogaster lineolata, the secretion was shown to be potently deterrent, indicating that the fluid plays a defensive role in nature. PMID:11997469

  20. De Novo Assembly and Developmental Transcriptome Analysis of the Small White Butterfly Pieris rapae

    PubMed Central

    Qi, Lixing; Fang, Qi; Zhao, Lei; Xia, Hao; Zhou, Yuxun; Xiao, Junhua; Li, Kai; Ye, Gongyin

    2016-01-01

    The small white butterfly Pieris rapae is one of the most destructive pests of Brassicaceae. Yet little is understood about its genes involved in development. To facilitate research on P. rapae, we sequenced the transcriptome of P. rapae during six developmental stages, including the egg, three larval stages, the pupa, and the adult. In total, 240 million high-quality reads were obtained. De novo assembly generated 96,069 unigenes with an average length of 1353 nt. Of these, 31,629 unigenes had homologs as determined by a blastx search against the NR database with a cut-off e-value of 10−5. Clusters of Orthologous Groups of proteins (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to functionally annotate those genes. Then, 849 genes involved in seven canonical development signaling pathway were identified, including dozens of key genes such as Hippo, Notch, and JAK2. A total of 21,883 differentially expressed (cut-off of 2-fold) unigenes were detected across the developmental stages, most of which were found between the egg and first larval stages. Interestingly, only 34 differentially expressed unigenes, most of which are cuticle protein related genes, were detected with a cut-off of 210-fold. Furthermore, we identified 32 heat shock protein (Hsp) genes that were expressed with complete open reading frames. Based on phylogenetic trees of the Hsp genes, we found that Hsp genes with close evolutionary relationships had similar expression pattern. Additionally, partial pattern recognition receptors genes were found to be developmental regulated. This study provides comprehensive sequence resources for P. rapae and numerous differential expressed genes, and these findings will lay the foundation for future functional genomics studies on this species. PMID:27428371

  1. Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa–B. oleracea monosomic alien addition lines

    PubMed Central

    Heneen, Waheeb K.; Geleta, Mulatu; Brismar, Kerstin; Xiong, Zhiyong; Pires, J. Chris; Hasterok, Robert; Stoute, Andrew I.; Scott, Roderick J.; King, Graham J.; Kurup, Smita

    2012-01-01

    Background and Aims Brassica rapa and B. oleracea are the progenitors of oilseed rape B. napus. The addition of each chromosome of B. oleracea to the chromosome complement of B. rapa results in a series of monosomic alien addition lines (MAALs). Analysis of MAALs determines which B. oleracea chromosomes carry genes controlling specific phenotypic traits, such as seed colour. Yellow-seeded oilseed rape is a desirable breeding goal both for food and livestock feed end-uses that relate to oil, protein and fibre contents. The aims of this study included developing a missing MAAL to complement an available series, for studies on seed colour control, chromosome homoeology and assignment of linkage groups to B. oleracea chromosomes. Methods A new batch of B. rapa–B. oleracea aneuploids was produced to generate the missing MAAL. Seed colour and other plant morphological features relevant to differentiation of MAALs were recorded. For chromosome characterization, Snow's carmine, fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used. Key Results The final MAAL was developed. Morphological traits that differentiated the MAALs comprised cotyledon number, leaf morphology, flower colour and seed colour. Seed colour was controlled by major genes on two B. oleracea chromosomes and minor genes on five other chromosomes of this species. Homoeologous pairing was largely between chromosomes with similar centromeric positions. FISH, GISH and a parallel microsatellite marker analysis defined the chromosomes in terms of their linkage groups. Conclusions A complete set of MAALs is now available for genetic, genomic, evolutionary and breeding perspectives. Defining chromosomes that carry specific genes, physical localization of DNA markers and access to established genetic linkage maps contribute to the integration of these approaches, manifested in the confirmed correspondence of linkage groups with specific chromosomes. Applications include marker

  2. Brassica napus Genome Possesses Extraordinary High Number of CAMTA Genes and CAMTA3 Contributes to PAMP Triggered Immunity and Resistance to Sclerotinia sclerotiorum.

