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Sample records for genetically diverse germplasm

  1. Assessing genetic diversity in Valencia peanut germplasm using SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Valencia peanuts (Arachis hypogaea L.ssp. fastigiata var. fastigiata) are well known for their in-shell market value. Assessment of genetic diversity of the available Valencia germplasm is key to the success of developing improved cultivars with desirable agronomic and quality traits. In the pres...

  2. Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

    PubMed Central

    Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun

    2013-01-01

    Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949

  3. Genetic diversity of water use efficiency in Jerusalem artichoke (Helianthus tuberosus L.) germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity in crop germplasm is an important resource for crop improvement, but information on genetic diversity is rare for Jerusalem artichoke, especially for traits related to water use efficiency. The objectives of this study were to investigate genetic variations for water use and water...

  4. Genetic diversity of worldwide Jerusalem artichoke (Helianthus tuberosus) germplasm as revealed by RAPD markers.

    PubMed

    Wangsomnuk, P P; Khampa, S; Wangsomnuk, P; Jogloy, S; Mornkham, T; Ruttawat, B; Patanothai, A; Fu, Y B

    2011-01-01

    Jerusalem artichoke (Helianthus tuberosus) is a wild relative of the cultivated sunflower (H. annuus); it is an old tuber crop that has recently received renewed interest. We used RAPD markers to characterize 147 Jerusalem artichoke accessions from nine countries. Thirty RAPD primers were screened; 13 of them detected 357 reproducible RAPD bands, of which 337 were polymorphic. Various diversity analyses revealed several different patterns of RAPD variation. More than 93% of the RAPD variation was found within accessions of a country. Weak genetic differentiation was observed between wild and cultivated accessions. Six groups were detected in this germplasm set. Four ancestral groups were found for the Canadian germplasm. The most genetically distinct accessions were identified. These findings provide useful diversity information for understanding the Jerusalem artichoke gene pool, for conserving Jerusalem artichoke germplasm, and for choosing germplasm for genetic improvement. PMID:22194201

  5. Genetic diversity in the germplasm of black pepper determined by EST-SSR markers.

    PubMed

    Wu, B D; Fan, R; Hu, L S; Wu, H S; Hao, C Y

    2016-01-01

    This study aimed to assess genetic diversity in the germplasm of black pepper from around the world using SSR markers from EST. In total, 13 markers were selected and successfully amplified the target loci across the black pepper germplasm. All the EST-SSR markers showed high levels of polymorphisms with an average polymorphism information content of 0.93. The genetic similarity coefficients among all accessions ranged from 0.724 to 1.000, with an average of 0.867. These results indicated that black pepper germplasms possess a complex genetic background and high genetic diversity. Based on a cluster analysis, 148 black pepper germplasms were grouped in two major clades: the Neotropics and the Asian tropics. Peperomia pellucida was grouped separately and distantly from all other accessions. These results generally agreed with the genetic and geographic distances. However, the Asian tropics clade did not cluster according to their geographic origins. In addition, compared with the American accessions, the Asian wild accessions and cultivated accessions grouped together, indicating a close genetic relationship. This verified the origin of black pepper. The newly developed EST-SSRs are highly valuable resources for the conservation of black pepper germplasm diversity and for black pepper breeding. PMID:27050963

  6. Genome-wide distribution of genetic diversity and linkage disequilibrium in elite sugar beet germplasm

    PubMed Central

    2011-01-01

    Background Characterization of population structure and genetic diversity of germplasm is essential for the efficient organization and utilization of breeding material. The objectives of this study were to (i) explore the patterns of population structure in the pollen parent heterotic pool using different methods, (ii) investigate the genome-wide distribution of genetic diversity, and (iii) assess the extent and genome-wide distribution of linkage disequilibrium (LD) in elite sugar beet germplasm. Results A total of 264 and 238 inbred lines from the yield type and sugar type inbreds of the pollen parent heterotic gene pools, respectively, which had been genotyped with 328 SNP markers, were used in this study. Two distinct subgroups were detected based on different statistical methods within the elite sugar beet germplasm set, which was in accordance with its breeding history. MCLUST based on principal components, principal coordinates, or lapvectors had high correspondence with the germplasm type information as well as the assignment by STRUCTURE, which indicated that these methods might be alternatives to STRUCTURE for population structure analysis. Gene diversity and modified Roger's distance between the examined germplasm types varied considerably across the genome, which might be due to artificial selection. This observation indicates that population genetic approaches could be used to identify candidate genes for the traits under selection. Due to the fact that r2 >0.8 is required to detect marker-phenotype association explaining less than 1% of the phenotypic variance, our observation of a low proportion of SNP loci pairs showing such levels of LD suggests that the number of markers has to be dramatically increased for powerful genome-wide association mapping. Conclusions We provided a genome-wide distribution map of genetic diversity and linkage disequilibrium for the elite sugar beet germplasm, which is useful for the application of genome-wide association

  7. Gene banks offer breeders access to germplasm: Germplasm collections help to preserve genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This article describes a coordinated system for conserving woody landscape plant germplasm in the United States. It provides an overview of the woody landscape plant germplasm collections of the USDA/ARS National Plant Germplasm System, a description of the Woody Landscape Plant Crop Germplasm Comm...

  8. Diversity of the breadfruit complex (Artocarpus, Moraceae): Genetic characterization of critical germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breadfruit (Artocarpus altilis, Moraceae) is a traditional staple starch crop in Oceania and has been introduced throughout the tropics. This study uses microsatellite markers to characterize the genetic diversity of breadfruit and its wild relatives housed in the USDA National Plant Germplasm Syste...

  9. Genetic Diversity of Lablab (L. purpureus) Germplasm Assessed by SSR Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of the USDA Lablab purpureus germplasm collection is unknown and was assessed by using polymorphic simple sequence repeat (SSR) markers derived from Medicago, soybean and cowpea. Phylogenetic analysis partitioned 47 representative accessions into two main clades (wild clade pr...

  10. Evaluation of Genetic Diversity of the USDA Lablab Purpureus Germplasm Collection Using Simple Sequence Repeat Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of the USDA Lablab purpureus germplasm collection is unknown and was assessed by using polymorphic simple sequence repeat (SSR) markers derived from Medicago, soybean and cowpea. Phylogenetic analysis paritioned 47 representative accessions into two main clades (wild clade prod...

  11. Genetic diversity of sweet sorghum germplasm in Mexico using AFLP and SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this work was to evaluate the diversity and genetic relationships between lines and varieties of the sweet sorghum (Sorghum bicolor) germplasm bank of the National Institute for Forestry, Agriculture and Livestock Research, Mexico, using AFLP and SSR markers. The molecular markers ...

  12. Genetic Diversity and Agronomic Improvement of North American Soybean Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    From 1970 to 2008 there were 2,242 soybean cultivars registered in North America through U.S. PVP, U.S. utility patent, and journal registration. Of these, 80% were developed through proprietary and 20% through public programs. The most frequently used germplasm for cultivar development were the cul...

  13. Genetic diversity assessment of Musa spp. germplasm using SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-ARS Tropical Agriculture Research Station is responsible for conserving germplasm of a number of important agricultural crop species. Among these, a Musa spp. collection has been established and is comprised of diploid, triploid and tetraploid accessions of cultivated, ornamental, wild and...

  14. Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics

    PubMed Central

    Melgarejo, Pablo; Legua, Pilar; Garcia-Sanchez, Francisco; Hernández, Francisca

    2016-01-01

    Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop’s wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop’s great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as

  15. Genetic diversity of pomegranate germplasm collection from Spain determined by fruit, seed, leaf and flower characteristics.

    PubMed

    Martinez-Nicolas, Juan J; Melgarejo, Pablo; Legua, Pilar; Garcia-Sanchez, Francisco; Hernández, Francisca

    2016-01-01

    Background. Miguel Hernandez University (Spain) created a germplasm bank of the varieties of pomegranate from different Southeastern Spain localities in order to preserve the crop's wide genetic diversity. Once this collection was established, the next step was to characterize the phenotype of these varieties to determine the phenotypic variability that existed among all the different pomegranate genotypes, and to understand the degree of polymorphism of the morphometric characteristics among varieties. Methods. Fifty-three pomegranate (Punica granatum L.) accessions were studied in order to determine their degree of polymorphism and to detect similarities in their genotypes. Thirty-one morphometric characteristics were measured in fruits, arils, seeds, leaves and flowers, as well as juice characteristics including content, pH, titratable acidity, total soluble solids and maturity index. ANOVA, principal component analysis, and cluster analysis showed that there was a considerable phenotypic diversity (and presumably genetic). Results. The cluster analysis produced a dendrogram with four main clusters. The dissimilarity level ranged from 1 to 25, indicating that there were varieties that were either very similar or very different from each other, with varieties from the same geographical areas being more closely related. Within each varietal group, different degrees of similarity were found, although there were no accessions that were identical. These results highlight the crop's great genetic diversity, which can be explained not only by their different geographical origins, but also to the fact that these are native plants that have not come from genetic improvement programs. The geographic origin could be, in the cases where no exchanges of plant material took place, a key criterion for cultivar clustering. Conclusions. As a result of the present study, we can conclude that among all the parameters analyzed, those related to fruit and seed size as well as the

  16. Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers.

    PubMed

    Rai, Ved Prakash; Kumar, Rajesh; Kumar, Sanjay; Rai, Ashutosh; Kumar, Sanjeet; Singh, Major; Singh, Sheo Pratap; Rai, Awadesh Bahadur; Paliwal, Rajneesh

    2013-10-01

    A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24 %) detected a total of 76 alleles (average, 3.04; range, 2-5). The average polymorphic information content (PIC) was 0.69 (range, 0.29-0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44-0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin. PMID:24431527

  17. Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

    PubMed Central

    Wang, C-H; Zheng, X-M; Xu, Q; Yuan, X-P; Huang, L; Zhou, H-F; Wei, X-H; Ge, S

    2014-01-01

    Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm. On the basis of model-based grouping, neighbour-joining tree and principal coordinate analysis, we confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm. With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and showed that Chinese temperate japonica contained higher diversity than that of global samples, whereas Chinese indica and tropical japonica maintained slightly lower diversity than that present in the global samples. Particularly, we observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups of Chinese cultivars, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments. PMID:24326293

  18. Genetic diversity and relationship of global faba bean (Vicia faba L.) germplasm revealed by ISSR markers.

    PubMed

    Wang, Hai-Fei; Zong, Xu-Xiao; Guan, Jian-Ping; Yang, Tao; Sun, Xue-Lian; Ma, Yu; Redden, Robert

    2012-03-01

    Genetic diversity and relationships of 802 faba bean (Vicia faba L.) landraces and varieties from different geographical locations of China and abroad were examined using ISSR markers. A total of 212 repeatable amplified bands were generated with 11 ISSR primers, of which 209 were polymorphic. Accessions from North China showed highest genetic diversity, while accessions from central China showed low level of diversity. Chinese spring faba bean germplasm was clearly separated from Chinese winter faba bean, based on principal component analysis and UPGMA clustering analysis. Winter accessions from Zhejiang (East China), Jiangxi (East China), Sichuan (Southwest China) and Guizhou (Southwest China) were quite distinct to that from other provinces in China. Great differentiation between Chinese accessions and those from rest of the world was shown with a UPGMA dendrogram. AMOVA analyses demonstrated large variation and differentiation within and among groups of accessions from China. As a continental geographic group, accessions from Europe were genetically closer to those from North Africa. Based on ISSR data, grouping results of accessions from Asia, Europe and Africa were obviously associated with their geographical origin. The overall results indicated that the genetic relationship of faba bean germplasm was closely associated with their geographical origin and their ecological habit. PMID:22204023

  19. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

    PubMed Central

    2013-01-01

    Background The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. Results We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. Conclusions The comprehensive molecular characterization of our grape

  20. Genetic diversity and population structure of the Ethiopian sorghum [Sorghum bicolor (L.) Moench] germplasm collection maintained by the USDA-ARS, National Plant Germplasm System using SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity and population structure present in the Ethiopia sorghum collection maintained by the USDA-ARS, National Plant Germplasm System (USDA-ARS-NPGS) is unknown. In addition, passport information is absent for 83% of these accessions which limit its evaluation and utility. Therefor...

  1. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers.

    PubMed

    Smýkal, P; Bačová-Kerteszová, N; Kalendar, R; Corander, J; Schulman, A H; Pavelek, M

    2011-05-01

    Retrotransposon segments were characterized and inter-retrotransposon amplified polymorphism (IRAP) markers developed for cultivated flax (Linum usitatissimum L.) and the Linum genus. Over 75 distinct long terminal repeat retrotransposon segments were cloned, the first set for Linum, and specific primers designed for them. IRAP was then used to evaluate genetic diversity among 708 accessions of cultivated flax comprising 143 landraces, 387 varieties, and 178 breeding lines. These included both traditional and modern, oil (86), fiber (351), and combined-use (271) accessions, originating from 36 countries, and 10 wild Linum species. The set of 10 most polymorphic primers yielded 141 reproducible informative data points per accession, with 52% polymorphism and a 0.34 Shannon diversity index. The maximal genetic diversity was detected among wild Linum species (100% IRAP polymorphism and 0.57 Jaccard similarity), while diversity within cultivated germplasm decreased from landraces (58%, 0.63) to breeding lines (48%, 0.85) and cultivars (50%, 0.81). Application of Bayesian methods for clustering resulted in the robust identification of 20 clusters of accessions, which were unstratified according to origin or user type. This indicates an overlap in genetic diversity despite disruptive selection for fiber versus oil types. Nevertheless, eight clusters contained high proportions (70-100%) of commercial cultivars, whereas two clusters were rich (60%) in landraces. These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics. PMID:21293839

  2. Assessing and Broadening Genetic Diversity of Elymus sibiricus Germplasm for the Improvement of Seed Shattering.

    PubMed

    Zhang, Zongyu; Zhang, Junchao; Zhao, Xuhong; Xie, Wengang; Wang, Yanrong

    2016-01-01

    Siberian wild rye (Elymus sibiricus L.) is an important native grass in the Qinghai-Tibet Plateau of China. It is difficult to grow for commercial seed production, since seed shattering causes yield losses during harvest. Assessing the genetic diversity and relationships among germplasm from its primary distribution area contributes to evaluating the potential for its utilization as a gene pool to improve the desired agronomic traits. In the study, 40 EST-SSR primers were used to assess the genetic diversity and population structure of 36 E. sibiricus accessions with variation of seed shattering. A total of 380 bands were generated, with an average of 9.5 bands per primer. The polymorphic information content (PIC) ranged from 0.23 to 0.50. The percentage of polymorphic bands (P) for the species was 87.11%, suggesting a high degree of genetic diversity. Based on population structure analysis, four groups were formed, similar to results of principal coordinate analysis (PCoA). The molecular variance analysis (AMOVA) revealed the majority of genetic variation occurred within geographical regions (83.40%). Two genotypes from Y1005 and ZhN06 were used to generate seven F₁ hybrids. The molecular and morphological diversity analysis of F₁ population revealed rich genetic variation and high level of seed shattering variation in F₁ population, resulting in significant improvement of the genetic base and desired agronomic traits. PMID:27376263

  3. Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum l.) germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Utilization of crop diversity held in genebanks is dependent on knowledge of useful traits including those identified genotypically. Target region amplification polymorphism (TRAP) markers were used to evaluate the genetic diversity and relationship among a sample of 263 chickpea landrace germplasm ...

  4. Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic dive...

  5. Assessment of genetic diversity and anthracnose disease response among Zimbabwe sorghum germplasm.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-ARS National Plant Germplasm System maintains a Zimbabwe sorghum collection of 1,235 accessions from different provinces. This germplasm has not been extensively employed in U.S. breeding programs due to the lack of phenotypic and genetic characterization. Therefore, 68 accessions from th...

  6. Evaluation and characterization of a genetically diverse Musa germplasm core subset.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-ARS, Tropical Agriculture Research Station is responsible for curating germplasm of several regionally and internationally important agricultural crops. Evaluation and characterization of Musa (bananas) genetic resources are an important component of programmed research. In a global coll...

  7. Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example.

    PubMed

    Jones, H; Gosman, N; Horsnell, R; Rose, G A; Everest, L A; Bentley, A R; Tha, S; Uauy, C; Kowalski, A; Novoselovic, D; Simek, R; Kobiljski, B; Kondic-Spika, A; Brbaklic, L; Mitrofanova, O; Chesnokov, Y; Bonnett, D; Greenland, A

    2013-07-01

    Hexaploid bread wheat evolved from a rare hybridisation, which resulted in a loss of genetic diversity in the wheat D-genome with respect to the ancestral donor, Aegilops tauschii. Novel genetic variation can be introduced into modern wheat by recreating the above hybridisation; however, the information associated with the Ae. tauschii accessions in germplasm collections is limited, making rational selection of accessions into a re-synthesis programme difficult. We describe methodologies to identify novel diversity from Ae. tauschii accessions that combines Bayesian analysis of genotypic data, sub-species diversity and geographic information that summarises variation in climate and habitat at the collection point for each accession. Comparisons were made between diversity discovered amongst a panel of Ae. tauschii accessions, bread wheat varieties and lines from the CIMMYT synthetic hexaploid wheat programme. The selection of Ae. tauschii accessions based on differing approaches had significant effect on diversity within each set. Our results suggest that a strategy that combines several criteria will be most effective in maximising the sampled variation across multiple parameters. The analysis of multiple layers of variation in ex situ Ae. tauschii collections allows for an informed and rational approach to the inclusion of wild relatives into crop breeding programmes. PMID:23558983

  8. Extensive genetic diversity and low linkage disequilibrium within the COMT locus in Germplasm Enhancement of Maize populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Caffeic acid 3-O-methytransferase (COMT) gene is a prime candidate for cell wall digestibility improvement based on the characterization of brown midrib-3 mutants. We compared the genetic diversity and linkage disequilibrium at COMT locus between populations sampled within the Germplasm Enhance...

  9. Genetic diversity analysis of tree peony germplasm using iPBS markers.

    PubMed

    Duan, Y B; Guo, D L; Guo, L L; Wei, D F; Hou, X G

    2015-01-01

    We examined the genetic diversity of 10 wild species (populations) and 55 varieties of tree peony using inter-primer binding site (iPBS) markers. From a total of 36 iPBS primers, 16 were selected based on polymorphic amplification. The number of bands amplified by each primer ranged from 9 to 19, with an average of 12.88 bands per primer. The length of bands ranged from 100 to 2000 bp, concentrated at 200 to 1800 bp. Sixteen primers amplified 206 bands in total, of which 173 bands were polymorphic with a polymorphism ratio of 83.98%. Each primer amplified 10.81 polymorphic bands on average. The data were then used to construct a phylogenetic tree using unweighted pair group method with arithmetic mean methods. Clustering analysis showed that the genetic relationships among the varieties were not only related to the genetic background or geographic origin, but also to the flowering phase, flower color, and flower type. Our data also indicated that iPBS markers were useful tools for classifying tree peony germplasms and for tree peony breeding, and the specific bands were helpful for molecular identification of tree peony varieties. PMID:26214434

  10. Genetic diversity analysis in Tunisian perennial ryegrass germplasm as estimated by RAPD, ISSR, and morpho-agronomical markers.

    PubMed

    Ghariani, S; Elazreg, H; Chtourou-Ghorbel, N; Chakroun, M; Trifi-Farah, N

    2015-01-01

    Tunisia is rich in diverse forage and pasture species including perennial ryegrass. In order to enhance forage production and improve agronomic performance of this local germplasm, a molecular analysis was undertaken. Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and morpho-agronomical traits markers were used for genetic diversity estimation of ryegrass germplasm after screening 20 spontaneous accessions, including a local and an introduced cultivars. Same mean polymorphism information content values were obtained (0.37) for RAPD and ISSR suggesting that both marker systems were equally effective in determining polymorphisms. The average pairwise genetic distance values were 0.57 (morpho-agronomical traits), 0.68 (RAPD), and 0.51 (ISSR) markers data sets. A higher Shannon diversity index was obtained with ISSR marker (0.57) than for RAPD (0.54) and morpho-agronomical traits (0.36). The Mantel test based on genetic distances of a combination of molecular markers and morpho-agronomical data exhibited a significant correlation between RAPD and ISSR data, suggesting that the use of a combination of molecular techniques was a highly efficient method of estimating genetic variability levels among Tunisian ryegrass germplasm. In summary, results showed that combining molecular and morpho-agronomical markers is an efficient way in assessing the genetic variability among Tunisian ryegrass genotypes. In addition, the combined analysis provided an exhaustive coverage for the analyzed diversity and helped us to identify suitable accessions showed by Beja and Jendouba localities, which present large similarities with cultivated forms and can be exploited for designing breeding programmes, conservation of germplasm and management of ryegrass genetic resources. PMID:26782500

  11. Genetic diversity of wild germplasm of "yerba mate" (Ilex paraguariensis St. Hil.) from Uruguay.

    PubMed

    Cascales, Jimena; Bracco, Mariana; Poggio, Lidia; Gottlieb, Alexandra Marina

    2014-12-01

    The "yerba mate" tree, Ilex paraguariensis St. Hil., is a crop native to subtropical South America, marketed for the elaboration of the highly popular "mate" beverage. The Uruguayan germplasm occupies the southernmost area of the species distribution range and carries adaptations to environments that considerably differ from the current production area. We characterized the genetic variability of the germplasm from this unexplored area by jointly analyzing individuals from the diversification center (ABP, Argentina, Brazil and Paraguay) with 19 nuclear and 11 plastidic microsatellite markers. For the Uruguayan germplasm, we registered 55 alleles (18 % private), and 80 genotypes (44 % exclusive), whereas 63 alleles (28.6 % private) and 81 genotypes (42 % exclusive) were recorded for individuals from ABP. Only two plastidic haplotypes were detected. Distance-based and multilocus genotype analyses showed that individuals from ABP intermingle and that the Uruguayan germplasm is differentiated in three gene-pools. Significant positive correlations between genetic and geographic distances were detected. Our results concur in that ABP individuals harbor greater genetic variation than those from the tail of the distribution, as to the number of alleles (1.15-fold), He (1.19-fold), Rs (1.39-fold), and the between-group genetic distances (1.16-fold). Also the shape of the genetic landscape interpolation analysis suggests that the genetic variation decays southward towards the Uruguayan territory. We showed that Uruguayan germplasm hosts a combination of nuclear alleles not present in the central region, constituting a valuable breeding resource. Future conservation efforts should concentrate in collecting numerous individuals of "yerba mate" per site to gather the existent variation. PMID:25427938

  12. Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding*

    PubMed Central

    Wang, Jun-mei; Yang, Jian-ming; Zhu, Jing-huan; Jia, Qiao-jun; Tao, Yue-zhi

    2010-01-01

    The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat (SSR) genotyping data. The amplified fragments from SSR primers were highly polymorphic in the barley accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 barley accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China. PMID:20872987

  13. Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat

    PubMed Central

    Ren, Jing; Sun, Daokun; Chen, Liang; You, Frank M.; Wang, Jirui; Peng, Yunliang; Nevo, Eviatar; Sun, Dongfa; Luo, Ming-Cheng; Peng, Junhua

    2013-01-01

    Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity. PMID:23538839

  14. Detection and genetic diversity of Grapevine red blotch-associated virus isolates in table grape accessions in the National Clonal Germplasm Repository in California

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The National Germplasm Repository of grapevines and Mediterranean tree fruits, and nut crops maintained by the U.S. Department of Agriculture at the Wolfskill ranch in Winters, California, holds the most genetically diverse collection of grapevines (Vitis spp., Family Vitaceae) in the World. Many o...

  15. GENETIC VARIATION FOR SEED MINERAL AND PROTEIN CONCENTRATION IN DIVERSE GERMPLASM OF CHICKPEA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chickpea (Cicer arietinum) is an important food legume that can provide significant amounts of dietary minerals and protein to humans. In order to better understand the genetic diversity that exists for these nutrients, we have assessed seed mineral concentration and seed protein concentration in 2...

  16. Evaluation of Lespedeza Germplasm Genetic Diversity and Its Phylogenetic Relationship with the Genus Kummerowia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of the genus Lespedeza is not well known and the phylogenetic relationship of Lespedeza with the genus Kummerowia is unclear. We report the first study in which polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers derived from Medicago, cowpea and soybea...

  17. Genetic diversity analysis of faba bean (Vicia faba L.) germplasms using sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

    PubMed

    Hou, W W; Zhang, X J; Shi, J B; Liu, Y J

    2015-01-01

    To investigate genetic diversity and relationships of 101 faba bean (Vicia faba L.), landraces and varieties from different provinces of China and abroad were analyzed by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE). A total of 2625 unambiguous and stable bands from 101 germplasms were detected, and 36 different bands were classified according to the electrophoretic mobility patterns of the proteins as determined by the SDS-PAGE analysis, of which 16 were polymorphic. Besides the common bands, the protein bands of 92, 75, 62, 40, 34, 17, and 13 kDa presented the highest frequencies of 92.08, 90.10, 99.01, 95.05, 95.05, 98.02, and 95.05%, respectively. The other 29 polymorphic protein bands showed higher polymorphism with 16.09 polymorphic bands in average. The genetic similarity of the 101 genotypes tested varied from 0.6111 to 0.9722, with an average of 0.7122. Cluster analysis divided the 101 genotypes into six major clusters, which was consistent with the systematic classification of faba bean done in previous studies. The overall results indicated that SDS-PAGE was a useful tool for genetic diversity analysis and laid a solid foundation for future faba bean breeding. PMID:26535710

  18. Genetic diversity and spatial structure in cacao (Theobroma cacao L.) germplasm from Bolivia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cacao (Theobroma cacao L.) is an important economic crop widely cultivated in the Bolivian Amazon. The germplasm group used by the Bolivian farmers was called “Cacao Nacional Boliviano” (CNB). Wild cacao populations are also found in the Beni River and in the valleys of Andes foot hills. Using DNA...

  19. Genetic diversity analysis of Capsicum spp germplasm bank accessions based on α/β-esterase polymorphism.

    PubMed

    Monteiro, E R; Bronzato, A R; Orasmo, G R; Lopes, A C A; Gomes, R L F; Mangolin, C A; Machado, M F P S

    2013-01-01

    Genetic diversity and structure were analyzed in 10 accessions belonging to Banco Ativo de Germoplasma de Capsicum located at Federal University of Piauí in northwestern Brazil that receives pepper samples grown in community gardens in various regions and Brazilian states. Selections were made from seeds of C. chinense (4 accessions), C. annuum (5 accessions), and C. baccatum (1 accession). Samples consisting of leaves were collected from 4-10 plants of each accession (a total of 85 plants). Native polyacrylamide gel electrophoresis was used to identify α- and β-esterase polymorphisms. Polymorphism was clearly detected in 5 loci. Sixteen alleles were found at 5 α/β-esterase loci of the three Capsicum species. In the C. chinense samples, the highest HO and HE values were 0.3625 and 0.4395, respectively, whereas in C. annuum samples, HO and HE values were 0.2980 and 0.3310, respectively; the estimated HO and HE values in C. chinense samples were higher than those detected in C. annuum samples. A deficit of homozygous individuals was found in C. chinense (FIS = -0.6978) and C. annuum (FIS = 0.7750). Genetic differentiation between C. chinense and C. annuum at these loci was high (FST = 0.1867) indicating that C. chinense and C. annuum are genetically structured species for α/β- esterase isozymes. The esterase analysis showed high genetic diversity among the C. chinense and C. annuum samples and very high genetic differentiation (FST = 0.6321) among the C. chinense and C. annuum samples and the C. baccatum accession. PMID:23661440

  20. Genetic Variation and Association Mapping of Protein Concentration in Brown Rice Using a Diverse Rice Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Protein is the second most abundant constituent in the rice grain next to starch. Association analysis for protein concentration in brown rice was performed using a “Mini-Core” collection, which represents the germplasm diversity found in the USDA world rice collection. Protein concentration was det...

  1. Assessment of the genetic diversity of the Tunisian citrus rootstock germplasm

    PubMed Central

    2012-01-01

    Background Citrus represents a substantial income for farmers in the Mediterranean Basin. However, the Mediterranean citrus industry faces increasing biotic and abiotic constraints. Therefore the breeding and selection of new rootstocks are now of the utmost importance. In Tunisia, in addition to sour orange, the most widespread traditional rootstock of the Mediterranean area, other citrus rootstocks and well adapted to local environmental conditions, are traditionally used and should be important genetic resources for breeding. To characterize the diversity of Tunisian citrus rootstocks, two hundred and one local accessions belonging to four facultative apomictic species (C. aurantium, sour orange; C. sinensis, orange; C. limon, lemon; and C. aurantifolia, lime) were collected and genotyped using 20 nuclear SSR markers and four indel mitochondrial markers. Multi-locus genotypes (MLGs) were compared to references from French and Spanish collections. Results The differentiation of the four varietal groups was well-marked. The groups displayed a relatively high allelic diversity, primarily due to very high heterozygosity. Sixteen distinct MLGs were identified. Ten of these were noted in sour oranges. However, the majority of the analysed sour orange accessions corresponded with only two MLGs, differentiated by a single allele, likely due to a mutation. The most frequent MLG is shared with the reference sour oranges. No polymorphism was found within the sweet orange group. Two MLGs, differentiated by a single locus, were noted in lemon. The predominant MLG was shared with the reference lemons. Limes were represented by three genotypes. Two corresponded to the 'Mexican lime' and 'limonette de Marrakech' references. The MLG of 'Chiiri' lime was unique. Conclusions The Tunisian citrus rootstock genetic diversity is predominantly due to high heterozygosity and differentiation between the four varietal groups. The phenotypic diversity within the varietal groups has

  2. Genetic bottlenecks in Turkish okra germplasm and utility of iPBS retrotransposon markers for genetic diversity assessment.

    PubMed

    Yıldız, M; Koçak, M; Baloch, F S

    2015-01-01

    Lack of requisite genetic variation in Turkish okra has necessitated the use of different types of markers for estimating the genetic diversity and identifying the source of variation. Transposable elements, present abundantly in plant genomes, generate genomic diversity through their replication and are thus an excellent source of molecular markers. We hypothesized that inter-primer binding site (iPBS)-retrotransposons could be the source of variation because of their genome plasticity nature. In the present study, genetic diversity of 66 okra landraces was analyzed using iPBS-retrotransposon markers. iPBS-retrotransposons detected 88 bands with 40.2% polymorphism and an average of 6.8 bands per primer. Gene diversity and Shannon's information index ranged from 0.01 to 0.13 and 0.02 to 0.21 for iPBS-retrotransposons and from 0.06 to 0.46 and 0.14 to 0.65 for simple sequence repeat (SSR) markers, respectively. Polymorphism information content value for retrotransposons varied between 0.12 and 0.99, while that for SSR was from 0.52 to 0.81. Neighbor joining analysis based on retrotransposons and SSRs divided all the accessions into four clusters; however, SSR markers were more efficient in clustering the landraces based on their origin. Using the STRUCTURE software for determining population structure, and two populations (at the number of hypothetical subpopulations, K = 2) were identified among the landraces. Low genetic diversity in Turkish okra highlights the need for the introduction of plants from countries with greater genetic diversity for these crops. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in okra. PMID:26400290

  3. How do we address the disconnect between genetic and morphological diversity in germplasm collections

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Morphology has long provided key data to assess diversity in landrace collections in genebanks worldwide. We explored, through an F2 cross between two inbred diploid potato clones, the utility of tuber morphology to assess diversity of potato landraces. We assessed the F2 population created by self-...

  4. Genetic Perspectives on Loss of Diversity in Elite Maize Breeding Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Selection and genetic drift are two processes that are very well understood if treated separately, but very poorly understood when acting in concert. As a result, existing quantitative genetic theory does not provide any good methods for developing optimal strategies for maintaining sustainable sel...

  5. Germplasm dynamics: the role of ecotypic diversity in shaping the patterns of genetic variation in Lolium perenne.

    PubMed

    Blackmore, T; Thorogood, D; Skøt, L; McMahon, R; Powell, W; Hegarty, M

    2016-01-01

    Perennial ryegrass (Lolium perenne) is the most widely grown temperate grass species globally. Intensive plant breeding in ryegrass compared to many other crops species is a relatively recent exercise (last 100 years) and provides an interesting experimental system to trace the extent, impact and trajectory of undomesticated ecotypic variation represented in modern ryegrass cultivars. To explore germplasm dynamics in Lolium perenne, 2199 SNPs were genotyped in 716 ecotypes sampled from 90 European locations together with 249 cultivars representing 33 forage/amenity accessions. In addition three pseudo-cross mapping populations (450 individual recombinants) were genotyped to create a consensus genetic linkage map. Multivariate analyses revealed strong differentiation between cultivars with a small proportion of the ecotypic variation captured in improved cultivars. Ryegrass cultivars generated as part of a recurrent selection programme (RSP) are strongly associated with a small number of geographically localised Italian ecotypes which were among the founders of the RSP. Changes in haplotype frequency revealed signatures of selection in genes putatively involved in water-soluble carbohydrate (WSC) accumulation (a trait selected in the RSP). Retrospective analysis of germplasm in breeding programmes (germplasm dynamics) provides an experimental framework for the identification of candidate genes for novel traits such as WSC accumulation in ryegrass. PMID:26935901

  6. Germplasm dynamics: the role of ecotypic diversity in shaping the patterns of genetic variation in Lolium perenne

    PubMed Central

    Blackmore, T.; Thorogood, D.; Skøt, L.; McMahon, R.; Powell, W.; Hegarty, M.

    2016-01-01

    Perennial ryegrass (Lolium perenne) is the most widely grown temperate grass species globally. Intensive plant breeding in ryegrass compared to many other crops species is a relatively recent exercise (last 100 years) and provides an interesting experimental system to trace the extent, impact and trajectory of undomesticated ecotypic variation represented in modern ryegrass cultivars. To explore germplasm dynamics in Lolium perenne, 2199 SNPs were genotyped in 716 ecotypes sampled from 90 European locations together with 249 cultivars representing 33 forage/amenity accessions. In addition three pseudo-cross mapping populations (450 individual recombinants) were genotyped to create a consensus genetic linkage map. Multivariate analyses revealed strong differentiation between cultivars with a small proportion of the ecotypic variation captured in improved cultivars. Ryegrass cultivars generated as part of a recurrent selection programme (RSP) are strongly associated with a small number of geographically localised Italian ecotypes which were among the founders of the RSP. Changes in haplotype frequency revealed signatures of selection in genes putatively involved in water-soluble carbohydrate (WSC) accumulation (a trait selected in the RSP). Retrospective analysis of germplasm in breeding programmes (germplasm dynamics) provides an experimental framework for the identification of candidate genes for novel traits such as WSC accumulation in ryegrass. PMID:26935901

  7. Genetic diversity in cocoa (Theobroma cacao, L.) germplasm collection from Ghana

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Theobroma cacao L. with its center of diversity in Central and South America was first introduced to West Africa in the mid-19th century and today the region produces 70% of the world's cocoa. Several distinct cocoa types have been introduced, cultivated and intercrossed across the region. Also, bi-...

  8. Genetic Diversity of the Malus sieversii Collection in the USDA-ARS National Plant Germplasm System

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant explorers have gathered seeds from wild Malus sieversii trees in Kazakhstan which are believed to be one of the major progenitor species of the dessert apple, Malus x domestica. Large field and seed collections from these explorations are maintained at the Plant Genetic Resources Unit in Gene...

  9. AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set.

    PubMed

    Sorkheh, Karim; Masaeli, Mohammad; Chaleshtori, Maryam Hosseini; Adugna, Asfaw; Ercisli, Sezai

    2016-04-01

    Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs. PMID:26762294

  10. Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity

    PubMed Central

    Ophir, Ron; Sherman, Amir; Rubinstein, Mor; Eshed, Ravit; Sharabi Schwager, Michal; Harel-Beja, Rotem; Bar-Ya'akov, Irit; Holland, Doron

    2014-01-01

    Pomegranate is a valuable crop that is grown commercially in many parts of the world. Wild species have been reported from India, Turkmenistan and Socotra. Pomegranate fruit has a variety of health-beneficial qualities. However, despite this crop's importance, only moderate effort has been invested in studying its biochemical or physiological properties or in establishing genomic and genetic infrastructures. In this study, we reconstructed a transcriptome from two phenotypically different accessions using 454-GS-FLX Titanium technology. These data were used to explore the functional annotation of 45,187 fully annotated contigs. We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). A subset of 480 SNPs was sampled to investigate the genetic structure of the broad pomegranate germplasm collection at the Agricultural Research Organization (ARO), which includes accessions from different geographical areas worldwide. This subset of SNPs was found to be polymorphic, with 10.7% loci with minor allele frequencies of (MAF<0.05). These SNPs were successfully used to classify the ARO pomegranate collection into two major groups of accessions: one from India, China and Iran, composed of mainly unknown country origin and which was more of an admixture than the other major group, composed of accessions mainly from the Mediterranean basin, Central Asia and California. This study establishes a high-throughput transcriptome and genetic-marker infrastructure. Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature. PMID:24558460

  11. Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity.

    PubMed

    Ophir, Ron; Sherman, Amir; Rubinstein, Mor; Eshed, Ravit; Sharabi Schwager, Michal; Harel-Beja, Rotem; Bar-Ya'akov, Irit; Holland, Doron

    2014-01-01

    Pomegranate is a valuable crop that is grown commercially in many parts of the world. Wild species have been reported from India, Turkmenistan and Socotra. Pomegranate fruit has a variety of health-beneficial qualities. However, despite this crop's importance, only moderate effort has been invested in studying its biochemical or physiological properties or in establishing genomic and genetic infrastructures. In this study, we reconstructed a transcriptome from two phenotypically different accessions using 454-GS-FLX Titanium technology. These data were used to explore the functional annotation of 45,187 fully annotated contigs. We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs) and 6,500 single-nucleotide polymorphisms (SNPs). A subset of 480 SNPs was sampled to investigate the genetic structure of the broad pomegranate germplasm collection at the Agricultural Research Organization (ARO), which includes accessions from different geographical areas worldwide. This subset of SNPs was found to be polymorphic, with 10.7% loci with minor allele frequencies of (MAF<0.05). These SNPs were successfully used to classify the ARO pomegranate collection into two major groups of accessions: one from India, China and Iran, composed of mainly unknown country origin and which was more of an admixture than the other major group, composed of accessions mainly from the Mediterranean basin, Central Asia and California. This study establishes a high-throughput transcriptome and genetic-marker infrastructure. Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature. PMID:24558460

  12. Analysis of genetic diversity and population structure in a tomato (Solanum lycopersicum L.) germplasm collection based on single nucleotide polymorphism markers.

    PubMed

    Wang, T; Zou, Q D; Qi, S Y; Wang, X F; Wu, Y Y; Liu, N; Zhang, Y M; Zhang, Z J; Li, H T

    2016-01-01

    Knowledge of genetic diversity is important to assist breeders in the selection of parental materials and in the design of breeding programs. In this study, we genotyped 348 inbred tomato lines, representing vintage and contemporary fresh-market varieties, by using 52 single nucleotide polymorphisms (SNPs); 45 of these were found to be polymorphic. The average minor allele frequency and unbiased expected heterozygosity were 0.315 and 0.356, respectively. Population structure analysis revealed that contemporary germplasm could be distinctly divided into six subpopulations representing three market classes and breeding programs (pink, green, and red). Vintage germplasm could be separated into at least two subpopulations, and more admixtures were found in vintage lines than in contemporary lines. These findings indicate that contemporary inbred lines are more diversified than vintage inbred lines. AMOVA of vintage and contemporary lines was performed. A significant difference was found (P < 0.01), which explained 17.4% of the total genetic variance. Subsequently, we constructed a core collection using 45 polymorphic SNP markers. The data showed that all alleles were captured by only 2% of lines, indicating that more alleles, as well as rare alleles, could enable more variation to be captured in the core collection. These data allow us to discard redundant inbred tomato lines and to select elite inbred lines, which will accelerate the breeding process. PMID:27525883

  13. Analysis of Genetic Diversity and Population Structure of Rice Germplasm from North-Eastern Region of India and Development of a Core Germplasm Set

    PubMed Central

    Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Ahmad, Altaf; Singh, N. K.; Singh, Rakesh

    2014-01-01

    The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a

  14. Melon (Cucumis melo L.) Diversity Analyses Provide Strategies for Germplasm Curation, Genetic Improvement and Evidentiary Support of Domestication Patterns

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of melon market types (Cucumis melo L., 2n = 2x = 24) in China, an important secondary center of diversity, has not been examined. Therefore, reference accessions (India, Africa, Crete/Greece, Japan, Europe, USA, and Spain) and 68 Chinese cultigens (fresh market non-netted thi...

