Sample records for sarson
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Population Structure and Phylogenetic Relationships in a Diverse Panel of Brassica rapa L.
Bird, Kevin A.; An, Hong; Gazave, Elodie; Gore, Michael A.; Pires, J. Chris; Robertson, Larry D.; Labate, Joanne A.
2017-01-01
The crop species Brassica rapa L. has significant economic importance around the world. However, the global distribution and complex evolutionary history of the species has made investigating its genetic population structure difficult. Crop domestication and improvement has resulted in extreme phenotypic diversity and subspecies that are used for oilseed, food for human consumption, and fodder for livestock. These subspecies include the oilseed morphotypes. oleifera (turnip rape), ssp. dichotoma (brown sarson/toria), ssp. trilocularis (yellow sarson); ssp. rapa (turnip); and Asian leafy vegetables ssp. pekinensis (Chinese cabbage), ssp. chinensis (bok choy), ssp. nipposinica (mizuna/mibuna), ssp. rapifera (rapini/broccoli rabe), ssp. narinosa (tatsoi), ssp parachinensis (choy sum), and ssp. perviridis (komatsuna). To date, studies have had insufficient sampling to determine the relationship of all morphotypes, especially oilseed morphotypes, and questions remain over the contribution of morphotype and geographic origin to population structure. We used genotyping-by-sequencing to score 18,272 single nucleotide polymorphism markers in a globally diverse panel of 333 B. rapa National Plant Germplasm System accessions that included 10 recognized subspecies. Our population genetic and phylogenetic analyses were broadly congruent and revealed five subpopulations that were largely reflective of morphotype and geography. These subpopulations were 1. European turnips/oilseed, 2. Asian turnips/oilseed, 3. yellow/brown sarson (ssp. trilocularis and ssp. dichotoma), 4. Chinese cabbage (ssp. pekinensis), and 5. bok choy, choy sum, and tatsoi (ssp. chinensis, ssp. parachinensis, ssp. narinosa). Additionally, we found evidence of polyphyly and/or paraphyly, particularly for oilseed morphotypes (ssp. oleifera and ssp. dichotoma) and turnips. The results of this study have provided improved resolution to the genetic and phylogenetic relationships of subspecies within the species B. rapa. Understanding of these relationships is key to the future genetic study and improvement of this globally important crop species. PMID:28348571
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Kaur, Navneet; Bhullar, Makhan S
2015-05-01
Terminal residues of pendimethalin and oxyfluorfen applied in autumn sugarcane- and vegetables-based intercropping systems were analyzed in peas (Pisum sativum), cabbage (Brassica oleracea), garlic (Allium sativum), gobhi sarson (Brassica napus), and raya (Brassica juncea). The study was conducted in winter season in 2010-2011 and in 2011-2012 at Ludhiana, India. Pendimethalin at 0.56 kg and 0.75 kg ha(-1) was applied immediately after sowing of gobhi sarson, raya, peas, garlic, and 2 days before transplanting of cabbage seedlings. Oxyfluorfen at 0.17 kg and 0.23 kg ha(-1) was applied immediately after sowing of peas and garlic and 2 days before transplanting of cabbage seedlings intercropped in autumn sugarcane. Representative samples of these vegetables were collected at 75, 90, 100, and 165 days after application of herbicides and analyzed by high-performance liquid chromatograph (HPLC) with diode array detector for residues. The residue level of pendimethalin and oxyfluorfen in mature vegetables was found to be below the limit of quantification which is 0.05 mg kg(-1) for both the herbicides. The soil samples were collected at 0, 7, 15, 30, 45, and 60 days after the application of their herbicides. The residues of herbicides in soil samples were found to be below the detectability limit of 0.05 mg kg(-1) after 60 days in case of pendimethalin and after 45 days in case of oxyfluorfen.
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Genomic inferences of domestication events are corroborated by written records in Brassica rapa.