    PubMed

    Rahman, Hafizur; Xu, You-Ping; Zhang, Xuan-Rui; Cai, Xin-Zhong

    2016-01-01

    Calmodulin-binding transcription activators (CAMTAs) play important roles in various plant biological processes including disease resistance and abiotic stress tolerance. Oilseed rape (Brassica napus L.) is one of the most important oil-producing crops worldwide. To date, compositon of CAMTAs in genomes of Brassica species and role of CAMTAs in resistance to the devastating necrotrophic fungal pathogen Sclerotinia sclerotiorum are still unknown. In this study, 18 CAMTA genes were identified in oilseed rape genome through bioinformatics analyses, which were inherited from the nine copies each in its progenitors Brassica rapa and Brassica oleracea and represented the highest number of CAMTAs in a given plant species identified so far. Gene structure, protein domain organization and phylogentic analyses showed that the oilseed rape CAMTAs were structurally similar and clustered into three major groups as other plant CAMTAs, but had expanded subgroups CAMTA3 and CAMTA4 genes uniquely in rosids species occurring before formation of oilseed rape. A large number of stress response-related cis-elements existed in the 1.5 kb promoter regions of the BnCAMTA genes. BnCAMTA genes were expressed differentially in various organs and in response to treatments with plant hormones and the toxin oxalic acid (OA) secreted by S. sclerotiorum as well as the pathogen inoculation. Remarkably, the expression of BnCAMTA3A1 and BnCAMTA3C1 was drastically induced in early phase of S. sclerotiorum infection, indicating their potential role in the interactions between oilseed rape and S. sclerotiorum. Furthermore, inoculation analyses using Arabidopsis camta mutants demonstrated that Atcamta3 mutant plants exhibited significantly smaller disease lesions than wild-type and other Atcamta mutant plants. In addition, compared with wild-type plants, Atcamta3 plants accumulated obviously more hydrogen peroxide in response to the PAMP chitin and exhibited much higher expression of the CGCG

  3. Brassica napus Genome Possesses Extraordinary High Number of CAMTA Genes and CAMTA3 Contributes to PAMP Triggered Immunity and Resistance to Sclerotinia sclerotiorum

    PubMed Central

    Rahman, Hafizur; Xu, You-Ping; Zhang, Xuan-Rui; Cai, Xin-Zhong

    2016-01-01

    Calmodulin-binding transcription activators (CAMTAs) play important roles in various plant biological processes including disease resistance and abiotic stress tolerance. Oilseed rape (Brassica napus L.) is one of the most important oil-producing crops worldwide. To date, compositon of CAMTAs in genomes of Brassica species and role of CAMTAs in resistance to the devastating necrotrophic fungal pathogen Sclerotinia sclerotiorum are still unknown. In this study, 18 CAMTA genes were identified in oilseed rape genome through bioinformatics analyses, which were inherited from the nine copies each in its progenitors Brassica rapa and Brassica oleracea and represented the highest number of CAMTAs in a given plant species identified so far. Gene structure, protein domain organization and phylogentic analyses showed that the oilseed rape CAMTAs were structurally similar and clustered into three major groups as other plant CAMTAs, but had expanded subgroups CAMTA3 and CAMTA4 genes uniquely in rosids species occurring before formation of oilseed rape. A large number of stress response-related cis-elements existed in the 1.5 kb promoter regions of the BnCAMTA genes. BnCAMTA genes were expressed differentially in various organs and in response to treatments with plant hormones and the toxin oxalic acid (OA) secreted by S. sclerotiorum as well as the pathogen inoculation. Remarkably, the expression of BnCAMTA3A1 and BnCAMTA3C1 was drastically induced in early phase of S. sclerotiorum infection, indicating their potential role in the interactions between oilseed rape and S. sclerotiorum. Furthermore, inoculation analyses using Arabidopsis camta mutants demonstrated that Atcamta3 mutant plants exhibited significantly smaller disease lesions than wild-type and other Atcamta mutant plants. In addition, compared with wild-type plants, Atcamta3 plants accumulated obviously more hydrogen peroxide in response to the PAMP chitin and exhibited much higher expression of the CGCG

  4. Expression of leaf blight resistance in Brassica leafy greens under field conditions and inheritance of resistance in a Brassica juncea source

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Brassica leafy greens are one of the most economically important vegetable commodities grown in the southeastern United States, and more than 28,000 metric tons of these crops are harvested in the U.S. annually. Collards and kale (Brassica oleracea L.), mustard greens (Brassica juncea L.) and turni...