  15. Isolation Distance, Inflorescence Sampling, and Population Size: Maintaining Genetic Diversity in the U.S. Temperate Grass Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During the regeneration of cross-pollinating accessions, genetic contamination from foreign pollen and reduction of the effective population size can be a hindrance to maintaining the genetic diversity in the temperate grass collection at the Western Regional Plant Introduction Station (WRPIS). The...

  16. Genetic diversity in Gossypium genus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The overall objectives of this paper are to report on cotton germplasm resources, morphobiological and agronomic diversity of Gossypium genus and review efforts on molecular genetic diversity of cotton gene pools as well as on the challenges and perspectives of exploiting genetic diversity in cotton...

  17. Molecular characterization of the Gossypium diversity reference set of the US National Cotton Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An understanding of the genetic diversity of cotton (Gossypium spp.) is essential to develop strategies for collection, conservation, and utilization of these germplasm resources. The US National Cotton Germplasm Collection is one of the largest world collections and includes not only accessions wi...

  18. Genetic diversity and relationship among faba bean (Vicia faba L.) germplasm entries as revealed by TRAP markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Target region amplification polymorphism (TRAP) markers were used to assess genetic diversity and relationship among 151 world-wide collected faba bean (Vicia faba L.) entries (137 accessions maintained at the USDA-ARS, Pullman, WA, two commercial varieties and 12 elite cultivars and advanced breedi...

  19. Development of SSR markers and assessment of genetic diversity of alzuki bean in the Chinese germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Adzuki bean is an important food legume crop in East Asia. China is ranked as the number one country for its production and consumption. A large number of adzuki bean accessions are maintained in the Chinese national seed genebank. Tapping its genetic diversity may have potential in assisting breedi...

  20. Assessment of Genetic Diversity of Lespedeza Germplasm and Analysis of Its Phylogenetic Relationship with the Genus Kummerowia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity of genus Lespedeza is not well known and the phylogenetic relationship of Lespedeza with the genus Kummerowia is unclear. We report the first study in which polymorphic expressed sequence tag-simple sequence (EST-SSR) markers derived from Medicago, cowpea and soybean were used...

  1. Genetic diversity and population structure of elite foxtail millet [Setaria italica (L.) P. Beauv.] germplasm in China

    Technology Transfer Automated Retrieval System (TEKTRAN)

    China is among the countries that have the most severe water deficiency. Due to its excellent drought tolerance, foxtail millet [Setaria italica (L.) P. Beauv.] has become one of the important cereal crops in China. Information on genetic diversity and population structure of foxtail millet may faci...

  2. Diversity in global maize germplasm: characterization and utilization.

    PubMed

    Prasanna, B M

    2012-11-01

    Maize (Zea mays L.) is not only of worldwide importance as a food, feed and as a source of diverse industrially important products, but is also a model genetic organism with immense genetic diversity. Although it was first domesticated in Mexico, maize landraces are widely found across the continents. Several studies in Mexico and other countries highlighted the genetic variability in the maize germplasm. Applications of molecular markers, particularly in the last two decades, have led to new insights into the patterns of genetic diversity in maize globally, including landraces as well as wild relatives (especially teosintes) in Latin America, helping in tracking the migration routes of maize from the centers of origin, and understanding the fate of genetic diversity during maize domestication. The genome sequencing of B73 (a highly popular US Corn Belt inbred) and Palomero (a popcorn landrace in Mexico) in the recent years are important landmarks in maize research, with significant implications to our understanding of the maize genome organization and evolution. Next-generation sequencing and high-throughput genotyping platforms promise to further revolutionize our understanding of genetic diversity and for designing strategies to utilize the genomic information for maize improvement. However, the major limiting factor to exploit the genetic diversity in crops like maize is no longer genotyping, but high-throughput and precision phenotyping. There is an urgent need to establish a global phenotyping network for comprehensive and efficient characterization of maize germplasm for an array of target traits, particularly for biotic and abiotic stress tolerance and nutritional quality. 'Seeds of Discovery' (SeeD), a novel initiative by CIMMYT with financial support from the Mexican Government for generating international public goods, has initiated intensive exploration of phenotypic and molecular diversity of maize germplasm conserved in the CIMMYT Gene Bank; this is

  3. ANALYSIS OF GENETIC DIVERSITY AND POPULATION STRUCTURE WITHIN FLORIDA COCONUT (COCOS NUCIFERA L.) GERMPLASM USING MICROSATELLITE DNA, WITH SPECIAL EMPHASIS ON THE FIJI DWARF CULTIVAR

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using fifteen simple sequence repeat (SSR) microsatellite DNA loci, we analyzed genetic variation within Cocos nucifera germplasm collections at two locations in south Florida, representing eight cultivars. The loci were also used in a parentage analysis of progeny of the 'Fiji Dwarf' variety at bo...

  4. The Tropical and Subtropical Germplasm Repositories of The National Germplasm System

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Germplasm collections are viewed as a source of genetic diversity to support crop improvement and agricultural research, and germplasm conservation efforts. The United States Department of Agriculture's National Plant Germplasm Repository System (NPGS) is responsible for administering plant genetic ...

  5. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm.

    PubMed

    Abdurakhmonov, I Y; Kohel, R J; Yu, J Z; Pepper, A E; Abdullaev, A A; Kushanov, F N; Salakhutdinov, I B; Buriev, Z T; Saha, S; Scheffler, B E; Jenkins, J N; Abdukarimov, A

    2008-12-01

    The narrow genetic base of cultivated cotton germplasm is hindering the cotton productivity worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of linkage disequilibrium (LD)-based association mapping is an alternative powerful molecular tool to dissect and exploit the natural genetic diversity conserved within cotton germplasm collections, greatly accelerating still 'lagging' cotton marker-assisted selection (MAS) programs. However, the extent of genome-wide linkage disequilibrium (LD) has not been determined in cotton. We report the extent of genome-wide LD and association mapping of fiber quality traits by using a 95 core set of microsatellite markers in a total of 285 exotic Gossypium hirsutum accessions, comprising of 208 landrace stocks and 77 photoperiodic variety accessions. We demonstrated the existence of useful genetic diversity within exotic cotton germplasm. In this germplasm set, 11-12% of SSR loci pairs revealed a significant LD. At the significance threshold (r(2)>/=0.1), a genome-wide average of LD declines within the genetic distance at <10 cM in the landrace stocks germplasm and >30 cM in variety germplasm. Genome wide LD at r(2)>/=0.2 was reduced on average to approximately 1-2 cM in the landrace stock germplasm and 6-8 cM in variety germplasm, providing evidence of the potential for association mapping of agronomically important traits in cotton. We observed significant population structure and relatedness in assayed germplasm. Consequently, the application of the mixed liner model (MLM), considering both kinship (K) and population structure (Q) detected between 6% and 13% of SSR markers associated with the main fiber quality traits in cotton. Our results highlight for the first time the feasibility and potential of association mapping, with consideration of the population structure and

  6. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The narrow genetic base of cultivated cotton germplasm is hindering the cotton production worldwide. Although potential genetic diversity exists in Gossypium genus, it is largely 'underutilized' due to photoperiodism and the lack of innovative tools to overcome such challenges. The application of ...

  7. Genetic diversity analysis of sugarcane germplasm based on fluorescence-labeled simple sequence repeat markers and a capillary electrophoresis-based genotyping platform

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity analysis, which refers to the elaboration of total extent of genetic characteristics in the genetic makeup of a certain species, constitutes a classical strategy for the study of diversity, population genetic structure, and breeding practices. In this study, fluorescence-labeled se...

  8. Genetic diversity of Malus cultivars and wild relatives in the Chinese National Repository of Apple Germplasm Resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Research Institute of Pomology (IP), Chinese Academy of Agricultural Sciences (CAAS) in Xingcheng, China, maintains hundreds of apple accessions that originated from around the world. We have used 16 microsatellites to assess the diversity and differentiation of 391 accessions within the IP tha...

  9. Utilizing common-garden and genetic diversity structure analysis to determine strategies for releasing wildland plant germplasm for rangeland revegetation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Semi-arid rangelands in the western North America face many challenges due to invasive weedy species, wildfires, and past mismanagement. A diversity of plant species are needed to effectively revegetate degraded rangelands in this expansive area. Legumes native to western North America are of inte...

  10. Notice of release of Charleston Peak Germplasm: selected class, genetically manipulated track pre-variety germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-Agricultural Research Service (ARS) announces the release of Charleston Peak Germplasm slender wheatgrass [Elymus trachycaulus (Link) Gould ex Shinners] as a selected class, genetically manipulated track pre-variety germplasm selected directly from collection D-3269. This collection is uni...

  11. Employing microsatellite and SNP markers to track functional mutations and evaluate genetic diversity in the USDA Arachis germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanuts (Arachis hypogaea L.) are nutritious because their seeds typically contain high amounts of oil, protein and other phytochemicals such as folic acid, tocopherol, and antioxidants; therefore, they are an important oil seed crop worldwide. The USDA Plant Genetic Resources Conservation Unit mai...

  12. Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity of thirty five Psidium guajava accessions maintained at the USDA, National Plants Germplasm System, Hilo, HI, was characterized using 20 simple sequence repeat (SSR) markers. Diversity analysis detected a total of 178 alleles ranging from four to 16. The observed mean heterozygosit...

  13. Taxonomy and genetic differentiation among wild and cultivated germplasm of Solanum sect. Petota

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Due to their adaptation to a diverse set of habitats and stresses, wild species of cultivated crops offer new sources of genetic diversity for germplasm improvement. Using an Infinium array representing a genome-wide set of 8303 single nucleotide polymorphisms (SNPs), we evaluated phylogenetic relat...

  14. Diallel analysis of diverse maize germplasm lines for resistance to aflatoxin accumulation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aflatoxin, a carcinogenic mycotoxin, remains a major problem throughout the southern USA and World. In this study, diverse, novel maize germplasm from the Genetic Enhancement of Maize (GEM) project was screened to determine the combining ability and inheritance of ear rot resistance and resistance ...

  15. Genetic variation and association mapping of silica concentration in rice hulls using a germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association analysis on the genetic variability for silica concentration in rice hulls was performed using a “Mini-Core” set of 174 accessions representative of the germplasm diversity found in the USDA world collection of rice. Hull silica concentration was determined in replicated trials conducte...

  16. Sambucus genetic resources at the U.S.D.A. National Clonal Germplasm Repository, Corvallis, Oregon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), National Clonal Germplasm Repository (NCGR-Corvallis) preserves the genetic diversity of elderberry (Sambucus L.). This genebank preserves representatives of seven of the nine major world Sambucus species and 50 cultivar...

  17. The U. S. National Plant Germplasm System: preserving plant genetic resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Being one of the world’s largest national genebank networks, the U.S. National Plant Germplasm System (NPGS) focuses on preserving the genetic diversity of crop plants and their wild relatives. The documented history of official plant introduction can be traced back to 1898 when USDA created its Se...

  18. Temperate forage legume and grass genetic resources: capitalizing on the U.S. germplasm system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The U.S. germplasm collection for temperate forage legumes and grasses provides diverse genetic resources to support the development of fodder crops adapted to conventional and organic farming practices. The collection contains 12,000 accessions of Medicago, Trifolium and Lotus representing 368 taxa...

  19. Improving in vitro mineral nutrition for diverse germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complex chemical interactions in growth media and variation in genotype response make it very difficult to optimize mineral nutrition of in vitro plants. Germplasm collections contain diverse species and cultivars that often do not grow well on standard tissue culture media or do not grow at all. Se...

  20. Utilization of SNP, SSR, and biochemical data to evaluate genetic and phenotypic diversity in the U.S. peanut germplasm collection.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanuts (Arachis hypogaea L.) are nutritious because their seeds typically contain high amounts of oil, protein, phytochemicals such as resveratrol, and antioxidants such as tocopherol and folic acid; therefore, they are an important oil seed crop worldwide. The genetic diversity and population stru...

  1. EVALUATION OF GENETIC DIVERSITY AND GENOME-WIDE LINKAGE DISEQUILIBRIUM AMOUNG US WHEAT (TRITICUM AETIVUM L.) GERMPLASM REPRESENTING DIFFERENT MARKET CLASSES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity and genome-wide linkage disequilibrium (LD) were investigated among forty-three US wheat (Triticum aestivum L.) elite cultivars and breeding lines representing seven US wheat market classes using 242 wheat genomic simple sequence repeat (SSR) markers distributed throughout the whea...

  2. Evaluation of genetic diversity and genome-wide linkage disequilibrium among US wheat (Triticum aestivum L.) germplasm representing different market classes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity and genome-wide linkage disequilibrium (LD) were investigated among forty-three U.S. wheat (Triticum aestivum L.) elite cultivars and breeding lines representing seven U.S. wheat market classes using 242 wheat genomic simple sequence repeat (SSR) markers distributed throughout the ...

  3. Durango diversity panel: abiotic and biotic stress characterization and potential for introducing new germplasm into East Africa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Durango Diversity Panel (DDP) consists of 192 old and newly released US and Canadian cultivars and germplasm lines in the pinto, great northern, red, and pink bean market classes. The Durango Race provides genetic diversity for drought stress tolerance, and biotic stress resistance. Much disea...

  4. Genetic Stability of Cryopreserved Shoot Tips of Rubus Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Questions often arise concerning the genetic stability of plant materials stored in liquid nitrogen for long time periods. This study followed the genetic stability of cryopreserved shoot tips of Rubus germplasm that were stored in liquid nitrogen for over 12 years, then rewarmed and regrown. We a...

  5. Molecular characterization of genetic diversity, structure, and differentiation in the olive (Olea europaea L.) germplasm collection of the united states department of agriculture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fifteen microsatellite loci were used to genotype 108 accessions of cultivated olive, Olea europaea L. ssp. europaea var. europaea, and eight of O. europaea L. ssp. cuspidata (Wall. ex G. Don) Ciferri from the germplasm collection of the United States Department of Agriculture in Davis, California. ...

  6. Genetic variability in agronomic traits of a germplasm collection of hulless barley.

    PubMed

    Zeng, X Q

    2015-01-01

    Germplasm collections represent an important genetic source for crop improvements. In this study, 220 accessions of hulless barley were collected worldwide and their genetic diversity was investigated. Sixteen agronomic traits, including yield and yield components, grain morphology, leaf size, plant height, and lodging resistance, were assessed under field conditions. All studied traits exhibited large variation. Thousand seed weight determined yield, and was strongly affected by spike length and spike number. Four varieties, Gaoyuan Zao 1, Fu 8-4, Zang 0331, and Harry (WDM00618), showed high resistance to lodging. Significant correlations among the traits were observed, indicating trait interactions. Life cycle had the smallest coefficient of variation (CV) among native, foreign, and improved varieties, whereas the CV of cellulose content was more or less balanced. Among the accessions from domestic and foreign germplasm, the CV for life cycle remained the lowest, whereas those for carbon/nitrogen and spike number per plant were the highest. Interestingly, higher genetic diversity was observed in domestic than in foreign accessions. Together, our findings demonstrate that there is abundant diversity in worldwide hulless barley germplasm collections, which would be useful when introducing their desirable traits into cultivars of hulless barley to improve yield and other agronomic traits. PMID:26782483

  7. High-throughput genotyping for species identification and diversity assessment in germplasm collections.

    PubMed

    Mason, Annaliese S; Zhang, Jing; Tollenaere, Reece; Vasquez Teuber, Paula; Dalton-Morgan, Jessica; Hu, Liyong; Yan, Guijun; Edwards, David; Redden, Robert; Batley, Jacqueline

    2015-09-01

    Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers. PMID:25641370

  8. Chemical diversity in basil (Ocimum sp.) germplasm.

    PubMed

    da Costa, Andréa Santos; Arrigoni-Blank, Maria de Fátima; de Carvalho Filho, José Luiz Sandes; de Santana, Aléa Dayane Dantas; Santos, Darlisson de Alexandria; Alves, Péricles Barreto; Blank, Arie Fitzgerald

    2015-01-01

    The present study aimed to chemically characterize 31 accessions and seven cultivars of basil. The percentage composition of the essential oils of the accessions and cultivars was based on the 14 most abundant constituents: 1,8-cineole, linalool, methyl chavicol, neral, nerol, geraniol, geranial, methyl cinnamate, β-bourbonene, methyl eugenol, α-trans-bergamotene, germacrene-D, epi-α-cadinol, and δ-cadinene. The genetic materials were classified into eight clusters according to the chemical composition of the essential oils: Cluster 1--mostly linalool and 1,8-cineole; Cluster 2--mostly linalool, geraniol, and α-trans-bergamotene; Cluster 3--mostly linalool, methyl chavicol, methyl cinnamate, and β-bourbonene; Cluster 4--mostly linalool, methyl chavicol, epi-α-cadinol, and α-trans-bergamotene; Cluster 5--mainly linalool, methyl eugenol, α-trans-bergamotene, and epi-α-cadinol; Cluster 6--mainly linalool, geraniol, and epi-α-cadinol; Cluster 7--mostly linalool and methyl chavicol; Cluster 8--mainly geranial and neral. PMID:25629084

  9. Chemical Diversity in Basil (Ocimum sp.) Germplasm

    PubMed Central

    da Costa, Andréa Santos; Arrigoni-Blank, Maria de Fátima; de Carvalho Filho, José Luiz Sandes; de Santana, Aléa Dayane Dantas; Santos, Darlisson de Alexandria; Alves, Péricles Barreto; Blank, Arie Fitzgerald

    2015-01-01

    The present study aimed to chemically characterize 31 accessions and seven cultivars of basil. The percentage composition of the essential oils of the accessions and cultivars was based on the 14 most abundant constituents: 1,8-cineole, linalool, methyl chavicol, neral, nerol, geraniol, geranial, methyl cinnamate, β-bourbonene, methyl eugenol, α-trans-bergamotene, germacrene-D, epi-α-cadinol, and δ-cadinene. The genetic materials were classified into eight clusters according to the chemical composition of the essential oils: Cluster 1—mostly linalool and 1,8-cineole; Cluster 2—mostly linalool, geraniol, and α-trans-bergamotene; Cluster 3—mostly linalool, methyl chavicol, methyl cinnamate, and β-bourbonene; Cluster 4—mostly linalool, methyl chavicol, epi-α-cadinol, and α-trans-bergamotene; Cluster 5—mainly linalool, methyl eugenol, α-trans-bergamotene, and epi-α-cadinol; Cluster 6—mainly linalool, geraniol, and epi-α-cadinol; Cluster 7—mostly linalool and methyl chavicol; Cluster 8—mainly geranial and neral. PMID:25629084

  10. Assessment of genetic diversity in rice [Oryza sativa L.] germplasm based on agro-morphology traits and zinc-iron content for crop improvement.

    PubMed

    Roy, Subhas Chandra; Sharma, B D

    2014-04-01

    . Highest iron containing rice was Swetonunia with 34.8 μg/g and highest amount of Zn was found in Nepali Kalam which was 195.3 μg/g. Anaerobic germination (AG) was observed in 18 cultivars among 84 land races (viz. Jungli, Kumrogore, Dudheshwar, Rambhog and Tulsi etc.), the trait is highly desired by the rice breeder for the introgression of this gene (QTL) to the HYV for direct seeding in the field for saving labour cost and reduced maturity time. Dendrogram showed genetic diversity among 84 landraces by grouping them into five major clusters. All the descriptors evaluated in this study have showed that there is enough genetic diversity among landraces and this information can be helpful to the breeders to choose the right parent for crop improvement. PMID:24757325

  11. Genetic diversity and population structure of cucumber (Cucumis sativus L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding genetic variation in germplasm collection is essential for the conservation and their efficient use in plant breeding. Cucumber is an important vegetable crop worldwide. Previous studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structu...

  12. Gossypium Germplasm Resources for Cotton Improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Only a very small fraction of the genetic diversity residing in the Gossypium genus is represented in improved, elite cotton germplasm. Although genetic diversity in elite germplasm is reported to be narrow, diversity on the farm is narrower, due to preferential planting of successful cultivars, an...

  13. Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers

    PubMed Central

    Qiang, Haiping; Chen, Zhihong; Zhang, Zhengli; Wang, Xuemin; Gao, Hongwen; Wang, Zan

    2015-01-01

    Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding. PMID:25901573

  14. Update on the Comparative Assessment of Genetic Diversity Between Accessible and Remote Potato Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is limited information on the organization of potato genetic diversity (GD) in natural habitats. Answering questions on that topic has significant implications for germplasm conservation -- for example, targeting habitats and populations with greater genetic richness or distinctiveness for col...

  15. Germplasm Enhancement of Maize: Allelic Diversity and Double Haploid Update

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Germplasm Enhancement of Maize (GEM) Project is a collaborative effort of public and private sector researchers to broaden and enhance the germplasm base. To date, 235 germplasm lines have been released to cooperators representing approximately 25 races. These lines were selected based on yiel...

  16. Variability in four diverse cotton (Gossypium hirsutum L.) germplasm populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A broad range of cotton (Gossypium hirsutum L.) germplasm resources exist with characteristics useful for improving modern cotton cultivars. However, much of this germplasm is not well utilized. The objective of this study was to evaluate agronomic and fiber traits of four germplasm populations to...

  17. Genetic diversity of cultivated lentil (Lens culinaris Medik.) and its relation to the world’s agro-ecological zones

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Assessment of genetic diversity and population structure of germplasm collections plays a critical role in supporting conservation and crop genetic enhancement strategies. We used a cultivated lentil (Lens culinaris Medik.) collection consisting of 352 accessions originating from 54 diverse countrie...

  18. The Puzzle of Italian Rice Origin and Evolution: Determining Genetic Divergence and Affinity of Rice Germplasm from Italy and Asia

    PubMed Central

    Jiang, Zhuxi; Basso, Barbara; Sala, Francesco; Spada, Alberto; Grassi, Fabrizio; Lu, Bao-Rong

    2013-01-01

    The characterization of genetic divergence and relationships of a set of germplasm is essential for its efficient applications in crop breeding and understanding of the origin/evolution of crop varieties from a given geographical region. As the largest rice producing country in Europe, Italy holds rice germplasm with abundant genetic diversity. Although Italian rice varieties and the traditional ones in particular have played important roles in rice production and breeding, knowledge concerning the origin and evolution of Italian traditional varieties is still limited. To solve the puzzle of Italian rice origin, we characterized genetic divergence and relationships of 348 rice varieties from Italy and Asia based on the polymorphisms of microsatellite fingerprints. We also included common wild rice O. rufipogon as a reference in the characterization. Results indicated relatively rich genetic diversity (He = 0.63-0.65) in Italian rice varieties. Further analyses revealed a close genetic relationship of the Italian traditional varieties with those from northern China, which provides strong genetic evidence for tracing the possible origin of early established rice varieties in Italy. These findings have significant implications for the rice breeding programs, in which appropriate germplasm can be selected from a given region and utilized for transferring unique genetic traits based on its genetic diversity and evolutionary relationships. PMID:24265814

  19. MAINTAINING GENETIC FIDELITY IN GERMPLASM COLLECTIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The establishment of guidelines to define Best Practices for genebank management has been a topic of discussion for many years at several different venues. Most recently, at a 2004 workshop sponsored by the Genetic Resources Policy Committee and the Science Council of the Consultative Group on Inte...

  20. Assessment of molecular diversity and population structure of the Ethiopian sorghum [Sorghum bicolor L. (Moench)] germplasm collection maintained by the USDA-ARS National Plant Germplasm System using SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity and population structure present in the Ethiopian sorghum collection maintained at the USDA-ARS National Plant Germplasm System (NPGS) has not been studied. In addition, 83% of the accessions in the Ethiopian collection lack passport information which has constrained their eval...

  1. Genetic biodiversity of Italian olives (Olea europaea) germplasm analyzed by SSR markers.

    PubMed

    Muzzalupo, Innocenzo; Vendramin, Giuseppe Giovanni; Chiappetta, Adriana

    2014-01-01

    The olive is an important fruit species cultivated for oil and table olives in Italy and the Mediterranean basin. The conservation of cultivated plants in ex situ collections is essential for the optimal management and use of their genetic resources. The largest ex situ olive germplasm collection consists of approximately 500 Italian olive varieties and corresponding to 85% of the total Italian olive germplasm is maintained at the Consiglio per la Ricerca e sperimentazione per l'Agricoltura, Centro di Ricerca per l'Olivicoltura e l'Industria Olearia (CRA-OLI), in Italy. In this work, eleven preselected nuclear microsatellite markers were used to assess genetic diversity, population structure, and gene flows with the aim of assembling a core collection. The dendrogram obtained utilizing the unweighted pair group method highlights the presence of homonymy and synonymy in olive tree datasets analyzed in this study. 439 different unique genotype profiles were obtained with this combination of 11 loci nSSR, representing 89.8% of the varieties analyzed. The remaining 10.2% comprises different variety pairs in which both accessions are genetically indistinguishable. Clustering analysis performed using BAPS software detected seven groups in Italian olive germplasm and gene flows were determined among identified clusters. We proposed an Italian core collection of 23 olive varieties capturing all detected alleles at microsatellites. The information collected in this study regarding the CRA-OLI ex situ collection can be used for breeding programs, for germplasm conservation, and for optimizing a strategy for the management of olive gene pools. PMID:24723801

  2. Genetic Biodiversity of Italian Olives (Olea europaea) Germplasm Analyzed by SSR Markers

    PubMed Central

    Vendramin, Giuseppe Giovanni; Chiappetta, Adriana

    2014-01-01

    The olive is an important fruit species cultivated for oil and table olives in Italy and the Mediterranean basin. The conservation of cultivated plants in ex situ collections is essential for the optimal management and use of their genetic resources. The largest ex situ olive germplasm collection consists of approximately 500 Italian olive varieties and corresponding to 85% of the total Italian olive germplasm is maintained at the Consiglio per la Ricerca e sperimentazione per l'Agricoltura, Centro di Ricerca per l'Olivicoltura e l'Industria Olearia (CRA-OLI), in Italy. In this work, eleven preselected nuclear microsatellite markers were used to assess genetic diversity, population structure, and gene flows with the aim of assembling a core collection. The dendrogram obtained utilizing the unweighted pair group method highlights the presence of homonymy and synonymy in olive tree datasets analyzed in this study. 439 different unique genotype profiles were obtained with this combination of 11 loci nSSR, representing 89.8% of the varieties analyzed. The remaining 10.2% comprises different variety pairs in which both accessions are genetically indistinguishable. Clustering analysis performed using BAPS software detected seven groups in Italian olive germplasm and gene flows were determined among identified clusters. We proposed an Italian core collection of 23 olive varieties capturing all detected alleles at microsatellites. The information collected in this study regarding the CRA-OLI ex situ collection can be used for breeding programs, for germplasm conservation, and for optimizing a strategy for the management of olive gene pools. PMID:24723801

  3. Ginning Efficiency between Diverse Genetic Groups of Upland Cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rising cost of energy in ginning cotton necessitates the evaluation of a diverse array of germplasm, currently available, for improving ginning efficiency. The objective was to study genetic variability for net ginning energy requirement and speed of ginning among five diverse groups of upland c...

  4. Endemic insular and coastal Tunisian date palm genetic diversity.

    PubMed

    Zehdi-Azouzi, Salwa; Cherif, Emira; Guenni, Karim; Abdelkrim, Ahmed Ben; Bermil, Aymen; Rhouma, Soumaya; Salah, Mohamed Ben; Santoni, Sylvain; Pintaud, Jean Christophe; Aberlenc-Bertossi, Frédérique; Hannachi, Amel Salhi

    2016-04-01

    The breeding of crop species relies on the valorisation of ancestral or wild varieties to enrich the cultivated germplasm. The Tunisian date palm genetic patrimony is being threatened by diversity loss and global climate change. We have conducted a genetic study to evaluate the potential of spontaneous coastal resources to improve the currently exploited Tunisian date palm genetic pool. Eighteen microsatellite loci of Phoenix dactylifera L. were used to compare the genetic diversity of coastal accessions from Kerkennah, Djerba, Gabès and continental date palm accessions from Tozeur. A collection of 105 date palms from the four regions was analysed. This study has provided us with an extensive understanding of the local genetic diversity and its distribution. The coastal date palm genotypes exhibit a high and specific genetic diversity. These genotypes are certainly an untapped reservoir of agronomically important genes to improve cultivated germplasm in continental date palm. PMID:26895027

  5. Phenotypic and RAPD diversity among 80 germplasm accessions of the medicinal plant isabgol (Plantago ovata, Plantaginaceae).

    PubMed

    Singh, N; Lal, R K; Shasany, A K

    2009-01-01

    Plantago ovata, popularly known as isabgol, has great commercial and medicinal importance due to thin rosy white membranous seed husk. Isabgol seeds and husks have emollient, demulcent and laxative properties. We used both biometric and molecular techniques to assess the genetic variability and relatedness of 80 germplasm accessions of Plantago spp (P. ovata, P. lanceolata, and P. major) collected both from India and abroad. The range of D2 values (2.01-4890.73) indicated a very high degree of divergence among the accessions. Based on the degree of divergence, 80 accessions/genotypes were grouped into seven clusters. Thirty-six accessions were analyzed through RAPD profiling for similarity and genetic distances, using 20 random primers. Intraspecific differences in all three species were smaller [range for P. ovata (2-17%), P. lanceolata (3-15%), P. major (2-11%)] than interspecific diversity. These highly divergent lines could be used to produce superior hybrids. PMID:19876869

  6. Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection.

    PubMed

    Bulli, Peter; Zhang, Junli; Chao, Shiaoman; Chen, Xianming; Pumphrey, Michael

    2016-01-01

    Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs. PMID:27226168

  7. Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection

    PubMed Central

    Bulli, Peter; Zhang, Junli; Chao, Shiaoman; Chen, Xianming; Pumphrey, Michael

    2016-01-01

    Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs. PMID:27226168

  8. Genetic diversity in Capsicum baccatum is significantly influenced by its ecogeographical distribution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The structure of genetic diversity in a plant germplasm collection is significantly influenced by its ecogeographical distribution. Improved understanding of the combined effects of geology, ecology and human intervention is essential for efficient conservation and use of plant germplasm. In the pr...

  9. Genetic and phenotypic diversity in camelina germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Camelina is a new crop targeted for agronomic systems across the Midwest. Camelina is a promising bioenergy crop fitting the requirements for the biodiesel industry, especially for production of JP-5 fuel used in the aircraft industry. Moreover, its fatty acid profile satisfies the standards for nut...

  10. Genetic effect and genetic values of fiber properties in F2 and F3 hybrids between germplasm lines and high yield cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Utilization of cotton (Gossypium hirsutum L.) germplasm for genetic improvement of fiber properties requires determination of genetic effects for fiber properties in the germplasm lines. A study was designed to analyze genetic populations derived from multiple crosses between nine germplasm lines a...

  11. Soybean Molecular Genetic Diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A history of the various DNA marker types used in the assessment of molecular genetic diversity in soybean [Glycine max (L.) Merr.] is followed by a description of a number of studies on the assessment of genetic diversity. These studies include a review of reports on 1) the quantification and comp...

  12. Puroindoline allelic diversity in Indian wheat germplasm and identification of new allelic variants

    PubMed Central

    Kumar, Rohit; Arora, Shaweta; Singh, Kashmir; Garg, Monika

    2015-01-01

    Grain hardness is an important quality trait that influences product development in wheat. This trait is governed by variation in puroindoline proteins (PINA and PINB). Our study evaluated 551 Indian wheat germplasm lines for diversity in Pina and Pinb genes. Eighty-two lines were shortlisted for full length sequencing and grain hardness studies. Sequencing studies identified six unknown alleles: two for the Pina gene and four for the Pinb gene. Five of them were novel with non-synonymous changes in the corresponding amino acid sequences. Identified mutations in the deduced mature proteins and their pre- and pro-peptides influenced the hardness characteristics of the grain. We classified these 82 varieties into different hardness categories with reference to international and Indian systems of classification. The majority of Indian wheat varieties were categorized as hard. This study revealed that unexplored Indian wheat germplasm can be a good source of genetic variability for both Pina and Pinb genes, helping in marker-assisted breeding and in obtaining wheat with different textural properties. PMID:26366114

  13. Determinants of genetic diversity.

    PubMed

    Ellegren, Hans; Galtier, Nicolas

    2016-07-01

    Genetic polymorphism varies among species and within genomes, and has important implications for the evolution and conservation of species. The determinants of this variation have been poorly understood, but population genomic data from a wide range of organisms now make it possible to delineate the underlying evolutionary processes, notably how variation in the effective population size (Ne) governs genetic diversity. Comparative population genomics is on its way to providing a solution to 'Lewontin's paradox' - the discrepancy between the many orders of magnitude of variation in population size and the much narrower distribution of diversity levels. It seems that linked selection plays an important part both in the overall genetic diversity of a species and in the variation in diversity within the genome. Genetic diversity also seems to be predictable from the life history of a species. PMID:27265362

  14. Improving in vitro mineral nutrition for diverse pear germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mineral nutrition of in vitro plants is often difficult to optimize due to complex chemical interactions of required nutrients. The USDA-ARS National Clonal Germplasm Repository, Corvallis, Oregon has over 200 shoot cultures of pears, including 18 species and many cultivars. Plant growth response o...

  15. Optimized scarification protocols improve germination of diverse Rubus germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seed collections of the wild relatives of cultivated blackberry and raspberry (Rubus species) are maintained at the National Clonal Germplasm Repository, Corvallis, OR. Seeds of Rubus species are orthodox and can be stored dry and remain viable for many years; however germination is often poor or er...

  16. Registration of four diverse random-mated cotton germplasm populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dwarf GP (Reg. No. ______; PI ______), Fiber GP (Reg. No. ______; PI ______), Glandless GP (Reg. No. ______; PI ______), and Race GP (Reg. No. ______; PI ______) are four unique upland cotton (Gossypium hirsutum L.) germplasm populations (GP) released by the USDA-ARS. One is a four-parent, narrow-b...

  17. SUNFLOWER GERMPLASM DIVERSITY FOR SEED OIL SATURATED FATTY ACID CONTENT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dietary saturated fat has become an important concern of consumers in recent years, as studies have indicated that high levels of saturated fat consumption are correlated with increased risk of coronary heart disease. The purpose of the present study was to screen the USDA-ARS sunflower germplasm ac...

  18. NGS technologies for analyzing germplasm diversity in genebanks*

    PubMed Central

    Graner, Andreas

    2012-01-01

    More than 70 years after the first ex situ genebanks have been established, major efforts in this field are still concerned with issues related to further completion of individual collections and securing of their storage. Attempts regarding valorization of ex situ collections for plant breeders have been hampered by the limited availability of phenotypic and genotypic information. With the advent of molecular marker technologies first efforts were made to fingerprint genebank accessions, albeit on a very small scale and mostly based on inadequate DNA marker systems. Advances in DNA sequencing technology and the development of high-throughput systems for multiparallel interrogation of thousands of single nucleotide polymorphisms (SNPs) now provide a suite of technological platforms facilitating the analysis of several hundred of Gigabases per day using state-of-the-art sequencing technology or, at the same time, of thousands of SNPs. The present review summarizes recent developments regarding the deployment of these technologies for the analysis of plant genetic resources, in order to identify patterns of genetic diversity, map quantitative traits and mine novel alleles from the vast amount of genetic resources maintained in genebanks around the world. It also refers to the various shortcomings and bottlenecks that need to be overcome to leverage the full potential of high-throughput DNA analysis for the targeted utilization of plant genetic resources. PMID:22257472

  19. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome-wide molecular markers are readily being applied to evaluate genetic diversity in germplasm collections and for making genomic selections in breeding programs. To accurately predict phenotypes and assay genetic diversity, molecular markers should assay a representative sample of the polymorp...

  20. REGISTRATION OF MAIZE GERMPLASM LINE GEMS-0067

    Technology Transfer Automated Retrieval System (TEKTRAN)

    GEMS-0067 is a partially inbred germplasm line released by Truman State University (TSU) in accordance with the Germplasm Enhancement of Maize (GEM) protocol. This line is being released for use in the development of genetically diverse, elite, amylomaize class VII parental lines possessing modifie...

  1. Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers.

    PubMed

    Jain, Sunita; Jain, Rajinder K; McCouch, Susan R

    2004-09-01

    Genetic relationships among Indian aromatic and quality rice (Oryza sativa) germplasm were assessed using 30 fluorescently labeled rice microsatellite markers. The 69 rice genotypes used in this study included 52 Basmati and other scented/quality rice varieties from different parts of India and 17 indica and japonica varieties that served as controls. A total of 235 alleles were detected at the 30 simple sequence repeat (SSR) loci, 62 (26.4%) of which were present only in Basmati and other scented/quality rice germplasm accessions. The number of alleles per locus ranged from 3 to 22, with an average of 7.8, polymorphism information content (PIC) values ranged from 0.2 to 0.9, with an average of 0.6, and the size range between the smallest and the largest allele for a given microsatellite locus varied between 3 bp and 68 bp. Of the 30 SSR markers, 20 could distinguish traditional Basmati rice varieties, and a single panel of eight markers could be used to differentiate the premium traditional Basmati, cross-bred Basmati, and non-Basmati rice varieties having different commercial value in the market-place. When estimates of inferred ancestry or similarity coefficients were used to cluster varieties, the high-quality Indian aromatic and quality rice genotypes could be distinguished from both indica and japonica cultivars, and crossbred varieties could be distinguished from traditional Basmati rices. The results indicate that Indian aromatic and quality germplasm is genetically distinct from other groups within O. sativa and is the product of a long independent pattern of evolution. The data also suggest that there is scope for exploiting the genetic diversity of aromatic/quality rice germplasm available in India for national Basmati rice breeding programs. PMID:15309297

  2. Imposing genetic diversity.

    PubMed

    Sparrow, Robert

    2015-01-01

    The idea that a world in which everyone was born "perfect" would be a world in which something valuable was missing often comes up in debates about the ethics of technologies of prenatal testing and preimplantation genetic diagnosis (PGD). This thought plays an important role in the "disability critique" of prenatal testing. However, the idea that human genetic variation is an important good with significant benefits for society at large is also embraced by a wide range of figures writing in the bioethics literature, including some who are notoriously hostile to the idea that we should not select against disability. By developing a number of thought experiments wherein we are to contemplate increasing genetic diversity from a lower baseline in order to secure this value, I argue that this powerful intuition is more problematic than is generally recognized, especially where the price of diversity is the well-being of particular individuals. PMID:26030484

  3. Historical origins and genetic diversity of wine grapes.

    PubMed

    This, Patrice; Lacombe, Thierry; Thomas, Mark R

    2006-09-01

    The genomic resources that are available to the grapevine research community have increased enormously during the past five years, in parallel with a renewed interest in grapevine (Vitis vinifera L.) germplasm resources and analysis of genetic diversity in grapes. Genetic variation, either natural or induced, is invaluable for crop improvement and understanding gene function, and the same is true for the grapevine. The history and vineyard cultural practices have largely determined the genetic diversity that exists today in grapevines. In this article, we provide a synopsis of what is known about the origin and genetics of grapes and how molecular genetics is helping us understand more about this plant: its evolution, historical development, genetic diversity and potential for genetic improvement. PMID:16872714

  4. Genetic Diversity of Cultivated Lentil (Lens culinaris Medik.) and Its Relation to the World's Agro-ecological Zones

    PubMed Central

    Khazaei, Hamid; Caron, Carolyn T.; Fedoruk, Michael; Diapari, Marwan; Vandenberg, Albert; Coyne, Clarice J.; McGee, Rebecca; Bett, Kirstin E.