Qi, Xinshuai; An, Hong; Ragsdale, Aaron P; Hall, Tara E; Gutenkunst, Ryan N; Chris Pires, J; Barker, Michael S
2017-07-01
Demographic modelling is often used with population genomic data to infer the relationships and ages among populations. However, relatively few analyses are able to validate these inferences with independent data. Here, we leverage written records that describe distinct Brassica rapa crops to corroborate demographic models of domestication. Brassica rapa crops are renowned for their outstanding morphological diversity, but the relationships and order of domestication remain unclear. We generated genomewide SNPs from 126 accessions collected globally using high-throughput transcriptome data. Analyses of more than 31,000 SNPs across the B. rapa genome revealed evidence for five distinct genetic groups and supported a European-Central Asian origin of B. rapa crops. Our results supported the traditionally recognized South Asian and East Asian B. rapa groups with evidence that pak choi, Chinese cabbage and yellow sarson are likely monophyletic groups. In contrast, the oil-type B. rapa subsp. oleifera and brown sarson were polyphyletic. We also found no evidence to support the contention that rapini is the wild type or the earliest domesticated subspecies of B. rapa. Demographic analyses suggested that B. rapa was introduced to Asia 2,400-4,100 years ago, and that Chinese cabbage originated 1,200-2,100 years ago via admixture of pak choi and European-Central Asian B. rapa. We also inferred significantly different levels of founder effect among the B. rapa subspecies. Written records from antiquity that document these crops are consistent with these inferences. The concordance between our age estimates of domestication events with historical records provides unique support for our demographic inferences. © 2017 John Wiley & Sons Ltd.
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Basnet, Ram Kumar; Moreno-Pachon, Natalia; Lin, Ke; Bucher, Johan; Visser, Richard G F; Maliepaard, Chris; Bonnema, Guusje
2013-12-01
Brassica seeds are important as basic units of plant growth and sources of vegetable oil. Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. We conducted a global microarray gene co-expression analysis by measuring transcript abundance of developing seeds from two diverse B. rapa morphotypes: a pak choi (leafy-type) and a yellow sarson (oil-type), and two of their doubled haploid (DH) progenies, (1) to study the timing of metabolic processes in developing seeds, (2) to explore the major transcriptional differences in developing seeds of the two morphotypes, and (3) to identify the optimum stage for a genetical genomics study in B. rapa seed. Seed developmental stages were similar in developing seeds of pak choi and yellow sarson of B. rapa; however, the colour of embryo and seed coat differed among these two morphotypes. In this study, most transcriptional changes occurred between 25 and 35 DAP, which shows that the timing of seed developmental processes in B. rapa is at later developmental stages than in the related species B. napus. Using a Weighted Gene Co-expression Network Analysis (WGCNA), we identified 47 "gene modules", of which 27 showed a significant association with temporal and/or genotypic variation. An additional hierarchical cluster analysis identified broad spectra of gene expression patterns during seed development. The predominant variation in gene expression was according to developmental stages rather than morphotype differences. Since lipids are the major storage compounds of Brassica seeds, we investigated in more detail the regulation of lipid metabolism. Four co-regulated gene clusters were identified with 17 putative cis-regulatory elements predicted in their 1000 bp upstream region, either specific or common to different lipid metabolic pathways. This is the first study of genome-wide profiling of transcript abundance during seed development in B. rapa. The identification of key physiological events, major expression patterns, and putative cis-regulatory elements provides useful information to construct gene regulatory networks in B. rapa developing seeds and provides a starting point for a genetical genomics study of seed quality traits.
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Impact of distillery effluent on germination behaviour of Brassica napus L.
Malaviya, Piyush; Sharma, Anuradha
2011-01-01
The study has been focused on effect of untreated distillery effluent (Devans Breweries Ltd., Jammu) on germination of gobi sarson (Brassica napus. L. var. Punjabi Special). Six treatments (E0.... E100) each having three replicates were made. E0 was taken as control in which tap water was used for irrigation of the plants. For E20, E40, E60, E80 and E100, different concentrations i.e. 20, 40, 60, 80 and 100% of effluent were used for irrigation, respectively. The 100% sample of distillery effluent analyzed for various physicochemical parameters showed acidic nature (pH 4.0) and higher values of COD (2496 mg l(-1)), TDS (799.7 mg l(-1)) and chlorides (1408 mg l(-1)). The parameters e.g. percent germination, germination index, speed of germination, and peak value were highest in treatment receiving 20% effluent concentration which also showed minimum values for percent inhibition, germination period, and delay index.