  5. Construction of Near Isogenic Lines in Brassica oleracea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The single species Brassica oleracea encompasses a remarkable diversity of morphotypes, including cauliflower, broccoli, kohlrabi, marrowstem kale, cabbage, and Brussels sprouts as well as rapid-flowering morphologically simple genotypes reminiscent of Arabidopsis. To dissect the molecular basis of ...

  6. Ectopic expression of the Brassica SHOOTMERISTEMLESS attenuates the deleterious effects of the auxin transport inhibitor TIBA on somatic embryo number and morphology.

    PubMed

    Elhiti, Mohamed; Stasolla, Claudio

    2011-02-01

    The auxin transport inhibitor 2,3,5-triiodobenzoic acid (TIBA) is a useful compound for investigating the role of auxin flow during plant growth and development. In Arabidopsis lines, applications of TIBA during the induction phase of somatic embryogenesis inhibit embryo development and induce the differentiation of the meristematic cells of the shoot apical meristem (SAM), leading to the fusion of the cotyledons. These abnormalities were associated to changes in the expression levels of auxin transporter genes (PINs) and endogenous distribution of IAA. Treatments of TIBA caused a rapid accumulation of IAA within the epidermal and cortical root cells of the explants (bent-cotyledon zygotic embryos), as well as in the apical and sub-apical cells of the callus generated by the surface of the cotyledons of the explants. Within the callus only a few cells acquired meristematic characteristics, and this was associated to low expression levels of genes involved in embryogenic cell fate acquisition, such as WUSCHEL (WUS), LEAFY COTYLEDON 1 and 2. All these deleterious effects were attenuated when TIBA was administered to lines over-expressing SHOOT MERISTEMLESS (STM) isolated from Brassica oleracea (Bo), B. napus (Bn), and B. rapa (Br). Of interest, TIBA-treated explants of Arabidopsis lines over-expressing the Brassica STM were able to produce a large number of embryogenic cells and somatic embryos which exhibited a normal morphology and two distinct cotyledons. A proposed reason for this behaviour was ascribed to the ability of the transformed tissue to retain a normal distribution of auxin in the presence of TIBA. Proper localization of auxin might be required for the normal expression of several genes needed for the acquisition of embryogenic competence and formation of somatic embryos. PMID:21421384

  7. Four genes encoding MYB28, a major transcriptional regulator of the aliphatic glucosinolate pathway, are differentially expressed in the allopolyploid Brassica juncea.

    PubMed

    Augustine, Rehna; Majee, Manoj; Gershenzon, Jonathan; Bisht, Naveen C

    2013-11-01

    Glucosinolates are Capparales-specific secondary metabolites that have immense potential in human health and agriculture. Unlike Arabidopsis thaliana, our knowledge about glucosinolate regulators in the Brassica crops is sparse. In the current study, four MYB28 homologues were identified (BjuMYB28-1,-2,-3,-4) from the polyploid Brassica juncea, and the effects of allopolyploidization on the divergence of gene sequence, structure, function, and expression were assessed. The deduced protein sequences of the four BjuMYB28 genes showed 76.1-83.1% identity with the Arabidopsis MYB28. Phylogenetic analysis revealed that the four BjuMYB28 proteins have evolved via the hybridization and duplication processes forming the B. juncea genome (AABB) from B. rapa (AA) and B. nigra (BB), while retaining high levels of sequence conservation. Mutant complementation and over-expression studies in A. thaliana showed that all four BjuMYB28 genes encode functional MYB28 proteins and resulted in similar aliphatic glucosinolate composition and content. Detailed expression analysis using qRT-PCR assays and promoter-GUS lines revealed that the BjuMYB28 genes have both tissue- and cell-specific expression partitioning in B. juncea. The two B-genome origin BjuMYB28 genes had more abundant transcripts during the early stages of plant development than the A-genome origin genes. However, with the onset of the reproductive phase, expression levels of all four BjuMYB28 increased significantly, which may be necessary for producing and maintaining high amounts of aliphatic glucosinolates during the later stages of plant development. Taken together, our results suggest that the four MYB28 genes are differentially expressed and regulated in B. juncea to play discrete though overlapping roles in controlling aliphatic glucosinolate biosynthesis. PMID:24043856

  8. Expression of salicylic acid-related genes in Brassica oleracea var. capitata during Plasmodiophora brassicae infection.