    2016-01-01

    Assessment of genetic diversity and population structure of germplasm collections plays a critical role in supporting conservation and crop genetic enhancement strategies. We used a cultivated lentil (Lens culinaris Medik.) collection consisting of 352 accessions originating from 54 diverse countries to estimate genetic diversity and genetic structure using 1194 polymorphic single nucleotide polymorphism (SNP) markers which span the lentil genome. Using principal coordinate analysis, population structure analysis and UPGMA cluster analysis, the accessions were categorized into three major groups that prominently reflected geographical origin (world's agro-ecological zones). The three clusters complemented the origins, pedigrees, and breeding histories of the germplasm. The three groups were (a) South Asia (sub-tropical savannah), (b) Mediterranean, and (c) northern temperate. Based on the results from this study, it is also clear that breeding programs still have considerable genetic diversity to mine within the cultivated lentil, as surveyed South Asian and Canadian germplasm revealed narrow genetic diversity. PMID:27507980

  5. Genetic Diversity of Cultivated Lentil (Lens culinaris Medik.) and Its Relation to the World's Agro-ecological Zones.

    PubMed

    Khazaei, Hamid; Caron, Carolyn T; Fedoruk, Michael; Diapari, Marwan; Vandenberg, Albert; Coyne, Clarice J; McGee, Rebecca; Bett, Kirstin E

    2016-01-01

    Assessment of genetic diversity and population structure of germplasm collections plays a critical role in supporting conservation and crop genetic enhancement strategies. We used a cultivated lentil (Lens culinaris Medik.) collection consisting of 352 accessions originating from 54 diverse countries to estimate genetic diversity and genetic structure using 1194 polymorphic single nucleotide polymorphism (SNP) markers which span the lentil genome. Using principal coordinate analysis, population structure analysis and UPGMA cluster analysis, the accessions were categorized into three major groups that prominently reflected geographical origin (world's agro-ecological zones). The three clusters complemented the origins, pedigrees, and breeding histories of the germplasm. The three groups were (a) South Asia (sub-tropical savannah), (b) Mediterranean, and (c) northern temperate. Based on the results from this study, it is also clear that breeding programs still have considerable genetic diversity to mine within the cultivated lentil, as surveyed South Asian and Canadian germplasm revealed narrow genetic diversity. PMID:27507980

  6. Chemical Diversity in Lippia alba (Mill.) N. E. Brown Germplasm

    PubMed Central

    Camêlo, Lídia Cristina Alves; Pinheiro, José Baldin; Andrade, Thiago Matos; Alves, Péricles Barreto

    2015-01-01

    The aim of this study was to perform chemical characterization of Lippia alba accessions from the Active Germplasm Bank of the Federal University of Sergipe. A randomized block experimental design with two replications was applied. The analysis of the chemical composition of the essential oils was conducted using a gas chromatograph coupled to a mass spectrometer. The chemical composition of the essential oils allowed the accessions to be allocated to the following six groups: group 1: linalool, 1,8-cineole, and caryophyllene oxide; group 2: linalool, geranial, neral, 1,8-cineol, and caryophyllene oxide; group 3: limonene, carvone, and sabinene; group 4: carvone, limonene, g-muurolene, and myrcene; group 5: neral, geranial, and caryophyllene oxide; and group 6: geranial, neral, o-cymene, limonene, and caryophyllene oxide. PMID:26075292

  7. Genetic variation and selection within glandless cotton germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is a renewed interest in research and use of glandless (free of gossypol) cotton that can produce edible seeds for human food and animal feed. However, there was a lack of information on yield potential of existing glandless germplasm since intermittent breeding activities for glandless cotton...

  8. Germplasm for genetic improvement of lint yield in Upland cotton genetic analysis of lint yield with yield components

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Determination of genetic effects for lint yield and yield components in cotton (Gossypium hirsutum L.) germplasm is critical for its utilization in breeding programs. This study was designed to apply the conditional approach and an additive and dominant (AD) model to analyze genetic effects and gen...

  9. Tapping the US sweet sorghum collection to identify biofuel germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The narrow genetic base in sweet sorghum [Sorghum bicolor (L.) Moench] breeding programs is limiting the development of new varieties for biofuel production. Therefore, the identification of genetically diverse sweet sorghum germplasm in the U.S. National Plant Germplasm System (NPGS) collection is...

  10. 30 years of preserving clonal genetic resources in the U.S. National Plant Germplasm System

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For more than 30 years, the U.S. Department of Agriculture (USDA) Agricultural Research Service (ARS) National Plant Germplasm System (NPGS) has preserved clonal plant genetic resources of horticultural crops in field gene banks. Facilities in Hilo, Hawaii; Mayaguez, Puerto Rico; Miami, Florida; and...

  11. Reducing photoperiod response of tropical maize germplasm for use in Midwestern maize introgression

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Germplasm Enhancement of Maize Project (GEM) is a cooperative effort of USDA-ARS, public and private sector scientists to broaden the genetic diversity of maize germplasm. Tropical maize germplasm is an important source of alleles for biotic and abiotic stress resistance and numerous value-adde...

  12. Elaeis oleifera genomic-SSR markers: exploitation in oil palm germplasm diversity and cross-amplification in arecaceae.

    PubMed

    Zaki, Noorhariza Mohd; Singh, Rajinder; Rosli, Rozana; Ismail, Ismanizan

    2012-01-01

    Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (H(o)) (0.164) and highly positive fixation indices (F(is)) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family. PMID:22605966

  13. Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae

    PubMed Central

    Zaki, Noorhariza Mohd; Singh, Rajinder; Rosli, Rozana; Ismail, Ismanizan

    2012-01-01

    Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (Ho) (0.164) and highly positive fixation indices (Fis) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family. PMID:22605966

  14. The United States Arachis germplasm collection: a valuable genetic resource for mining useful traits to improve peanut quality and production

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA Plant Genetic Resources Conservation Unit maintains the second largest peanut germplasm collection in the world consisting of both cultivated and wild germplasm with a total of 9,924 Arachis accessions. A cultivated core (831 accessions) and mini core (112 accessions) collections were esta...

  15. The USDA collection of barley landraces and cultivars: genetic diversity, population structure, and potential for genome-wide association studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New sources of genetic diversity must to be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these re...

  16. Genetic diversity, population structure, conservation and utilization of Theobroma cacao L., genetic resources in the Dominican Republic

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cacao (Theobroma cacao L.) is a significant agricultural commodity in the Dominican Republic, which ranks 11th in the world and number one in organic cacao exports. In an effort to identify propagation mistakes, and estimate genetic diversity and population structure in cacao germplasm accessions a...

  17. Genetic diversity analysis of common beans based on molecular markers.

    PubMed

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

  18. Genetic diversity analysis of common beans based on molecular markers

    PubMed Central

    Gill-Langarica, Homar R.; Muruaga-Martínez, José S.; Vargas-Vázquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-01-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

  19. Diversity of potato genetic resources

    PubMed Central

    Machida-Hirano, Ryoko

    2015-01-01

    A considerable number of highly diverse species exist in genus Solanum. Because they can adapt to a broad range of habitats, potato wild relatives are promising sources of desirable agricultural traits. Potato taxonomy is quite complex because of introgression, interspecific hybridization, auto- and allopolyploidy, sexual compatibility among many species, a mixture of sexual and asexual reproduction, possible recent species divergence, phenotypic plasticity, and the consequent high morphological similarity among species. Recent researchers using molecular tools have contributed to the identification of genes controlling several types of resistance as well as to the revision of taxonomical relationships among potato species. Historically, primitive forms of cultivated potato and its wild relatives have been used in breeding programs and there is still an enormous and unimaginable potential for discovering desirable characteristics, particularly in wild species Different methods have been developed to incorporate useful alleles from these wild species into the improved cultivars. Potato germplasm comprising of useful alleles for different breeding objectives is preserved in various gene banks worldwide. These materials, with their invaluable information, are accessible for research and breeding purposes. Precise identification of species base on the new taxonomy is essential for effective use of the germplasm collection. PMID:25931978

  20. Determining redundancy of short-day onion accessions in a germplasm collection using microsatellite and targeted region amplified polymorphic markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The U.S. National Plant Germplasm System is one of the world’s largest national genebank networks focusing on preserving the genetic diversity of plants by acquiring, preserving, evaluat- ing, documenting and distributing crop-related germplasm to researchers worldwide. Maintaining viable germplasm ...

  1. Determining redundancy of short-day, onion (Allium cepa L. var. cepa) accessions in a germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The U.S. National Plant Germplasm System is one of the world’s largest national genebank networks focusing on preserving the genetic diversity of plants by acquiring, preserving, evaluating, documenting and distributing crop-related germplasm to researchers worldwide. Maintaining viable germplasm co...

  2. Status of the USA cotton germplasm collection and crop vulnerability

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The National Plant Germplasm System (NPGS) is a cooperative effort among State, Federal and Private organizations aimed at preserving one of agriculture’s greatest assets, plant genetic diversity. The NPGS serves the scientific community by collecting, storing, and distributing germplasm as well as ...

  3. Genetic diversity in wild and cultivated black raspberry evaluated by simple sequence repeat markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Breeding progress in black raspberry (Rubus occidentalis L.) has been limited by a lack of genetic diversity in elite germplasm. Black raspberry cultivars have been noted for showing very few phenotypic differences and seedlings from crosses between cultivars for a lack of segregation for important ...

  4. Extensive genetic diversity and low linkage disequilibrium within the COMT locus in maize exotic populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Caffeic acid 3-O-methytransferase (COMT) gene is a prime candidate for cell wall digestibility improvement based on the characterization of brown midrib-3 mutants. We compared the genetic diversity and linkage disequilibrium at COMT locus between populations sampled within the Germplasm Enhance...

  5. Genetic diversity of mango cultivars estimated using Start Codon Targeted (SCoT) markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diversity and genetic relationships among 23 mango germplasm accessions, collected from different locations in Guangxi province in China, were analyzed by using a novel and simple gene targeted DNA marker: Start Codon Targeted (SCoT) markers. This technique uses a single, 18-mer primer PCR amplifica...

  6. Usefulness of WRKY gene-derived markers for assessing genetic diversity of Florida coconut cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analysis of the genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm representing eight cultivars was previously described using 15 microsatellite (simple sequence repeat, SSR) markers. Here we report on the analysis of the same genotypes using 13 markers d...

  7. Genetic diversity analysis in Piper species (Piperaceae) using RAPD markers.

    PubMed

    Sen, Sandeep; Skaria, Reby; Abdul Muneer, P M

    2010-09-01

    The genetic diversity of eight species of Piper (Piperaceae) viz., P. nigrum, P. longum, P. betle, P. chaba, P. argyrophyllum, P. trichostachyon, P. galeatum, and P. hymenophyllum from Kerala state, India were analyzed by Random amplified polymorphic DNA (RAPD). Out of 22 10-mer RAPD primers screened, 11 were selected for comparative analysis of different species of Piper. High genetic variations were found among different Piper species studied. Among the total of 149 RAPD fragments amplified, 12 bands (8.05%) were found monomorphic in eight species. The remaining 137 fragments were found polymorphic (91.95%). Species-specific bands were found in all eight species studied. The average gene diversity or heterozygosity (H) was 0.33 across all the species, genetic distances ranged from 0.21 to 0.69. The results of this study will facilitate germplasm identification, management, and conservation. PMID:20383613

  8. Identification and conservation of apple genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-ARS National Plant Germplasm System (NPGS) maintains a vast collection of plant genetic resources that includes over 570,000 accessions representing nearly 15,000 species. This collection is dispersed amongst 17 active sites throughout the United States. The NPGS base collection at the Nati...

  9. Genetic and Metabolite Diversity of Sardinian Populations of Helichrysum italicum

    PubMed Central

    Melito, Sara; Sias, Angela; Petretto, Giacomo L.; Chessa, Mario; Pintore, Giorgio; Porceddu, Andrea

    2013-01-01

    Background Helichrysum italicum (Asteraceae) is a small shrub endemic to the Mediterranean Basin, growing in fragmented and diverse habitats. The species has attracted attention due to its secondary metabolite content, but little effort has as yet been dedicated to assessing the genetic and metabolite diversity present in these populations. Here, we describe the diversity of 50 H. italicum populations collected from a range of habitats in Sardinia. Methods H. italicum plants were AFLP fingerprinted and the composition of their leaf essential oil characterized by GC-MS. The relationships between the genetic structure of the populations, soil, habitat and climatic variables and the essential oil chemotypes present were evaluated using Bayesian clustering, contingency analyses and AMOVA. Key results The Sardinian germplasm could be partitioned into two AFLP-based clades. Populations collected from the southwestern region constituted a homogeneous group which remained virtually intact even at high levels of K. The second, much larger clade was more diverse. A positive correlation between genetic diversity and elevation suggested the action of natural purifying selection. Four main classes of compounds were identified among the essential oils, namely monoterpenes, oxygenated monoterpenes, sesquiterpenes and oxygenated sesquiterpenes. Oxygenated monoterpene levels were significantly correlated with the AFLP-based clade structure, suggesting a correspondence between gene pool and chemical diversity. Conclusions The results suggest an association between chemotype, genetic diversity and collection location which is relevant for the planning of future collections aimed at identifying valuable sources of essential oil. PMID:24260149

  10. Genetic Diversity and Human Equality.

    ERIC Educational Resources Information Center

    Dobzhansky, Theodosius

    The idea of equality often, if not frequently, bogs down in confusion and apparent contradictions; equality is confused with identity, and diversity with inequality. It would seem that the easiest way to discredit the idea of equality is to show that people are innately, genetically, and, therefore, irremediably diverse and unlike. The snare is,…

  11. Genetic Diversity of Toscana Virus

    PubMed Central

    Collao, Ximena; Palacios, Gustavo; Sanbonmatsu-Gámez, Sara; Pérez-Ruiz, Mercedes; Negredo, Ana I.; Navarro-Marí, José-María; Grandadam, Marc; Aransay, Ana Maria; Lipkin, W. Ian; Tenorio, Antonio

    2009-01-01

    Distribution of Toscana virus (TOSV) is evolving with climate change, and pathogenicity may be higher in nonexposed populations outside areas of current prevalence (Mediterranean Basin). To characterize genetic diversity of TOSV, we determined the coding sequences of isolates from Spain and France. TOSV is more diverse than other well-studied phleboviruses (e.g.,Rift Valley fever virus). PMID:19331735

  12. Sequence-Related Amplified Polymorphism (SRAP) markers for assessing interrelationships and genetic diversity among members of the Saccharum complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Characterization of wild germplasm provides essential information on genetic diversity that breeders utilize for crop improvement. The potential of the sequence-related amplified polymorphism (SRAP) technique, which preferentially amplifies gene-rich regions, was evaluated to assess the genetic rela...

  13. Registration of N6202 soybean germplasm with high protein, good yield potential, large seed and diverse pedigree

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘N6202’ soybean [Glycine max (L.,) Merr.] was cooperatively developed and released by the USDA-ARS and the North Carolina Agricultural Research Service in 2009 as a Maturity Group VI germplasm with high-protein seed, good yield potential, large-seed size, and diverse pedigree. The unusual combinati...

  14. Analysis of genetic and nutritional diversity among selected accessions of dry beans and nuña beans (Phaseolus vulgaris L.) from the USDA-ARS National Plant Germplasm System

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beans (Phaseolus spp.) are one of the most economically and nutritionally important crops world-wide, with a value of over $17 billion harvested annually. They are one of the most ancient crops of the New World, having been cultivated for thousands of years. They are an environmentally diverse crop...

  15. Seed oil and protein diversity among Gossypium accessions in the U.S. National Cotton Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Identifying and reporting genetic variability is an important tool to increase the utilization of germplasm collections. In an effort to further realize the potential of cottonseed, we have characterized seed composition traits of Gossypium spp. accessions available in the U.S. National Cotton Germ...

  16. Population genetics related to adaptation in elite oat germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Six hundred thirty five oat lines and 2,635 SNP loci were used to evaluate population structure, linkage disequilibrium (LD) and genotype-phenotype association with heading date. The first five principal components (PC) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 2...

  17. Anthracnose disease response for photoperiod-insensitive Ethiopian germplasm from the U.S. sorghum collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ethiopia is an important center of genetic diversity for sorghum germplasm; however, photoperiod-sensitivity limits the utilization of this genetic resource. The United States National Plant Germplasm System maintains 180 Ethiopian sorghum accessions that are less sensitive to photoperiod and these...

  18. Genetic diversity in Napier grass (Pennisetum purpureum) cultivars: implications for breeding and conservation.

    PubMed

    Wanjala, Bramwel W; Obonyo, Meshack; Wachira, Francis N; Muchugi, Alice; Mulaa, Margaret; Harvey, Jagger; Skilton, Robert A; Proud, Janice; Hanson, Jean

    2013-01-01

    Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to be highly significant (P < 0.001), indicating more variation within (91 %) than between populations (9 %). Results suggested moderate genetic differentiation among Napier grass populations sampled, which could imply a high germplasm exchange within the region. The AFLP markers used in this study efficiently discriminate among cultivars and could be useful in identification and germplasm conservation. PMID:23671788

  19. Genetic diversity in Napier grass (Pennisetum purpureum) cultivars: implications for breeding and conservation

    PubMed Central

    Wanjala, Bramwel W.; Obonyo, Meshack; Wachira, Francis N.; Muchugi, Alice; Mulaa, Margaret; Harvey, Jagger; Skilton, Robert A.; Proud, Janice; Hanson, Jean

    2013-01-01

    Napier grass is an important forage crop for dairy production in the tropics; as such, its existing genetic diversity needs to be assessed for conservation. The current study assessed the genetic variation of Napier grass collections from selected regions in Eastern Africa and the International Livestock Research Institute Forage Germplasm-Ethiopia. The diversity of 281 cultivars was investigated using five selective amplified fragment length polymorphism (AFLP) markers and classical population genetic parameters analysed using various software. The number of bands generated was 216 with fragments per primer set ranging from 50 to 115. Mean percentage polymorphic loci was 63.40. Genetic diversity coefficients based on Nei's genetic diversity ranged from 0.0783 to 0.2142 and Shannon's information index ranged from 0.1293 to 0.3445. The Fst value obtained was moderately significant (Fst = 0.1688). Neighbour-joining analysis gave two distinct clusters which did not reflect geographical locations. Analysis of molecular variance showed all variance components to be highly significant (P < 0.001), indicating more variation within (91 %) than between populations (9 %). Results suggested moderate genetic differentiation among Napier grass populations sampled, which could imply a high germplasm exchange within the region. The AFLP markers used in this study efficiently discriminate among cultivars and could be useful in identification and germplasm conservation. PMID:23671788

  20. Characterizing Croatian Wheat Germplasm Diversity and Structure in a European Context by DArT Markers

    PubMed Central

    Novoselović, Dario; Bentley, Alison R.; Šimek, Ruđer; Dvojković, Krešimir; Sorrells, Mark E.; Gosman, Nicolas; Horsnell, Richard; Drezner, Georg; Šatović, Zlatko

    2016-01-01

    Narrowing the genetic base available for future genetic progress is a major concern to plant breeders. In order to avoid this, strategies to characterize and protect genetic diversity in regional breeding pools are required. In this study, 89 winter wheat cultivars released in Croatia between 1936 and 2006 were genotyped using 1,229 DArT (diversity array technology) markers to assess the diversity and population structure. In order to place Croatian breeding pool (CBP) in a European context, Croatian wheat cultivars were compared to 523 European cultivars from seven countries using a total of 166 common DArT markers. The results show higher genetic diversity in the wheat breeding pool from Central Europe (CE) as compared to that from Northern and Western European (NWE) countries. The most of the genetic diversity was attributable to the differences among cultivars within countries. When the geographical criterion (CE vs. NWE) was applied, highly significant difference between regions was obtained that accounted for 16.19% of the total variance, revealing that the CBP represents genetic variation not currently captured in elite European wheat. The current study emphasizes the important contribution made by plant breeders to maintaining wheat genetic diversity and suggests that regional breeding is essential to the maintenance of this diversity. The usefulness of open-access wheat datasets is also highlighted. PMID:26941756

  1. Characterizing Croatian Wheat Germplasm Diversity and Structure in a European Context by DArT Markers.

    PubMed

    Novoselović, Dario; Bentley, Alison R; Šimek, Ruđer; Dvojković, Krešimir; Sorrells, Mark E; Gosman, Nicolas; Horsnell, Richard; Drezner, Georg; Šatović, Zlatko

    2016-01-01

    Narrowing the genetic base available for future genetic progress is a major concern to plant breeders. In order to avoid this, strategies to characterize and protect genetic diversity in regional breeding pools are required. In this study, 89 winter wheat cultivars released in Croatia between 1936 and 2006 were genotyped using 1,229 DArT (diversity array technology) markers to assess the diversity and population structure. In order to place Croatian breeding pool (CBP) in a European context, Croatian wheat cultivars were compared to 523 European cultivars from seven countries using a total of 166 common DArT markers. The results show higher genetic diversity in the wheat breeding pool from Central Europe (CE) as compared to that from Northern and Western European (NWE) countries. The most of the genetic diversity was attributable to the differences among cultivars within countries. When the geographical criterion (CE vs. NWE) was applied, highly significant difference between regions was obtained that accounted for 16.19% of the total variance, revealing that the CBP represents genetic variation not currently captured in elite European wheat. The current study emphasizes the important contribution made by plant breeders to maintaining wheat genetic diversity and suggests that regional breeding is essential to the maintenance of this diversity. The usefulness of open-access wheat datasets is also highlighted. PMID:26941756

  2. Genetic variation of germination cold tolerance in Japanese rice germplasm

    PubMed Central

    Bosetti, Fátima; Montebelli, Camila; Novembre, Ana Dionísia L.C.; Chamma, Helena Pescarin; Pinheiro, José Baldin

    2012-01-01

    Low temperatures at the initial stages of rice development prevent fast germination and seedling establishment and may cause significant productivity losses. In order to develop rice cultivars exhibiting cold tolerance, it is necessary to investigate genetic resources, providing basic knowledge to allow the introduction of genes involved in low temperature germination ability from accessions into elite cultivars. Japanese rice accessions were evaluated at the germination under two conditions: 13°C for 28 days (cold stress) and 28°C for seven days (optimal temperature). The traits studied were coleoptile and radicle length under optimal temperature, coleoptile and radicle length under cold and percentage of the reduction in coleptile and radicle length due to low temperature. Among the accessions studied, genetic variation for traits related to germination under low temperatures was observed and accessions exhibiting adequate performance for all investigated traits were identified. The use of multivariate analysis allowed the identification of the genotypes displaying cold tolerance by smaller reductions in coleoptile and radicle lenght in the presence of cold and high vigour, by higher coleoptile and radicle growth under cold. PMID:23226080

  3. Farming practices and genetic characterization of Nicobari pig, an indigenous pig germplasm of Nicobar group of islands, India.

    PubMed

    De, Arun Kumar; Jeyakumar, S; Kundu, Madhu Sudan; Kundu, Anandamoy; Sunder, Jai; Ramachandran, M

    2014-04-01

    The Nicobari pig, locally known as Ha-un, is an indigenous pig germplasm located only in the Nicobar group of islands, India. The present study documents the Nicobari pig-rearing practices of the tribal farmers and genetically characterizes them using 23 FAO-recommended microsatellite markers. The study was conducted over a period of 3 years (2010-2012) in Car Nicobar, India. A total of 225 farmers were surveyed (15 farmers per village of 15 villages). Information on herd statistics, husbandry practices, and constraints faced by the farmers in pig production were collected. The pigs were reared in a free-range system. Mean pig herd size per house hold was 8.9, and main feed for pigs was coconut and some indigenous feed materials such as pandanus, bread fruit, and Nicobari alu. The main constraints faced by the farmers were lack of feed after the tsunami, different disease conditions, piglet mortality, and predator attack. The Nicobari pigs were genotyped by 23 FAO-recommended microsatellite markers. The mean observed number of alleles for all 23 loci in Nicobari pigs was 6.96 ± 0.31. The mean observed and expected heterozygosities were 0.66 ± 0.02 and 0.75 ± 0.01, respectively. It was found that the genetic diversity of this pig breed was very high compared to Large White Yorkshire and other European pig breeds. This genetic characterization of the pig breed will be helpful in their conservation effort. PMID:24595559

  4. Nucleotide diversity estimates of tomatillo (Physalis philadelphica) accessions including nine new inbred lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To help support utilization of germplasm resources for tomatillo (Physalis philadelphica) crop improvement, we characterized genetic diversity in the National Plant Germplasm System (NPGS) collection. Genotyping by sequencing (GBS), a method of high throughput DNA sequencing of reduced representati...

  5. Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm Based on nSSR Markers and cpDNA Sequences

    PubMed Central

    Wambulwa, Moses C.; Meegahakumbura, Muditha K.; Kamunya, Samson; Muchugi, Alice; Möller, Michael; Liu, Jie; Xu, Jian-Chu; Ranjitkar, Sailesh; Li, De-Zhu; Gao, Lian-Ming

    2016-01-01

    Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (HS) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed “mosaic” group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study

  6. Insights into the Genetic Relationships and Breeding Patterns of the African Tea Germplasm Based on nSSR Markers and cpDNA Sequences.

    PubMed

    Wambulwa, Moses C; Meegahakumbura, Muditha K; Kamunya, Samson; Muchugi, Alice; Möller, Michael; Liu, Jie; Xu, Jian-Chu; Ranjitkar, Sailesh; Li, De-Zhu; Gao, Lian-Ming

    2016-01-01

    Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (H S) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents

  7. Unlocking the Genetic Diversity of Maize Landraces with Doubled Haploids Opens New Avenues for Breeding

    PubMed Central

    Strigens, Alexander; Schipprack, Wolfgang; Reif, Jochen C.; Melchinger, Albrecht E.

    2013-01-01

    Landraces are valuable genetic resources for broadening the genetic base of elite germplasm in maize. Extensive exploitation of landraces has been hampered by their genetic heterogeneity and heavy genetic load. These limitations may be overcome by the in-vivo doubled haploid (DH) technique. A set of 132 DH lines derived from three European landraces and 106 elite flint (EF) lines were genotyped for 56,110 single nucleotide polymorphism (SNP) markers and evaluated in field trials at five locations in Germany in 2010 for several agronomic traits. In addition, the landraces were compared with synthetic populations produced by intermating DH lines derived from the respective landrace. Our objectives were to (1) evaluate the phenotypic and molecular diversity captured within DH lines derived from European landraces, (2) assess the breeding potential (usefulness) of DH lines derived from landraces to broaden the genetic base of the EF germplasm, and (3) compare the performance of each landrace with the synthetic population produced from the respective DH lines. Large genotypic variances among DH lines derived from landraces allowed the identification of DH lines with grain yields comparable to those of EF lines. Selected DH lines may thus be introgressed into elite germplasm without impairing its yield level. Large genetic distances of the DH lines to the EF lines demonstrated the potential of DH lines derived from landraces to broaden the genetic base of the EF germplasm. The comparison of landraces with their respective synthetic population showed no yield improvement and no reduction of phenotypic diversity. Owing to the low population structure and rapid decrease of linkage disequilibrium within populations of DH lines derived from landraces, these would be an ideal tool for association mapping. Altogether, the DH technology opens new opportunities for characterizing and utilizing the genetic diversity present in gene bank accessions of maize. PMID:23451190

  8. Genetic diversity in Trichomonas vaginalis.

    PubMed

    Meade, John C; Carlton, Jane M

    2013-09-01

    Recent advances in genetic characterisation of Trichomonas vaginalis isolates show that the extensive clinical variability in trichomoniasis and its disease sequelae are matched by significant genetic diversity in the organism itself, suggesting a connection between the genetic identity of isolates and their clinical manifestations. Indeed, a high degree of genetic heterogeneity in T vaginalis isolates has been observed using multiple genotyping techniques. A unique two-type population structure that is both local and global in distribution has been identified, and there is evidence of recombination within each group, although sexual recombination between the groups appears to be constrained. There is conflicting evidence in these studies for correlations between T vaginalis genetic identity and clinical presentation, metronidazole susceptibility, and the presence of T vaginalis virus, underscoring the need for adoption of a common standard for genotyping the parasite. Moving forward, microsatellite genotyping and multilocus sequence typing are the most robust techniques for future investigations of T vaginalis genotype-phenotype associations. PMID:23702460

  9. Genetic selection and conservation of genetic diversity*.

    PubMed

    Blackburn, H D

    2012-08-01

    For 100s of years, livestock producers have employed various types of selection to alter livestock populations. Current selection strategies are little different, except our technologies for selection have become more powerful. Genetic resources at the breed level have been in and out of favour over time. These resources are the raw materials used to manipulate populations, and therefore, they are critical to the past and future success of the livestock sector. With increasing ability to rapidly change genetic composition of livestock populations, the conservation of these genetic resources becomes more critical. Globally, awareness of the need to steward genetic resources has increased. A growing number of countries have embarked on large scale conservation efforts by using in situ, ex situ (gene banking), or both approaches. Gene banking efforts have substantially increased and data suggest that gene banks are successfully capturing genetic diversity for research or industry use. It is also noteworthy that both industry and the research community are utilizing gene bank holdings. As pressures grow to meet consumer demands and potential changes in production systems, the linkage between selection goals and genetic conservation will increase as a mechanism to facilitate continued livestock sector development. PMID:22827378

  10. Distribution of SUN, OVATE, LC, and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity1[C][W][OA

    PubMed Central

    Rodríguez, Gustavo R.; Muños, Stéphane; Anderson, Claire; Sim, Sung-Chur; Michel, Andrew; Causse, Mathilde; Gardener, Brian B. McSpadden; Francis, David; van der Knaap, Esther

    2011-01-01

    Phenotypic diversity within cultivated tomato (Solanum lycopersicum) is particularly evident for fruit shape and size. Four genes that control tomato fruit shape have been cloned. SUN and OVATE control elongated shape whereas FASCIATED (FAS) and LOCULE NUMBER (LC) control fruit locule number and flat shape. We investigated the distribution of the fruit shape alleles in the tomato germplasm and evaluated their contribution to morphology in a diverse collection of 368 predominantly tomato and tomato var. cerasiforme accessions. Fruits were visually classified into eight shape categories that were supported by objective measurements obtained from image analysis using the Tomato Analyzer software. The allele distribution of SUN, OVATE, LC, and FAS in all accessions was strongly associated with fruit shape classification. We also genotyped 116 representative accessions with additional 25 markers distributed evenly across the genome. Through a model-based clustering we demonstrated that shape categories, germplasm classes, and the shape genes were nonrandomly distributed among five genetic clusters (P < 0.001), implying that selection for fruit shape genes was critical to subpopulation differentiation within cultivated tomato. Our data suggested that the LC, FAS, and SUN mutations arose in the same ancestral population while the OVATE mutation arose in a separate lineage. Furthermore, LC, OVATE, and FAS mutations may have arisen prior to domestication or early during the selection of cultivated tomato whereas the SUN mutation appeared to be a postdomestication event arising in Europe. PMID:21441384

  11. Genetics of the ovule fiberless and foliar glabrous traits in the Gossypium arboreum germplasm line in PI 529740

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Accession PI 529740 from the Gossypium arboreum (G. arboreum) germplasm collection and characterized by fiberless seeds and glabrous leaves and stems was crossed with two G. arboreum accessions, PI 417890 or PI 529729, to develop F2 populations for genetic analysis. Segregation data indicated these...

  12. Diverse germplasm to devleop male-sterile lines for hybrid breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hybrid rice breeding in the US has depended largely upon male-sterile lines originating in China or from other Asian sources. By contrast, the program in Arkansas has developed all of its male-sterile lines at Stuttgart,AR using germplasm accessions available in the USDA Rice Germplasm Collection st...

  13. Genetic diversity of medlar (Mespilus germanica) germplasm using microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The medlar (Mespilus germanica) is a pome fruit related to pear (Pyrus sp.) and hawthorn (Crataegus sp.) that has been cultivated for many centuries for its edible fruit. It was also an important medicinal plant in the Middle Ages. The center of origin for Mespilus is the Trans-Caucasus region and t...

  14. Availability of genotypic data for USDA-ARS National Plant Germplasm System accessions using the Genetic Resources Information Network (GRIN) database

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The National Plant Germplasm System (NPGS) provides critical genetic resources to researchers and breeders world wide. Users of the NPGS materials need access to both genotypic and phenotypic data for accessions. Descriptor records at the accession level within the Germplasm Resources Information ...

  15. Genetic diversity and population structure of an important wild berry crop.

    PubMed

    Zoratti, Laura; Palmieri, Luisa; Jaakola, Laura; Häggman, Hely

    2015-01-01

    The success of plant breeding in the coming years will be associated with access to new sources of variation, which will include landraces and wild relatives of crop species. In order to access the reservoir of favourable alleles within wild germplasm, knowledge about the genetic diversity and the population structure of wild species is needed. Bilberry (Vaccinium myrtillus) is one of the most important wild crops growing in the forests of Northern European countries, noted for its nutritional properties and its beneficial effects on human health. Assessment of the genetic diversity of wild bilberry germplasm is needed for efforts such as in situ conservation, on-farm management and development of plant breeding programmes. However, to date, only a few local (small-scale) genetic studies of this species have been performed. We therefore conducted a study of genetic variability within 32 individual samples collected from different locations in Iceland, Norway, Sweden, Finland and Germany, and analysed genetic diversity among geographic groups. Four selected inter-simple sequence repeat primers allowed the amplification of 127 polymorphic loci which, based on analysis of variance, made it possible to identify 85 % of the genetic diversity within studied bilberry populations, being in agreement with the mixed-mating system of bilberry. Significant correlations were obtained between geographic and genetic distances for the entire set of samples. The analyses also highlighted the presence of a north-south genetic gradient, which is in accordance with recent findings on phenotypic traits of bilberry. PMID:26483325

  16. Genetic diversity and population structure of an important wild berry crop

    PubMed Central

    Zoratti, Laura; Palmieri, Luisa; Jaakola, Laura; Häggman, Hely

    2015-01-01

    The success of plant breeding in the coming years will be associated with access to new sources of variation, which will include landraces and wild relatives of crop species. In order to access the reservoir of favourable alleles within wild germplasm, knowledge about the genetic diversity and the population structure of wild species is needed. Bilberry (Vaccinium myrtillus) is one of the most important wild crops growing in the forests of Northern European countries, noted for its nutritional properties and its beneficial effects on human health. Assessment of the genetic diversity of wild bilberry germplasm is needed for efforts such as in situ conservation, on-farm management and development of plant breeding programmes. However, to date, only a few local (small-scale) genetic studies of this species have been performed. We therefore conducted a study of genetic variability within 32 individual samples collected from different locations in Iceland, Norway, Sweden, Finland and Germany, and analysed genetic diversity among geographic groups. Four selected inter-simple sequence repeat primers allowed the amplification of 127 polymorphic loci which, based on analysis of variance, made it possible to identify 85 % of the genetic diversity within studied bilberry populations, being in agreement with the mixed-mating system of bilberry. Significant correlations were obtained between geographic and genetic distances for the entire set of samples. The analyses also highlighted the presence of a north–south genetic gradient, which is in accordance with recent findings on phenotypic traits of bilberry. PMID:26483325

  17. Using genetic diversity information to establish core collections of Stylosanthes capitata and Stylosanthes macrocephala

    PubMed Central

    Santos-Garcia, Melissa Oliveira; de Toledo-Silva, Guilherme; Sassaki, Rodrigo Possidonio; Ferreira, Thais Helena; Resende, Rosângela Maria Simeão; Chiari, Lucimara; Karia, Cláudio Takao; Carvalho, Marcelo Ayres; Faleiro, Fábio Gelape; Zucchi, Maria Imaculada; de Souza, Anete Pereira

    2012-01-01

    Stylosanthes species are important forage legumes in tropical and subtropical areas. S. macrocephala and S. capitata germplasm collections that consist of 134 and 192 accessions, respectively, are maintained at the Brazilian Agricultural Research Corporation Cerrados (Embrapa-Cerrados). Polymorphic microsatellite markers were used to assess genetic diversity and population structure with the aim to assemble a core collection. The mean values of HO and HE for S. macrocephala were 0.08 and 0.36, respectively, whereas the means for S. capitata were 0.48 and 0.50, respectively. Roger’s genetic distance varied from 0 to 0.83 for S. macrocephala and from 0 to 0.85 for S. capitata. Analysis with STRUCTURE software distinguished five groups among the S. macrocephala accessions and four groups among those of S. capitata. Nei’s genetic diversity was 27% in S. macrocephala and 11% in S. capitata. Core collections were assembled for both species. For S. macrocephala, all of the allelic diversity was represented by 23 accessions, whereas only 13 accessions were necessary to represent all allelic diversity for S. capitata. The data presented herein evidence the population structure present in the Embrapa-Cerrados germplasm collections of S. macrocephala and S. capitata, which may be useful for breeding programs and germplasm conservation. PMID:23271947

  18. Genetic diversity in peach [Prunus persica (L.) Batsch] at the University of Florida: past present and future

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The University of Florida (UF) stone fruit breeding and genetics program was created in 1952 to develop early ripening stone fruit cultivars with high quality, adaptation to summer rainfall, low chilling requirements, and the ability to withstand high disease pressure. Diverse germplasm sources were...

  19. Development of single nucleotide polymorphism (SNP) markers from the mango (Mangiferaindica) transcriptome for mapping and estimation of genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of resources for genomic studies in Mangifera indica (mango) will allow marker-assisted selection and identification of genetically diverse germplasm, greatly aiding mango breeding programs. We report here a first step in developing such resources, our identification of thousands una...

  20. Centennial olive trees as a reservoir of genetic diversity

    PubMed Central

    Díez, Concepción M.; Trujillo, Isabel; Barrio, Eladio; Belaj, Angjelina; Barranco, Diego; Rallo, Luis

    2011-01-01

    Background and Aims Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin. Methods The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars. Key Results Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives. Conclusions This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity. PMID:21852276

  1. Cryopreservation of citrus in the USDA-ARS national plant germplasm system collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diverse Citrus germplasm from the USDA-ARS National Plant Germplasm System, University of California Riverside, and the California citrus industry is at risk of being lost as a result of disease infestations and unexpected weather disasters. At the National Center for Genetic Resources Preservation ...

  2. High-throughput genotyping of Lesquerella (physaria and paysonia) Germplasm collections using DArT markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Physaria (syn. Lesquerella) and Paysonia germplasm collection of the U.S. National Plant Germplasm System has not been fully characterized for genetic diversity. There are currently more than 200 accessions being managed ex situ to support new crop research and development activities. To bette...

  3. Proanthocyanidin diversity in the EU 'HealthyHay' sainfoin (Onobrychis viciifolia) germplasm collection.

    PubMed

    Stringano, Elisabetta; Hayot Carbonero, Christine; Smith, Lydia M J; Brown, Ronald H; Mueller-Harvey, Irene

    2012-05-01

    This study investigated 37 diverse sainfoin (Onobrychis viciifolia Scop.) accessions from the EU 'HealthyHay' germplasm collection for proanthocyanidin (PA) content and composition. Accessions displayed a wide range of differences: PA contents varied from 0.57 to 2.80 g/100 g sainfoin; the mean degree of polymerisation from 12 to 84; the proportion of prodelphinidin tannins from 53% to 95%, and the proportion of trans-flavanol units from 12% to 34%. A positive correlation was found between PA contents (thiolytic versus acid-butanol degradation; P<0.001; R(2)=0.49). A negative correlation existed between PA content (thiolysis) and mDP (P<0.05; R(2)=-0.30), which suggested that accessions with high PA contents had smaller PA polymers. Cluster analysis revealed that European accessions clustered into two main groups: Western Europe and Eastern Europe/Asia. In addition, accessions from USA, Canada and Armenia tended to cluster together. Overall, there was broad agreement between tannin clusters and clusters that were based on morphological and agronomic characteristics. PMID:22313998

  4. Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm

    PubMed Central

    Micheletti, Diego; Dettori, Maria Teresa; Micali, Sabrina; Aramini, Valeria; Pacheco, Igor; Da Silva Linge, Cassia; Foschi, Stefano; Banchi, Elisa; Barreneche, Teresa; Quilot-Turion, Bénédicte; Lambert, Patrick; Pascal, Thierry; Iglesias, Ignasi; Carbó, Joaquim; Wang, Li-rong; Ma, Rui-juan; Li, Xiong-wei; Gao, Zhong-shan; Nazzicari, Nelson; Troggio, Michela; Bassi, Daniele; Rossini, Laura; Verde, Ignazio; Laurens, François; Arús, Pere; Aranzana, Maria José

    2015-01-01

    Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs. PMID:26352671

  5. Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.).