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Datta, J K; Banerjee, A; Sikdar, M Saha; Gupta, S; Mondal, N K
2009-09-01
Field experiment was carried out during November 2006 to February 2007 under old alluvial soil to evaluate the impact of combined dose of chemical fertilizer, biofertilizer in combination with compost for the yellow sarson (Brassica campestries cv. B9) in a randomized block design replicated thrice. Various morpho-physiological parameters viz., plant population, length of shoot and root, leaf area index (LAI), crop growth rate (CGR), net assimilation rate (NAR), yield attributes viz., number of siliquae per plant, number of seeds/siliquae, 1000 seed weight (test weight), seed yield, stover yield and physiological and biochemical parameters viz., pigment content, sugar, amino acid, protein, ascorbic acid content in physiologically active leaf were performed. The treatment T1 i.e., 40% less N fertilizer 25% less P fertilizer K fertilizer constant + 12 kg ha(-1) biofertilizer (Azophos) and organic manure (compost) @ 5Mt ha(-1), showed the maximum chlorophyll accumulation (10. 231 mg g(-1) freshweight), highest seed/siliquae (25.143), test weight of seeds (4. 861g) and highest seed yield (10.661 tha(-1)). A comparison between all the morphological, anatomical, physiological and biochemical parameters due to application of chemical fertilizer; bio-fertilizer and compost alone and in combination and their impact on soil microorganism, flora and fauna will throw a sound environmental information.
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Tuning growth cycles of Brassica crops via natural antisense transcripts of BrFLC.
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. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
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Genetic architecture of the circadian clock and flowering time in Brassica rapa.
Lou, P; Xie, Q; Xu, X; Edwards, C E; Brock, M T; Weinig, C; McClung, C R
2011-08-01
The circadian clock serves to coordinate physiology and behavior with the diurnal cycles derived from the daily rotation of the earth. In plants, circadian rhythms contribute to growth and yield and, hence, to both agricultural productivity and evolutionary fitness. Arabidopsis thaliana has served as a tractable model species in which to dissect clock mechanism and function, but it now becomes important to define the extent to which the Arabidopsis model can be extrapolated to other species, including crops. Accordingly, we have extended our studies to the close Arabidopsis relative and crop species, Brassica rapa. We have investigated natural variation in circadian function and flowering time among multiple B. rapa collections. There is wide variation in clock function, based on a robust rhythm in cotyledon movement, within a collection of B. rapa accessions, wild populations and recombinant inbred lines (RILs) derived from a cross between parents from two distinct subspecies, a rapid cycling Chinese cabbage (ssp. pekinensis) and a Yellow Sarson oilseed (ssp. trilocularis). We further analyzed the RILs to identify the quantitative trait loci (QTL) responsible for this natural variation in clock period and temperature compensation, as well as for flowering time under different temperature and day length settings. Most clock and flowering-time QTL mapped to overlapping chromosomal loci. We have exploited micro-synteny between the Arabidopsis and B. rapa genomes to identify candidate genes for these QTL.
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Genetic Dissection of Leaf Development in Brassica rapa Using a Genetical Genomics Approach1[W
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
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Mind the Roots: Phenotyping Below-Ground Crop Diversity and Its Influence on Final Yield
NASA Astrophysics Data System (ADS)
Nieters, C.; Guadagno, C. R.; Lemli, S.; Hosseini, A.; Ewers, B. E.
2017-12-01
Changes in global climate patterns and water regimes are having profound impacts on worldwide crop production. An ever-growing population paired with increasing temperatures and unpredictable periods of severe drought call for accurate modeling of future crop yield. Although novel approaches are being developed in high-throughput, above-ground image phenotyping, the below-ground plant system is still poorly phenotyped. Collection of plant root morphology and hydraulics are needed to inform mathematical models to reliably estimate yields of crops grown in sub-optimal conditions. We used Brassica rapa to inform our model as it is a globally cultivated crop with several functionally diverse cultivars. Specifically, we use 7 different accessions from oilseed (R500 and Yellow Sarson), leafy type (Pac choi and Chinese cabbage), a vegetable turnip, and two Wisconsin Fast Plants (Imb211 and Fast Plant self-compatible), which have shorter life cycles and potentially large differences in allocation to roots. Bi-weekly, we harvested above and below-ground biomass to compare the varieties in terms of carbon allocation throughout their life cycle. Using WinRhizo software, we analyzed root system length and surface area to compare and contrast root morphology among cultivars. Our results confirm that root structural characteristics are crucial to explain plant water use and carbon allocation. The root:shoot ratio reveals a significant (p < 0.01) difference among crop accession. To validate the procedure across different varieties and life stages we also compared surface area results from the image-based technology to dry biomass finding a strong linear relationship (R2= 0.85). To assess the influence of a diverse above-ground morphology on the root system we also measured above-ground anatomical and physiological traits such as gas exchange, chlorophyll content, and chlorophyll a fluorescence. A thorough analysis of the root system will clarify carbon dynamics and hydraulics at the whole-plant level, improving final yield predictions.
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NASA Astrophysics Data System (ADS)
Tackley, P. J.; Aurnou, J. M.; Aubert, J.