    PubMed

    Manoharan, Ranjith Kumar; Shanmugam, Ashokraj; Hwang, Indeok; Park, Jong-In; Nou, Ill-Sup

    2016-06-01

    Brassica oleracea var. capitata (cabbage) is an important vegetable crop in Asian countries such as Korea, China, and Japan. Cabbage production is severely affected by clubroot disease caused by the soil-borne plant pathogen Plasmodiophora brassicae. During clubroot development, methyl salicylate (MeSA) is biosynthesized from salicylic acid (SA) by methyltransferase. In addition, methyl salicylate esterase (MES) plays a major role in the conversion of MeSA back into free SA. The interrelationship between MES and methytransferases during clubroot development has not been fully explored. To begin to examine these relationships, we investigated the expression of MES genes in disease-susceptible and disease-resistant plants during clubroot development. We identified three MES-encoding genes potentially involved in the defense against pathogen attack. We found that SS1 was upregulated in both the leaves and roots of B. oleracea during P. brassicae infection. These results support the conclusion that SA biosynthesis is suppressed during pathogen infection in resistant plants. We also characterized the expression of a B. oleracea BSMT gene, which appears to be involved in glycosylation rather than MeSA biosynthesis. Our results provide insight into the functions and interactions of genes for MES and methyltransferase during infection. Taken together, our findings indicate that MES genes are important candidates for use to control clubroot diseases. PMID:27171821

  9. Oil body biogenesis during Brassica napus embryogenesis.

    PubMed

    He, Yu-Qing; Wu, Yan

    2009-08-01

    Although the oil body is known to be an important membrane enclosed compartment for oil storage in seeds, we have little understanding about its biogenesis during embryogenesis. In the present study we investigated the oil body emergence and variations in Brassica napus cv. Topas. The results demonstrate that the oil bodies could be detected already at the heart stage, at the same time as the embryos began to turn green, and the starch grains accumulated in the chloroplast stroma. In comparison, we have studied the development of oil bodies between Arabidopsis thaliana wild type (Col) and the low-seed-oil mutant wrinkled1-3. We observed that the oil body development in the embryos of Col is similar to that of B. napus cv. Topas, and that the size of the oil bodies was obviously smaller in the embryos of wrinkled1-3. Our results suggest that the oil body biogenesis might be coupled with the embryo chloroplast. PMID:19686376

  10. Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors under Multiple Stresses in Brassica napus.

    PubMed

    He, Yajun; Mao, Shaoshuai; Gao, Yulong; Zhu, Liying; Wu, Daoming; Cui, Yixin; Li, Jiana; Qian, Wei

    2016-01-01

    WRKY transcription factors play important roles in responses to environmental stress stimuli. Using a genome-wide domain analysis, we identified 287 WRKY genes with 343 WRKY domains in the sequenced genome of Brassica napus, 139 in the A sub-genome and 148 in the C sub-genome. These genes were classified into eight groups based on phylogenetic analysis. In the 343 WRKY domains, a total of 26 members showed divergence in the WRKY domain, and 21 belonged to group I. This finding suggested that WRKY genes in group I are more active and variable compared with genes in other groups. Using genome-wide identification and analysis of the WRKY gene family in Brassica napus, we observed genome duplication, chromosomal/segmental duplications and tandem duplication. All of these duplications contributed to the expansion of the WRKY gene family. The duplicate segments that were detected indicated that genome duplication events occurred in the two diploid progenitors B. rapa and B. olearecea before they combined to form B. napus. Analysis of the public microarray database and EST database for B. napus indicated that 74 WRKY genes were induced or preferentially expressed under stress conditions. According to the public QTL data, we identified 77 WRKY genes in 31 QTL regions related to various stress tolerance. We further evaluated the expression of 26 BnaWRKY genes under multiple stresses by qRT-PCR. Most of the genes were induced by low temperature, salinity and drought stress, indicating that the WRKYs play important roles in B. napus stress responses. Further, three BnaWRKY genes were strongly responsive to the three multiple stresses simultaneously, which suggests that these 3 WRKY may have multi-functional roles in stress tolerance and can potentially be used in breeding new rapeseed cultivars. We also found six tandem repeat pairs exhibiting similar expression profiles under the various stress conditions, and three pairs were mapped in the stress related QTL regions