    PubMed

    Li, Pirui; Zhang, Fei; Chen, Sumei; Jiang, Jiafu; Wang, Haibin; Su, Jiangshuo; Fang, Weimin; Guan, Zhiyong; Chen, Fadi

    2016-06-01

    Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits. PMID:26780102

  6. Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set.

    PubMed

    Hinze, Lori L; Gazave, Elodie; Gore, Michael A; Fang, David D; Scheffler, Brian E; Yu, John Z; Jones, Don C; Frelichowski, James; Percy, Richard G

    2016-05-01

    A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources. PMID:26774060

  7. Genetic Diversity among Enterococcus faecalis

    PubMed Central

    McBride, Shonna M.; Fischetti, Vincent A.; LeBlanc, Donald J.; Moellering, Robert C.; Gilmore, Michael S.

    2007-01-01

    Enterococcus faecalis, a ubiquitous member of mammalian gastrointestinal flora, is a leading cause of nosocomial infections and a growing public health concern. The enterococci responsible for these infections are often resistant to multiple antibiotics and have become notorious for their ability to acquire and disseminate antibiotic resistances. In the current study, we examined genetic relationships among 106 strains of E. faecalis isolated over the past 100 years, including strains identified for their diversity and used historically for serotyping, strains that have been adapted for laboratory use, and isolates from previously described E. faecalis infection outbreaks. This collection also includes isolates first characterized as having novel plasmids, virulence traits, antibiotic resistances, and pathogenicity island (PAI) components. We evaluated variation in factors contributing to pathogenicity, including toxin production, antibiotic resistance, polymorphism in the capsule (cps) operon, pathogenicity island (PAI) gene content, and other accessory factors. This information was correlated with multi-locus sequence typing (MLST) data, which was used to define genetic lineages. Our findings show that virulence and antibiotic resistance traits can be found within many diverse lineages of E. faecalis. However, lineages have emerged that have caused infection outbreaks globally, in which several new antibiotic resistances have entered the species, and in which virulence traits have converged. Comparing genomic hybridization profiles, using a microarray, of strains identified by MLST as spanning the diversity of the species, allowed us to identify the core E. faecalis genome as consisting of an estimated 2057 unique genes. PMID:17611618

  8. Genetic diversity and recombination analysis of sweepoviruses from Brazil

    PubMed Central

    2012-01-01

    Background Monopartite begomoviruses (genus Begomovirus, family Geminiviridae) that infect sweet potato (Ipomoea batatas) around the world are known as sweepoviruses. Because sweet potato plants are vegetatively propagated, the accumulation of viruses can become a major constraint for root production. Mixed infections of sweepovirus species and strains can lead to recombination, which may contribute to the generation of new recombinant sweepoviruses. Results This study reports the full genome sequence of 34 sweepoviruses sampled from a sweet potato germplasm bank and commercial fields in Brazil. These sequences were compared with others from public nucleotide sequence databases to provide a comprehensive overview of the genetic diversity and patterns of genetic exchange in sweepoviruses isolated from Brazil, as well as to review the classification and nomenclature of sweepoviruses in accordance with the current guidelines proposed by the Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV). Co-infections and extensive recombination events were identified in Brazilian sweepoviruses. Analysis of the recombination breakpoints detected within the sweepovirus dataset revealed that most recombination events occurred in the intergenic region (IR) and in the middle of the C1 open reading frame (ORF). Conclusions The genetic diversity of sweepoviruses was considerably greater than previously described in Brazil. Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of sweepovirus species and strains and provided valuable new information for understanding the diversity and evolution of sweepoviruses. PMID:23082767

  9. Diversity among melon (Cucumis melo L.) landraces from the Indo-Gangetic plains of India and their genetic relationship with U.S.A. melon cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report here the first broad genetic characterization of farmer-developed land races of melon (Cucumis melo L.) from the Indo-Gangetic plains of India, an area overlooked in previous genetic diversity analyses of Indian melon germplasm. Eighty-eight landraces from three melon groups in two subspec...

  10. Nuclear and chloroplast diversity and phenotypic distribution of rice (Oryza sativa L.) germplasm from the democratic people’s republic of Korea (DPRK; North Korea)

    PubMed Central

    2014-01-01

    Background Rice accounts for 43% of staple food production in the Democratic People’s Republic of Korea (DPRK). The most widely planted rice varieties were developed from a limited number of ancestral lines that were repeatedly used as parents in breeding programs. However, detailed pedigrees are not publicly available and little is known about the genetic, phenotypic, and geographical variation of DPRK varieties. Results We evaluated 80 O. sativa accessions from the DPRK, consisting of 67 improved varieties and 13 landraces. Based on nuclear SSR analysis, we divide the varieties into two genetic groups: Group 1 corresponds to the temperate japonica subpopulation and represents 78.75% of the accessions, while Group 2 shares recent ancestry with indica varieties. Interestingly, members of Group 1 are less diverse than Group 2 at the nuclear level, but are more diverse at the chloroplast level. All Group 2 varieties share a single Japonica maternal-haplotype, while Group 1 varieties trace maternal ancestry to both Japonica and Indica. Phenotypically, members of Group 1 have shorter grains than Group 2, and varieties from breeding programs have thicker and wider grains than landraces. Improved varieties in Group 1 also show similar and/or better levels of cold tolerance for most traits, except for spikelet number per panicle. Finally, geographic analysis demonstrates that the majority of genetic variation is located within regions that have the most intensive rice cultivation, including the Western territories near the capital city Pyungyang. This is consistent with the conscious and highly centralized role of human selection in determining local dispersion patterns of rice in the DPRK. Conclusions Diversity studies of DPRK rice germplasm revealed two genetic groups. The most widely planted group has a narrow genetic base and would benefit from the introduction of new genetic variation from cold tolerant landraces, wild accessions, and/or cultivated gene pools to

  11. Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers

    PubMed Central

    Xu, Chaoqun; Gao, Jiao; Du, Zengfeng; Li, Dengke; Wang, Zhe; Li, Yingyue; Pang, Xiaoming

    2016-01-01

    Ziziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources. PMID:27531220

  12. Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers.

    PubMed

    Xu, Chaoqun; Gao, Jiao; Du, Zengfeng; Li, Dengke; Wang, Zhe; Li, Yingyue; Pang, Xiaoming

    2016-01-01

    Ziziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources. PMID:27531220

  13. Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation.

    PubMed

    Dossa, Komivi; Wei, Xin; Zhang, Yanxin; Fonceka, Daniel; Yang, Wenjuan; Diouf, Diaga; Liao, Boshou; Cissé, Ndiaga; Zhang, Xiurong

    2016-01-01

    Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs), Eastern Asia (EAs), and Western Africa (WAf) were highly diversified, while those from Western Asia (WAs), Northern Africa (NAf), and Southeastern Africa (SAf) had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions. PMID:27077887

  14. Analysis of Genetic Diversity and Population Structure of Sesame Accessions from Africa and Asia as Major Centers of Its Cultivation

    PubMed Central

    Dossa, Komivi; Wei, Xin; Zhang, Yanxin; Fonceka, Daniel; Yang, Wenjuan; Diouf, Diaga; Liao, Boshou; Cissé, Ndiaga; Zhang, Xiurong

    2016-01-01

    Sesame is an important oil crop widely cultivated in Africa and Asia. Understanding the genetic diversity of accessions from these continents is critical to designing breeding methods and for additional collection of sesame germplasm. To determine the genetic diversity in relation to geographical regions, 96 sesame accessions collected from 22 countries distributed over six geographic regions in Africa and Asia were genotyped using 33 polymorphic SSR markers. Large genetic variability was found within the germplasm collection. The total number of alleles was 137, averaging 4.15 alleles per locus. The accessions from Asia displayed more diversity than those from Africa. Accessions from Southern Asia (SAs), Eastern Asia (EAs), and Western Africa (WAf) were highly diversified, while those from Western Asia (WAs), Northern Africa (NAf), and Southeastern Africa (SAf) had the lowest diversity. The analysis of molecular variance revealed that more than 44% of the genetic variance was due to diversity among geographic regions. Five subpopulations, including three in Asia and two in Africa, were cross-identified through phylogenetic, PCA, and STRUCTURE analyses. Most accessions clustered in the same population based on their geographical origins. Our results provide technical guidance for efficient management of sesame genetic resources in breeding programs and further collection of sesame germplasm from these different regions. PMID:27077887

  15. Peach genetic resources: diversity, population structure and linkage disequilibrium

    PubMed Central

    2013-01-01

    was considerable LD extension while no variation of LD with physical distance was observed in the landraces. From the first STRUCTURE result, LG1 had the greatest proportion of alleles in LD within all three subpopulations. Conclusions Our study demonstrates a high level of genetic diversity and relatively fast decay of LD in the Oriental peach breeding program. Inclusion of Chinese landraces will have a greater effect on increasing genetic diversity in Occidental breeding programs. Fingerprinting with genotype data for all 658 cultivars will be used for accession management in different germplasms. A higher density of markers are needed for association mapping in Oriental germplasm due to the low extension of LD. Population structure and evaluation of LD provides valuable information for GWAS experiment design in peach. PMID:24041442

  16. Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L.) Landraces from North-Eastern India

    PubMed Central

    Mawkhlieng, Bandapkuper; Misra, A. K.; Pattanayak, A.; Harish, G. D.; Singh, S. K.; Ngachan, S. V.; Bansal, K. C.

    2015-01-01

    The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, chakhao rice germplasm from Manipur; and P3, aromatic rice accessions from Nagaland. Pair-wise FST between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (Indica and Japonica) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and quality rice

  17. Germplasm Preservation of Vegetatively-propagated Crops at the National Center for Genetic Resources Preservation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Out of 476,049 germplasm accessions maintained by the USDA, ARS, National Plant Germplasm System (NPS), ca. 30,000 are vegetatively-propagated and as such require preservation as non seed propagules. Numerous research reports have demonstrated the advantages of long-term storage of plant tissues in ...

  18. GRAPE GENETIC RESOURCES AND RESEARCH AT THE DAVIS CALIFORNIA NATIONAL CLONAL GERMPLASM REPOSITORY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Davis, California National Clonal Germplasm Repository (NCGR) houses most Mediterranean-adapted fruit and nut crop collections in the U.S., including grapes (Vitis). The NCGR is part of the USDA National Plant Germplasm System (NPGS). Our missions are to acquire, preserve, characterize and dis...

  19. Ploidy Variation and Genetic Diversity in Dichroa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent evidence suggests a close genetic relationship between Hydrangea macrophylla and D. febrifuga, which supports previous morphological and DNA sequence data. This relationship was confirmed by the production of fertile intergeneric hybrids. Here we characterize the genetic diversity of availab...

  20. Screening a diverse soybean germplasm collection for reaction to purple seed stain caused by Cercospora kikuchii

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Purple seed stain (PSS), caused by Cercospora kikuchii, is a prevalent soybean disease that causes latent seed infection, seed decay, purple seed discoloration, and overall quality deterioration. The objective of this research was to screen soybean accessions from the USDA germplasm collection for r...

  1. Diversity in Tolerance of Soybean (Glycine max L. Merr.) Germplasm to Soil Waterlogging

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean (Glycine max L. Merr.) cultivars from the U.S. are generally intolerant to flooding stress. Soybean germplasm and cultivars originating from other countries potentially could have better flooding tolerance. Screen house and field tests were conducted to determine differences in waterlogging ...

  2. Registration of LG04-6863 Soybean Germplasm Line with Diverse Pedigree

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean [Glycine max (L.) Merr.] germplasm line LG04-6863 was developed and released by the University of Missouri Agricultural Experiment Station, Delta Center, Portageville, MO, the USDA-Agricultural Research Service and the Illinois Agricultural Experiment Station, Urbana IL. It was approved for ...

  3. Genetic Diversity and Societally Important Disparities

    PubMed Central

    Rosenberg, Noah A.; Kang, Jonathan T. L.

    2015-01-01

    The magnitude of genetic diversity within human populations varies in a way that reflects the sequence of migrations by which people spread throughout the world. Beyond its use in human evolutionary genetics, worldwide variation in genetic diversity sometimes can interact with social processes to produce differences among populations in their relationship to modern societal problems. We review the consequences of genetic diversity differences in the settings of familial identification in forensic genetic testing, match probabilities in bone marrow transplantation, and representation in genome-wide association studies of disease. In each of these three cases, the contribution of genetic diversity to social differences follows from population-genetic principles. For a fourth setting that is not similarly grounded, we reanalyze with expanded genetic data a report that genetic diversity differences influence global patterns of human economic development, finding no support for the claim. The four examples describe a limit to the importance of genetic diversity for explaining societal differences while illustrating a distinction that certain biologically based scenarios do require consideration of genetic diversity for solving problems to which populations have been differentially predisposed by the unique history of human migrations. PMID:26354973

  4. SSR mining in oil palm EST database: application in oil palm germplasm diversity studies.

    PubMed

    Ting, Ngoot-Chin; Zaki, Noorhariza Mohd; Rosli, Rozana; Low, Eng-Ti Leslie; Ithnin, Maizura; Cheah, Suan-Choo; Tan, Soon-Guan; Singh, Rajinder

    2010-08-01

    This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group (45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT (7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification. PMID:20861564

  5. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    PubMed Central

    Küpper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sérgio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

    2011-01-01

    A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm. PMID:21637550

  6. Personalized medicine and human genetic diversity.

    PubMed

    Lu, Yi-Fan; Goldstein, David B; Angrist, Misha; Cavalleri, Gianpiero

    2014-09-01

    Human genetic diversity has long been studied both to understand how genetic variation influences risk of disease and infer aspects of human evolutionary history. In this article, we review historical and contemporary views of human genetic diversity, the rare and common mutations implicated in human disease susceptibility, and the relevance of genetic diversity to personalized medicine. First, we describe the development of thought about diversity through the 20th century and through more modern studies including genome-wide association studies (GWAS) and next-generation sequencing. We introduce several examples, such as sickle cell anemia and Tay-Sachs disease that are caused by rare mutations and are more frequent in certain geographical populations, and common treatment responses that are caused by common variants, such as hepatitis C infection. We conclude with comments about the continued relevance of human genetic diversity in medical genetics and personalized medicine more generally. PMID:25059740

  7. Personalized Medicine and Human Genetic Diversity

    PubMed Central

    Lu, Yi-Fan; Goldstein, David B.; Angrist, Misha; Cavalleri, Gianpiero

    2014-01-01

    Human genetic diversity has long been studied both to understand how genetic variation influences risk of disease and infer aspects of human evolutionary history. In this article, we review historical and contemporary views of human genetic diversity, the rare and common mutations implicated in human disease susceptibility, and the relevance of genetic diversity to personalized medicine. First, we describe the development of thought about diversity through the 20th century and through more modern studies including genome-wide association studies (GWAS) and next-generation sequencing. We introduce several examples, such as sickle cell anemia and Tay–Sachs disease that are caused by rare mutations and are more frequent in certain geographical populations, and common treatment responses that are caused by common variants, such as hepatitis C infection. We conclude with comments about the continued relevance of human genetic diversity in medical genetics and personalized medicine more generally. PMID:25059740

  8. The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis

    PubMed Central

    2010-01-01

    Background The genetic diversity of crop species is the result of natural selection on the wild progenitor and human intervention by ancient and modern farmers and breeders. The genomes of modern cultivars, old cultivated landraces, ecotypes and wild relatives reflect the effects of these forces and provide insights into germplasm structural diversity, the geographical dimension to species diversity and the process of domestication of wild organisms. This issue is also of great practical importance for crop improvement because wild germplasm represents a rich potential source of useful under-exploited alleles or allele combinations. The aim of the present study was to analyse a major Pisum germplasm collection to gain a broad understanding of the diversity and evolution of Pisum and provide a new rational framework for designing germplasm core collections of the genus. Results 3020 Pisum germplasm samples from the John Innes Pisum germplasm collection were genotyped for 45 retrotransposon based insertion polymorphism (RBIP) markers by the Tagged Array Marker (TAM) method. The data set was stored in a purpose-built Germinate relational database and analysed by both principal coordinate analysis and a nested application of the Structure program which yielded substantially similar but complementary views of the diversity of the genus Pisum. Structure revealed three Groups (1-3) corresponding approximately to landrace, cultivar and wild Pisum respectively, which were resolved by nested Structure analysis into 14 Sub-Groups, many of which correlate with taxonomic sub-divisions of Pisum, domestication related phenotypic traits and/or restricted geographical locations. Genetic distances calculated between these Sub-Groups are broadly supported by principal coordinate analysis and these, together with the trait and geographical data, were used to infer a detailed model for the domestication of Pisum. Conclusions These data provide a clear picture of the major distinct gene

  9. Developing single nucleotide polymorphism (SNP) markers from transcriptome sequences for identification of longan (Dimocarpus longan) germplasm

    PubMed Central

    Wang, Boyi; Tan, Hua-Wei; Fang, Wanping; Meinhardt, Lyndel W; Mischke, Sue; Matsumoto, Tracie; Zhang, Dapeng

    2015-01-01

    Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in 50 longan germplasm accessions, including cultivated varieties and wild germplasm; and designated 25 SNP markers that unambiguously identified all tested longan varieties with high statistical rigor (P<0.0001). Multiple trees from the same clone were verified and off-type trees were identified. Diversity analysis revealed genetic relationships among analyzed accessions. Cultivated varieties differed significantly from wild populations (Fst=0.300; P<0.001), demonstrating untapped genetic diversity for germplasm conservation and utilization. Within cultivated varieties, apparent differences between varieties from China and those from Thailand and Hawaii indicated geographic patterns of genetic differentiation. These SNP markers provide a powerful tool to manage longan genetic resources and breeding, with accurate and efficient genotype identification. PMID:26504559

  10. Development and genetic analyses of early season cold tolerant sorghum germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sorghum is one of the most versatile & resilient crop species with vast genetic diversity. To date sorghum provides commodity products for grain, forage & bioenergy industries. It is also well-known for excellent drought and high temperature tolerance; and is considered as water and climate susta...

  11. Genetic diversity of natural populations of Machilus thunbergii, an endangered tree species in eastern China, determined with ISSR analysis.

    PubMed

    Liu, J; Sun, H G; Jiang, J M; Shao, W H; Luan, Q F

    2013-01-01

    The genetic diversity of 10 Machilus thunbergii populations in eastern China was analyzed using inter-simple sequence repeat markers. The populations showed high genetic diversity, with an overall population genetic diversity of 0.2343. Genetic diversity varied largely among populations, and populations with the highest genetic diversity were mainly from the eastern and western parts of the natural distribution area. Small populations, lack of effective gene flow, and fragmentation of habitats have led to greater genetic differentiation among populations, with 41.18% of genetic variation existing among populations. Unweighted pair-group method with arithmetic mean cluster analysis indicated that populations distributed between latitudes 25° and 31°N were clustered together and should be prioritized for in situ conservation. Northern, eastern, and southern populations were located in peripheral areas of the distribution range and were clustered separately. Collection of distinctive germplasm from peripheral populations should be promoted and ex situ conservation of elite germplasm should be implemented. PMID:23546979

  12. Genetic diversity in Capsicum baccatum is significantly influenced by its ecogeographical distribution

    PubMed Central

    2012-01-01

    Background The exotic pepper species Capsicum baccatum, also known as the aji or Peruvian hot pepper, is comprised of wild and domesticated botanical forms. The species is a valuable source of new genes useful for improving fruit quality and disease resistance in C. annuum sweet bell and hot chile pepper. However, relatively little research has been conducted to characterize the species, thus limiting its utilization. The structure of genetic diversity in a plant germplasm collection is significantly influenced by its ecogeographical distribution. Together with DNA fingerprints derived from AFLP markers, we evaluated variation in fruit and plant morphology of plants collected across the species native range in South America and evaluated these characters in combination with the unique geography, climate and ecology at different sites where plants originated. Results The present study mapped the ecogeographic distribution, analyzed the spatial genetic structure, and assessed the relationship between the spatial genetic pattern and the variation of morphological traits in a diverse C. baccatum germplasm collection spanning the species distribution. A combined diversity analysis was carried out on the USDA-ARS C. baccatum germplasm collection using data from GIS, morphological traits and AFLP markers. The results demonstrate that the C. baccatum collection covers wide geographic areas and is adapted to divergent ecological conditions in South America ranging from cool Andean highland to Amazonia rainforest. A high level of morphological diversity was evident in the collection, with fruit weight the leading variable. The fruit weight distribution pattern was compatible to AFLP-based clustering analysis for the collection. A significant spatial structure was observed in the C. baccatum gene pool. Division of the domesticated germplasm into two major regional groups (Western and Eastern) was further supported by the pattern of spatial population structure. Conclusions

  13. Genetic Diversity of A-Genome Cotton.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Since Upland cotton (Gossypium hirsutum L.) is known to have relatively low levels of genetic diversity or variation in genetic makeup among individuals, a better understanding of this variation and relationships among possible sources of novel genes would be valuable. Therefore, analysis of genetic...

  14. Analysis of genetic diversity of southern Spain fig tree (Ficus carica L.) and reference materials as a tool for breeding and conservation.

    PubMed

    Perez-Jiménez, M; López, B; Dorado, G; Pujadas-Salvá, A; Guzmán, G; Hernandez, P

    2012-06-01

    The common fig tree (Ficus carica L.) is a Mediterranean crop with problematic cultivar identification. The recovery and conservation of possible local varieties for ecological production requires the previous genetic characterization of the available germplasm. In this context, 42 lines corresponding to 12 local varieties and two caprifigs, in addition to 15 reference samples have been fingerprinted using 21 SSR markers. A total of 77 alleles were revealed, detecting a useful level of genetic variability within the local germplasm pools. UPGMA clustering analysis has revealed the genetic structure and relationships among the local and reference germplasm. Eleven of the local varieties could be identified and defined as obtained clusters, showing that SSR analysis is an efficient method to evaluate the Andalusian fig tree diversity for on-farm conservation. PMID:22804343

  15. Genetic Diversity Strategy for the Management and Use of Rubber Genetic Resources: More than 1,000 Wild and Cultivated Accessions in a 100-Genotype Core Collection.

    PubMed

    de Souza, Livia Moura; Le Guen, Vincent; Cerqueira-Silva, Carlos Bernardo Moreno; Silva, Carla Cristina; Mantello, Camila Campos; Conson, Andre Ricardo Oliveira; Vianna, João Paulo Gomes; Zucchi, Maria Imaculada; Scaloppi Junior, Erivaldo José; Fialho, Josefino de Freitas; de Moraes, Mario Luis Teixeira; Gonçalves, Paulo de Souza; Souza, Anete Pereira de

    2015-01-01

    The rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] is the only plant species worldwide that is cultivated for the commercial production of natural rubber. This study describes the genetic diversity of the Hevea spp. complex that is available in the main ex situ collections of South America, including Amazonian populations that have never been previously described. Genetic data were analyzed to determine the genetic structure of the wild populations, quantify the allelic diversity and suggest the composition of a core collection to capture the maximum genetic diversity within a minimal sample size. A total of 1,117 accessions were genotyped with 13 microsatellite markers. We identified a total of 408 alleles, 319 of which were shared between groups and 89 that were private in different groups of accessions. In a population structure and principal component analysis, the level of clustering reflected a primary division into the following two subgroups: cluster 1, which consisted of varieties from the advanced breeding germplasm that originated from the Wickham and Mato Grosso accessions; and cluster 2, which consisted of the wild germplasm from the Acre, Amazonas, Pará and Rondônia populations and Hevea spp. The analyses revealed a high frequency of gene flow between the groups, with the genetic differentiation coefficient (GST) estimated to be 0.018. Additionally, no distinct separation among the H. brasiliensis accessions and the other species from Amazonas was observed. A core collection of 99 accessions was identified that captured the maximum genetic diversity. Rubber tree breeders can effectively utilize this core collection for cultivar improvement. Furthermore, such a core collection could provide resources for forming an association panel to evaluate traits with agronomic and commercial importance. Our study generated a molecular database that should facilitate the management of the Hevea germplasm and its use for subsequent genetic

  16. Genetic Diversity Strategy for the Management and Use of Rubber Genetic Resources: More than 1,000 Wild and Cultivated Accessions in a 100-Genotype Core Collection

    PubMed Central

    Cerqueira-Silva, Carlos Bernardo Moreno; Silva, Carla Cristina; Mantello, Camila Campos; Conson, Andre Ricardo Oliveira; Vianna, João Paulo Gomes; Zucchi, Maria Imaculada; Scaloppi Junior, Erivaldo José; Fialho, Josefino de Freitas; de Moraes, Mario Luis Teixeira; Gonçalves, Paulo de Souza; de Souza, Anete Pereira

    2015-01-01

    The rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] is the only plant species worldwide that is cultivated for the commercial production of natural rubber. This study describes the genetic diversity of the Hevea spp. complex that is available in the main ex situ collections of South America, including Amazonian populations that have never been previously described. Genetic data were analyzed to determine the genetic structure of the wild populations, quantify the allelic diversity and suggest the composition of a core collection to capture the maximum genetic diversity within a minimal sample size. A total of 1,117 accessions were genotyped with 13 microsatellite markers. We identified a total of 408 alleles, 319 of which were shared between groups and 89 that were private in different groups of accessions. In a population structure and principal component analysis, the level of clustering reflected a primary division into the following two subgroups: cluster 1, which consisted of varieties from the advanced breeding germplasm that originated from the Wickham and Mato Grosso accessions; and cluster 2, which consisted of the wild germplasm from the Acre, Amazonas, Pará and Rondônia populations and Hevea spp. The analyses revealed a high frequency of gene flow between the groups, with the genetic differentiation coefficient (GST) estimated to be 0.018. Additionally, no distinct separation among the H. brasiliensis accessions and the other species from Amazonas was observed. A core collection of 99 accessions was identified that captured the maximum genetic diversity. Rubber tree breeders can effectively utilize this core collection for cultivar improvement. Furthermore, such a core collection could provide resources for forming an association panel to evaluate traits with agronomic and commercial importance. Our study generated a molecular database that should facilitate the management of the Hevea germplasm and its use for subsequent genetic

  17. Geographic description of genetic diversity and genetic relationships in the USDA Rice World Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Asian cultivated rice (Oryza sativa L.) is structured into five genetic groups, indica, AUS, tropical japonica, temperate japonica and aromatic. Genetic characterization of a global rice collection could help better serve the global research community. Collecting worldwide rice germplasm started in ...

  18. How does ecological disturbance influence genetic diversity?

    PubMed

    Banks, Sam C; Cary, Geoffrey J; Smith, Annabel L; Davies, Ian D; Driscoll, Don A; Gill, A Malcolm; Lindenmayer, David B; Peakall, Rod

    2013-11-01

    Environmental disturbance underpins the dynamics and diversity of many of the ecosystems of the world, yet its influence on the patterns and distribution of genetic diversity is poorly appreciated. We argue here that disturbance history may be the major driver that shapes patterns of genetic diversity in many natural populations. We outline how disturbance influences genetic diversity through changes in both selective processes and demographically driven, selectively neutral processes. Our review highlights the opportunities and challenges presented by genetic approaches, such as landscape genomics, for better understanding and predicting the demographic and evolutionary responses of natural populations to disturbance. Developing this understanding is now critical because disturbance regimes are changing rapidly in a human-modified world. PMID:24054910

  19. Development of corn inbred lines with reduced preharvest aflatoxin contamination and identification of genes/markers for breeding and germplasm evaluation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Host plant resistance is a highly desirable tactic that can be used to manage aflatoxin contamination. Screening and identification of corn germplasm for resistant traits for crop improvement and molecular marker development will bring new genetic diversity into US corn germplasm. Using the combinat...

  20. Genetic diversity of Aquilegia (Ranunculaceae) species and cultivars assessed by AFLPs.

    PubMed

    Zhu, R R; Gao, Y K; Xu, L J; Zhang, Q X

    2011-01-01

    Species of the genus Aquilegia are exceptionally diverse in their floral morphology and color, commonly known as columbine. They are widely planted ornamentals and are highly attractive for hummingbirds. However, little is known about their genetic diversity. We examined the genetic diversity of the species and cultivars using amplified fragment length polymorphism (AFLP) markers. Sixteen EcoRI/MseI AFLP primer combinations produced 327 informative polymorphic bands, with a mean of 20.4 bands scored per primer. Jaccard's coefficient of similarity varied from 0.61 to 0.93, indicative of high levels of genetic variation. Cluster analysis using the unweighted pair group method with arithmetic mean algorithm placed the 64 accessions into two main clusters, each divided into two sub-clusters. The AFLP variability was significantly associated with the geographic origins, as the Asian species and the North American species grouped into two distinct clusters. The genetic diversity found among Aquilegia demonstrated the potential value of Chinese germplasm for cultivar improvement and for widening the genetic basis of breeding programs and breeding material selection. We concluded that AFLPs are informative and can provide significant insights for genetic diversity research in columbine species. PMID:21574138

  1. Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter

    PubMed Central

    Assefa, Kebebew; Cannarozzi, Gina; Girma, Dejene; Kamies, Rizqah; Chanyalew, Solomon; Plaza-Wüthrich, Sonia; Blösch, Regula; Rindisbacher, Abiel; Rafudeen, Suhail; Tadele, Zerihun

    2015-01-01

    Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding. PMID:25859251

  2. Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter].

    PubMed

    Assefa, Kebebew; Cannarozzi, Gina; Girma, Dejene; Kamies, Rizqah; Chanyalew, Solomon; Plaza-Wüthrich, Sonia; Blösch, Regula; Rindisbacher, Abiel; Rafudeen, Suhail; Tadele, Zerihun

    2015-01-01

    Tef [Eragrostis tef (Zucc.) Trotter] is a cereal crop resilient to adverse climatic and soil conditions, and possessing desirable storage properties. Although tef provides high quality food and grows under marginal conditions unsuitable for other cereals, it is considered to be an orphan crop because it has benefited little from genetic improvement. Hence, unlike other cereals such as maize and wheat, the productivity of tef is extremely low. In spite of the low productivity, tef is widely cultivated by over six million small-scale farmers in Ethiopia where it is annually grown on more than three million hectares of land, accounting for over 30% of the total cereal acreage. Tef, a tetraploid with 40 chromosomes (2n = 4x = 40), belongs to the family Poaceae and, together with finger millet (Eleusine coracana Gaerth.), to the subfamily Chloridoideae. It was originated and domesticated in Ethiopia. There are about 350 Eragrostis species of which E. tef is the only species cultivated for human consumption. At the present time, the gene bank in Ethiopia holds over five thousand tef accessions collected from geographical regions diverse in terms of climate and elevation. These germplasm accessions appear to have huge variability with regard to key agronomic and nutritional traits. In order to properly utilize the variability in developing new tef cultivars, various techniques have been implemented to catalog the extent and unravel the patterns of genetic diversity. In this review, we show some recent initiatives investigating the diversity of tef using genomics, transcriptomics and proteomics and discuss the prospect of these efforts in providing molecular resources that can aid modern tef breeding. PMID:25859251

  3. Collecting in Central Asia: National Plant Germplasm System Plant Explorations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-ARS National Plant Germplasm System is charged with the preservation of economically important crop plants and their wild relatives. Curators in the System strive to develop collections capturing the genetic diversity of each species. One mechanism for filling gaps in collections is through...

  4. Capturing Positive Transgressive Variation From Wild And Exotic Germplasm Resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Only a small fraction of the naturally occurring genetic diversity available in rice germplasm repositories around the world has been explored to date. This is beginning to change with the advent of affordable, high throughput genotyping approaches coupled with robust statistical analysis methods th...

  5. Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

    NASA Astrophysics Data System (ADS)

    Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

    2013-03-01

    Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

  6. Germplasm Preservation of Vegetatively-propagated Crops at the National Center for Genetic Resources Preservation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Out of 476,049 germpaslm accessions maintained by the USDA, ARS, National Plant Germplasm System (NPGS), ca. 30,000 are vegetaively-propagated and as such require preservation as non seed propagules. Numerous research reports demonstrated the advantages of long term storage of plant tissues in liqui...

  7. Evaluating wild grapevine germplasm with genotyping-by-sequencing methods for conservation, preservation, genetics and breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-ARS cold hardy grapevine germplasm represents one of the best collections of publically available grapevine material for grape breeding and improvement. The repository holds in excess of 1300 different grapevine genotypes, with roughly a quarter made up of wild grapevine species. Efforts ...

  8. Biobanking genetic resources: Challenges and implementation at the USDA National Animal Germplasm Program

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is adequate infrastructure in the US to identify and acquire germplasm from the major beef and dairy cattle and swine breeds. However, when we venture outside these species the same tasks become more difficult because of a lack of breed associations, databases that include genotypic and pheno...

  9. Genetic resources for table grapes in the National Plant Germplasm System

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grapes, members of the genus Vitis, have been used by man for at least 23,000 years and actively cultivated for 5000+ years. Grape germplasm has long been selected for table use, as many old cultivars have markedly larger fruit, crisp flesh, larger clusters, seedlessness, and other traits very diffe...

  10. Population genetics and structure of a global foxtail millet germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foxtail millet is one among the most ancient crops of dryland agriculture. It is the second most important crop among millets, grown for grains or forage. Foxtail millet germplasm resources provide reservoirs of novel alleles and genes for crop improvement that have remained mostly unexplored. We ge...

  11. Development of DArT Marker Platforms and Genetic Diversity Assessment of the U.S. Collection of the New Oilseed Crop Lesquerella and Related Species

    PubMed Central

    Cruz, Von Mark V.; Kilian, Andrzej; Dierig, David A.

    2013-01-01

    The advantages of using molecular markers in modern genebanks are well documented. They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of germplasm collections. We describe the development of two types of DArT molecular marker platforms for the new oilseed crop lesquerella (Physaria spp.), a member of the Brassicaceae family, to characterize a collection in the National Plant Germplasm System (NPGS) with relatively little known in regards to the genetic diversity and traits. The two types of platforms were developed using a subset of the germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed a total of 2,833 polymorphic markers with an average genotype call rate of 98.4% and a scoring reproducibility of 99.7%. On the other hand, the DArTseq platform developed for SNP and DArT markers from short sequence reads showed a total of 27,748 high quality markers. Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa. PMID:23724020

  12. Interspecific Chromosome Substitution Lines as Genetic Resources for Improvement, Trait Analyses and Genomic Inference

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three of the research areas likely to very significantly impact genetic improvement of cotton are interspecific introgression, genetic dissection of complex traits and sequencing of [AD] genomes. Interspecific introgression is expected to increase genetic diversity of breeding germplasm, creating op...

  13. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil.

    PubMed

    Santos, Elisa S L; Cerqueira-Silva, Carlos Bernard M; Mori, Gustavo M; Ahnert, Dário; Mello, Durval L N; Pires, José Luis; Corrêa, Ronan X; de Souza, Anete P

    2015-01-01

    Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called 'Bahian cacao' or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide. PMID:26675449

  14. Genetic Structure and Molecular Diversity of Cacao Plants Established as Local Varieties for More than Two Centuries: The Genetic History of Cacao Plantations in Bahia, Brazil

    PubMed Central

    Santos, Elisa S. L.; Cerqueira-Silva, Carlos Bernard M.; Mori, Gustavo M.; Ahnert, Dário; Mello, Durval L. N.; Pires, José Luis; Corrêa, Ronan X.; de Souza, Anete P.

    2015-01-01

    Bahia is the most important cacao-producing state in Brazil, which is currently the sixth-largest country worldwide to produce cacao seeds. In the eighteenth century, the Comum, Pará and Maranhão varieties of cacao were introduced into southern Bahia, and their descendants, which are called ‘Bahian cacao’ or local Bahian varieties, have been cultivated for over 200 years. Comum plants have been used to start plantations in African countries and extended as far as countries in South Asia and Oceania. In Brazil, two sets of clones selected from Bahian varieties and their mutants, the Agronomic Institute of East (SIAL) and Bahian Cacao Institute (SIC) series, represent the diversity of Bahian cacao in germplasm banks. Because the genetic diversity of Bahian varieties, which is essential for breeding programs, remains unknown, the objective of this work was to assess the genetic structure and diversity of local Bahian varieties collected from farms and germplasm banks. To this end, 30 simple sequence repeat (SSR) markers were used to genotype 279 cacao plants from germplasm and local farms. The results facilitated the identification of 219 cacao plants of Bahian origin, and 51 of these were SIAL or SIC clones. Bahian cacao showed low genetic diversity. It could be verified that SIC and SIAL clones do not represent the true diversity of Bahian cacao, with the greatest amount of diversity found in cacao trees on the farms. Thus, a core collection to aid in prioritizing the plants to be sampled for Bahian cacao diversity is suggested. These results provide information that can be used to conserve Bahian cacao plants and applied in breeding programs to obtain more productive Bahian cacao with superior quality and tolerance to major diseases in tropical cacao plantations worldwide. PMID:26675449

  15. Genetic diversity of the two commercial tetraploid cotton species in the Gossypium Diversity Reference Set

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A diversity reference set has been constructed for the Gossypium accessions in the U.S. National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers were used to study the alleli...

  16. Implications of recurrent disturbance for genetic diversity.

    PubMed

    Davies, Ian D; Cary, Geoffrey J; Landguth, Erin L; Lindenmayer, David B; Banks, Sam C

    2016-02-01

    Exploring interactions between ecological disturbance, species' abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well-understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance-induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes. PMID:26839689

  17. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites.

    PubMed Central

    Liu, Kejun; Goodman, Major; Muse, Spencer; Smith, J Stephen; Buckler, Ed; Doebley, John

    2003-01-01

    Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize. PMID:14704191

  18. Maintaining Medicinal Plant Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For all plant genetic resources collections, including medicinal plant germplasm, maintaining the genetic integrity of material held ex situ is of major importance. This holds true for all intended end uses of the material whether it is as a source for crop improvement, medical research, as voucher...

  19. Genetic Diversity and Population Structure of Siberian apricot (Prunus sibirica L.) in China

    PubMed Central

    Li, Ming; Zhao, Zhong; Miao, Xingjun; Zhou, Jingjing

    2014-01-01

    The genetic diversity and population genetic structure of 252 accessions from 21 Prunus sibirica L. populations were investigated using 10 ISSR, SSR, and SRAP markers. The results suggest that the entire population has a relatively high level of genetic diversity, with populations HR and MY showing very high diversity. A low level of inter-population genetic differentiation and a high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow, and largely attributable to the cross-pollination and self-incompatibility reproductive system. A STRUCTURE (model-based program) analysis revealed that the 21 populations can be divided into two main groups, mainly based on geographic differences and genetic exchanges. The entire wild Siberia apricot population in China could be divided into two subgroups, including 107 accessions in subgroup (SG) 1 and 147 accessions in SG 2. A Mantel test revealed a significant positive correlation between genetic and geographic distance matrices, and there was a very significant positive correlation among three marker datasets. Overall, we recommend a combination of conservation measures, with ex situ and in situ conservation that includes the construction of a core germplasm repository and the implement of in situ conservation for populations HR, MY, and ZY. PMID:24384840

  20. Identification of several gy4 nulls from the USDA soybean germplasm collection provides new genetic resources for the development of high-quality tofu cultivars.