2009-04-01
Due to the absence of an atmosphere and proximity to the Sun, Mercury's surface temperature varies laterally by several 100s K, even when averaged over long time periods. The dominant variation in time-averaged surface T occurs from pole to equator (~225 K) [1]. The resonant relationship between Mercury's orbit and rotation results in a smaller longitudinal variation (~100 K) [1]. Here we demonstrate, using models of mantle convection in a 3-D spherical shell, that this stationary lateral variation in surface temperature has a small but significant influence on mantle convection and on the lateral variation of heat flux across the core-mantle boundary (CMB). We evaluate the possible observational signature of this laterally-varying convection in terms of boundary topography, stress distribution, gravity and moment of inertia tensor. We furthermore test whether the lateral variation in CMB flux is capable of driving a thermal wind dynamo, i.e., weak dynamo action with no internally-driven core convective motions. For Mercury's mantle we assume a dry olivine rheology including both diffusion creep and disclocation creep with rheological parameters such as activation energy and volume taken from the synthesis of [2]. We assume decaying radiogenic heat sources with the same concentration as in the bulk silicate Earth, and a parameterised model of core cooling. The models are run for 4.5 Ga from a relatively hot initial state with random initial perturbations. We use the code StagYY, which uses a finite-volume discretization on a spherical yin-yang grid and a multigrid solver [3]. Results in spherical axisymmetric geometry, compare a case with constant surface temperature to one with a latitude-dependent surface temperature. The system forms about 3 convection cells from pole to equator. Although the results look similar to first order, in the latitude-dependent case the convection is noticably more sluggish and colder towards the pole. In CMB flux, both cases display large oscillations due to convection cells. A pole-to-equator trend is superimposed on this for the case with laterally-varying surface temperature. Although the amplitude of this long-wavelength variation is smaller than that of the within-cell variation, its long-wavelength nature might be effective in driving thermal winds in the core. Results in a full 3-D spherical shell indicate that convection adopts a cellular structure with a polygonal network of downwellings and plume-like upwellings, as is usually obtained for stagnant lid convection, for example, in the recent 3-D spherical Mercury models of [4]. This is in notable contrast to the models of [5], in which linear upwellings were obtained. This difference could be because the initial perturbations used by [5] used a small number of low-order spherical harmonics, i.e., a long-wavelength pattern with particular symmetries, whereas our initial perturbations are random white noise. The origin of this difference requires further investigation. The pattern of CMB heat flux shows a strong l=2, m=0 pattern, again with superimposed small-scale variations due to convection cells. The surface geoid displays an very dominant (2,0) pattern, which would be a strong diagnostic of this behaviour. These models are being further analysed for boundary topography and stress distribution. Models of planetary dynamos have traditionally depended upon the concept that secular cooling and internal radioactive decay are responsible for genererating convective fluid motions within the core [e.g. 6]. Some models, of Earth's dynamo in particular, also include thermal winds --shear flows driven by heat flux variations along the core-mantle boundary -- that modify the dynamo process [e.g. 7]. We have now shown, following the work of [8], that thermal winds themselves are capable of driving dynamo action in planetary cores (Fig. 4). In fully self-consistent, three-dimensional models, we find that thermal wind dynamos do not require a net heat flux to emanate from the core and can operate even when the core fluid is neutrally stratified. In these models, the dynamo is powered externally by thermal energy stored in the mantle. This dynamo mechanism can occur on planetary bodies, such as Mercury, which are likely to have weak net heat fluxes from their cores but possess significant core-mantle boundary heat flux variations (Figures 1 - 3). We plan to use the pattern of CMB heat flux from the mantle models as a boundary condition for core models, in order to determine the feasibility of thermal wind dynamo action occurring in Mercury's core. References [1] Aharonson, O., et al. (2004) EPSL, 218, 261-268. [2] Karato, S. and Wu, P. (1993) Sci., 260, 771-778. [3] Tackley, P. J. (2008) PEPI, doi: 10.1016/j.pepi.2008.08.005.. [4] Breuer, D. et al. (2007) Sp. Sci. Rev., 132, 229-260. [5] King, S. D. (2008) Nature Geoscience, 1, 229-232. [5] Heimpel, M. H. et al. (2005) EPSL, 236, 542-557. [7] Willis, A., et al. (2007) PEPI, 165, 83-92. [8] Sarson, G., (2003) PRSL A, 459, 1241-1259. [9] Aubert, J., et al. (2008) GJI, 172, 945-956.