  11. Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors under Multiple Stresses in Brassica napus

    PubMed Central

    He, Yajun; Mao, Shaoshuai; Gao, Yulong; Zhu, Liying; Wu, Daoming; Cui, Yixin; Li, Jiana; Qian, Wei

    2016-01-01

    WRKY transcription factors play important roles in responses to environmental stress stimuli. Using a genome-wide domain analysis, we identified 287 WRKY genes with 343 WRKY domains in the sequenced genome of Brassica napus, 139 in the A sub-genome and 148 in the C sub-genome. These genes were classified into eight groups based on phylogenetic analysis. In the 343 WRKY domains, a total of 26 members showed divergence in the WRKY domain, and 21 belonged to group I. This finding suggested that WRKY genes in group I are more active and variable compared with genes in other groups. Using genome-wide identification and analysis of the WRKY gene family in Brassica napus, we observed genome duplication, chromosomal/segmental duplications and tandem duplication. All of these duplications contributed to the expansion of the WRKY gene family. The duplicate segments that were detected indicated that genome duplication events occurred in the two diploid progenitors B. rapa and B. olearecea before they combined to form B. napus. Analysis of the public microarray database and EST database for B. napus indicated that 74 WRKY genes were induced or preferentially expressed under stress conditions. According to the public QTL data, we identified 77 WRKY genes in 31 QTL regions related to various stress tolerance. We further evaluated the expression of 26 BnaWRKY genes under multiple stresses by qRT-PCR. Most of the genes were induced by low temperature, salinity and drought stress, indicating that the WRKYs play important roles in B. napus stress responses. Further, three BnaWRKY genes were strongly responsive to the three multiple stresses simultaneously, which suggests that these 3 WRKY may have multi-functional roles in stress tolerance and can potentially be used in breeding new rapeseed cultivars. We also found six tandem repeat pairs exhibiting similar expression profiles under the various stress conditions, and three pairs were mapped in the stress related QTL regions

  12. RapA2 Is a Calcium-binding Lectin Composed of Two Highly Conserved Cadherin-like Domains That Specifically Recognize Rhizobium leguminosarum Acidic Exopolysaccharides*

    PubMed Central

    Abdian, Patricia L.; Caramelo, Julio J.; Ausmees, Nora; Zorreguieta, Angeles

    2013-01-01

    In silico analyses have revealed a conserved protein domain (CHDL) widely present in bacteria that has significant structural similarity to eukaryotic cadherins. A CHDL domain was shown to be present in RapA, a protein that is involved in autoaggregation of Rhizobium cells, biofilm formation, and adhesion to plant roots as shown by us and others. Structural similarity to cadherins suggested calcium-dependent oligomerization of CHDL domains as a mechanistic basis for RapA action. Here we show by circular dichroism spectroscopy, light scattering, isothermal titration calorimetry, and other methods that RapA2 from Rhizobium leguminosarum indeed exhibits a cadherin-like β-sheet conformation and that its proper folding and stability are dependent on the binding of one calcium ion per protein molecule. By further in silico analysis we also reveal that RapA2 consists of two CHDL domains and expand the range of CHDL-containing proteins in bacteria and archaea. However, light scattering assays at various concentrations of added calcium revealed that RapA2 formed neither homo-oligomers nor hetero-oligomers with RapB (a distinct CHDL protein), indicating that RapA2 does not mediate cellular interactions through a cadherin-like mechanism. Instead, we demonstrate that RapA2 interacts specifically with the acidic exopolysaccharides (EPSs) produced by R. leguminosarum in a calcium-dependent manner, sustaining a role of these proteins in the development of the biofilm matrix made of EPS. Because EPS binding by RapA2 can only be attributed to its two CHDL domains, we propose that RapA2 is a calcium-dependent lectin and that CHDL domains in various bacterial and archaeal proteins confer carbohydrate binding activity to these proteins. PMID:23235153

  13. Genome-wide identification, phylogeny, duplication, and expression analyses of two-component system genes in Chinese cabbage (Brassica rapa ssp. pekinensis).