    PubMed

    Kim, Won-Seok; Ho, Heo Jae; Nelson, Randall L; Krishnan, Hari B

    2008-12-10

    Tofu, a cheese-like food made by curdling soy milk, is a major dietary staple of Asian countries. Consumption of tofu and other soy products is steadily increasing in North America due to its well-known health benefits. Soybean A(5), A(4), and B(3) peptide null lines 'Enrei' and 'Raiden' are commonly utilized in breeding programs to develop high-quality tofu cultivars. To expand the genetic diversity it is desirable to identify and utilize other A(5), A(4), and B(3) null genotypes in the development of improved tofu cultivars that are adapted to North American conditions. In this study were screened diverse soybean accessions from the USDA Soybean Germplasm Collection to identify Gy4 mutants, the locus that controls A(5), A(4), and B(3) peptide production. Analysis of total seed proteins from 485 soybean lines by SDS-PAGE enabled the identification of 38 accessions that lacked the A(5), A(4), and B(3) peptides. These accessions showed marked differences in seed size and seed coat color and represented different maturity groups ranging from 0 to IX. To ascertain the molecular basis for the lack of A(5), A(4), and B(3) peptides in the newly identified Gy4 mutants, the nucleotide sequence of a portion of the Gy4 gene was determined from eight soybean accessions representing different maturity groups. These eight Gy4 mutants revealed a single point mutation that changed the translation initiation codon ATG to ATA, resulting in the A(5), A(4), and B(3) null phenotype. The newly identified Gy4 mutants from this study will enable plant breeders to expand the genetic diversity of North American food-quality soybeans and also aid in the development of hypoallergenic soybeans. PMID:18991447

  1. Genetic diversity and population structure of an extremely endangered species: the world's largest Rhododendron

    PubMed Central

    Wu, Fu Qin; Shen, Shi Kang; Zhang, Xin Jun; Wang, Yue Hua; Sun, Wei Bang

    2015-01-01

    Comprehensive studies on the genetic diversity and structure of endangered species are urgently needed to promote effective conservation and management activities. The big tree rhododendron, Rhododendron protistum var. giganteum, is a highly endangered species with only two known endemic populations in a small area in the southern part of Yunnan Province in China. Unfortunately, limited information is available regarding the population genetics of this species. Therefore, we conducted amplified fragment length polymorphism (AFLP) analysis to characterize the genetic diversity and variation of this species within and between remaining populations. Twelve primer combinations of AFLP produced 447 unambiguous and repetitious bands. Among these bands, 298 (66.67 %) were polymorphic. We found high genetic diversity at the species level (percentage of polymorphic loci = 66.67 %, h = 0.240, I = 0.358) and low genetic differentiation (Gst = 0.110) between the two populations. Gene flow between populations (Nm) was relatively high at 4.065. Analysis of molecular variance results revealed that 22 % of the genetic variation was partitioned between populations and 78 % of the genetic variation was within populations. The presence of moderate to high genetic diversity and low genetic differentiation in the two populations can be explained by life history traits, pollen dispersal and high gene flow (Nm = 4.065). Bayesian structure and principal coordinate analysis revealed that 56 sampled trees were clustered into two groups. Our results suggest that some rare and endangered species are able to maintain high levels of genetic diversity even at small population sizes. These results will assist with the design of conservation and management programmes, such as in situ and ex situ conservation, seed collection for germplasm conservation and reintroduction. PMID:25477251

  2. Genetic diversity analysis of sweet kernel apricot in China based on SSR and ISSR markers.

    PubMed

    Liu, M P; Du, H Y; Zhu, G P; Fu, D L; Tana, W Y

    2015-01-01

    Simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) markers were used to evaluate genetic diversity among 22 sweet kernel apricot accessions and 12 cultivars in China to provide information on how to improve the utilization of kernel apricot germplasms. The results showed that 10 pairs of SSR primers screened from 40 primer pairs amplified 43 allelic variants, all of which were polymorphic (100%), and 9 ISSR primers selected from 100 primers amplified 67 allelic variants with 50 polymorphic bands (74.63%). There was a relatively distant genetic relationship between the 34 samples, where their genetic similarity coefficient was between 0.62 and 0.99. The UPGMA dendrogram constructed using combined data of the two marker systems separated the genotypes into three main clusters. PMID:26345904

  3. Potential of Start Codon Targeted (SCoT) markers to estimate genetic diversity and relationships among Chinese Elymus sibiricus accessions.

    PubMed

    Zhang, Junchao; Xie, Wengang; Wang, Yanrong; Zhao, Xuhong

    2015-01-01

    Elymus sibiricus as an important forage grass and gene pool for improving cereal crops, that is widely distributed in West and North China. Information on its genetic diversity and relationships is limited but necessary for germplasm collection, conservation and future breeding. Start Codon Targeted (SCoT) markers were used for studying the genetic diversity and relationships among 53 E. sibiricus accessions from its primary distribution area in China. A total of 173 bands were generated from 16 SCoT primers, 159 bands of which were polymorphic with the percentage of polymorphic bands (PPB) of 91.91%. Based upon population structure analysis five groups were formed. The cluster analysis separated the accessions into two major clusters and three sub-clusters, similar to results of principal coordinate analysis (PCoA). The molecular variance analysis (AMOVA) showed that genetic variation was greater within geographical regions (50.99%) than between them (49.01%). Furthermore, the study also suggested that collecting and evaluating E. sibiricus germplasm for major geographic regions and special environments broadens the available genetic base and illustrates the range of variation. The results of the present study showed that SCoT markers were efficient in assessing the genetic diversity among E. sibiricus accessions. PMID:25853316

  4. Development of a core set of SSR markers for the characterization of Gossypium germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular markers such as simple sequence repeats (SSR) are a useful tool for characterizing genetic diversity of Gossypium germplasm collections. Genetic profiles by DNA fingerprinting of cotton accessions can only be compared among different collections if a common set of molecular markers are us...

  5. Variation for seed minerals and protein concentrations in diverse germplasm of lentil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lentil (Lens culinaris) is an important food legume that can provide significant amounts of dietary minerals and other essential nutrients to humans. To understand the nutritional diversity that exists within this species, we measured seed mineral and protein concentrations in 350 diverse accessions...

  6. Genetic diversity, seed size associations and population structure of a core collection of common beans (Phaseolus vulgaris L.).

    PubMed

    Blair, Matthew W; Díaz, Lucy M; Buendía, Hector F; Duque, Myriam C

    2009-10-01

    Cultivated common bean germplasm is especially diverse due to the parallel domestication of two genepools in the Mesoamerican and Andean centers of diversity and introgression between these gene pools. Classification into morphological races has helped to provide a framework for utilization of this cultivated germplasm. Meanwhile, core collections along with molecular markers are useful tools for organizing and analyzing representative sets of these genotypes. In this study, we evaluated 604 accessions from the CIAT core germplasm collection representing wide genetic variability from both primary and secondary centers of diversity with a newly developed, fluorescent microsatellite marker set of 36 genomic and gene-based SSRs to determine molecular diversity and with seed protein analysis to determine phaseolin alleles. The entire collection could be divided into two genepools and five predominant races with the division between the Mesoamerica race and the Durango-Jalisco group showing strong support within the Mesoamerican genepool and the Nueva Granada and Peru races showing less diversity overall and some between-group admixture within the Andean genepool. The Chile race could not be distinguished within the Andean genepool but there was support for the Guatemala race within the Mesoamerican genepool and this race was unique in its high level of diversity and distance from other Mesoamerican races. Based on this population structure, significant associations were found between SSR loci and seed size characteristics, some on the same linkage group as the phaseolin locus, which previously had been associated with seed size, or in other regions of the genome. In conclusion, this study has shown that common bean has very significant population structure that can help guide the construction of genetic crosses that maximize diversity as well as serving as a basis for additional association studies. PMID:19688198

  7. Diversity captured in the USDA-ARS National Plant Germplasm System apple core collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Core collections have been used widely in genetic resources to provide a representative and compact sample to use in breeding evaluation. In the 1990s a core set was developed by the USDA-ARS Plant Genetic Resources Unit (PGRU) in Geneva, NY. Using data available at the time, a core set was develo...

  8. Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers.

    PubMed

    Dinarti, Diny; Susilo, Agung W; Meinhardt, Lyndel W; Ji, Kun; Motilal, Lambert A; Mischke, Sue; Zhang, Dapeng

    2015-12-01

    Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers' fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. PMID:26719747

  9. Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers

    PubMed Central

    Dinarti, Diny; Susilo, Agung W.; Meinhardt, Lyndel W.; Ji, Kun; Motilal, Lambert A.; Mischke, Sue; Zhang, Dapeng

    2015-01-01

    Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers’ fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. PMID:26719747

  10. Genetic diversity in pollen abiotic stress tolerance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity in reproductive abiotic stress tolerance has been investigated by cotton breeders throughout the public and private sectors. The primary focus of these studies has been the evaluation of abiotic stress responses during the development of the flower prior to anthesis. Sterility in...

  11. Molecular phylogeny and genetic diversity of Lygus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inter- and intraspecific genetic diversity in North American Lygus was using nuclear and mitochondrial DNA. DNA sequences have been obtained from the mitochondrial cox1 and cox2 genes, the nuclear ITS1 spacer, and regions flanking microsatellites (MSFR). The Fargo lab sequenced a region overlapp...

  12. Genetic Diversity in Pollen Abiotic Stress Tolerance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity in reproductive abiotic stress tolerance has been investigated by cotton breeders throughout the public and private sectors. The primary focus of these studies has been the evaluation of abiotic stress responses during the development of the flower prior to anthesis. Sterility in...

  13. Genetic diversity of Lycoris endemic to Korea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Extensive taxonomic relationships among Lycoris Herb. (Amaryllidaceae) taxa native to Korea have not been analyzed previously. This study was carried out to investigate the hybrid origin, genetic diversity, and relationships of Lycoris taxa (L. flavescens, L. uydoensis, L. chejuensis, L. chinensis ...

  14. Genetic Diversity of Natural Crossing in Cotton

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have shown previously genetic diversity in mature cotton pollen sensitivity to low humidity. This study investigated the impact of pollen sensitivity to low humidity on the amount of outcrossing to neighboring plants. We utilized “red” and “green” pigmented cotton, in addition to gossypol glan...

  15. Genetic Diversity for Concentration of Sixteen Mineral Elements Among Diverse Rice Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mineral nutrients such as Ca, Fe, and Zn play critical roles in human health, with over 3 billion people suffering from Fe and Zn deficiencies. Rice provides the major source of nutrition for a large proportion of the world’s population, but unfortunately, rice grain is not a good source of mineral...

  16. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)

    PubMed Central

    2010-01-01

    Background Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci. Results Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74%) followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population ϕPT values, p < 0.01). Conclusion Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity. PMID:20082707

  17. Assessing phenotypic, biochemical, and molecular diversity in coriander (Coriandrum sativum L.) germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This research was conducted to elucidate phenotypic and biochemical diversity in 60 coriander (Coriandrum sativum L.) accessions maintained at the North Central Regional Plant Introduction Station and examine relationships between amplified fragment length polymorphisms (AFLP) and patterns of phenot...

  18. Susceptibility of fruit from diverse apple and crabapple germplasm to attack from plum curculio, Conotrachelus nenuphar (Herbst) (Coleoptera: Curculionidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plum curculio, Conotrachelus nenuphar (Herbst) (Coleoptera: Curculionidae) is an important apple pest that significantly hinders sustainable apple production in eastern North America. The potential for host plant resistance to plum curculio among apple (Malus) germplasm has never been rigorously ev...

  19. Managing the U.S. germplasm collection of temperate forage legumes to serve diverse collection users and global conservation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Alfalfa and other forage legume crops support livestock production around the world. Breeders and scientists have long capitalized on the genetic diversity in the U.S. Temperate Forage Legume Collection to support a wide range of crop improvement and scientific inquiries. The Collection also serves...

  20. Baby leaf lettuce germplasm enhancement: developing diverse populations with resistance to bacterial leaf spot caused by Xanthomonas campestris pv. vitians

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Baby leaf lettuce cultivars with resistance to bacterial leaf spot (BLS) caused by Xanthomonas campestris pv. vitians (Xcv) are needed to reduce crop losses. The objectives of this research were to assess the genetic diversity for BLS resistance in baby leaf lettuce cultivars and to select early gen...

  1. Genetic diversity, population structure and marker trait associations for seed quality traits in cotton (Gossypium hirsutum).

    PubMed

    Badigannavar, Ashok; Myers, Gerald O

    2015-03-01

    Cottonseed contains 16% seed oil and 23% seed protein by weight. High levels of palmitic acid provides a degree of stability to the oil, while the presence of bound gossypol in proteins considerably changes their properties, including their biological value. This study uses genetic principles to identify genomic regions associated with seed oil, protein and fibre content in upland cotton cultivars. Cotton association mapping panel representing the US germplasm were genotyped using amplified fragment length polymorphism markers, yielding 234 polymorphic DNA fragments. Phenotypic analysis showed high genetic variability for the seed traits, seed oil range from 6.47-25.16%, protein from 1.85-28.45% and fibre content from 15.88-37.12%. There were negative correlations between seed oil and protein content.With reference to genetic diversity, the average estimate of FST was 8.852 indicating a low level of genetic differentiation among subpopulations. The AMOVA test revealed that variation was 94% within and 6% among subpopulations. Bayesian population structure identified five subpopulations and was in agreement with their geographical distribution. Among the mixed models analysed, mixed linear model (MLM) identified 21 quantitative trait loci for lint percentage and seed quality traits, such as seed protein and oil. Establishing genetic diversity, population structure and marker trait associations for the seed quality traits could be valuable in understanding the genetic relationships and their utilization in breeding programmes. PMID:25846880

  2. Screening and association mapping of rice blast disease resistance using a diverse collection of rice germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice blast, caused by the fungus Magnaporthe oryzae B. Couch, is a very serious disease in rice (Oryza sativa L.) worldwide. Incorporation of new blast resistance genes into breeding lines is an important objective of many rice breeding programs. A diverse collection of 409 O. sativa accessions des...

  3. Diversity in seed production characteristics within the USDA-ARS Limnanthes alba germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Meadowfoam (L. alba) seeds are a source of long chain fatty acids which are stable under diverse environmental conditions. The fatty acid composition makes the oil valuable for use in cosmetics, lubricants, rubber additives, and plastics. While a few meadowfoam cultivars have been developed, high se...

  4. Non-destructive measurements of cottonseed nutritional trait diversity in the US National Cotton Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent studies have suggested that cottonseed (Gossypium spp.) has the potential to contribute to the effort against world hunger, particularly by providing a high-quality protein source. This report analyzed the diversity in protein content and other seed quality factors in the U.S. National Cotton...

  5. Non-destructive measurements of cottonseed nutritional trait diversity in the US National Cotton Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent studies have suggested that cottonseed (Gossypium spp.) has the potential to contribute to the effort against world hunger, particularly by providing a high quality protein source. This report analyzed the diversity in protein content and other seed quality factors in the US National Cotton ...

  6. Bread matters: a national initiative to profile the genetic diversity of Australian wheat.

    PubMed

    Edwards, David; Wilcox, Stephen; Barrero, Roberto A; Fleury, Delphine; Cavanagh, Colin R; Forrest, Kerrie L; Hayden, Matthew J; Moolhuijzen, Paula; Keeble-Gagnère, Gabriel; Bellgard, Matthew I; Lorenc, Michał T; Shang, Catherine A; Baumann, Ute; Taylor, Jennifer M; Morell, Matthew K; Langridge, Peter; Appels, Rudi; Fitzgerald, Anna

    2012-08-01

    The large and complex genome of wheat makes genetic and genomic analysis in this important species both expensive and resource intensive. The application of next-generation sequencing technologies is particularly resource intensive, with at least 17 Gbp of sequence data required to obtain minimal (1×) coverage of the genome. A similar volume of data would represent almost 40× coverage of the rice genome. Progress can be made through the establishment of consortia to produce shared genomic resources. Australian wheat genome researchers, working with Bioplatforms Australia, have collaborated in a national initiative to establish a genetic diversity dataset representing Australian wheat germplasm based on whole genome next-generation sequencing data. Here, we describe the establishment and validation of this resource which can provide a model for broader international initiatives for the analysis of large and complex genomes. PMID:22681313

  7. Genetic Diversity of Fragaria iinumae and F. nipponica Based on Microsatellite Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) - National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, is a genebank that preserves strawberry genetic resources. The Fragaria L. collection consists of accessions from 17 species and 37 countries. ...

  8. Novel Use of Alfalfa Leafcutting Bees (Megachile rotundata) for Plant Genetic Resource Conservation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The North Central Regional Plant Introduction Station (NCRPIS) located in Ames, Iowa maintains a large collection of diverse plant germplasm. Controlled pollination of individual accessions is necessary to preserve the original genetic diversity. Some plants, especially those with conspicuous flowe...

  9. Nineteenth century French rose (Rosa sp.) germplasm shows a shift over time from a European to an Asian genetic background

    PubMed Central

    Liorzou, Mathilde; Pernet, Alix; Li, Shubin; Chastellier, Annie; Thouroude, Tatiana; Michel, Gilles; Malécot, Valéry; Gaillard, Sylvain; Briée, Céline; Foucher, Fabrice; Oghina-Pavie, Cristiana; Clotault, Jérémy; Grapin, Agnès

    2016-01-01

    Hybridization with introduced genetic resources is commonly practiced in ornamental plant breeding to introgress desired traits. The 19th century was a golden age for rose breeding in France. The objective here was to study the evolution of rose genetic diversity over this period, which included the introduction of Asian genotypes into Europe. A large sample of 1228 garden roses encompassing the conserved diversity cultivated during the 18th and 19th centuries was genotyped with 32 microsatellite primer pairs. Its genetic diversity and structure were clarified. Wide diversity structured in 16 genetic groups was observed. Genetic differentiation was detected between ancient European and Asian accessions, and a temporal shift from a European to an Asian genetic background was observed in cultivated European hybrids during the 19th century. Frequent crosses with Asian roses throughout the 19th century and/or selection for Asiatic traits may have induced this shift. In addition, the consistency of the results with respect to a horticultural classification is discussed. Some horticultural groups, defined according to phenotype and/or knowledge of their pedigree, seem to be genetically more consistent than others, highlighting the difficulty of classifying cultivated plants. Therefore, the horticultural classification is probably more appropriate for commercial purposes rather than genetic relatedness, especially to define preservation and breeding strategies. PMID:27406785

  10. EPA'S GENETIC DIVERSITY RESEARCH PROGRAM: ECOLOGICAL INDICATOR DEVELOPMENT

    EPA Science Inventory

    Genetic diversity is a fundamental component of biodiversity that is affected by environmental stressors in predictable ways and limits potential responses of a population to future stressors. Understanding patterns of genetic diversity enhances the value and interpretation of o...

  11. Inbreeding levels in swine: Ramifications for Genetic Diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Globally, genetic diversity of livestock populations is contracting. Knowing the true extent of the contraction is needed to develop effective conservation strategies. While contractions of genetic diversity have been documented at the breed level, little within breed documentation has occurred. ...

  12. Genetic Diversity of Grasspea and Its Relative Species Revealed by SSR Markers

    PubMed Central

    Wang, Fang; Yang, Tao; Burlyaeva, Marina; Li, Ling; Jiang, Junye; Fang, Li; Redden, Robert; Zong, Xuxiao

    2015-01-01

    The study of genetic diversity between Lathyrus sativus L. and its relative species may yield fundamental insights into evolutionary history and provide options to meet the challenge of climate changes. 30 SSR loci were employed to assess the genetic diversity and population structure of 283 individuals from wild and domesticated populations from Africa, Europe, Asia and ICARDA. The allele number per loci ranged from 3 to 14. The average gene diversity index and average polymorphism information content (PIC) was 0.5340 and 0.4817, respectively. A model based population structure analysis divided the germplasm resources into three subgroups: the relative species, the grasspea from Asia, and the grasspea from Europe and Africa. The UPGMA dendrogram and PCA cluster also demonstrated that Asian group was convincingly separated from the other group. The AMOVA result showed that the cultivated species was quite distinct from its relative species, however a low level of differentiation was revealed among their geographic origins. In all, these results provided a molecular basis for understanding genetic diversity of L. sativus and its relatives. PMID:25793712

  13. Long-term preservation of new industrial crop germplasm at the National Center for Genetic Resources Preservation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Cropdatabase of the New Crops Crop Germplasm Committee within the Germplasm Resource Information System (GRIN) lists 118 species in 42 genera as having potential uses as industrial crops (http://www.ars-grin.gov/npgs/cgc reports). It is challenging to choose an appropriate long-term storage cond...

  14. Genetic improvement of the Pee Dee cotton germplasm collection following seventy years of plant breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term plant breeding programs develop genetic resources that constitute the baseline potential of crop production systems. Over the course of time, through long-term plant breeding efforts, the volume of genetic resources developed is extensive. Knowledge of the performance and genetic propertie...

  15. Genetic diversity of wild Malus orientalis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seeds from wild populations of Malus orientalis were collected in southern Russia and Turkey in 1998 and 1999. Seedling trees from these populations are now maintained in the USDA-National Plant Germplasm System Malus collection. Four hundred ninety-six individuals representing 85 half-sib familie...

  16. Assessing genetic diversity among six populations of Gossypium arboreum L. using microsatellites markers.

    PubMed

    Sethi, Khushboo; Siwach, Priyanka; Verma, Surender Kumar

    2015-10-01

    Among the four cultivated cotton species, G. hirsutum (allotetraploid) presently holds a primary place in cultivation. Efforts to further improve this primary cotton face the constraints of its narrow genetic base due to repeated selective breeding and hence demands enrichment of diversity in the gene pool. G. arboreum (diploid species) is an invaluable genetic resource with great potential in this direction. Based on the dispersal and domestication in different directions from Indus valley, different races of G. arboreum have evolved, each having certain traits like drought and disease resistance, which the tetraploid cotton lack. Due to lack of systematic, race wise characterization of G. arboreum germplasm, it  has not been explored fully. During the present study, 100 polymorphic SSR loci were  used to genotype 95 accessions belonging to 6 races of G. arboreum producing 246 polymorphic alleles; mean number of effective alleles was 1.505. AMOVA showed 14 % of molecular variance among population groups, 34 % among individuals and remaining 52 % within individuals. UPGMA dendrogram, based on Nei's genetic distance, distributed the six populations in two major clusters of 3 populations each; race 'bengalense' was found more close to 'cernuum' than the others. The clustering of 95 genotypes by UPGMA tree generation as well as PCoA analysis clustered 'bengalense' genotypes into one group along with some genotypes of 'cernuum', while rest of the genotypes made separate clusters. Outcomes of this research should be helpful in identifying the genotypes for their further utilization in hybridization program to obtain high level of germplasm diversity. PMID:26600679

  17. Comparison of “Remote” Versus “Easy” In Situ Collection Locations for USA Wild Solanum (Potato) Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A basic question in germplasm collecting is whether the in situ genetic diversity in a given geographic range has been adequately sampled. While one would ideally sample all diverse sites with appropriate habitat, there is usually a practical bias against visiting relatively inaccessible sites. For ...

  18. The Wukong Terminal-Repeat Retrotransposon in Miniature (TRIM) Elements in Diverse Maize Germplasm

    PubMed Central

    Liu, Zhen; Li, Xinxin; Wang, Tingzhang; Messing, Joachim; Xu, Jian-Hong

    2015-01-01

    TRIMs (terminal-repeat retrotransposons in miniature), which are characterized by their small size, have been discovered in all investigated vascular plants and even in animals. Here, we identified a highly conservative TRIM family referred to as Wukong elements in the maize genome. The Wukong family shows a distinct pattern of tandem arrangement in the maize genome suggesting a high rate of unequal crossing over. Estimation of insertion times implies a burst of retrotransposition activity of the Wukong family after the allotetraploidization of maize. Using next-generation sequencing data, we detected 87 new Wukong insertions in parents of the maize NAM population relative to the B73 reference genome and found abundant insertion polymorphism of Wukong elements in 75 re-sequenced maize lines, including teosinte, landraces, and improved lines. These results suggest that Wukong elements possessed a persistent retrotransposition activity throughout maize evolution. Moreover, the phylogenetic relationships among 76 maize inbreds and their relatives based on insertion polymorphisms of Wukong elements should provide us with reliable molecular markers for biodiversity and genetics studies. PMID:26019188

  19. Genetic diversity of koala retroviral envelopes.

    PubMed

    Xu, Wenqin; Gorman, Kristen; Santiago, Jan Clement; Kluska, Kristen; Eiden, Maribeth V

    2015-03-01

    Genetic diversity, attributable to the low fidelity of reverse transcription, recombination and mutation, is an important feature of infectious retroviruses. Under selective pressure, such as that imposed by superinfection interference, gammaretroviruses commonly adapt their envelope proteins to use alternative receptors to overcome this entry block. The first characterized koala retroviruses KoRV subgroup A (KoRV-A) were remarkable in their absence of envelope genetic variability. Once it was determined that KoRV-A was present in all koalas in US zoos, regardless of their disease status, we sought to isolate a KoRV variant whose presence correlated with neoplastic malignancies. More than a decade after the identification of KoRV-A, we isolated a second subgroup of KoRV, KoRV-B from koalas with lymphomas. The envelope proteins of KoRV-A and KoRV-B are sufficiently divergent to confer the ability to bind and employ distinct receptors for infection. We have now obtained a number of additional KoRV envelope variants. In the present studies we report these variants, and show that they differ from KoRV-A and KoRV-B envelopes in their host range and superinfection interference properties. Thus, there appears to be considerable variation among KoRVs envelope genes suggesting genetic diversity is a factor following the KoRV-A infection process. PMID:25789509

  20. Five-year agronomic and phenotypic data summary for a replicated cacao (Theobroma cacao L.) germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Loss of genetic diversity found in centers of origin necessitates the establishment of ex situ germplasm collections for long-term conservation. Cacao genetic resources have been acquired, preserved and evaluated at the USDA-ARS, Tropical Agriculture Research Station in Mayaguez (TARS), Puerto Rico...

  1. Genetic diversity in aspen and its relation to arthropod abundance

    PubMed Central

    Zhang, Chunxia; Vornam, Barbara; Volmer, Katharina; Prinz, Kathleen; Kleemann, Frauke; Köhler, Lars; Polle, Andrea; Finkeldey, Reiner

    2015-01-01

    The ecological consequences of biodiversity have become a prominent public issue. Little is known on the effect of genetic diversity on ecosystem services. Here, a diversity experiment was established with European and North American aspen (Populus tremula, P. tremuloides) planted in plots representing either a single deme only or combinations of two, four and eight demes. The goals of this study were to explore the complex inter- and intraspecific genetic diversity of aspen and to then relate three measures for diversity (deme diversity, genetic diversity determined as Shannon index or as expected heterozygosity) to arthropod abundance. Microsatellite and AFLP markers were used to analyze the genetic variation patterns within and between the aspen demes and deme mixtures. Large differences were observed regarding the genetic diversity within demes. An analysis of molecular variance revealed that most of the total genetic diversity was found within demes, but the genetic differentiation among demes was also high. The complex patterns of genetic diversity and differentiation resulted in large differences of the genetic variation within plots. The average diversity increased from plots with only one deme to plots with two, four, and eight demes, respectively and separated plots with and without American aspen. To test whether intra- and interspecific diversity impacts on ecosystem services, arthropod abundance was determined. Increasing genetic diversity of aspen was related to increasing abundance of arthropods. However, the relationship was mainly driven by the presence of American aspen suggesting that species identity overrode the effect of intraspecific variation of European aspen. PMID:25674097

  2. Study Of Genetic Diversity Between Grasspea Landraces Using Morphological And Molecular Marker

    NASA Astrophysics Data System (ADS)

    Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood

    2008-01-01

    Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.

  3. Molecular genetic variation in cultivated peanuts germplasm of Henan and detection of their elite allelic variations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Groundnut or peanut (Arachis hypogaea L.) is an economically important crop worldwide as a source of protein and cooking oil, particularly in developing countries. Because of its narrow genetic background and shortage of polymorphic genetic markers, molecular characterization of cultivated peanuts i...

  4. Comparison of single nucleotide polymorphisms and simple sequence repeats in genotype identification and diversity assessment of cacao germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Accurate identification of individual genotypes in an efficient manner is especially important for cacao (Theobroma cacao L.) germplasm conservation and breeding. The development of single nucleotide polymorphism (SNP) markers in cacao offers the opportunity to use a high throughput genotyping syste...

  5. A SOLCAP STRATEGY TO EVALUATE ALLELIC DIVERSITY OF CULTIVATED AND WILD SOLANUM GERMPLASM AND ACCESS ECONOMICALLY IMPORTANT GENES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Solanaceae Coordinated Agricultural Project (SolCAP) is an effort to organize a community of public and private researchers for “translational genomics”, the utilization of information derived from genome technologies for crop improvement. Standard germplasm panels will be developed that represe...

  6. Linkage Disequilibrium Based Association Mapping of Fiber Quality Traits in Cotton Using Diverse Cotton Germplasm from Uzbekistan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    QTL-mapping, a now-classical approach to identify molecular markers linked to complex traits in specific experimental populations, is extremely time-consuming, high-risk, and expensive work - prohibitively expensive if dozens, let alone hundreds or thousands, of germplasm accessions are to be examin...

  7. Susceptibility of fruit from diverse apple and crabapple germplasm to attack from apple maggot, Rhagoletis pomonella (Walsh) (Diptera: Tephritidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Apple maggot, Rhagoletis pomonella (Walsh) is a pest of major concern to apple, Malus x domestica (Borkh.) production in eastern North America. Host-plant resistance to apple maggot among apple germplasm has been previously evaluated among a small number of exotic Malus accessions and domestic hyb...

  8. A SolCAP strategy to evaluate allelic diversity of cultivated and wild Solanum germplasm and access economically important genes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    THE Solanaceae Coordinated Agricultural Project (SolCAP) is an effort to organize a community of public and private researchers for “translational genomics”, the utilization of information derived from genome technologies for crop improvement. Standard germplasm panels will be developed that represe...

  9. Malus sieversii: a diverse Central Asian apple species in the USDA-ARS National Plant Germplasm System

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are several Central Asian Malus species and varieties in the USDA-ARS National Plant Germplasm System (NPGS) apple collection. Malus sieversii is the most comprehensively collected species native to Central Asia. Other taxa such as M. sieversii var. kirghisorum, M. sieversii var. turkmenorum, ...

  10. Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L.) germplasm

    PubMed Central

    2012-01-01

    Background The goals of our study were to assess the phylogeny and the population structure of tobacco accessions representing a wide range of genetic diversity; identify a subset of accessions as a core collection capturing most of the existing genetic diversity; and estimate, in the tobacco core collection, the extent of linkage disequilibrium (LD) in seven genomic regions using simple sequence repeat (SSR) markers. To this end, a collection of accessions were genotyped with SSR markers. Molecular diversity was evaluated and LD was analyzed across seven regions of the genome. Results A genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA) and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2). The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure. Conclusions A global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure. PMID:22435796

  11. New carrot and garlic germplasm to advance breeding and understand crop origins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic variation provided by diverse plant germplasm is the basic building material used for crop improvement that shapes the crops we grow today. Wild carrot from the U.S. provided the cytoplasm used to develop a reliable system to produce hybrid carrots that account for most of the commercial...

  12. Performance and phenology of wild black raspberry (Rubus occidentalis L.) germplasm in a common garden

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A lack of genetic diversity in cultivated black raspberry (Rubus occidentalis L.) germplasm has been widely recognized as a major factor limiting progress towards breeding improved cultivars. Despite this, little effort has been made since the early twentieth century to systematically collect and ev...

  13. Collecting in Central Asia and the Caucasus: US National Plant Germplasm System Plant Explorations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-ARS National Plant Germplasm System (NPGS) is charged with the preservation of economically important crop plants and their wild relatives. Curators in the System strive to develop collections capturing the genetic diversity of each species. One mechanism for filling gaps in collections...

  14. Response to anthracnose infection for a random selection of sorghum germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Anthracnose is one of the most important diseases of sorghum and substantial grain yield losses can occur during disease epidemics. The disease can be successfully managed through the use of resistant cultivars. Germplasm collections provide important sources of genetic diversity for the identific...

  15. Genetic diversity and identification of Chinese-grown pecan using ISSR and SSR markers.

    PubMed

    Jia, Xiao-Dong; Wang, Tao; Zhai, Min; Li, Yong-Rong; Guo, Zhong-Ren

    2011-01-01

    Pecan is an important horticultural nut crop originally from North America and now widely cultivated in China for its high ecological, ornamental and economic value. Currently, there are over one hundred cultivars grown in China, including introduced American cultivars and Chinese seedling breeding cultivars. Molecular markers were used to assess the genetic diversity of these cultivars and to identify the pedigrees of fine pecan plants with good characteristics and no cultivar-related data. A total of 77 samples grown in China were studied, including 14 introduced cultivars, 12 domestic seedling breeding cultivars, and 49 fine pecan plants with no cultivar data, together with Carya cathayensis and Juglans nigra. A total of 77 ISSR and 19 SSR primers were prescreened; 10 ISSR and eight SSR primers were selected, yielding a total of 94 amplified bands (100% polymorphic) in the range of 140-1,950 bp for the ISSR and 70 amplified bands (100% polymorphic) in the range of 50-350 bp for SSR markers. Genetic diversity analyses indicated Chinese-grown pecan cultivars and fine plants had significant diversity at the DNA level. The dengrograms constructed with ISSR, SSR or combined data were very similar, but showed very weak grouping association with morphological characters. However, the progeny were always grouped with the parents. The great diversity found among the Chinese cultivars and the interesting germplasm of the fine pecan plants analyzed in this study are very useful for increasing the diversity of the pecan gene pool. All 77 accessions in this study could be separated based on the ISSR and SSR fingerprints produced by one or more primers. The results of our study also showed that ISSR and SSR techniques were both suitable for genetic diversity analyses and the identification of pecan resources. PMID:22146370

  16. The silent threat of low genetic diversity

    USGS Publications Warehouse

    Hunter, Margaret E.

    2013-01-01

    Across the Caribbean, protected coastal waters have served as primary feeding and breeding grounds for the endangered Antillean manatee. Unfortunately, these same coastal waters are also a popular “habitat” for humans. In the past, the overlap between human and manatee habitat allowed for manatee hunting and threatened the survival of these gentle marine mammals. Today, however, threats are much more inadvertent and are often related to coastal development, degraded habitats and boat strikes. In the state of Florida, decades of research on the species’ biological needs have helped conservationists address threats to its survival. For example, low wake zones and boater education have protected manatees from boat strikes, and many of their critical winter refuges are now protected. The Florida population has grown steadily, thus increasing from approximately 1,200 in 1991 to more than 5,000 in 2010. It is conceivable that in Florida manatees may one day be reclassified as “threatened” rather than “endangered.” Yet, in other parts of the Caribbean, threats still loom. This includes small, isolated manatee populations found on islands that can be more susceptible to extinction and lack of genetic diversity. To ensure the species’ long-term viability, scientists have turned their sights to the overall population dynamics of manatees throughout the Caribbean. Molecular genetics has provided new insights into long-term threats the species faces. Fortunately, the emerging field of conservation genetics provides managers with tools and strategies for protecting the species’ long-term viability.

  17. Diversity and Domestication of Apples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species within Malus are genetically diverse. Individuals within the USDA-ARS National Plant Germplasm System have been identified with ploidies ranging from diploid to hexaploid. Chloroplast sequence data from seven regions have revealed genetic relationships among apple species and has aided in ...

  18. In vitro conservation of Dendrobium germplasm.

    PubMed

    Teixeira da Silva, Jaime A; Zeng, Songjun; Galdiano, Renato Fernandes; Dobránszki, Judit; Cardoso, Jean Carlos; Vendrame, Wagner A

    2014-09-01

    Dendrobium is a large genus in the family Orchidaceae that exhibits vast diversity in floral characteristics, which is of considerable importance to orchid breeders, biotechnologists and collectors. Native species have high value as a result of their medicinal properties, while their hybrids are important as ornamental commodities, either as cut flowers or potted plants and are thus veritable industrial crops. Thus, preservation of Dendrobium germplasm is valuable for species conservation, breeding programs and the floriculture industry. Cryopreservation represents the only safe, efficient and cost-effective long-term storage option to facilitate the conservation of genetic resources of plant species. This review highlights 16 years of literature related to the preservation of Dendrobium germplasm and comprises the most comprehensive assessment of thorough studies performed to date, which shows reliable and reproducible results. Air-drying, encapsulation-dehydration, encapsulation-vitrification, vitrification and droplet-vitrification are the current cryopreservation methodologies that have been used to cryopreserve Dendrobium germplasm. Mature seeds, pollen, protoplasts, shoot primordia, protocorms and somatic embryos or protocorm-like bodies (PLBs) have been cryopreserved with different levels of success. Encapsulation-vitrification and encapsulation-dehydration are the most used protocol, while PLBs represent the main explant explored. PMID:24845051

  19. The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies.

    PubMed

    Muñoz-Amatriaín, María; Cuesta-Marcos, Alfonso; Endelman, Jeffrey B; Comadran, Jordi; Bonman, John M; Bockelman, Harold E; Chao, Shiaoman; Russell, Joanne; Waugh, Robbie; Hayes, Patrick M; Muehlbauer, Gary J

    2014-01-01

    New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections. PMID:24732668

  20. The USDA Barley Core Collection: Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies

    PubMed Central

    Endelman, Jeffrey B.; Comadran, Jordi; Bonman, John M.; Bockelman, Harold E.; Chao, Shiaoman; Russell, Joanne; Waugh, Robbie; Hayes, Patrick M.; Muehlbauer, Gary J.

    2014-01-01

    New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define ‘mini-core’ sets of accessions capturing the majority of the allelic diversity present in the core collection. These ‘mini-core’ sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of ‘hull cover’, ‘spike row number’, and ‘heading date’ demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections. PMID:24732668

  1. Genetic Stability of In Vitro Conserved Germplasm of Humulus Lupulus L.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic and epigenetic stability of hop accessions after being cryopreserved for one year or cold stored for three years were evaluated using several molecular markers (RAPDs, AFLPs and MSAPs) and clear, repetitive and specific patterns were obtained among accessions and between control and trea...

  2. 'HoneySweet' plum - a valuable genetically engineered fruit-tree cultivar and germplasm resource

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ‘HoneySweet’ is a plum variety developed through genetic engineering to be highly resistant to plum pox potyvirus (PPV), the causal agent of sharka disease, that threatens stone-fruit industries world-wide and most specifically, in Europe. Field testing for over 15 years in Europe has demonstrated ...

  3. Genetic structural analysis for germplasm accessions in the USDA Rice World Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice is grouped into five genetic structures including indica, aus, aromatic, temperate japonica, and tropical japonica. A core collection having 1,785 accessions from 114 countries has been developed that is representative of the USDA rice world collection which includes over 18,000 accessions. The...

  4. CFP Positive Progeny from Genetic Crosses of Elite Germplasm with a Transgenic Sugar Beet

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Resistance to Cercospora leaf spot disease, a serious problem for sugar beet production in most growing regions, has historically not been very amenable to genetic improvement by traditional means since only moderate resistance occurs naturally and it is multigenic with low heritability. Therefore, ...

  5. Genetic variation and association mapping of protein concentration in rice using a germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice protein is an important source of nutrition and energy for a majority of the world’s population. However, the protein concentration in rice can have an impact on its flavor, texture, cooking and processing quality, thus, affecting its acceptability. It is therefore important to know if genet...

  6. Poultry germplasm preservation: modulating membrane lipids for successful cryopreservation of semen from valuable genetic stocks

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The goal of this project is to provide the content for development of a single nucleotide polymorphism (SNP) chip for use by the commercial turkey industry to interrogate genetic differences (single nucleotide variations in the genome’s DNA) and potentially enable the selection for preferred traits ...

  7. Genetic structure and genetic diversity of single-variety Lonicera macranthoides populations in China, as indicated by SCoT markers.

    PubMed

    Chen, D X; Li, L Y; Zhang, X; Wang, Y

    2015-01-01

    Lonicera macranthoides is an important traditional Chinese herb. The lack of information regarding the genetic structure and genetic relationships among its cultivars has hindered the conservation and utilization of this resource. This study used start codon targeted markers to assess the genetic diversity and other genetic characteristics of five single-variety L. macranthoides populations in China. Using 22 primers produced a total of 266 bands, of which 227 were polymorphic, indicating a high level of polymorphism. At the species level, genetic diversity was high: percentage of polymorphic loci (PPB) = 85.34%, effective number of alleles (NE) = 1.3479, Nei's gene diversity (H) = 0.2075, and Shannon's information index (Hsp, species level) = 0.3198. However, at the varietal population level, genetic diversity was lower, with averages of: PPB = 19.74%, NE = 1.0946, H = 0.0561, Hpop = 0.0850 (population level). Nei's genetic differentiation coefficient was 0.7319, which is consistent with Shannon's population genetic differentiation coefficient (0.7324). This indicates that most of the genetic variation in this species exists among the varietal populations. The differentiation among varieties may have been caused by artificial selection, mode of reproduction, and barriers to gene flow (0.1831). The genetic similarity coefficient ranged from 0.7222 to 0.9419. Phylogenetic analysis showed the five varieties to form two major clades. Results suggest that cultivar breeders should strengthen the exchange of germplasm and increase the mutual penetration of useful genes, which would broaden the hereditary basis of L. macranthoides. PMID:26214488

  8. Genetic diversity and species diversity of stream fishes covary across a land-use gradient

    USGS Publications Warehouse

    Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

  9. Preserving oak (Quercus sp.) germplasm to promote ex situ conservation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Germplasm banks are increasingly used as an ex situ conservation strategy. Germplasm banks are able to maintain extraordinary levels of diversity for long periods at relatively low cost. Studies using seeds – the preferred propagules in plant germplasm banks – have revealed the underlying reasons wh...

  10. Genetic Diversity Increases Insect Herbivory on Oak Saplings

    PubMed Central

    Castagneyrol, Bastien; Lagache, Lélia; Giffard, Brice; Kremer, Antoine; Jactel, Hervé

    2012-01-01

    A growing body of evidence from community genetics studies suggests that ecosystem functions supported by plant species richness can also be provided by genetic diversity within plant species. This is not yet true for the diversity-resistance relationship as it is still unclear whether damage by insect herbivores responds to genetic diversity in host plant populations. We developed a manipulative field experiment based on a synthetic community approach, with 15 mixtures of one to four oak (Quercus robur) half-sib families. We quantified genetic diversity at the plot level by genotyping all oak saplings and assessed overall damage caused by ectophagous and endophagous herbivores along a gradient of increasing genetic diversity. Damage due to ectophagous herbivores increased with the genetic diversity in oak sapling populations as a result of higher levels of damage in mixtures than in monocultures for all families (complementarity effect) rather than because of the presence of more susceptible oak genotypes in mixtures (selection effect). Assemblages of different oak genotypes would benefit polyphagous herbivores via improved host patch location, spill over among neighbouring saplings and diet mixing. By contrast, genetic diversity was a poor predictor of the abundance of endophagous herbivores, which increased with individual sapling apparency. Plant genetic diversity may not provide sufficient functional contrast to prevent tree sapling colonization by specialist herbivores while enhancing the foraging of generalist herbivores. Long term studies are nevertheless required to test whether the effect of genetic diversity on herbivory change with the ontogeny of trees and local adaptation of specialist herbivores. PMID:22937168

  11. The USDA Pearl Millet Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA National Plant Germplasm System pearl millet collection is maintained at the Plant Genetic Resources Conservation Unit located in Griffin, Ga. The germplasm collection contains 1297 unique accessions collected from 31 different countries. The majority of the accessions were collected or d...

  12. Does genetic diversity limit disease spread in natural host populations?

    PubMed Central

    King, K C; Lively, C M

    2012-01-01

    It is a commonly held view that genetically homogenous host populations are more vulnerable to infection than genetically diverse populations. The underlying idea, known as the ‘monoculture effect,' is well documented in agricultural studies. Low genetic diversity in the wild can result from bottlenecks (that is, founder effects), biparental inbreeding or self-fertilization, any of which might increase the risk of epidemics. Host genetic diversity could buffer populations against epidemics in nature, but it is not clear how much diversity is required to prevent disease spread. Recent theoretical and empirical studies, particularly in Daphnia populations, have helped to establish that genetic diversity can reduce parasite transmission. Here, we review the present theoretical work and empirical evidence, and we suggest a new focus on finding ‘diversity thresholds.' PMID:22713998

  13. Population genetic diversity and fitness in multiple environments

    PubMed Central

    2010-01-01

    Background When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater) and stressful conditions (diluted seawater). The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis. Results Populations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation between AFLP diversity and

  14. Cereal Germplasm Resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Germplasm resources for the cereals are available from several sources. This paper discusses the history of germplasm banks, types of germplasm available and where to request seeds for different cereal species from....

  15. Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity.

    USGS Publications Warehouse

    Vandergast, Amy G.; Perry, William M.; Lugo, Roberto V.; Hathaway, Stacie A.

    2011-01-01

    The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS, to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.

  16. Assessment of genetic diversity in lentils (Lens culinaris Medik.) based on SNPs.

    PubMed

    Basheer-Salimia, R; Camilli, B; Scacchi, S; Noli, E; Awad, M

    2015-01-01

    This study is the first attempt to establish an SNP database for the purpose of estimating the genetic diversity and relatedness of Palestinian lentil genotypes. A total of 14 lentil accessions (11 local, two supplied by ICARDA, and one introduced from Italy) were investigated. By sequencing two genes, lectin and lipid transfer protein 5 (LTP5), four SNPs were detected (three in the first and one in latter gene) with average frequencies of one SNP every 228 and 578 bp, respectively. In addition, in LTP5 two single-nucleotide indels were observed in the non-coding part of the gene. Four haplotypes were identified in the lectin gene, three in LTP5. One lectin haplotype coincided with that present in GenBank belonging to two cultivated varieties, two were rather similar to this, whereas the last one turned out closer to the sequence of one wild lentil accession, indicating the existence of diversity in the Palestinian germplasm. These results, enhancing the available knowledge of lentil genetic resources in Palestine, may contribute to their conservation and utilization in breeding projects. PMID:26125786

  17. Genetic diversity of the Chinese traditional herb Blumea balsamifera (Asteraceae) based on AFLP markers.

    PubMed

    Pang, Y X; Wang, W Q; Zhang, Y B; Yuan, Y; Yu, J B; Zhu, M; Chen, Y Y

    2014-01-01

    Blumea balsamifera is a commercially important medicinal herb in China and other parts of Asia. It is used to produce borneol. This plant grows in the wild, but resources have diminished greatly in recent years. We examined the genetic diversity of this species to help develop conservation strategies; 35 plants from five provinces were analyzed using AFLPs. Eight AFLP primer combinations generated 1367 fragments, giving a mean of 172 fragments per primer combination. Polymorphism in the germplasm analysis was found for 1360 (99.48%) of the fragments, of which 264 (19.27%) fragments were unique (accession specific) and 423 (25.33%) of the fragments were rare (present in less than 10% of the accessions). The polymorphic fragments were used to group the accessions in a UPGMA phenogram. Most grouping was geographical. In general, accessions coming from Guizhou and Guangxi showed higher diversities as these accessions were scattered in different groups. The genetic distance estimated by Jaccard similarity coefficient index showed low variability among genotypes (coefficient value ranged from 0.60 to 0.95). More attention should be given to the study and conservation of the biodiversity of this economically important genus. PMID:24782086

  18. Status of genetic diversity of U. S. dairy goat breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity underpins the livestock breeders’ ability to improve the production potential of their livestock. Therefore, it is important to periodically assess genetic diversity within a breed. Such an analysis was conducted on U.S. dairy goat breeds: Alpine, LaMancha, Nigerian Dwarf, Nubian, ...

  19. Comparison of Genetic Diversity Between US and Kazak Sheep Breeds.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To secure US genetic diversity it is beneficial to compare US and non-US breeds. Such information may also be used to identify areas of sampling for diverse genetic resources. Kazakhstan (KZ) provides an interesting comparison due to its history of sheep production and proximity to the Silk Route, w...

  20. Status of genetic diversity of U. S. dairy goat breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity underpins the livestock breeders’ ability to improve the production potential of their livestock. Therefore, it is important to periodically assess genetic diversity within a breed. Such an analysis was conducted on U.S. dairy goat breeds and this article is an overview of that wo...

  1. Exploring Germplasm Diversity to Understand the Domestication Process in Cicer spp. Using SNP and DArT Markers

    PubMed Central

    Roorkiwal, Manish; von Wettberg, Eric J.; Upadhyaya, Hari D.; Warschefsky, Emily; Rathore, Abhishek; Varshney, Rajeev K.

    2014-01-01

    To estimate genetic diversity within and between 10 interfertile Cicer species (94 genotypes) from the primary, secondary and tertiary gene pool, we analysed 5,257 DArT markers and 651 KASPar SNP markers. Based on successful allele calling in the tertiary gene pool, 2,763 DArT and 624 SNP markers that are polymorphic between genotypes from the gene pools were analyzed further. STRUCTURE analyses were consistent with 3 cultivated populations, representing kabuli, desi and pea-shaped seed types, with substantial admixture among these groups, while two wild populations were observed using DArT markers. AMOVA was used to partition variance among hierarchical sets of landraces and wild species at both the geographical and species level, with 61% of the variation found between species, and 39% within species. Molecular variance among the wild species was high (39%) compared to the variation present in cultivated material (10%). Observed heterozygosity was higher in wild species than the cultivated species for each linkage group. Our results support the Fertile Crescent both as the center of domestication and diversification of chickpea. The collection used in the present study covers all the three regions of historical chickpea cultivation, with the highest diversity in the Fertile Crescent region. Shared alleles between different gene pools suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of divergence and fusion of wild chickpea taxa in the past. PMID:25010059

  2. Plant Germplasm Centers and Microbial Culture Collections: A User’s Guide to Key Genetic Resources for Plant Pathology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This User's Guide to microbial culture collections and collections of germplasm of higher plants contains a variety of instructional material. It specifies to potential users amongst the plant science community, but especially plant pathologists, how to locate collections on line or via corresponde...

  3. EcoTurf - a case study: genetic variation and agronomic potential of bermudagrass (Cynodon spp.) germplasm collected from Australian biodiversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Australian Cynodon germplasm has not been comprehensively exploited for bermudagrass improvement. In this paper we will describe ‘EcoTurf’ a four year (2007-2011) project to develop water and nutrient use efficient bermudagrasses from Australian biodiversity. We describe the sampling strategies of A...

  4. Physicochemical properties and aroma volatile profiles in a diverse collection of California-grown pomegranate (Punica granatum L.) germplasm.

    PubMed

    Beaulieu, J C; Lloyd, S W; Preece, J E; Moersfelder, J W; Stein-Chisholm, R E; Obando-Ulloa, J M

    2015-08-15

    Colorful antioxidant-rich fruits often convey astringency and sourness that juice consumers may not appreciate. We assessed properties in juices from a collection of California-grown pomegranate from the National Clonal Germplasm Repository. The goal was to evaluate overall differences in germplasm with quality traits classified as sweet, sweet-sour and sour. Previous relationships noted in sweet and sour cultivar attributes were observed. Wonderful generally clustered with sweet-sour and sour cultivars. Sweet low acid cultivars occasionally clustered closely with Wonderful which is hard to rationalize. The dominant compounds were 3-hexenol and 1-hexanol which allowed separation of Kara Gul, Haku-botan and Wonderful. Aldehyde and terpene content can be used to characterize cultivars. The study represents the first data on variation in juice qualities in different sweet, sweet-sour and sour cultivars, grown in California, compared with Wonderful. Data may help the juice industry better select raw juice materials in order to ultimately satisfy consumers. PMID:25794761

  5. Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes

    PubMed Central

    Osborne, Megan J; Perkin, Joshuah S.; Gido, Keith B.; Turner, Thomas F.

    2014-01-01

    We used comparative landscape genetics to examine the relative roles of historical events, intrinsic traits, and landscape factors in determining the distribution of genetic diversity of river fishes across the North American Great Plains. Spatial patterns of diversity were overlaid on a patch-based graphical model, and then compared within and among three species that co-occurred across five Great Plains watersheds. Species differing in reproductive strategy (benthic vs. pelagic spawning) were hypothesized to have different patterns of genetic diversity, but the overriding factor shaping contemporary patterns of diversity was the signature of past climates and geological history. Allelic diversity was significantly higher at southern latitudes for Cyprinella lutrensis and Hybognathus placitus, consistent with northward expansion from southern Pleistocene refugia. Within the historical context, all species exhibited lowered occupancy and abundance in heavily fragmented and drier upstream reaches, particularly H. placitus; a pelagic-spawning species, suggesting rates of extirpation have outpaced losses of genetic diversity in this species. Within most basins, genetically diverse populations of each species persisted. Hence, reconnecting genetically diverse populations with those characterized by reduced diversity (regardless of their position within the riverine network) would provide populations with greater genetic and demographic resilience. We discuss cases where cross-basin transfer may be appropriate to enhance genetic diversity and mitigate negative effects of climate change. Overall, striking similarities in genetic patterns and response to fragmentation and dewatering suggest a common strategy for genetic resource management in this unique riverine fish assemblage. PMID:25327780

  6. Beauveria bassiana: Quercetinase production and genetic diversity

    PubMed Central

    Eula Maria de M. B., Costa; Fabiana Cristina, Pimenta; Christian, Luz; Valéria de, Oliveira; Marília, Oliveira; Elda, Bueno; Silvana, Petrofeza

    2011-01-01

    Beauveria bassiana genetic diversity and ability to synthesize quercetin 2,3-dioxygenase (quercetinase) were analyzed. B. bassiana isolates, obtained from Brazilian soil samples, produced quercetinase after induction using 0.5 g/L quercetin. B. bassiana ATCC 7159 (29.6 nmol/mL/min) and isolate IP 11 (27.5 nmol/ml/min) showed the best performances and IP 3a (9.5 nmol/mL/min) presented the lowest level of quercetinase activity in the culture supernatant. A high level of polymorphism was detected by random amplified polymorphic DNA (RAPD) analysis. The use of internal-transcribed-spacer ribosomal region restriction fragment length polymorphism (ITS-RFLP) did not reveal characteristic markers to differentiate isolates. However, the ITS1-5.8S-ITS2 region sequence analysis provided more information on polymorphism among the isolates, allowing them to be clustered by relative similarity into three large groups. Correlation was tested according to the Person's correlation. Data of our studies showed, that lower associations among groups, level of quercetinase production, or geographical origin could be observed. This study presents the production of a novel biocatalyst by B. bassiana and suggests the possible industrial application of this fungal species in large-scale biotechnological manufacture of quercetinase. PMID:24031599

  7. Multiple paternity does not depend on male genetic diversity

    PubMed Central

    Thonhauser, Kerstin E.; Raveh, Shirley; Penn, Dustin J.

    2014-01-01

    Polyandry is common in many species and it has been suggested that females engage in multiple mating to increase the genetic diversity of their offspring (genetic diversity hypothesis). Multiple paternity occurs in 30% of litters in wild populations of house mice, Mus musculus musculus, and multiple-sired litters are genetically more diverse than single-sired ones. Here, we aimed to test whether female house mice produce multiple-sired litters when they have the opportunity to produce genetically diverse litters. We assessed the rates of multiple paternity when females could choose to mate with two males that were genetically dissimilar to each other (i.e. nonsiblings and MHC dissimilar) compared with when females could choose to mate with two males that were genetically similar to each other (i.e. siblings and shared MHC alleles). Multiple mating may depend upon a female's own condition, and, therefore, we also tested whether inbred (from full-sibling matings) females were more likely to produce multiple-sired progeny than outbred controls. Overall we found that 29% of litters had multiple sires, but we found no evidence that females were more likely to produce multiple-sired litters when they had the opportunity to mate with genetically dissimilar males compared with controls, regardless of whether females were inbred or outbred. Thus, our findings do not support the idea that female mice increase multiple paternity when they have the opportunity to increase the genetic diversity of their offspring, as expected from the genetic diversity hypothesis. PMID:25018559

  8. Ploidy level and genomic composition of the USDA-ARS Tropical Agriculture Research Station Musa sp. Germplasm Collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant germplasm collections serve as repositories for important genes. However, insufficient and inaccurate characterization of the genetic diversity in a collection slows and can prevent full utilization of these collections to maximum potential. Bananas and plantains (Musa sp., Colla) are some o...

  9. Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives

    PubMed Central

    Govindaraj, M.; Vetriventhan, M.; Srinivasan, M.

    2015-01-01

    The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable

  10. Genetic diversity for grain nutrients in wild emmer wheat: potential for wheat improvement

    PubMed Central

    Chatzav, Merav; Peleg, Zvi; Ozturk, Levent; Yazici, Atilla; Fahima, Tzion; Cakmak, Ismail; Saranga, Yehoshua

    2010-01-01

    Background and Aims Micronutrient malnutrition, particularly zinc and iron deficiency, afflicts over three billion people worldwide due to low dietary intake. In the current study, wild emmer wheat (Triticum turgidum ssp. dicoccoides), the progenitor of domesticated wheat, was tested for (1) genetic diversity in grain nutrient concentrations, (2) associations among grain nutrients and their relationships with plant productivity, and (3) the association of grain nutrients with the eco-geographical origin of wild emmer accessions. Methods A total of 154 genotypes, including wild emmer accessions from across the Near Eastern Fertile Crescent and diverse wheat cultivars, were characterized in this 2-year field study for grain protein, micronutrient (zinc, iron, copper and manganese) and macronutrient (calcium, magnesium, potassium, phosphorus and sulphur) concentrations. Key Results Wide genetic diversity was found among the wild emmer accessions for all grain nutrients. The concentrations of grain zinc, iron and protein in wild accessions were about two-fold greater than in the domesticated genotypes. Concentrations of these compounds were positively correlated with one another, with no clear association with plant productivity, suggesting that all three nutrients can be improved concurrently with no yield penalty. A subset of 12 populations revealed significant genetic variation between and within populations for all minerals. Association between soil characteristics at the site of collection and grain nutrient concentrations showed negative associations between soil clay content and grain protein and between soil-extractable zinc and grain zinc, the latter suggesting that the greatest potential for grain nutrient minerals lies in populations from micronutrient-deficient soils. Conclusions Wild emmer wheat germplasm offers unique opportunities to exploit favourable alleles for grain nutrient properties that were excluded from the domesticated wheat gene pool. PMID

  11. Romanian Maize (Zea mays) Inbred Lines as a Source of Genetic Diversity in SE Europe, and Their Potential in Future Breeding Efforts

    PubMed Central

    Haș, Voichița; Haș, Ioan; Miclăuș, Mihai

    2013-01-01

    Maize has always been under constant human selection ever since it had been domesticated. Intensive breeding programs that resulted in the massive use of hybrids nowadays have started in the 60s. That brought significant yield increases but reduced the genetic diversity at the same time. Consequently, breeders and researchers alike turned their attention to national germplasm collections established decades ago in many countries, as they may hold allelic variations that could prove useful for future improvements. These collections are mainly composed of inbred lines originating from well-adapted local open pollinated varieties. However, there is an overall lack of data in the literature about the genetic diversity of maize in SE Europe, and its potential for future breeding efforts. There are no data, whatsoever, on the nutritional quality of the grain, primarily dictated by the zein proteins. We therefore sought to use the Romanian maize germplasm as an entry point in understanding the molecular make-up of maize in this part of Europe. By using 80 SSR markers, evenly spread throughout the genome, on 82 inbred lines from various parts of the country, we were able to decipher population structure and the existing relationships between those and the eight international standards used, including the reference sequenced genome B73. Corroborating molecular data with a standardized morphological, physiological, and biochemical characterization of all 90 inbred lines, this is the first comprehensive such study on the existing SE European maize germplasm. The inbred lines we present here are an important addition to the ever-shrinking gene pool that the breeding programs are faced-with, because of the allelic richness they hold. They may serve as parental lines in crosses that will lead to new hybrids, characterized by a high level of heterosis, nationwide and beyond, due to their existing relationship with the international germplasm. PMID:24392016

  12. Extreme genetic diversity in asexual grass thrips populations.

    PubMed

    Fontcuberta García-Cuenca, A; Dumas, Z; Schwander, T

    2016-05-01

    The continuous generation of genetic variation has been proposed as one of the main factors explaining the maintenance of sexual reproduction in nature. However, populations of asexual individuals may attain high levels of genetic diversity through within-lineage diversification, replicate transitions to asexuality from sexual ancestors and migration. How these mechanisms affect genetic variation in populations of closely related sexual and asexual taxa can therefore provide insights into the role of genetic diversity for the maintenance of sexual reproduction. Here, we evaluate patterns of intra- and interpopulation genetic diversity in sexual and asexual populations of Aptinothrips rufus grass thrips. Asexual A. rufus populations are found throughout the world, whereas sexual populations appear to be confined to few locations in the Mediterranean region. We found that asexual A. rufus populations are characterized by extremely high levels of genetic diversity, both in comparison with their sexual relatives and in comparison with other asexual species. Migration is extensive among asexual populations over large geographic distances, whereas close sexual populations are strongly isolated from each other. The combination of extensive migration with replicate evolution of asexual lineages, and a past demographic expansion in at least one of them, generated high local clone diversities in A. rufus. These high clone diversities in asexual populations may mimic certain benefits conferred by sex via genetic diversity and could help explain the extreme success of asexual A. rufus populations. PMID:26864612

  13. [Analysis of genetic diversity on 9 wild stocks of taimen (Hucho taimen) by microsatellite markers].

    PubMed

    Liu, Bo; Kuang, You-Yi; Tong, Guang-Xiang; Yin, Jia-Sheng

    2011-12-01

    Taimen (Hucho taimen) is a native fish species in China and it is in the state of endangerment. To explain clearly the genetic diversity and genetic structure, 9 wild populations of taimen were investigated using 20 microsatellite markers. The results showed that their observed heterozygosity ranged from 0.0994 to 0.8882, the expected heterozygosity varied from 0.2005 to 0.8759, and the range of PIC index was from 0.3432 to 0.5261 while population from Huma River had low genetic diversity. Fst of matching group ranged from 0.0246 to 0.2333 (P <0.0001)and Nm varied among 0.8216 to 9.9292, which indicated that the genetic differentiation was remarkable among populations.The half/full-sib family tests detected a proportion of half/full-sib family groups varying among 27.78% to 90.91%, showing a high inbred pressure and a risk of bottlenecks experienced by most groups. The AMOVA results showed that the global Fst was 0.1081; the clustering result showed that individuals from Beiji tributary of Heilongjiang River clustered as one clade, all individuals from Huma River and Wusuli River clustered as one clade and all individuals from the upper reaches of the Heilongjiang River clustered as another clade. All these results indicated that the decrease of taimen resource has affected the gene exchange among their populations. In order to achieve full protection of taimen germplasm resources, we should put an end to the destructive fishing for taimen and promotegene exchange among their populations. PMID:22184017

  14. Genetic diversity of cultivated and wild tomatoes revealed by morphological traits and SSR markers.

    PubMed

    Zhou, R; Wu, Z; Cao, X; Jiang, F L

    2015-01-01

    In the current study, morphological traits and molecular markers were used to assess the genetic diversity of 29 cultivated tomatoes, 14 wild tomatoes and seven introgression lines. The three components of the principal component analysis (PCA) explained 78.54% of the total morphological variation in the 50 tomato genotypes assessed. Based on these morphological traits, a three-dimensional PCA plot separated the 50 genotypes into distinct groups, and a dendrogram divided them into six clusters. Fifteen polymorphic genomic simple- sequence repeat (genomic-SSR) and 13 polymorphic expressed sequence tag-derived SSR (EST-SSR) markers amplified 1115 and 780 clear fragments, respectively. Genomic-SSRs detected a total of 64 alleles, with a mean of 4 alleles per primer, while EST-SSRs detected 52 alleles, with a mean of 4 alleles per primer. The polymorphism information content was slightly higher in genomic-SSRs (0.49) than in EST-SSRs (0.45). The mean similarity coefficient among the wild tomatoes was lower than the mean similarity coefficient among the cultivated tomatoes. The dendrogram based on genetic distance divided the 50 tomato genotypes into eight clusters. The Mantel test between genomic-SSR and EST-SSR matrices revealed a good correlation, whereas the morphological matrices and the molecular matrices were weakly correlated. We confirm the applicability of EST-SSRs in analyzing genetic diversity among cultivated and wild tomatoes. High variability of the 50 tomato genotypes was observed at the morphological and molecular level, indicating valuable tomato germplasm, especially in the wild tomatoes, which could be used for further genetic studies. PMID:26535702

  15. Molecular characterization of patchouli (Pogostemon spp) germplasm.

    PubMed

    Sandes, S S; Zucchi, M I; Pinheiro, J B; Bajay, M M; Batista, C E A; Brito, F A; Arrigoni-Blank, M F; Alvares-Carvalho, S V; Silva-Mann, R; Blank, A F

    2016-01-01

    Patchouli [Pogostemon cablin (Blanco) Benth.] is an aromatic, herbaceous plant belonging to the Lamiaceae family native to Southeast Asia. Its leaves produce an essential oil regularly used by the perfume and cosmetics industries. However, since patchouli from the Philippines and India were described and named Pogostemon patchouli, there has been a divergence in the identity of these species. The objective of the current study was to study the genetic diversity of patchouli accessions in the Active Germplasm Bank of Universidade Federal de Sergipe using microsatellite and inter simple sequence repeat markers. The results of both types of molecular markers showed that there are two well-defined clusters of accessions that harbor exclusive alleles. It was observed that these two clusters are genetically distant, suggesting that they belong to two different species. Based on the results, two accessions were classified as Pogostemon heyneanus and the remaining accessions were classified as P. cablin. PMID:26909987

  16. Genetic conservation, characterization and utilization of wild relatives of fruit and nut crops at the USDA Germplasm Repository in Davis, California

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The National Clonal Germplasm Repository (NCGR) in Davis is one among the nine repositories in the National Plant Germplasm System, USDA-ARS that is responsible for conservation of clonally propagated woody perennial subtropical and temperate fruit and nut crop germplasm. Currently the repository ho...

  17. Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from the East African highlands.

    PubMed

    Asfaw, Asrat; Blair, Matthew W; Almekinders, Conny

    2009-12-01

    The East African highlands are a region of important common bean production and high varietal diversity for the crop. The objective of this study was to uncover the diversity and population structure of 192 landraces from Ethiopia and Kenya together with four genepool control genotypes using morphological phenotyping and microsatellite marker genotyping. The germplasm represented different common bean production ecologies and seed types common in these countries. The landraces showed considerable diversity that corresponded well to the two recognized genepools (Andean and Mesoamerican) with little introgression between these groups. Mesoamerican genotypes were predominant in Ethiopia while Andean genotypes were predominant in Kenya. Within each country, landraces from different collection sites were clustered together indicating potential gene flow between regions within Kenya or within Ethiopia. Across countries, landraces from the same country of origin tended to cluster together indicating distinct germplasm at the national level and limited gene flow between the two countries highlighting divided social networks within the regions and a weak trans-national bean seed exchange especially for landrace varieties. One exception to this may be the case of small red-seeded beans where informal cross-border grain trade occurs. We also observed that genetic divergence was slightly higher for the Ethiopian landraces compared to Kenyan landraces and that Mesoamerican genotypes were more diverse than the Andean genotypes. Common beans in eastern Africa are often cultivated in marginal, risk-prone farming systems and the observed landrace diversity should provide valuable alleles for adaptation to stressful environments in future breeding programs in the region. PMID:19756469

  18. Application of Association Mapping to Understanding the Genetic Diversity of Plant Germplasm Resources

    PubMed Central

    Abdurakhmonov, Ibrokhim Y.; Abdukarimov, Abdusattor

    2008-01-01

    Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a “powerful gene tagging” tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application. PMID:18551188

  19. Haplotype Structure and Genetic Diversity at Fusarium Head Blight Resistance QTLs in Soft Winter Wheat Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several quantitative trait loci (QTLs) for resistance to Fusarium head blight (FHB) have been mapped in wheat. Haplotyping strategies make use of previous QTL mapping and molecular marker information. In our study we selected markers reported to be near FHB resistance QTL mapped in Sumai 3, Wuhan 1 ...

  20. Genetic diversity in the USDA Limnanthes germplasm collection assessed by simple sequence repeats

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Limnanthes, also known as meadowfoam, has attracted attention for industrial use due to the unique characteristics of its seed oil. Samples from wild populations showed variability in agronomically important traits involved in seed oil yield, warranting the establishment and continued dev...

  1. Genetic Diversity and Population Structure of Chinese Foxtail Millet [Setaria italica (L.) Beauv.] Landraces

    PubMed Central

    Wang, Chunfang; Jia, Guanqing; Zhi, Hui; Niu, Zhengang; Chai, Yang; Li, Wei; Wang, Yongfang; Li, Haiquan; Lu, Ping; Zhao, Baohua; Diao, Xianmin

    2012-01-01

    As an ancient cereal of great importance for dryland agriculture even today, foxtail millet (Setaria italica) is fast becoming a new plant genomic model crop. A genotypic analysis of 250 foxtail millet landraces, which represent 1% of foxtail millet germplasm kept in the Chinese National Gene Bank (CNGB), was conducted with 77 SSRs covering the foxtail millet genome. A high degree of molecular diversity among the landraces was found, with an average of 20.9 alleles per locus detected. STRUCTURE, neighbor-jointing, and principal components analyses classify the accessions into three clusters (topmost hierarchy) and, ultimately, four conservative subgroups (substructuring within the topmost clusters) in total, which are in good accordance with eco-geographical distribution in China. The highest subpopulation diversity was identified in the accessions of Pop3 from the middle regions of the Yellow River, followed by accessions in Pop1 from the downstream regions of the Yellow River, suggesting that foxtail millet was domesticated in the Yellow River drainage area first and then spread to other parts of the country. Linkage disequilibrium (LD) decay of less than 20 cM of genetic distance in the foxtail millet landrace genome was observed, which suggests that it could be possible to achieve resolution down to the 20 cM level for association mapping. PMID:22870400

  2. Genetic diversity assessment of wild Southeastern American Vaccinium using microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The United States Department of Agriculture (USDA)-Agricultural Research Service (ARS)-National Clonal Germplasm Repository (NCGR) in Corvallis Oregon preserves genetic resources of more than 1700 Vaccinium accessions from 33 countries. Wild Vaccinium species from northwestern, central and south Flo...

  3. Genetic diversity of diploid Japanese strawberry species based on microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) - National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, is a genebank that preserves strawberry genetic resources. In 2004, representatives of two Japanese diploid species, F. iinumae Makino and F. n...

  4. The NCRPIS - Providing Diverse Plant Genetic Resources for Worldwide Research and Development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The North Central Regional Plant Introduction Station (NCRPIS) is an active plant genebank of the U.S. National Plant Germplasm System (NPGS). Dedicated to conserving and providing plant genetic resources and valuable information to researchers worldwide, the NPGS is a network of federal and state ...

  5. Melon fruits: genetic diversity, physiology, and biotechnology features.

    PubMed

    Nuñez-Palenius, Hector G; Gomez-Lim, Miguel; Ochoa-Alejo, Neftali; Grumet, Rebecca; Lester, Gene; Cantliffe, Daniel J

    2008-01-01

    Among Cucurbitaceae, Cucumis melo is one of the most important cultivated cucurbits. They are grown primarily for their fruit, which generally have a sweet aromatic flavor, with great diversity and size (50 g to 15 kg), flesh color (orange, green, white, and pink), rind color (green, yellow, white, orange, red, and gray), form (round, flat, and elongated), and dimension (4 to 200 cm). C. melo can be broken down into seven distinct types based on the previously discussed variations in the species. The melon fruits can be either climacteric or nonclimacteric, and as such, fruit can adhere to the stem or have an abscission layer where they will fall from the plant naturally at maturity. Traditional plant breeding of melons has been done for 100 years wherein plants were primarily developed as open-pollinated cultivars. More recently, in the past 30 years, melon improvement has been done by more traditional hybridization techniques. An improvement in germplasm is relatively slow and is limited by a restricted gene pool. Strong sexual incompatibility at the interspecific and intergeneric levels has restricted rapid development of new cultivars with high levels of disease resistance, insect resistance, flavor, and sweetness. In order to increase the rate and diversity of new traits in melon it would be advantageous to introduce new genes needed to enhance both melon productivity and melon fruit quality. This requires plant tissue and plant transformation techniques to introduce new or foreign genes into C. melo germplasm. In order to achieve a successful commercial application from biotechnology, a competent plant regeneration system of in vitro cultures for melon is required. More than 40 in vitro melon regeneration programs have been reported; however, regeneration of the various melon types has been highly variable and in some cases impossible. The reasons for this are still unknown, but this plays a heavy negative role on trying to use plant transformation technology

  6. Demographic Events and Evolutionary Forces Shaping European Genetic Diversity

    PubMed Central

    Veeramah, Krishna R.; Novembre, John

    2014-01-01

    Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease. PMID:25059709

  7. Demographic events and evolutionary forces shaping European genetic diversity.

    PubMed

    Veeramah, Krishna R; Novembre, John

    2014-09-01

    Europeans have been the focus of some of the largest studies of genetic diversity in any species to date. Recent genome-wide data have reinforced the hypothesis that present-day European genetic diversity is strongly correlated with geography. The remaining challenge now is to understand more precisely how patterns of diversity in Europe reflect ancient demographic events such as postglacial expansions or the spread of farming. It is likely that recent advances in paleogenetics will give us some of these answers. There has also been progress in identifying specific segments of European genomes that reflect adaptations to selective pressures from the physical environment, disease, and dietary shifts. A growing understanding of how modern European genetic diversity has been shaped by demographic and evolutionary forces is not only of basic historical and anthropological interest but also aids genetic studies of disease. PMID:25059709

  8. Sexual selection and individual genetic diversity in a songbird.

    PubMed

    Marshall, Rupert C; Buchanan, Katherine L; Catchpole, Clive K

    2003-11-01

    Here, we report for the first time, to our knowledge, a strong correlation between a measure of individual genetic diversity and song complexity, a sexually selected male trait in sedge warblers, Acrocephalus schoenobaenus. We also find that females prefer to mate with males who will maximize this diversity in individual progeny. The genetic diversity of each offspring is further increased by means of nonrandom fertilization, as we also show that the fertilizing sperm contains a haplotype more genetically distant to that of the egg than expected by chance. These findings suggest that species' mating preferences may be subject to fine tuning aimed at increasing offspring viability through increased genetic diversity. This includes external and internal mechanisms of selection, even within the ejaculate of a single male. PMID:14667396

  9. Genetic diversity and structure in two protected Posidonia oceanica meadows.

    PubMed

    Micheli, Carla; D'Esposito, Daniela; Belmonte, Alessandro; Peirano, Andrea; Valiante, Luigi Maria; Procaccini, Gabriele

    2015-08-01

    Posidonia oceanica meadows growing along the west Mediterranean coastline are under continuous anthropogenic pressure. The way meadow health correlates with genetic and genotypic diversity in P. oceanica, is still under debate. Here we report a microsatellite analysis of two P. oceanica meadows living in protected areas of the Ligurian (Monterosso al Mare, MPA of "Cinque Terre") and central Tyrrhenian Sea (Santa Marinella, regional Site of Community Importance). Both meadows were recently classified as "disturbed", according to shoot density and other phenological parameters. Between the two meadows, Santa Marinella showed higher genetic diversity, while clear genetic substructure was present in both sites, reflecting high spatial heterogeneity. The present study suggests that genetic diversity does not match unequivocally with shoot density and leaf morphology and that small scale intra-meadow heterogeneity is an important factor to consider for establishing the relation between genetic/genotypic variability and health of natural seagrass meadows. PMID:26164681

  10. Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip

    PubMed Central

    Hill, Theresa A.; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W.; Van Deynze, Allen

    2013-01-01

    The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome

  11. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

    PubMed

    Hill, Theresa A; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W; Van Deynze, Allen

    2013-01-01

    The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome

  12. Implications of the apportionment of human genetic diversity for the apportionment of human phenotypic diversity

    PubMed Central

    Edge, Michael D.; Rosenberg, Noah A.

    2015-01-01

    Researchers in many fields have considered the meaning of two results about genetic variation for concepts of “race.” First, at most genetic loci, apportionments of human genetic diversity find that worldwide populations are genetically similar. Second, when multiple genetic loci are examined, it is possible to distinguish people with ancestry from different geographical regions. These two results raise an important question about human phenotypic diversity: To what extent do populations typically differ on phenotypes determined by multiple genetic loci? It might be expected that such phenotypes follow the pattern of similarity observed at individual loci. Alternatively, because they have a multilocus genetic architecture, they might follow the pattern of greater differentiation suggested by multilocus ancestry inference. To address the question, we extend a well-known classification model of Edwards (2003) by adding a selectively neutral quantitative trait. Using the extended model, we show, in line with previous work in quantitative genetics, that regardless of how many genetic loci influence the trait, one neutral trait is approximately as informative about ancestry as a single genetic locus. The results support the relevance of single-locus genetic-diversity partitioning for predictions about phenotypic diversity. PMID:25677859

  13. Inference of genetic diversity in popcorn S3 progenies.

    PubMed

    Pena, G F; do Amaral, A T; Ribeiro, R M; Ramos, H C C; Boechat, M S B; Santos, J S; Mafra, G S; Kamphorst, S H; de Lima, V J; Vivas, M; de Souza Filho, G A

    2016-01-01

    Molecular markers are a useful tool for identification of complementary heterotic groups in breeding programs aimed at the production of superior hybrids, particularly for crops such as popcorn in which heterotic groups are not well-defined. The objective of the present study was to analyze the genetic diversity of 47 genotypes of tropical popcorn to identify possible heterotic groups for the development of superior hybrids. Four genotypes of high genetic value were studied: hybrid IAC 125, strain P2, and varieties UENF 14 and BRS Angela. In addition, 43 endogamous S3 progenies obtained from variety UENF 14 were used. Twenty-five polymorphic SSR-EST markers were analyzed. A genetic distance matrix was obtained and the following molecular diversity parameters were estimated: number of alleles, number of effective alleles, polymorphism information content (PIC), observed and expected heterozygosities, Shannon diversity index, and coefficient of inbreeding. We found a moderate PIC and high diversity index, indicating that the studied population presents both good discriminatory ability and high informativeness for the utilized markers. The dendrogram built based on the dissimilarity matrix indicated six distinct groups. Our findings demonstrate the genetic diversity among the evaluated genotypes and provide evidence for heterotic groups in popcorn. Furthermore, the functional genetic diversity indicates that there are informative genetic markers for popcorn. PMID:27173336

  14. Genetic Diversity in Cotton Out-Crossing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previously we have reported on the finding of genetic differences in the abiotic stress tolerance of cotton pollen. Genetic differences in sensitivity to humidity were observed impacting pollen survival in dry environments. The present study evaluated out-crossing rates in cotton lines whose polle...

  15. Cotton gene flow: Genetic diversity in outcrossing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Previously we have reported on the finding of genetic differences in the abiotic stress tolerance of cotton pollen. Genetic differences in sensitivity to humidity were observed impacting pollen survival in dry environments. The present study evaluated out-crossing rates in cotton lines whose pollen ...

  16. Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers

    PubMed Central

    2010-01-01

    Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections. PMID:21637613

  17. Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers.

    PubMed

    Palmieri, Darío A; Bechara, Marcelo D; Curi, Rogério A; Monteiro, Jomar P; Valente, Sérgio E S; Gimenes, Marcos A; Lopes, Catalina R

    2010-01-01

    Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections. PMID:21637613

  18. Assessment of Platycodon grandiflorum germplasm resources from northern Anhui province based on ISSR analysis.

    PubMed

    Nie, Chuanpeng; Liu, Ruijiao; Li, Shangbo; Li, Yanyan

    2014-12-01

    Based on genetic diversity analysis with ISSR-PCR, this study was to access the germplasm resources of Platycodon grandiflorum in northern Anhui province. Ten primers that could produce more distinct and repeatable bands were used for ISSR-PCR. Statistic analysis was conducted by POPGENE v. 1.32, Arlequin3.l, NTSYS-pc version 2.1. (1) Seventy-four polymorphic bands (76.29 %) out of a total of 97 were generated from 105 individuals in five populations. (2) Shannon index of diversity ranged from 0.307 to 0.260, diversity at species level was 0.3581, which means superior genetic diversity. (3) Genetic diversity across all the populations revealed by AMOVA indicated that 86.02 % occurred within populations. (4) The Fst value was 0.1398, indicating a intermediate genetic differentiation among populations. (5) Dendrogram relationship illustrated genetic distance was correlated with geographic distance. ISSR markers can be used for studying genetic diversity of P. grandiflorum. Degradation of populations doesn't happen in northern Anhui province, bank of germplasm preservation should be established for cultivation of excellent variety of P. grandiflorum. PMID:25200435

  19. Understanding Genetic Diversity of Sorghum Using Quantitative Traits

    PubMed Central

    Sinha, Sweta; Kumaravadivel, N.