    PubMed

    Liu, Zhenning; Zhang, Mei; Kong, Lijun; Lv, Yanxia; Zou, Minghua; Lu, Gang; Cao, Jiashu; Yu, Xiaolin

    2014-08-01

    In plants, a two component system (TCS) composed of sensor histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs) has been employed in cytokinin signal transduction. A TCS exhibits important functions in diverse biological processes, including plant growth, development, and response to environmental stimuli. Conducting an exhaustive search of the Chinese cabbage genome, a total of 20 HK(L) (11 HKs and 9 HKLs), 8 HP (7 authentic and 1 pseudo), and 57 RR (21 Type-A, 17 Type-B, 4 Type-C, and 15 pseudo) proteins were identified. The structures, conserved domains, and phylogenetic relationships of these protein-coding genes were analysed in detail. The duplications, evolutionary patterns, and divergence of the TCS genes were investigated. The transcription levels of TCS genes in various tissues, organs, and developmental stages were further analysed to obtain information of the functions of these genes. Cytokinin-related binding elements were found in the putative promoter regions of Type-A BrRR genes. Furthermore, gene expression patterns to adverse environmental stresses (drought and high salinity) and exogenous phytohormones (tZ and ABA) were investigated. Numerous stress-responsive candidate genes were obtained. Our systematic analyses provided insights into the characterization of the TCS genes in Chinese cabbage and basis for further functional studies of such genes. PMID:24585003

  14. Fine mapping and identification of candidate Bo-or gene controlling orange head of Chinese cabbage (Brassica rapa L. ssp. Pekinensis)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Orange head Chinese cabbage accumulates significant amounts of carotenoids with enhanced nutritional quality. To develop molecular markers for breeding of Chinese cabbage lines with high carotenoid content and to isolate the candidate gene underlying carotenoid synthesis, we performed fine mapping ...

  15. Beyond Punnett Squares: Student Word Association and Explanations of Phenotypic Variation through an Integrative Quantitative Genetics Unit Investigating Anthocyanin Inheritance and Expression in "Brassica rapa" Fast Plants

    ERIC Educational Resources Information Center

    Batzli, Janet M.; Smith, Amber R.; Williams, Paul H.; McGee, Seth A.; Dosa, Katalin; Pfammatter, Jesse

    2014-01-01

    Genetics instruction in introductory biology is often confined to Mendelian genetics and avoids the complexities of variation in quantitative traits. Given the driving question "What determines variation in phenotype (Pv)? (Pv=Genotypic variation Gv + environmental variation Ev)," we developed a 4-wk unit for an inquiry-based laboratory…

  16. Cyanide detoxification in an insect herbivore: Molecular identification of β-cyanoalanine synthases from Pieris rapae.

    PubMed

    van Ohlen, Maike; Herfurth, Anna-Maria; Kerbstadt, Henrike; Wittstock, Ute

    2016-03-01

    Cyanogenic compounds occur widely in the plant kingdom. Therefore, many herbivores are adapted to the presence of these compounds in their diet by either avoiding cyanide release or by efficient cyanide detoxification mechanisms. The mechanisms of adaptation are not fully understood. Larvae of Pieris rapae (Lepidoptera: Pieridae) are specialist herbivores on glucosinolate-containing plants. They are exposed to cyanide during metabolism of phenylacetonitrile, a product of benzylglucosinolate breakdown catalyzed by plant myrosinases and larval nitrile-specifier protein (NSP) in the gut. Cyanide is metabolized to β-cyanoalanine and thiocyanate in the larvae. Here, we demonstrate that larvae of P. rapae possess β-cyanoalanine activity in their gut. We have identified three gut-expressed cDNAs designated PrBSAS1-PrBSAS3 which encode proteins with similarity to β-substituted alanine synthases (BSAS). Characterization of recombinant PrBSAS1-PrBSAS3 shows that they possess β-cyanoalanine activity. In phylogenetic trees, PrBSAS1-PrBSAS3, the first characterized insect BSAS, group together with a characterized mite β-cyanoalanine synthase and bacterial enzymes indicating a similar evolutionary history. PMID:26714205

  17. Use of nucleotide sequence data to identify a microsporidian pathogen of Pieris rapae (Lepidoptera, Pieridae).

    PubMed

    Malone, L A; McIvor, C A

    1996-11-01

    Nucleotide sequence was determined for a portion of genomic DNA which spans the V4 variable region of the small subunit ribosomal RNA gene of an unidentified microsporidium from the cabbage white butterfly, Pieris rapae (174 base pairs). Comparison with equivalent sequence data obtained here for two other microsporidian species, Nosema bombycis (240 base pairs) and Nosema bombi (200 base pairs), and from the GenBank database for 11 other microsporidian species suggests that the unidentified species from P. rapae is most closely related to some Vairimorpha species. Light and electron microscopic observations of the developmental stages of this parasite were in accord with this. Infection experiments conducted at 20 and 26 degrees C demonstrated temperature-dependent dimorphism, with the production of both binucleate free spores (mean dimensions: 3.8 x 1.8 microns; 10-13 polar filament coils) and membrane-bound uninucleate octospores (mean dimensions: 3.1 x 1.9 microns). Macrospores (mean dimensions 8.0 x 2.1 microns) were also observed. Sites of infection were the gut epithelium, the Malpighian tubules, the salivary glands, and the fat body. Infections were found in all insect life stages, including the egg. This microsporidium was found to be indistinguishable from both Nosema mesnili (Paillot) and Microsporidium (Thelohania) mesnili (Paillot) and we propose that these species be combined and transferred to the genus Vairimorpha Pilley. PMID:8931362

  18. Remote sensing and the assessment of prehistoric productivity in cultivation practices of Rapa Nui, Chile

    NASA Astrophysics Data System (ADS)

    Kovalchik, Jacob

    While there is a tradition that the population of Rapa Nui was large during prehistory, there is remarkably little evidence used to support to these claims. This study represents an empirically-based estimate of pre-contact agricultural productivity to create a sound evaluation of Rapa Nui's prehistoric population. In this study, I map the spatial distributions of lithic mulching using satellite imagery, RPV aerial photography, in situ spectral reflectance analyses, and supervised and sub-pixel image classification methods. Using the results of these analyses, I estimate the total mapped lithic mulch area and combine this estimate with previously documented distributions of manavai. Together these analyses provide an estimate of the extent of these two important cultivation practices and an upper-limit magnitude of prehistoric food production. The spatial data, when evaluated in conjunction with appropriate agricultural cultivation statistic proxies, are then used to conservatively quantify the island's carrying capacity. In my final analysis, I argue that the prehistoric productivity was insufficient to support the large populations that have been suggested.

  19. Morphological Clines and Weak Drift along an Urbanization Gradient in the Butterfly, Pieris rapae

    PubMed Central

    Schoville, Sean D.; Widmer, Ivo; Deschamps-Cottin, Magali; Manel, Stéphanie

    2013-01-01

    Urban areas are increasing globally, providing opportunities for biodiversity researchers to study the process in which species become established in novel, highly disturbed habitats. This ecological process can be understood through analyses of morphological and genetic variation, which can shed light on patterns of neutral and adaptive evolution. Previous studies have shown that urban populations often diverge genetically from non-urban source populations. This could occur due to neutral genetic drift, but an alternative is that selection could lead to allele frequency changes in urban populations. The development of genome scan methods provides an opportunity to investigate these outcomes from samples of genetic variation taken along an urbanization gradient. Here we examine morphological variation in wing size and diversity at neutral amplified fragment length polymorphisms in the butterfly Pieris rapae L. (Lepidoptera, Pieridae) sampled from the center to the periphery of Marseille. We utilize established and novel environmental correlation approaches to scan genetic variation for evidence of selection. We find significant morphological differences in urban populations, as well as weak genetic structure and decreased genetic diversity in urban versus non-urban sites. However, environmental correlation tests provide little support for selection in our dataset. Our comparison of different methods and allele frequency clines suggests that loci identified as significant are false positives. Although there is some indication that selection may be acting on wing size in urban butterflies, genetic analyses suggest P. rapae are undergoing neutral drift. PMID:24386146

  20. [Role of Bacterial Adhesin RAPA1 in Formation of Efficient Symbiosis of Rhizobium leguminosarum with Bean Plants].