    2016-01-01

    Sorghum is the important cereal crop around the world and hence understanding and utilizing the genetic variation in sorghum accessions are essential for improving the crop. A good understanding of genetic variability among the accessions will enable precision breeding. So profiling the genetic diversity of sorghum is imminent. In the present investigation, forty sorghum accessions consisting of sweet sorghum, grain sorghum, forage sorghum, mutant lines, maintainer lines, and restorer lines were screened for genetic diversity using quantitative traits. Observations were recorded on 14 quantitative traits, out of which 9 diverse traits contributing to maximum variability were selected for genetic diversity analysis. The principle component analysis revealed that the panicle width, stem girth, and leaf breadth contributed maximum towards divergence. By using hierarchical cluster analysis, the 40 accessions were grouped under 6 clusters. Cluster I contained maximum number of accessions and cluster VI contained the minimum. The maximum intercluster distance was observed between cluster VI and cluster IV. Cluster III had the highest mean value for hundred-seed weight and yield. Hence the selection of parents must be based on the wider intercluster distance and superior mean performance for yield and yield components. Thus in the present investigation quantitative data were able to reveal the existence of a wide genetic diversity among the sorghum accessions used providing scope for further genetic improvement. PMID:27382499

  20. Diversity in global gene expression and morphology across a watercress (Nasturtium officinale R. Br.) germplasm collection: first steps to breeding.

    PubMed

    Payne, Adrienne C; Clarkson, Graham J J; Rothwell, Steve; Taylor, Gail

    2015-01-01

    Watercress (Nasturtium officinale R. Br.) is a nutrient intense, leafy crop that is consumed raw or in soups across the globe, but for which, currently no genomic resources or breeding programme exists. Promising morphological, biochemical and functional genomic variation was identified for the first time in a newly established watercress germplasm collection, consisting of 48 watercress accessions sourced from contrasting global locations. Stem length, stem diameter and anti-oxidant (AO) potential varied across the accessions. This variation was used to identify three extreme contrasting accessions for further analysis. Variation in global gene expression was investigated using an Affymetrix Arabidopsis ATH1 microarray gene chip, using the commercial control (C), an accession selected for dwarf phenotype with a high AO potential (dwarfAO, called 'Boldrewood') and one with high AO potential alone. A set of transcripts significantly differentially expressed between these three accessions, were identified, including transcripts involved in the regulation of growth and development and those involved in secondary metabolism. In particular, when differential gene expression was compared between C and dwarfAO, the dwarfAO was characterised by increased expression of genes encoding glucosinolates, which are known precursors of phenethyl isothiocyanate, linked to the anti-carcinogenic effects well-documented in watercress. This study provides the first analysis of natural variation across the watercress genome and has identified important underpinning information for future breeding for enhanced anti-carcinogenic properties and morphology traits in this nutrient-intense crop. PMID:26504575

  1. Diversity in global gene expression and morphology across a watercress (Nasturtium officinale R. Br.) germplasm collection: first steps to breeding

    PubMed Central

    Payne, Adrienne C.; Clarkson, Graham J.J.; Rothwell, Steve; Taylor, Gail

    2015-01-01

    Watercress (Nasturtium officinale R. Br.) is a nutrient intense, leafy crop that is consumed raw or in soups across the globe, but for which, currently no genomic resources or breeding programme exists. Promising morphological, biochemical and functional genomic variation was identified for the first time in a newly established watercress germplasm collection, consisting of 48 watercress accessions sourced from contrasting global locations. Stem length, stem diameter and anti-oxidant (AO) potential varied across the accessions. This variation was used to identify three extreme contrasting accessions for further analysis. Variation in global gene expression was investigated using an Affymetrix Arabidopsis ATH1 microarray gene chip, using the commercial control (C), an accession selected for dwarf phenotype with a high AO potential (dwarfAO, called ‘Boldrewood’) and one with high AO potential alone. A set of transcripts significantly differentially expressed between these three accessions, were identified, including transcripts involved in the regulation of growth and development and those involved in secondary metabolism. In particular, when differential gene expression was compared between C and dwarfAO, the dwarfAO was characterised by increased expression of genes encoding glucosinolates, which are known precursors of phenethyl isothiocyanate, linked to the anti-carcinogenic effects well-documented in watercress. This study provides the first analysis of natural variation across the watercress genome and has identified important underpinning information for future breeding for enhanced anti-carcinogenic properties and morphology traits in this nutrient-intense crop. PMID:26504575

  2. Accumulation of genetic diversity in the US Potato Genebank

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Efficient management of ex-situ collections includes understanding how conservation technologies impact the genetic diversity and integrity of these collections. For over 60 years, research at the US Potato Genebank has produced helpful scientific insights on diverse aspects of potato conservation. ...

  3. TEMPORAL CHANGES OF GENETIC DIVERSITY IN SUGARCANE BREEDING POPULATIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Concerns about decline of genetic diversity in sugarcane (Saccharum spp.) breeding programs need be addressed to define better breeding strategies aimed at achieving greater genetic gains. The objectives of this study were to reconstruct the divergence in the Canal Point breeding populations as temp...

  4. Genetic diversity of Toxoplama gondii isolates from Ethiopian feral cats

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent studies indicate greater genetic variability among isolates of Toxoplasma gondii worldwide than previously thought. However, there is no information on genetic diversity of T. gondii from any host in Ethiopia. In the present study, genotyping was performed on viable T. gondii isolates by bioa...

  5. Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers

    PubMed Central

    Fernandez i Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font i Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

    2012-01-01

    Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3′ untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3′ UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, “Stella” was separated from “Compact Stella.” This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3′ UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry. PMID:22737155

  6. Present Spatial Diversity Patterns of Theobroma cacao L. in the Neotropics Reflect Genetic Differentiation in Pleistocene Refugia Followed by Human-Influenced Dispersal

    PubMed Central

    Thomas, Evert; van Zonneveld, Maarten; Loo, Judy; Hodgkin, Toby; Galluzzi, Gea; van Etten, Jacob

    2012-01-01

    Cacao (Theobroma cacao L.) is indigenous to the Amazon basin, but is generally believed to have been domesticated in Mesoamerica for the production of chocolate beverage. However, cacao’s distribution of genetic diversity in South America is also likely to reflect pre-Columbian human influences that were superimposed on natural processes of genetic differentiation. Here we present the results of a spatial analysis of the intra-specific diversity of cacao in Latin America, drawing on a dataset of 939 cacao trees genotypically characterized by means of 96 SSR markers. To assess continental diversity patterns we performed grid-based calculations of allelic richness, Shannon diversity and Nei gene diversity, and distinguished different spatially coherent genetic groups by means of cluster analysis. The highest levels of genetic diversity were observed in the Upper Amazon areas from southern Peru to the Ecuadorian Amazon and the border areas between Colombia, Peru and Brazil. On the assumption that the last glaciation (22,000–13,000 BP) had the greatest pre-human impact on the current distribution and diversity of cacao, we modeled the species’ Pleistocene niche suitability and overlaid this with present-day diversity maps. The results suggest that cacao was already widely distributed in the Western Amazon before the onset of glaciation. During glaciations, cacao populations were likely to have been restricted to several refugia where they probably underwent genetic differentiation, resulting in a number of genetic clusters which are representative for, or closest related to, the original wild cacao populations. The analyses also suggested that genetic differentiation and geographical distribution of a number of other clusters seem to have been significantly affected by processes of human management and accompanying genetic bottlenecks. We discuss the implications of these results for future germplasm collection and in situ, on farm and ex situ conservation of

  7. Limited Genetic Diversity in the Endophytic Sugarcane Bacterium Acetobacter diazotrophicus

    PubMed Central

    Caballero-Mellado, Jesus; Martinez-Romero, Esperanza

    1994-01-01

    Acetobacter diazotrophicus isolates that originated from different sugarcane cultivars growing in diverse geographic regions of Mexico and Brazil were shown to have limited genetic diversity. Measurements of polymorphism in the electrophoretic mobilities of metabolic enzymes revealed that the mean genetic diversity per enzyme locus (among the four electrophoretic types distinguished) was 0.064. The results of the genetic analysis indicate that the genetic structure of A. diazotrophicus is clonal, with one largely predominant clone. Plasmids were present in 20 of 24 isolates, and the molecular sizes of the plasmids ranged from 2.0 to 170 kb. Two plasmids (a 20- to 24-kb plasmid detected in all 20 plasmid-containing isolates and a 170-kb plasmid observed in 14 isolates) were highly conserved among the isolates examined. Regardless of the presence of plasmids, all of the isolates shared a common pattern of nif structural gene organization on the chromosome. Images PMID:16349254

  8. Genetic diversity, parasite prevalence and immunity in wild bumblebees

    PubMed Central

    Whitehorn, Penelope R.; Tinsley, Matthew C.; Brown, Mark J. F.; Darvill, Ben; Goulson, Dave

    2011-01-01

    Inbreeding and a consequent loss of genetic diversity threaten small, isolated populations. One mechanism by which genetically impoverished populations may become extinct is through decreased immunocompetence and higher susceptibility to parasites. Here, we investigate the relationship between immunity and inbreeding in bumblebees, using Hebridean island populations of Bombus muscorum. We sampled nine populations and recorded parasite prevalence and measured two aspects of immunity: the encapsulation response and levels of phenoloxidase (PO). We found that prevalence of the gut parasite Crithidia bombi was higher in populations with lower genetic diversity. Neither measure of immune activity was correlated with genetic diversity. However, levels of PO declined with age and were also negatively correlated with parasite abundance. Our results suggest that as insect populations lose heterozygosity, the impact of parasitism will increase, pushing threatened populations closer to extinction. PMID:20926436

  9. Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly

    PubMed Central

    Swaegers, J; Mergeay, J; Therry, L; Larmuseau, M H D; Bonte, D; Stoks, R

    2013-01-01

    Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations. PMID:23820582

  10. Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly.

    PubMed

    Swaegers, J; Mergeay, J; Therry, L; Larmuseau, M H D; Bonte, D; Stoks, R

    2013-11-01

    Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations. PMID:23820582

  11. Assessment of Genetic Diversity of Sweet Potato in Puerto Rico

    PubMed Central

    Rodriguez-Bonilla, Lorraine; Cuevas, Hugo E.; Montero-Rojas, Milly; Bird-Pico, Fernando; Luciano-Rosario, Dianiris; Siritunga, Dimuth

    2014-01-01

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand for food and the need for conservation of agricultural and genetic resources. In Puerto Rico (PR), the genetic diversity of sweet potato has been poorly understood, although it has been part of the diet since Pre-Columbus time. Thus, 137 landraces from different localities around PR were collected and subjected to a genetic diversity analysis using 23 SSR-markers. In addition, 8 accessions from a collection grown in Gurabo, PR at the Agricultural Experimental Station (GAES), 10 US commercial cultivars and 12 Puerto Rican accessions from the USDA repository collection were included in this assessment. The results of the analysis of the 23 loci showed 255 alleles in the 167 samples. Observed heterozygosity was high across populations (0.71) while measurements of total heterozygosity revealed a large genetic diversity throughout the population and within populations. UPGMA clustering method revealed two main clusters. Cluster 1 contained 12 PR accessions from the USDA repository collection, while cluster 2 consisted of PR landraces, US commercial cultivars and the PR accessions from GAES. Population structure analysis grouped PR landraces in five groups including four US commercial cultivars. Our study shows the presence of a high level of genetic diversity of sweet potato across PR which can be related to the genetic makeup of sweet potato, human intervention and out-crossing nature of the plant. The history of domestication and dispersal of sweet potato in the Caribbean and the high levels of genetic diversity found through this study makes sweet potato an invaluable resource that needs to be protected and further studied. PMID:25551388

  12. Theory predicts the uneven distribution of genetic diversity within species.

    PubMed

    Rauch, Erik M; Bar-Yam, Yaneer

    2004-09-23

    Global efforts to conserve species have been strongly influenced by the heterogeneous distribution of species diversity across the Earth. This is manifest in conservation efforts focused on diversity hotspots. The conservation of genetic diversity within an individual species is an important factor in its survival in the face of environmental changes and disease. Here we show that diversity within species is also distributed unevenly. Using simple genealogical models, we show that genetic distinctiveness has a scale-free power law distribution. This property implies that a disproportionate fraction of the diversity is concentrated in small sub-populations, even when the population is well-mixed. Small groups are of such importance to overall population diversity that even without extrinsic perturbations, there are large fluctuations in diversity owing to extinctions of these small groups. We also show that diversity can be geographically non-uniform--potentially including sharp boundaries between distantly related organisms--without extrinsic causes such as barriers to gene flow or past migration events. We obtained these results by studying the fundamental scaling properties of genealogical trees. Our theoretical results agree with field data from global samples of Pseudomonas bacteria. Contrary to previous studies, our results imply that diversity loss owing to severe extinction events is high, and focusing conservation efforts on highly distinctive groups can save much of the diversity. PMID:15386012

  13. The structural diversity of artificial genetic polymers.

    PubMed

    Anosova, Irina; Kowal, Ewa A; Dunn, Matthew R; Chaput, John C; Van Horn, Wade D; Egli, Martin

    2016-02-18

    Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson-Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space. PMID:26673703

  14. Unlocking the genetic diversity of Creole wheats.

    PubMed

    Vikram, Prashant; Franco, Jorge; Burgueño-Ferreira, Juan; Li, Huihui; Sehgal, Deepmala; Saint Pierre, Carolina; Ortiz, Cynthia; Sneller, Clay; Tattaris, Maria; Guzman, Carlos; Sansaloni, Carolina Paola; Fuentes-Davila, Guillermo; Reynolds, Matthew; Sonders, Kai; Singh, Pawan; Payne, Thomas; Wenzl, Peter; Sharma, Achla; Bains, Navtej Singh; Singh, Gyanendra Pratap; Crossa, José; Singh, Sukhwinder

    2016-01-01

    Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement. PMID:26976656

  15. The structural diversity of artificial genetic polymers

    PubMed Central

    Anosova, Irina; Kowal, Ewa A.; Dunn, Matthew R.; Chaput, John C.; Van Horn, Wade D.; Egli, Martin

    2016-01-01

    Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson–Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space. PMID:26673703

  16. Unlocking the genetic diversity of Creole wheats

    PubMed Central

    Vikram, Prashant; Franco, Jorge; Burgueño-Ferreira, Juan; Li, Huihui; Sehgal, Deepmala; Saint Pierre, Carolina; Ortiz, Cynthia; Sneller, Clay; Tattaris, Maria; Guzman, Carlos; Sansaloni, Carolina Paola; Fuentes-Davila, Guillermo; Reynolds, Matthew; Sonders, Kai; Singh, Pawan; Payne, Thomas; Wenzl, Peter; Sharma, Achla; Bains, Navtej Singh; Singh, Gyanendra Pratap; Crossa, José; Singh, Sukhwinder

    2016-01-01

    Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement. PMID:26976656

  17. Regional specificity of genetically diverse garlic varieties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Garlic is a profitable crop for small to medium-sized vegetable farmers. Despite the increasing market for specialty garlic, it is remarkable how little is known about the diverse types of garlic available. Farmers need to know which garlic types perform well under their growing conditions, and th...

  18. Temporal changes in population genetic diversity and structure in red and white clover grown in three contrasting environments in northern Europe

    PubMed Central

    Collins, Rosemary P.; Helgadóttir, Áslaug; Frankow-Lindberg, Bodil E.; Skøt, Leif; Jones, Charlotte; Skøt, Kirsten P.

    2012-01-01

    Backgound and Aims Extending the cultivation of forage legume species into regions where they are close to the margin of their natural distribution requires knowledge of population responses to environmental stresses. This study was conducted at three north European sites (Iceland, Sweden and the UK) using AFLP markers to analyse changes in genetic structure over time in two population types of red and white clover (Trifolium pratense and T. repens, respectively): (1) standard commercial varieties; (2) wide genetic base (WGB) composite populations constructed from many commercial varieties plus unselected material obtained from germplasm collections. Methods At each site populations were grown in field plots, then randomly sampled after 3–5 years to obtain survivor populations. AFLP markers were used to calculate genetic differentiation within and between original and survivor populations. Key Results No consistent changes in average genetic diversity were observed between original and survivor populations. In both species the original varieties were always genetically distinct from each other. Significant genetic shift was observed in the white clover ‘Ramona’ grown in Sweden. The WGB original populations were more genetically similar. However, genetic differentiation occurred between original and survivor WGB germplasm in both species, particularly in Sweden. Regression of climatic data with genetic differentiation showed that low autumn temperature was the best predictor. Within the set of cold sites the highest level of genetic shift in populations was observed in Sweden. Conclusions The results suggest that changes in population structure can occur within a short time span in forage legumes, resulting in the rapid formation of distinct survivor populations in environmentally challenging sites. PMID:22437665

  19. Utilizing the genetic diversity within rice cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant breeding of rice emphasizes improvement in yield, disease resistance, and milling quality. Numerous other traits (e.g., bran carotenoids) that historically have not been selected for could provide added value in expanding niche markets, as well as be useful tools for understanding the genetic ...

  20. Genetic Diversity and Genome Complexity of Sugarcane

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane (Saccharum spp.) as a C4 plant, is one of the most efficient crops in converting solar energy into chemical energy. Sugarcane cultivar improvement programs have not yet systematically utilized the most of the genetic sources of yield potential and resistance to stresses that may exist in t...

  1. Genetic Diversity of US Sheep Breeds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the genetic relationships between US sheep breeds is useful in developing conservation strategies and actions. A broad sampling of individual sheep from 28 breeds was performed. Breed types included: fine wool, meat types, long wool, hair, prolific, and fat tailed. Blood and semen samp...

  2. Genetic Diversity for Aluminum Tolerance in Sorghum

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Significant genetic variation for aluminum (Al) tolerance in many plant species has allowed the development of cultivars that are high yielding on acidic, Al toxic soils. However, knowledge of intraspecific variation for Al tolerance control is needed in order to assess the potential for further Al ...

  3. Global resources of genetic diversity in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Collecting and preserving genetic resources is critical in order to improve agricultural production around the world. Ensuring enough food to provide adequate nutrition for the global population is going to be a hugh challenge for plant breeders going forward as the human populations increases. Fa...

  4. Polishing the craft of genetic diversity creation in directed evolution.

    PubMed

    Tee, Kang Lan; Wong, Tuck Seng

    2013-12-01

    Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field. PMID:24012599

  5. Genotyping by sequencing reveals the genetic diversity of the USDA pisum diversity collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA expanded Pisum Single Plant (PSP) core collection is a unique resource that represents the breadth of the genetic diversity of the genus in an inbred format that facilitates genetic study. The collection includes inbred accessions from the refined pea core collection, parent lines of USDA r...

  6. Genetic Linkage Maps: Strategies, Resources and Achievements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This book chapter is for the sunflower volume in the Crop GGB (Genetics, Genomics and Breeding) Book Series. The book includes chapters covering basic information about the sunflower plant, germplasm diversity, classical genetics and traditional breeding, genome mapping, regulation of seed oil conte...

  7. Genetic diversity and genetic differentiation in Daphnia metapopulations with subpopulations of known age.

    PubMed

    Haag, Christoph R; Riek, Myriam; Hottinger, Jürgen W; Pajunen, V Ilmari; Ebert, Dieter

    2005-08-01

    If colonization of empty habitat patches causes genetic bottlenecks, freshly founded, young populations should be genetically less diverse than older ones that may have experienced successive rounds of immigration. This can be studied in metapopulations with subpopulations of known age. We studied allozyme variation in metapopulations of two species of water fleas (Daphnia) in the skerry archipelago of southern Finland. These populations have been monitored since 1982. Screening 49 populations of D. longispina and 77 populations of D. magna, separated by distances of 1.5-2180 m, we found that local genetic diversity increased with population age whereas pairwise differentiation among pools decreased with population age. These patterns persisted even after controlling for several potentially confounding ecological variables, indicating that extinction and recolonization dynamics decrease local genetic diversity and increase genetic differentiation in these metapopulations by causing genetic bottlenecks during colonization. We suggest that the effect of these bottlenecks may be twofold, namely decreasing genetic diversity by random sampling and leading to population-wide inbreeding. Subsequent immigration then may not only introduce new genetic material, but also lead to the production of noninbred hybrids, selection for which may cause immigrant alleles to increase in frequency, thus leading to increased genetic diversity in older populations. PMID:15937138

  8. Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

    PubMed Central

    Barik, Saumya Ranjan; Sahoo, Ambika; Mohapatra, Sudipti; Nayak, Deepak Kumar; Mahender, Anumalla; Meher, Jitandriya; Anandan, Annamalai

    2016-01-01

    Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance. PMID:27494320

  9. Genetic diversity and association mapping of bacterial blight and other horticulturally important traits with microsatellite markers in pomegranate from India.

    PubMed

    Singh, Nripendra Vikram; Abburi, Venkata Lakshmi; Ramajayam, D; Kumar, Ravinder; Chandra, Ram; Sharma, Kuldeep Kumar; Sharma, Jyotsana; Babu, K Dhinesh; Pal, Ram Krishna; Mundewadikar, Dhananjay M; Saminathan, Thangasamy; Cantrell, Robert; Nimmakayala, Padma; Reddy, Umesh K

    2015-08-01

    This genetic diversity study aimed to estimate the population structure and explore the use of association mapping strategies to identify linked markers for bacterial resistance, growth and fruit quality in pomegranate collections from India. In total, 88 accessions including 37 cultivated types were investigated. A total of 112 alleles were amplified by use of 44 publicly available microsatellites for estimating molecular genetic diversity and population structure. Neighbor-joining analysis, model-based population structure and principal component analysis corroborated the genetic relationships among wild-type and cultivated pomegranate collections from India. Our study placed all 88 germplasm into four clusters. We identified a cultivated clade of pomegranates in close proximity to Daru types of wild-type pomegranates that grow naturally near the foothills of the Himalayas. Admixture analysis sorted various lineages of cultivated pomegranates to their respective ancestral forms. We identified four linked markers for fruit weight, titratable acidity and bacterial blight severity. PGCT001 was found associated with both fruit weight and bacterial blight, and the association with fruit weight during both seasons analyzed was significant after Bonferroni correction. This research demonstrates effectiveness of microsatellites to resolve population structure among the wild and cultivar collection of pomegranates and future use for association mapping studies. PMID:25675870

  10. Genetic diversity and population differentiation of Sclerotinia sclerotiorum collected from canola in China and in USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic and phenotypic diversity and population differentiation of Sclerotinia sclerotiorum isolates infecting canola from China and the United States were investigated. Genetic diversity was assessed with eight microsatellite markers and mycelial compatibility groups (MCGs). Phenotypic diversity wa...

  11. Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae).

    PubMed

    Kwak, Myounghai; Gepts, Paul

    2009-03-01

    Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUCTURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F(ST), and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F(ST) value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race. PMID:19130029

  12. Genetic Diversity in the Interference Selection Limit

    PubMed Central

    Good, Benjamin H.; Walczak, Aleksandra M.; Neher, Richard A.; Desai, Michael M.

    2014-01-01

    Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics fails to account for interference between linked mutations, which grows increasingly severe as the density of selected polymorphisms increases. Here, we describe a simple limit that emerges when interference is common, in which the fitness effects of individual mutations play a relatively minor role. Instead, similar to models of quantitative genetics, molecular evolution is determined by the variance in fitness within the population, defined over an effectively asexual segment of the genome (a “linkage block”). We exploit this insensitivity in a new “coarse-grained” coalescent framework, which approximates the effects of many weakly selected mutations with a smaller number of strongly selected mutations that create the same variance in fitness. This approximation generates accurate and efficient predictions for silent site variability when interference is common. However, these results suggest that there is reduced power to resolve individual selection pressures when interference is sufficiently widespread, since a broad range of parameters possess nearly identical patterns of silent site variability. PMID:24675740

  13. Evaluation of genetic potential of the polyvoltine silkworm (Bombyx mori L.) germplasm and identification of parents for breeding programme*

    PubMed Central

    Rao, C.G.P.; Seshagiri, S.V.; Ramesh, C.; Ibrahim, Basha K.; Nagaraju, H.; Chandrashekaraiah

    2006-01-01

    In the present study, polyvoltine germplasm stock of Andhra Pradesh State Sericulture Research and Development, Institute (APSSRDI) was evaluated for its performance based on quantitative and qualitative traits. Twenty-one oval and 10 peanut cocoon shaped lines were reared in different seasons of the year. Since the polyvoltines are non-diapausing, six generations were reared and evaluated for various economically important traits based on evaluation index and sub-ordinate function statistical methods. Ten top ranked lines obtained by using both the methods were identified as potential parental strains. Among oval lines, APM14, APM11, APM18, APMW9, and APM19, and among peanut lines APMD5, APMD1, APMD3, APMD9 and APMD8 were selected as base material. The identified high yielding lines will be used in various breeding programmes as initial parents for the synthesis of superior polyvoltine breeds/hybrids. PMID:16502509

  14. Potato germplasm enhancement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Madison USDA-ARS Germplasm Enhancement Program focuses on the development of parents for breeding programs by putting novel valuable traits into adapted, fertile germplasm. The first germplasm release from this program is five clones with resistance to cold sweetening. These clones are named M1-...

  15. Genetic Diversity and Population Structure of Haemonchus contortus.

    PubMed

    Gilleard, J S; Redman, E

    2016-01-01

    Haemonchus contortus is one of the most successful and problematic livestock parasites worldwide. From its apparent evolutionary origins in sub-Saharan Africa, it is now found in small ruminants in almost all regions of the globe, and can infect a range of different domestic and wildlife artiodactyl hosts. It has a remarkably high propensity to develop resistance to anthelmintic drugs, making control increasingly difficult. The success of this parasite is, at least in part, due to its extremely high levels of genetic diversity that, in turn, provide a high adaptive capacity. Understanding this genetic diversity is important for many areas of research including anthelmintic resistance, epidemiology, control, drug/vaccine development and molecular diagnostics. In this article, we review the current knowledge of H. contortus genetic diversity and population structure for both field isolates and laboratory strains. We highlight the practical relevance of this knowledge with a particular emphasis on anthelmintic resistance research. PMID:27238002

  16. Inbreeding and genetic diversity analysis in a hatchery release population and clones of Rhopilema esculentum based on microsatellite markers

    NASA Astrophysics Data System (ADS)

    Tian, Tao; Chen, Zaizhong; Wang, Mosang; Hu, Yulong; Wang, Weiji

    2016-07-01

    Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye (Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed (H o) and expected (H e) heterozygosity ranged from 0.152 to 0.839 (mean=0.464) and from 0.235 to 0.821 (mean=0.618), respectively. The polymorphism information content (PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.

  17. Genetic Diversity among Ancient Nordic Populations

    PubMed Central

    Melchior, Linea; Lynnerup, Niels; Siegismund, Hans R.; Kivisild, Toomas; Dissing, Jørgen

    2010-01-01

    Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (∼2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture. PMID:20689597

  18. Genetic diversity of rhg1 and Rhg4 loci in wild soybeans resistant to soybean cyst nematode race 3.

    PubMed

    Yuan, C P; Wang, Y J; Zhao, H K; Zhang, L; Wang, Y M; Liu, X D; Zhong, X F; Dong, Y S

    2016-01-01

    Over-utilization of germplasms that are resistant to the soybean cyst nematode (SCN) in soybean breeding programs can lead to genetic vulnerability in resistant cultivars. Resistant wild soybean (Glycine soja) is considered an invaluable gene source for increasing the genetic diversity of SCN resistance. In this study, we genotyped 23 G. soja accessions that are resistant to SCN race 3 for polymorphisms in the resistance genes, rhg1, Rhg4, and SHMT, and investigated their genetic relationship with eight Glycine max resistant cultivars. We identified 89 single nucleotide polymorphisms (SNPs) and 11 DNA insertion-deletions (InDels), of which 70 SNPs and 8 InDels were found in rhg1, 9 SNPs were found in Rhg4, and 10 SNPs and 3 InDels were found in SHMT. Nucleotide diversity was π = 0.00238 and θ = 0.00235, and haplotype diversity was 1.000. A phylogenetic tree comprising four clusters was constructed using sequence variations of the 23 G. soja and 8 G. max resistant accessions. Five G. soja accessions in subcluster A2, and four G. soja accessions in cluster B were genetically distant from G. max genotypes. Eight resistance-associated SNPs in the three resistance genes formed nine haplotypes in total. G. soja resistant accessions had different haplotypes (H2, H4, H5, H6, H7, and H8) compared with those of G. max (H1, H3, and H9). These results provide vital information on the use of wild soybeans for broadening the genetic base of SCN resistance. PMID:27323148

  19. Genetic variation in transpiration efficiency and relationships between whole plant and leaf gas exchange measurements in Saccharum spp. and related germplasm.

    PubMed

    Jackson, Phillip; Basnayake, Jaya; Inman-Bamber, Geoff; Lakshmanan, Prakash; Natarajan, Sijesh; Stokes, Chris

    2016-02-01

    Fifty-one genotypes of sugarcane (Saccharum spp.) or closely related germplasm were evaluated in a pot experiment to examine genetic variation in transpiration efficiency. Significant variation in whole plant transpiration efficiency was observed, with the difference between lowest and highest genotypes being about 40% of the mean. Leaf gas exchange measurements were made across a wide range of conditions. There was significant genetic variation in intrinsic transpiration efficiency at a leaf level as measured by leaf internal CO2 (Ci) levels. Significant genetic variation in Ci was also observed within subsets of data representing narrow ranges of stomatal conductance. Ci had a low broad sense heritability (Hb = 0.11) on the basis of single measurements made at particular dates, because of high error variation and genotype × date interaction, but broad sense heritability for mean Ci across all dates was high (Hb = 0.81) because of the large number of measurements taken at different dates. Ci levels among genotypes at mid-range levels of conductance had a strong genetic correlation (-0.92 ± 0.30) with whole plant transpiration efficiency but genetic correlations between Ci and whole plant transpiration efficiency were weaker or not significant at higher and lower levels of conductance. Reduced Ci levels at any given level of conductance may result in improved yields in water-limited environments without trade-offs in rates of water use and growth. Targeted selection and improvement of lowered Ci per unit conductance via breeding may provide longer-term benefits for water-limited environments but the challenge will be to identify a low-cost screening methodology. PMID:26628517

  20. Genetic variation in transpiration efficiency and relationships between whole plant and leaf gas exchange measurements in Saccharum spp. and related germplasm

    PubMed Central

    Jackson, Phillip; Basnayake, Jaya; Inman-Bamber, Geoff; Lakshmanan, Prakash; Natarajan, Sijesh; Stokes, Chris

    2016-01-01

    Fifty-one genotypes of sugarcane (Saccharum spp.) or closely related germplasm were evaluated in a pot experiment to examine genetic variation in transpiration efficiency. Significant variation in whole plant transpiration efficiency was observed, with the difference between lowest and highest genotypes being about 40% of the mean. Leaf gas exchange measurements were made across a wide range of conditions. There was significant genetic variation in intrinsic transpiration efficiency at a leaf level as measured by leaf internal CO2 (Ci) levels. Significant genetic variation in Ci was also observed within subsets of data representing narrow ranges of stomatal conductance. Ci had a low broad sense heritability (Hb = 0.11) on the basis of single measurements made at particular dates, because of high error variation and genotype × date interaction, but broad sense heritability for mean Ci across all dates was high (Hb = 0.81) because of the large number of measurements taken at different dates. Ci levels among genotypes at mid-range levels of conductance had a strong genetic correlation (−0.92 ± 0.30) with whole plant transpiration efficiency but genetic correlations between Ci and whole plant transpiration efficiency were weaker or not significant at higher and lower levels of conductance. Reduced Ci levels at any given level of conductance may result in improved yields in water-limited environments without trade-offs in rates of water use and growth. Targeted selection and improvement of lowered Ci per unit conductance via breeding may provide longer-term benefits for water-limited environments but the challenge will be to identify a low-cost screening methodology. PMID:26628517

  1. Evaluation of soybean germplasm conserved in NIAS genebank and development of mini core collections

    PubMed Central

    Kaga, Akito; Shimizu, Takehiko; Watanabe, Satoshi; Tsubokura, Yasutaka; Katayose, Yuichi; Harada, Kyuya; Vaughan, Duncan A.; Tomooka, Norihiko

    2012-01-01

    Genetic variation and population structure among 1603 soybean accessions, consisted of 832 Japanese landraces, 109 old and 57 recent Japanese varieties, 341 landrace from 16 Asian countries and 264 wild soybean accessions, were characterized using 191 SNP markers. Although gene diversity of Japanese soybean germplasm was slight lower than that of exotic soybean germplasm, population differentiation and clustering analyses indicated clear genetic differentiation among Japanese cultivated soybeans, exotic cultivated soybeans and wild soybeans. Nine hundred ninety eight Japanese accessions were separated to a certain extent into groups corresponding to their agro-morphologic characteristics such as photosensitivity and seed characteristics rather than their geographical origin. Based on the assessment of the SNP markers and several agro-morphologic traits, accessions that retain gene diversity of the whole collection were selected to develop several soybean sets of different sizes using an heuristic approach; a minimum of 12 accessions can represent the observed gene diversity; a mini-core collection of 96 accession can represent a major proportion of both geographic origin and agro-morphologic trait variation. These selected sets of germplasm will provide an effective platform for enhancing soybean diversity studies and assist in finding novel traits for crop improvement. PMID:23136496

  2. Assessment of genetic diversity in Brazilian barley using SSR markers

    PubMed Central

    Ferreira, Jéssica Rosset; Pereira, Jorge Fernando; Turchetto, Caroline; Minella, Euclydes; Consoli, Luciano; Delatorre, Carla Andréa

    2016-01-01

    Abstract Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs. PMID:27007902

  3. Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis

    PubMed Central

    Chan, Agnes P.; Williams, Amber L.; Rice, Danny W.; Liu, Xinyue; Melake-Berhan, Admasu; Huot Creasy, Heather; Puiu, Daniela; Rosovitz, M. J.; Khouri, Hoda M.; Beckstrom-Sternberg, Stephen M.; Allan, Gerard J.; Keim, Paul; Ravel, Jacques; Rabinowicz, Pablo D.

    2011-01-01

    Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade. PMID:21750729

  4. Genetic diversity and differentiation of Mongolian and Russian yak populations.

    PubMed

    Xuebin, Q; Jianlin, H; Lkhagva, B; Chekarova, I; Badamdorj, D; Rege, J E O; Hanotte, O

    2005-04-01

    In this study we examined the genetic diversity of yak populations in the northernmost part of their current global distribution. Five Mongolian and one Russian yak populations as well as one Chinese yak population from the Qinghai-Tibetan Plateau, the putative centre of yak domestication, were analysed with 15 microsatellite loci to determine the level of genetic variation within populations as well as the genetic differentiation and relationship between populations. A total of 116 microsatellite alleles were identified. The mean number of alleles per locus (MNA) across populations was 7.73 +/- 1.98 and the mean expected heterozygosity (HE) was 0.696 +/- 0.026. The relative magnitude of gene differentiation (F(ST)) among populations was 4.1%, and all genetic differentiations (F(ST)) between populations were significant (p < 0.001). A significant inbreeding effect (F(IS)) was detected in the Hovsgol yak (p < 0.01). There was no indication of a recent bottleneck in any of the populations studied. The results showed that yak populations in Mongolia and Russia have maintained high genetic diversity within populations and a low, although significant, genetic differentiation between populations. Both phylogenetic and principal component analyses support a close genetic relationship between the Gobi Altai, south Gobi and north Hangai populations, and between the Hovsgol and Buryatia populations respectively. Our results indicate that these yak populations should be considered as distinct genetic entities in respect of conservation and breeding programmes. PMID:16130478

  5. Roads, interrupted dispersal, and genetic diversity in timber rattlesnakes.

    PubMed

    Clark, Rulon W; Brown, William S; Stechert, Randy; Zamudio, Kelly R

    2010-08-01

    Anthropogenic habitat modification often creates barriers to animal movement, transforming formerly contiguous habitat into a patchwork of habitat islands with low connectivity. Roadways are a feature of most landscapes that can act as barriers or filters to migration among local populations. Even small and recently constructed roads can have a significant impact on population genetic structure of some species, but not others. We developed a research approach that combines fine-scale molecular genetics with behavioral and ecological data to understand the impacts of roads on population structure and connectivity. We used microsatellite markers to characterize genetic variation within and among populations of timber rattlesnakes (Crotalus horridus) occupying communal hibernacula (dens) in regions bisected by roadways. We examined the impact of roads on seasonal migration, genetic diversity, and gene flow among populations. Snakes in hibernacula isolated by roads had significantly lower genetic diversity and higher genetic differentiation than snakes in hibernacula in contiguous habitat. Genetic-assignment analyses revealed that interruption to seasonal migration was the mechanism underlying these patterns. Our results underscore the sizeable impact of roads on this species, despite their relatively recent construction at our study sites (7 to 10 generations of rattlesnakes), the utility of population genetics for studies of road ecology, and the need for mitigating effects of roads. PMID:20151984

  6. Indian Plant Germplasm on the Global Platter: An Analysis

    PubMed Central

    Jacob, Sherry R.; Tyagi, Vandana; Agrawal, Anuradha; Chakrabarty, Shyamal K.; Tyagi, Rishi K.

    2015-01-01

    , about 50% of the Indian-origin accessions deposited in SGSV are traditional varieties or landraces with defined traits which form the backbone of any crop gene pool. This paper is also attempting to correlate the global data on Indian-origin germplasm with the national germplasm export profile. The analysis from this paper is discussed with the perspective of possible implications in the access and benefit sharing regime of both the International Treaty on Plant Genetic Resources for Food and Agriculture and the newly enforced Nagoya Protocol under the Convention on Biological Diversity. PMID:25974270

  7. Indian plant germplasm on the global platter: an analysis.

    PubMed

    Jacob, Sherry R; Tyagi, Vandana; Agrawal, Anuradha; Chakrabarty, Shyamal K; Tyagi, Rishi K

    2015-01-01

    , about 50% of the Indian-origin accessions deposited in SGSV are traditional varieties or landraces with defined traits which form the backbone of any crop gene pool. This paper is also attempting to correlate the global data on Indian-origin germplasm with the national germplasm export profile. The analysis from this paper is discussed with the perspective of possible implications in the access and benefit sharing regime of both the International Treaty on Plant Genetic Resources for Food and Agriculture and the newly enforced Nagoya Protocol under the Convention on Biological Diversity. PMID:25974270

  8. Genetic Diversity and Population Structure of Teosinte

    PubMed Central

    Fukunaga, Kenji; Hill, Jason; Vigouroux, Yves; Matsuoka, Yoshihiro; Sanchez G., Jesus; Liu, Kejun; Buckler, Edward S.; Doebley, John

    2005-01-01

    The teosintes, the closest wild relatives of maize, are important resources for the study of maize genetics and evolution and for plant breeding. We genotyped 237 individual teosinte plants for 93 microsatellites. Phylogenetic relationships among species and subspecific taxa were largely consistent with prior analyses for other types of molecular markers. Plants of all species formed monophyletic clades, although relationships among species were not fully resolved. Phylogenetic analysis indicated that the Mexican annual teosintes divide into two clusters that largely correspond to the previously defined subspecies, Z. mays ssp. parviglumis and ssp. mexicana, although there are a few samples that represent either evolutionary intermediates or hybrids between these two subspecies. The Mexican annual teosintes show genetic substructuring along geographic lines. Hybridization or introgression between some teosintes and maize occurs at a low level and appears most common with Z. mays ssp. mexicana. Phylogeographic and phylogenetic analyses of the Mexican annual teosintes indicated that ssp. parviglumis diversified in the eastern part of its distribution and spread from east to west and that ssp. mexicana diversified in the Central Plateau of Mexico and spread along multiple paths to the north and east. We defined core sets of collections of Z. mays ssp. mexicana and ssp. parviglumis that attempt to capture the maximum number of microsatellite alleles for given sample sizes. PMID:15687282

  9. Genetic diversity of and differentiation among five populations of blunt snout bream (Megalobrama amblycephala) revealed by SRAP markers: implications for conservation and management.