    PubMed

    Nigmatullina, L R; Lavina, A M; Vershinina, Z R; Baimiev, Al Kh

    2015-01-01

    Bacterial adhesins, the proteins responsible for attachment of plant growth-promoting rhizobacteria to plant roots, are involved in formation of stable associative symbioses. In the present work enhanced expression of the rapA1 adhesin gene in Rhizobium leguminosarum PVu5 was shown to improve the efficiency of nodulation on bean roots inoculated with the modified strain. The rapA1 gene was cloned into the pJN105Turbo plasmid, this construct was used for transformation of R. leguminosarum PVu5, bean plants were inoculated by this transgenic strain, and efficiency of root nodule formation was determined. In the plants treated with rapA1-transgenic rhizobia, the number of root nodules was on average two times higher than in the plants inoculated with the original strain. Aggregation of R. leguminosarum was achieved when the rapA1 gene expression was enhanced either in rhizobia or in the co-cultured modified strain E. coli pJN105TurboRapA1. PMID:26964360

  1. A Novel Formulation of Bacillus thuringiensis for the Control of Brassica Leaf Beetle, Phaedon brassicae (Coleoptera: Chrysomelidae).

    PubMed

    Kim, Eunseong; Jeoung, Sujin; Park, Youngjin; Kim, Kunwoo; Kim, Yonggyun

    2015-12-01

    Cabbage is a major vegetable crop over the world. Various insect pests can affect cabbage production. Excessive spray of chemical insecticides can lead to the development of insecticide resistance with various adverse effects on the environment and humans. Brassica leaf beetle, Phaedon brassicae Baly, is a coleopteran pest. Both larvae and adults cause damages to cabbage. The objective of this study was to develop an effective microbial insecticide against P. brassicae by adding an immunosuppressive agent to Bacillus thuringiensis (Bt). The immunosuppressive agent was chosen from bacterial cultured broth of Photorhabdus temperata subsp. temperata (Ptt). Reverse phase HPLC revealed that Ptt-cultured broth possessed at least two eicosanoid biosynthesis inhibitors (oxindole and indole) in its hexane extract. The bacterial cultured broth exhibited potent immunosuppressive activity against P. brassicae. Based on toxicity results, B. thuringiensis subsp. tenebrionis (BtT) was selected from four strains of Bts. When Ptt-cultured broth was added to spore-producing BtT cells, the insecticidal activities of BtT against both larvae and adults of P. brassicae were significantly increased. This bacterial mixture applied to develop a "Bt-Plus," which was formulated by mixing BtT cells (10(11) spores per ml) and 48-h Ptt-cultured broth along with additives (surfactant and preservative). When Bt-Plus was sprayed to cabbage infested by P. brassicae at 1,000-fold dilution, the mixture exhibited much higher control efficacy than BtT treatment alone, suggesting it could be used as a novel Bt insecticide for the control of P. brassicae. PMID:26470390

  2. Induced polyploidization in Brassica campestris L. (Brassicaceae).

    PubMed

    Kumar, G; Dwivedi, K

    2014-01-01

    Present experimental design has been made up to obtain crop with higher ploidy level via synthetic polyploidization. Since ploidy manipulation is generally associated with the obtainment of some increased enviable traits of the crop and also provides them greater adaptability to unfavorable or harsh circumstances as compared to its diploids counterparts. Thus, herein present research autotetraploids of Brassica campestris L. have been lucratively achieved by the application of colchicine. Two methods of treatment were utilized i.e. seed treatment and seedling treatment. No polyploidy could be obtained through seed treatment while seedling treatment responded well towards polyploidy. However, the status of autotetraploidy has been confirmed by cytomorphological investigations of treated plants as against its diploids counterparts. For the purpose, morphological parameters such as increased stomata size, pollen diameter, flower size, reproductive organs whereas reduction in plant height, leaf length, leaf breadth, stomata frequency, number of flowers/inflorescence etc. were appraised. Further, cytological observations w