    PubMed

    Ji, Wei; Zhang, Gui-Rong; Ran, Wei; Gardner, Jonathan P A; Wei, Kai-Jian; Wang, Wei-Min; Zou, Gui-Wei

    2014-01-01

    The blunt snout bream (Megalobrama amblycephala) is an important freshwater aquaculture fish throughout China. Because of widespread introductions of this species to many regions, the genetic diversity of wild and natural populations is now threatened. In the present study, SRAP (sequence-related amplified polymorphism) markers were used to assess genetic diversity of blunt snout bream. Three natural populations (Liangzi Lake, Poyang Lake and Yuni Lake, one cultured population (Nanxian) and one genetic strain ('Pujiang No. 1') of blunt snout bream were screened with 88 SRAP primer combinations, of which 13 primer pairs produced stable and reproducible amplification patterns. In total, 172 bands were produced, of which 132 bands were polymorphic. Nei's gene diversity (h) and Shannon's information index (I) values provided evidence of differences in genetic diversity among the five populations (Poyang Lake>Liangzi Lake>Nanxian>'Pujiang No. 1'>Yuni Lake). Based on cluster analysis conducted on genetic distance values, the five blunt snout bream populations were divided into three groups, Poyang Lake and Liangzi Lake (natural populations), Nanxian and 'Pujiang No. 1' (cultured population and genetically selected strain), and Yuni Lake (natural population). Significant genetic differentiation was found among the five populations using analysis of molecular variance (AMOVA), with more genetic divergence existing among populations (55.49%), than within populations (44.51%). This molecular marker technique is a simple and efficient method to quantify genetic diversity within and among fish populations, and is employed here to help manage and conserve germplasm variability of blunt snout bream and to support the ongoing selective breeding programme for this fish. PMID:25265288

  10. Genetic Diversity of and Differentiation among Five Populations of Blunt Snout Bream (Megalobrama amblycephala) Revealed by SRAP Markers: Implications for Conservation and Management

    PubMed Central

    Ran, Wei; Gardner, Jonathan P. A.; Wei, Kai-Jian; Wang, Wei-Min; Zou, Gui-Wei

    2014-01-01

    The blunt snout bream (Megalobrama amblycephala) is an important freshwater aquaculture fish throughout China. Because of widespread introductions of this species to many regions, the genetic diversity of wild and natural populations is now threatened. In the present study, SRAP (sequence-related amplified polymorphism) markers were used to assess genetic diversity of blunt snout bream. Three natural populations (Liangzi Lake, Poyang Lake and Yuni Lake, one cultured population (Nanxian) and one genetic strain (‘Pujiang No. 1’) of blunt snout bream were screened with 88 SRAP primer combinations, of which 13 primer pairs produced stable and reproducible amplification patterns. In total, 172 bands were produced, of which 132 bands were polymorphic. Nei's gene diversity (h) and Shannon's information index (I) values provided evidence of differences in genetic diversity among the five populations (Poyang Lake>Liangzi Lake>Nanxian>‘Pujiang No. 1’>Yuni Lake). Based on cluster analysis conducted on genetic distance values, the five blunt snout bream populations were divided into three groups, Poyang Lake and Liangzi Lake (natural populations), Nanxian and ‘Pujiang No. 1’ (cultured population and genetically selected strain), and Yuni Lake (natural population). Significant genetic differentiation was found among the five populations using analysis of molecular variance (AMOVA), with more genetic divergence existing among populations (55.49%), than within populations (44.51%). This molecular marker technique is a simple and efficient method to quantify genetic diversity within and among fish populations, and is employed here to help manage and conserve germplasm variability of blunt snout bream and to support the ongoing selective breeding programme for this fish. PMID:25265288

  11. Mitochondrial DNA perspective of Serbian genetic diversity.

    PubMed

    Davidovic, Slobodan; Malyarchuk, Boris; Aleksic, Jelena M; Derenko, Miroslava; Topalovic, Vladanka; Litvinov, Andrey; Stevanovic, Milena; Kovacevic-Grujicic, Natasa

    2015-03-01

    Although south-Slavic populations have been studied to date from various aspects, the population of Serbia, occupying the central part of the Balkan Peninsula, is still genetically understudied at least at the level of mitochondrial DNA (mtDNA) variation. We analyzed polymorphisms of the first and the second mtDNA hypervariable segments (HVS-I and HVS-II) and informative coding-region markers in 139 Serbians to shed more light on their mtDNA variability, and used available data on other Slavic and neighboring non-Slavic populations to assess their interrelations in a broader European context. The contemporary Serbian mtDNA profile is consistent with the general European maternal landscape having a substantial proportion of shared haplotypes with eastern, central, and southern European populations. Serbian population was characterized as an important link between easternmost and westernmost south-Slavic populations due to the observed lack of genetic differentiation with all other south-Slavic populations and its geographical positioning within the Balkan Peninsula. An increased heterogeneity of south Slavs, most likely mirroring turbulent demographic events within the Balkan Peninsula over time (i.e., frequent admixture and differential introgression of various gene pools), and a marked geographical stratification of Slavs to south-, east-, and west-Slavic groups, were also found. A phylogeographic analyses of 20 completely sequenced Serbian mitochondrial genomes revealed not only the presence of mtDNA lineages predominantly found within the Slavic gene pool (U4a2a*, U4a2a1, U4a2c, U4a2g, HV10), supporting a common Slavic origin, but also lineages that may have originated within the southern Europe (H5*, H5e1, H5a1v) and the Balkan Peninsula in particular (H6a2b and L2a1k). PMID:25418795

  12. Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla)

    PubMed Central

    Hao, Wei; Wang, Shengji; Liu, Huajing; Zhou, Boru; Wang, Xinwang; Jiang, Tingbo

    2015-01-01

    In order to study genetic diversity of white birch (Betula platyphylla), 544 primer pairs were designed based on the genome-wide Solexa sequences. Among them, 215 primer pairs showed polymorphism between five genotypes and 111 primer pairs that presented clear visible bands in genotyping 41 white birch plants that were collected from 6 different geographical regions. A total of 717 alleles were obtained at 111 loci with a range of 2 to 12 alleles per locus. The results of statistic analysis showed that polymorphic frequency of the alleles ranged from 17% to 100% with a mean of 55.85%; polymorphism information content (PIC) of the loci was from 0.09 to 0.58 with a mean of 0.30; and gene diversity between the tested genotypes was from 0.01 to 0.66 with a mean of 0.36. The results also indicated that major allele frequency ranged from 0.39 to 1.00 with an mean of 0.75; expected heterozygosity from 0.22 to 0.54 with a mean of 0.46; observed heterozygosity from 0.02 to 0.95 with a mean of 0.26; Nei's index from 0.21 to 0.54 with a mean of 0.46; and Shannon's Information from 0.26 to 0.87 with a mean of 0.66. The 41 white birch genotypes at the 111 selected SSR loci showed low to moderate similarity (0.025-0.610), indicating complicated genetic diversity among the white birch collections. The UPGMA-based clustering analysis of the allelic constitution of 41 white birch genotypes at 111 SSR loci suggested that the six different geographical regions can be further separated into four clusters at a similarity coefficient of 0.22. Genotypes from Huanren and Liangshui provenances were grouped into Cluster I, genotypes from Xiaobeihu and Qingyuan provenances into Cluster II, genotypes from Finland provenance into Cluster III, and genotypes from Maoershan into Cluster IV. The information provided in this study could help for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program. PMID:25923698

  13. Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla).

    PubMed

    Hao, Wei; Wang, Shengji; Liu, Huajing; Zhou, Boru; Wang, Xinwang; Jiang, Tingbo

    2015-01-01

    In order to study genetic diversity of white birch (Betula platyphylla), 544 primer pairs were designed based on the genome-wide Solexa sequences. Among them, 215 primer pairs showed polymorphism between five genotypes and 111 primer pairs that presented clear visible bands in genotyping 41 white birch plants that were collected from 6 different geographical regions. A total of 717 alleles were obtained at 111 loci with a range of 2 to 12 alleles per locus. The results of statistic analysis showed that polymorphic frequency of the alleles ranged from 17% to 100% with a mean of 55.85%; polymorphism information content (PIC) of the loci was from 0.09 to 0.58 with a mean of 0.30; and gene diversity between the tested genotypes was from 0.01 to 0.66 with a mean of 0.36. The results also indicated that major allele frequency ranged from 0.39 to 1.00 with an mean of 0.75; expected heterozygosity from 0.22 to 0.54 with a mean of 0.46; observed heterozygosity from 0.02 to 0.95 with a mean of 0.26; Nei's index from 0.21 to 0.54 with a mean of 0.46; and Shannon's Information from 0.26 to 0.87 with a mean of 0.66. The 41 white birch genotypes at the 111 selected SSR loci showed low to moderate similarity (0.025-0.610), indicating complicated genetic diversity among the white birch collections. The UPGMA-based clustering analysis of the allelic constitution of 41 white birch genotypes at 111 SSR loci suggested that the six different geographical regions can be further separated into four clusters at a similarity coefficient of 0.22. Genotypes from Huanren and Liangshui provenances were grouped into Cluster I, genotypes from Xiaobeihu and Qingyuan provenances into Cluster II, genotypes from Finland provenance into Cluster III, and genotypes from Maoershan into Cluster IV. The information provided in this study could help for genetic improvement and germplasm conservation, evaluation and utilization in white birch tree breeding program. PMID:25923698

  14. Genetic diversity and conservation in a small endangered horse population.

    PubMed

    Janova, Eva; Futas, Jan; Klumplerova, Marie; Putnova, Lenka; Vrtkova, Irena; Vyskocil, Mirko; Frolkova, Petra; Horin, Petr

    2013-08-01

    The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes and one major histocompatibility (MHC-DRA) gene were studied for assessing genetic diversity after 15 years of conservation. The results were compared to values obtained in a similar study 13 years ago. The extent of genetic diversity of the current population was comparable to other breeds, despite its small size and isolation. The comparison between 1997 and 2010 did not show differences in the extent of genetic diversity and no loss of allele richness and/or heterozygosity was observed. Genetic differences identified between the black and grey sub-populations observed 13 years ago persisted. Deviations from the Hardy-Weinberg equilibrium found in 19 microsatellite loci and in five SNP loci are probably due to selective breeding. No differences between neutral and immunity-related markers were found. No changes in the frequencies of markers associated with two diseases, melanoma and insect bite hypersensitivity, were observed, due probably to the short interval of time between comparisons. It, thus, seems that, despite its small size, previous bottlenecks and inbreeding, the molecular variation of Old Kladruber horses is comparable to other horse breeds and that the current breeding policy does not compromise genetic variation of this endangered population. PMID:23649723

  15. Genetic diversity of Kenyan native oyster mushroom (Pleurotus).

    PubMed

    Otieno, Ojwang D; Onyango, Calvin; Onguso, Justus Mungare; Matasyoh, Lexa G; Wanjala, Bramwel W; Wamalwa, Mark; Harvey, Jagger J W

    2015-01-01

    Members of the genus Pleurotus, also commonly known as oyster mushroom, are well known for their socioeconomic and biotechnological potentials. Despite being one of the most important edible fungi, the scarce information about the genetic diversity of the species in natural populations has limited their sustainable utilization. A total of 71 isolates of Pleurotus species were collected from three natural populations: 25 isolates were obtained from Kakamega forest, 34 isolates from Arabuko Sokoke forest and 12 isolates from Mount Kenya forest. Amplified fragment length polymorphism (AFLP) was applied to thirteen isolates of locally grown Pleurotus species obtained from laboratory samples using five primer pair combinations. AFLP markers and internal transcribed spacer (ITS) sequences of the ribosomal DNA were used to estimate the genetic diversity and evaluate phylogenetic relationships, respectively, among and within populations. The five primer pair combinations generated 293 polymorphic loci across the 84 isolates. The mean genetic diversity among the populations was 0.25 with the population from Arabuko Sokoke having higher (0.27) diversity estimates compared to Mount Kenya population (0.24). Diversity between the isolates from the natural population (0.25) and commercial cultivars (0.24) did not differ significantly. However, diversity was greater within (89%; P > 0.001) populations than among populations. Homology search analysis against the GenBank database using 16 rDNA ITS sequences randomly selected from the two clades of AFLP dendrogram revealed three mushroom species: P. djamor, P. floridanus and P. sapidus; the three mushrooms form part of the diversity of Pleurotus species in Kenya. The broad diversity within the Kenyan Pleurotus species suggests the possibility of obtaining native strains suitable for commercial cultivation. PMID:25344263

  16. Assessment of genetic diversity of sweet potato in Puerto Rico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sweet potato (Ipomoea batatas L.) is the seventh most important food crop due to its distinct advantages, such as adaptability to different environmental conditions and high nutritional value. Assessing the genetic diversity of this important crop is necessary due to the constant increase of demand ...

  17. Genetic diversity and differentiation of Pseudophoenix (Arecaceae) in Hispaniola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Technical Abstract Pseudophoenix ekmanii Burret, P. lediniana Read, and P. vinifera (Mart.) Becc. (Arecaceae) are endemic to Hispaniola. The more wide-ranging P. sargentii H.Wendl. ex Sarg. occurs on this island as well. The population genetic diversity and structure of Pseudophoenix was investigate...

  18. Bovine Genetic Diversity Revealed By mtDNA Sequence Variation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mitochondrial DNA single nucleotide polymorphism (SNP) data were used to determine genetic distance, nucleotide diversity, construction of haplotypes, estimation of information contents, and phylogenic relationships in bovine HapMap breeds. The Bovine International HapMap panel consists of 720 anima...

  19. Estimation of genetic diversity using SSR markers in sunflower

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sunflower is a major oilseed crop in central Asia, but little is known of the molecular diversity among collections of sunflower from Pakistan region. This paper described inherent genetic relationships among sunflower collections using Simple Sequence Repeat molecular markers. Results should help...

  20. Parasites and genetic diversity in an invasive bumblebee

    PubMed Central

    Jones, Catherine M; Brown, Mark J F; Ings, Thomas

    2014-01-01

    Biological invasions are facilitated by the global transportation of species and climate change. Given that invasions may cause ecological and economic damage and pose a major threat to biodiversity, understanding the mechanisms behind invasion success is essential. Both the release of non-native populations from natural enemies, such as parasites, and the genetic diversity of these populations may play key roles in their invasion success. We investigated the roles of parasite communities, through enemy release and parasite acquisition, and genetic diversity in the invasion success of the non-native bumblebee, Bombus hypnorum, in the United Kingdom. The invasive B. hypnorum had higher parasite prevalence than most, or all native congeners for two high-impact parasites, probably due to higher susceptibility and parasite acquisition. Consequently parasites had a higher impact on B. hypnorum queens’ survival and colony-founding success than on native species. Bombus hypnorum also had lower functional genetic diversity at the sex-determining locus than native species. Higher parasite prevalence and lower genetic diversity have not prevented the rapid invasion of the United Kingdom by B. hypnorum. These data may inform our understanding of similar invasions by commercial bumblebees around the world. This study suggests that concerns about parasite impacts on the small founding populations common to re-introduction and translocation programs may be less important than currently believed. PMID:24749545

  1. Genetic diversity within and between natural populations of Rattus norvegicus.

    PubMed

    Cramer, D V; Chakravarti, A; Arenas, O; Humprieres, J; Mowery, P A

    1988-01-01

    The levels of gene diversity for 17 polymorphic loci in natural populations of wild rats were examined for three separate locations in North and South America. The level of gene diversity in the total sample for the RT1.A locus, the dominant class I histocompatibility locus in the major histocompatibility (RT1) complex of the rat, was 0.807. The degree of gene diversity for nonalloantigenic loci scattered throughout the rat genome was 0.215, a level comparable to, if not slightly higher than, that for other mammalian species. The large and consistent levels of diversity for individuals within each population suggest that significant deviations from random mating have occurred within each group. Conclusions from analyzing genetic distance and the index of genetic differentiation between the three populations are consistent with these populations' geographic isolation and small effective population size. Assuming that the separation of the North and South American groups has existed for approximately 300 years, the effective size of these populations is estimated to be approximately 1,500 individuals. Apparent differences in the distribution of the number and frequency of alleles in the major histocompatibility complexes of mice and rats and the level of genetic differentiation among separate rat populations may be due to the effects of genetic drift in small populations. PMID:3183358

  2. Population genetic structure and genetic diversity of soybean aphids from USA, Korea and Japan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Following its recent invasion of North America, the soybean aphid (Aphis glycines Matsumura) has become the number one insect pest of soybean (Glycine max L. Merr.) in the north central states of USA. Very little is known about the population genetic structure and genetic diversity of the soybean ap...

  3. Genetic variation for agronomic and fiber quality traits in a population derived from high-quality cotton germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic improvement of fiber quality is necessary to meet the requirements of processors and users of cotton fiber. To foster genetic improvement of cotton fiber quality, adequate genetic variation for the quantitatively inherited physical properties of cotton is required. Additionally, knowledge of...

  4. Relationships Between Oases and Germplasm Collections

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Traditional date palm oases have served as conservators of date palm genetic resources. There have been only a few studies on the population structure of these oases or evaluations of non-fruit-related characteristics. A system is needed in which regional germplasm repositories for date palm genetic...

  5. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems

    PubMed Central

    van der Meer, Sascha; Jacquemyn, Hans

    2015-01-01

    Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68), which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G”ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively) and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands. PMID:26079603

  6. Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

    PubMed

    Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

    2015-01-01

    Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species. PMID:26662418

  7. Polyphenols in whole rice grain: genetic diversity and health benefits.

    PubMed

    Shao, Yafang; Bao, Jinsong

    2015-08-01

    Polyphenols, such as phenolic acid, anthocyanin and proanthocyanidins, have both nutraceutical properties and functional significance for human health. Identification of polyphenolic compounds and investigation of their genetic basis among diverse rice genotypes provides the basis for the improvement of the nutraceutical properties of whole rice grain. This review focuses on current information on the identification, genetic diversity, formation and distribution patterns of the phenolic acid, anthocyanin, and proanthocyanidins in whole rice grain. The genetic analysis of polyphenol content and antioxidant capacity allows the identification of several candidate genes or quantitative trait loci (QTL) responsible for polyphenol variation, which may be useful in improvement of these phytochemicals by breeding. Future challenges such as how to mitigate the effects of climate change while improving nutraceutical properties in whole grain, and how to use new technology to develop new rice high in nutraceutical properties are also presented. PMID:25766805

  8. Synthetic biology: advancing the design of diverse genetic systems

    PubMed Central

    Wang, Yen-Hsiang; Wei, Kathy Y.; Smolke, Christina D.

    2013-01-01

    A main objective of synthetic biology is to make the process of designing genetically-encoded biological systems more systematic, predictable, robust, scalable, and efficient. The examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from a simple genetic switch to search-and-destroy systems. While significant advances in synthesis capabilities support the potential for the implementation of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Synthetic biology offers much promise in developing systems to address challenges faced in manufacturing, the environment and sustainability, and health and medicine, but the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems. PMID:23413816

  9. [Screening of peafowl microsatellite primers and analysis of genetic diversity].

    PubMed

    Bao, Wen-Bin; Chen, Guo-Hong; Shu, Jing-Ting; Xu, Qi; Li, Hui-Fang

    2006-10-01

    The applicability of chicken microsatellite primers to peafowl population was analyzed in the present paper, and the results showed 14 of 29 pairs of microsatellite primers from chicken could amplify peafowl DNA and produce specific allele patterns. A mean of 1.71 alleles was found for each locus. Seven pairs were highly polymorphic, and MCW0080 and MCW0098 were ideal markers for peafowl. Genetic diversity analysis within and between the green peafowl and the blue peafowl populations demonstrated that the expected heterozygosity of two peafowl populations were 0.2482 and 0.2744, respectively. The inbreeding index (FST), Reynolds' genetic distance and gene flow between the two populations were 0.078, 0.0603 and 3.896 respectively. These results indicate that the heterozygosity and the genetic diversity of these two peafowl populations were very low, and suggest a tendency towards intermixing. PMID:17035182

  10. Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest

    PubMed Central

    Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

    2016-01-01

    A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community. PMID:26860815

  11. Soil properties drive a negative correlation between species diversity and genetic diversity in a tropical seasonal rainforest.

    PubMed

    Xu, Wumei; Liu, Lu; He, Tianhua; Cao, Min; Sha, Liqing; Hu, Yuehua; Li, Qiaoming; Li, Jie

    2016-01-01

    A negative species-genetic diversity correlation (SGDC) could be predicted by the niche variation hypothesis, whereby an increase in species diversity within community reduces the genetic diversity of the co-occurring species because of the reduction in average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of the species within community. We tested these predictions within a 20 ha tropical forest dynamics plot (FDP) in the Xishuangbanna tropical seasonal rainforest. We established 15 plots within the FDP and investigated the soil properties, tree diversity, and genetic diversity of a common tree species Beilschmiedia roxburghiana within each plot. We observed a significant negative correlation between tree diversity and the genetic diversity of B. roxburghiana within the communities. Using structural equation modeling, we further determined that the inter-plot environmental characteristics (soil pH and phosphorus availability) directly affected tree diversity and that the tree diversity within the community determined the genetic diversity of B. roxburghiana. Increased soil pH and phosphorus availability might promote the coexistence of more tree species within community and reduce genetic diversity of B. roxburghiana for the reduced average niche breadth; alternatively, competition could reduce effective population size and therefore genetic diversity of B. roxburghiana within community. PMID:26860815

  12. Expansion of the USDA-ARS Germplasm Resources Information Network (GRIN) database to accommodate molecular data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-ARS National Plant Germplasm System (NPGS) provides both germplasm and data on genetic resources to researchers and breeders world wide. New tables and codes that hold data relating to molecular markers and multi-locus genotypes have been added to the Germplasm Resources Information Networ...

  13. RECOVERY OF EXOTIC ALLELES IN ENHANCED TROPICAL YELLOW GERMPLASM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enhancement of overall diversity levels and the incorporation of new favorable traits are major benefits of using exotic germplasm in elite breeding programs. Agronomic deficiencies and poor adaptation often limits use of exotic germplasm in plant breeding programs. To introgress exotic alleles into...

  14. Recovery of Exotic Alleles in Enhanced Tropical Yellow Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Enhancement of overall diversity levels and the incorporation of new favorable traits are major benefits of using exotic germplasm in elite breeding programs. Agronomic deficiencies and poor adaptation often limits use of exotic germplasm in plant breeding programs. To introgress exotic alleles into...

  15. Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic diversity present in crop landraces represents a valuable genetic resource for breeding and genetic studies. Bottle gourd (Lagenaria siceraria) landraces in Turkey are highly genetically diverse. However, the limited genomic resources available for this crop hinder the molecular characte...

  16. Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene.

    PubMed

    Martin, Simon H; Möst, Markus; Palmer, William J; Salazar, Camilo; McMillan, W Owen; Jiggins, Francis M; Jiggins, Chris D

    2016-05-01

    A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects. PMID:27017626

  17. Extraordinary Genetic Diversity in a Wood Decay Mushroom.

    PubMed

    Baranova, Maria A; Logacheva, Maria D; Penin, Aleksey A; Seplyarskiy, Vladimir B; Safonova, Yana Y; Naumenko, Sergey A; Klepikova, Anna V; Gerasimov, Evgeny S; Bazykin, Georgii A; James, Timothy Y; Kondrashov, Alexey S

    2015-10-01

    Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10(-8) (95% CI: 1.1 × 10(-8) to 4.1 × 10(-8)) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics. PMID:26163667

  18. Extraordinary Genetic Diversity in a Wood Decay Mushroom

    PubMed Central

    Baranova, Maria A.; Logacheva, Maria D.; Penin, Aleksey A.; Seplyarskiy, Vladimir B.; Safonova, Yana Y.; Naumenko, Sergey A.; Klepikova, Anna V.; Gerasimov, Evgeny S.; Bazykin, Georgii A.; James, Timothy Y.; Kondrashov, Alexey S.

    2015-01-01

    Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10−8 (95% CI: 1.1 × 10−8 to 4.1 × 10−8) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics. PMID:26163667

  19. Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

    PubMed Central

    Martin, Simon H.; Möst, Markus; Palmer, William J.; Salazar, Camilo; McMillan, W. Owen; Jiggins, Francis M.; Jiggins, Chris D.

    2016-01-01

    A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila. A more complete understanding of these forces will come from analyzing other taxa that differ in population demography and other aspects of biology. We have analyzed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of Heliconius melpomene and another 21 resequenced genomes representing 11 related species. By comparing intraspecific diversity and interspecific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as nonsynonymous substitutions and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial nonsynonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies, a fact that curiously results in very similar levels of neutral diversity in these very different insects. PMID:27017626

  20. Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach

    PubMed Central

    2010-01-01

    Background Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size. Results The thematic core collection obtained meets the minimum requirements for a core sample - maintenance of at least 80% of the allelic richness of the thematic collection, with, approximately, 15% of its size. The method was compared with other methodologies based on the M strategy, and also with a core collection generated by random sampling. Higher proportions of retained alleles (in a core collection of equal size) or similar proportions of retained alleles (in a core collection of smaller size) were detected in the two methods based on the M strategy compared to the proposed methodology. Core sub-collections constructed by different methods were compared regarding the increase or maintenance of phenotypic diversity. No change on phenotypic diversity was detected by measuring the trait "Weight of 100 Seeds", for the tested sampling methods. Effects on linkage disequilibrium between unlinked microsatellite loci, due to sampling, are discussed. Conclusions Building of a thematic core collection was here defined by prior selection of accessions which are diverse for the trait of interest, and then by pairwise genetic distances, estimated by DNA polymorphism analysis at molecular marker loci. The resulting thematic core collection potentially reflects the maximum

  1. Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

    PubMed Central

    Garzón-Martínez, Gina A.; Osorio-Guarín, Jaime A.; Delgadillo-Durán, Paola; Mayorga, Franklin; Enciso-Rodríguez, Felix E.; Landsman, David

    2015-01-01

    The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation FST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies. PMID:26550601

  2. Diversity of genetic backgrounds modulating the durability of a major resistance gene. Analysis of a core collection of pepper landraces resistant to Potato virus Y.

    PubMed

    Quenouille, Julie; Saint-Felix, Ludovic; Moury, Benoit; Palloix, Alain

    2016-02-01

    The evolution of resistance-breaking capacity in pathogen populations has been shown to depend on the plant genetic background surrounding the resistance genes. We evaluated a core collection of pepper (Capsicum annuum) landraces, representing the worldwide genetic diversity, for its ability to modulate the breakdown frequency by Potato virus Y of major resistance alleles at the pvr2 locus encoding the eukaryotic initiation factor 4E (eIF4E). Depending on the pepper landrace, the breakdown frequency of a given resistance allele varied from 0% to 52.5%, attesting to their diversity and the availability of genetic backgrounds favourable to resistance durability in the plant germplasm. The mutations in the virus genome involved in resistance breakdown also differed between plant genotypes, indicating differential selection effects exerted on the virus population by the different genetic backgrounds. The breakdown frequency was positively correlated with the level of virus accumulation, confirming the impact of quantitative resistance loci on resistance durability. Among these loci, pvr6, encoding an isoform of eIF4E, was associated with a major effect on virus accumulation and on the breakdown frequency of the pvr2-mediated resistance. This exploration of plant genetic diversity delivered new resources for the control of pathogen evolution and the increase in resistance durability. PMID:25967744

  3. Low genetic diversity in a marine nature reserve: re-evaluating diversity criteria in reserve design

    PubMed Central

    Bell, J.J; Okamura, B

    2005-01-01

    Little consideration has been given to the genetic composition of populations associated with marine reserves, as reserve designation is generally to protect specific species, communities or habitats. Nevertheless, it is important to conserve genetic diversity since it provides the raw material for the maintenance of species diversity over longer, evolutionary time-scales and may also confer the basis for adaptation to environmental change. Many current marine reserves are small in size and isolated to some degree (e.g. sea loughs and offshore islands). While such features enable easier management, they may have important implications for the genetic structure of protected populations, the ability of populations to recover from local catastrophes and the potential for marine reserves to act as sources of propagules for surrounding areas. Here, we present a case study demonstrating genetic differentiation, isolation, inbreeding and reduced genetic diversity in populations of the dogwhelk Nucella lapillus in Lough Hyne Marine Nature Reserve (an isolated sea lough in southern Ireland), compared with populations on the local adjacent open coast and populations in England, Wales and France. Our study demonstrates that this sea lough is isolated from open coast populations, and highlights that there may be long-term genetic consequences of selecting reserves on the basis of isolation and ease of protection. PMID:16024366

  4. Genetic diversity and phylogenetic relationship among Tunisian cactus species (Opuntia) as revealed by random amplified microsatellite polymorphism markers.

    PubMed

    Bendhifi Zarroug, M; Baraket, G; Zourgui, L; Souid, S; Salhi Hannachi, A

    2015-01-01

    Opuntia ficus indica is one of the most economically important species in the Cactaceae family. Increased interest in this crop stems from its potential contribution to agricultural diversification, application in the exploitation of marginal lands, and utility as additional income sources for farmers. In Tunisia, O. ficus indica has been affected by drastic genetic erosion resulting from biotic and abiotic stresses. Thus, it is imperative to identify and preserve this germplasm. In this study, we focused on the use of random amplified microsatellite polymorphisms to assess genetic diversity among 25 representatives of Tunisian Opuntia species maintained in the collection of the National Institute of Agronomic Research of Tunisia. Seventy-two DNA markers were screened to discriminate accessions using 16 successful primer combinations. The high percentage of polymorphic band (100%), the resolving power value (5.68), the polymorphic information content (0.94), and the marker index (7.2) demonstrated the efficiency of the primers tested. Therefore, appropriate cluster analysis used in this study illustrated a divergence among the cultivars studied and exhibited continuous variation that occurred independently of geographic origin. O. ficus indica accessions did not cluster separately from the other cactus pear species, indicating that their current taxonomical classifications are not well aligned with their genetic variability or locality of origin. PMID:25730081

  5. Genetic Diversity and Population Structure of Theileria annulata in Oman

    PubMed Central

    Al-Hamidhi, Salama; H. Tageldin, Mohammed.; Weir, William; Al-Fahdi, Amira; Johnson, Eugene H.; Bobade, Patrick; Alqamashoui, Badar; Beja-Pereira, Albano; Thompson, Joanne; Kinnaird, Jane; Shiels, Brian; Tait, Andy; Babiker, Hamza

    2015-01-01

    Background Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle. Methods Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman. Results We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise FST values being less than 0.03. Slightly higher FST values (GST

  6. Determinants of Genetic Diversity of Spontaneous Drug Resistance in Bacteria.

    PubMed

    Couce, Alejandro; Rodríguez-Rojas, Alexandro; Blázquez, Jesús

    2016-07-01

    Any pathogen population sufficiently large is expected to harbor spontaneous drug-resistant mutants, often responsible for disease relapse after antibiotic therapy. It is seldom appreciated, however, that while larger populations harbor more mutants, the abundance distribution of these mutants is expected to be markedly uneven. This is because a larger population size allows early mutants to expand for longer, exacerbating their predominance in the final mutant subpopulation. Here, we investigate the extent to which this reduction in evenness can constrain the genetic diversity of spontaneous drug resistance in bacteria. Combining theory and experiments, we show that even small variations in growth rate between resistant mutants and the wild type result in orders-of-magnitude differences in genetic diversity. Indeed, only a slight fitness advantage for the mutant is enough to keep diversity low and independent of population size. These results have important clinical implications. Genetic diversity at antibiotic resistance loci can determine a population's capacity to cope with future challenges (i.e., second-line therapy). We thus revealed an unanticipated way in which the fitness effects of antibiotic resistance can affect the evolvability of pathogens surviving a drug-induced bottleneck. This insight will assist in the fight against multidrug-resistant microbes, as well as contribute to theories aimed at predicting cancer evolution. PMID:27182949

  7. Genetic diversity of Microcystis cyanophages in two different freshwater environments.

    PubMed

    Nakamura, Ginji; Kimura, Shigeko; Sako, Yoshihiko; Yoshida, Takashi

    2014-06-01

    Bacteriophages rapidly diversify their genes through co-evolution with their hosts. We hypothesize that gene diversification of phages leads to locality in phages genome. To test this hypothesis, we investigated the genetic diversity and composition of Microcystis cyanophages using 104 sequences of Ma-LMM01-type cyanophages from two geographically distant sampling sites. The intergenetic region between the ribonucleotide reductase genes nrdA and nrdB was used as the genetic marker. This region contains the host-derived auxiliary metabolic genes nblA, an unknown function gene g04, and RNA ligase gene g03. The sequences obtained were conserved in the Ma-LMM01 gene order and contents. Although the genetic diversity of the sequences was high, it varied by gene. The genetic diversity of nblA was the lowest, suggesting that nblA is a highly significant gene that does not allow mutation. In contrast, g03 sequences had many point mutations. RNA ligase is involved in the counter-host's phage defense mechanism, suggesting that phage defense also plays an important role for rapid gene diversification. The maximum parsimony network and phylogenic analysis showed the sequences from the two sampling sites were distinct. These findings suggest Ma-LMM01-type phages rapidly diversify their genomes through co-evolution with hosts in each location and eventually provided locality of their genomes. PMID:24671440

  8. The influence of recombination on human genetic diversity.

    PubMed

    Spencer, Chris C A; Deloukas, Panos; Hunt, Sarah; Mullikin, Jim; Myers, Simon; Silverman, Bernard; Donnelly, Peter; Bentley, David; McVean, Gil

    2006-09-22

    In humans, the rate of recombination, as measured on the megabase scale, is positively associated with the level of genetic variation, as measured at the genic scale. Despite considerable debate, it is not clear whether these factors are causally linked or, if they are, whether this is driven by the repeated action of adaptive evolution or molecular processes such as double-strand break formation and mismatch repair. We introduce three innovations to the analysis of recombination and diversity: fine-scale genetic maps estimated from genotype experiments that identify recombination hotspots at the kilobase scale, analysis of an entire human chromosome, and the use of wavelet techniques to identify correlations acting at different scales. We show that recombination influences genetic diversity only at the level of recombination hotspots. Hotspots are also associated with local increases in GC content and the relative frequency of GC-increasing mutations but have no effect on substitution rates. Broad-scale association between recombination and diversity is explained through covariance of both factors with base composition. To our knowledge, these results are the first evidence of a direct and local influence of recombination hotspots on genetic variation and the fate of individual mutations. However, that hotspots have no influence on substitution rates suggests that they are too ephemeral on an evolutionary time scale to have a strong influence on broader scale patterns of base composition and long-term molecular evolution. PMID:17044736

  9. Population genetic diversity and hybrid detection in captive zebras

    PubMed Central

    Ito, Hideyuki; Langenhorst, Tanya; Ogden, Rob; Inoue-Murayama, Miho

    2015-01-01

    Zebras are members of the horse family. There are three species of zebras: the plains zebra Equus quagga, the Grevy’s zebra E. grevyi and the mountain zebra E. zebra. The Grevy’s zebra and the mountain zebra are endangered, and hybridization between the Grevy’s zebra and the plains zebra has been documented, leading to a requirement for conservation genetic management within and between the species. We characterized 28 microsatellite markers in Grevy’s zebra and assessed cross-amplification in plains zebra and two of its subspecies, as well as mountain zebra. A range of standard indices were employed to examine population genetic diversity and hybrid populations between Grevy’s and plains zebra were simulated to investigate subspecies and hybrid detection. Microsatellite marker polymorphism was conserved across species with sufficient variation to enable individual identification in all populations. Comparative diversity estimates indicated greater genetic variation in plains zebra and its subspecies than Grevy’s zebra, despite potential ascertainment bias. Species and subspecies differentiation were clearly demonstrated and F1 and F2 hybrids were correctly identified. These findings provide insights into captive population genetic diversity in zebras and support the use of these markers for identifying hybrids, including the known hybrid issue in the endangered Grevy’s zebra. PMID:26294133

  10. Genetic diversity and population genetics of large lungworms (Dictyocaulus, Nematoda) in wild deer in Hungary.

    PubMed

    Ács, Zoltán; Hayward, Alexander; Sugár, László

    2016-09-01

    Dictyocaulus nematode worms live as parasites in the lower airways of ungulates and can cause significant disease in both wild and farmed hosts. This study represents the first population genetic analysis of large lungworms in wildlife. Specifically, we quantify genetic variation in Dictyocaulus lungworms from wild deer (red deer, fallow deer and roe deer) in Hungary, based on mitochondrial cytochrome c oxidase subunit 1 (cox1) sequence data, using population genetic and phylogenetic analyses. The studied Dictyocaulus taxa display considerable genetic diversity. At least one cryptic species and a new parasite-host relationship are revealed by our molecular study. Population genetic analyses for Dictyocaulus eckerti revealed high gene flow amongst weakly structured spatial populations that utilise the three host deer species considered here. Our results suggest that D. eckerti is a widespread generalist parasite in ungulates, with a diverse genetic backround and high evolutionary potential. In contrast, evidence of cryptic genetic structure at regional geographic scales was observed for Dictyocaulus capreolus, which infects just one host species, suggesting it is a specialist within the studied area. D. capreolus displayed lower genetic diversity overall, with only moderate gene flow compared to the closely related D. eckerti. We suggest that the differing vagility and dispersal behaviour of hosts are important contributing factors to the population structure of lungworms, and possibly other nematode parasites with single-host life cycles. Our findings are of relevance for the management of lungworms in deer farms and wild deer populations. PMID:27150969

  11. Genetic diversity affects colony survivorship in commercial honey bee colonies

    NASA Astrophysics Data System (ADS)

    Tarpy, David R.; vanEngelsdorp, Dennis; Pettis, Jeffrey S.

    2013-08-01

    Honey bee ( Apis mellifera) queens mate with unusually high numbers of males (average of approximately 12 drones), although there is much variation among queens. One main consequence of such extreme polyandry is an increased diversity of worker genotypes within a colony, which has been shown empirically to confer significant adaptive advantages that result in higher colony productivity and survival. Moreover, honey bees are the primary insect pollinators used in modern commercial production agriculture, and their populations have been in decline worldwide. Here, we compare the mating frequencies of queens, and therefore, intracolony genetic diversity, in three commercial beekeeping operations to determine how they correlate with various measures of colony health and productivity, particularly the likelihood of queen supersedure and colony survival in functional, intensively managed beehives. We found the average effective paternity frequency ( m e ) of this population of honey bee queens to be 13.6 ± 6.76, which was not significantly different between colonies that superseded their queen and those that did not. However, colonies that were less genetically diverse (headed by queens with m e ≤ 7.0) were 2.86 times more likely to die by the end of the study when compared to colonies that were more genetically diverse (headed by queens with m e > 7.0). The stark contrast in colony survival based on increased genetic diversity suggests that there are important tangible benefits of increased queen mating number in managed honey bees, although the exact mechanism(s) that govern these benefits have not been fully elucidated.

  12. Genetic diversity affects colony survivorship in commercial honey bee colonies.

    PubMed

    Tarpy, David R; Vanengelsdorp, Dennis; Pettis, Jeffrey S

    2013-08-01

    Honey bee (Apis mellifera) queens mate with unusually high numbers of males (average of approximately 12 drones), although there is much variation among queens. One main consequence of such extreme polyandry is an increased diversity of worker genotypes within a colony, which has been shown empirically to confer significant adaptive advantages that result in higher colony productivity and survival. Moreover, honey bees are the primary insect pollinators used in modern commercial production agriculture, and their populations have been in decline worldwide. Here, we compare the mating frequencies of queens, and therefore, intracolony genetic diversity, in three commercial beekeeping operations to determine how they correlate with various measures of colony health and productivity, particularly the likelihood of queen supersedure and colony survival in functional, intensively managed beehives. We found the average effective paternity frequency (m e ) of this population of honey bee queens to be 13.6 ± 6.76, which was not significantly different between colonies that superseded their queen and those that did not. However, colonies that were less genetically diverse (headed by queens with m e  ≤ 7.0) were 2.86 times more likely to die by the end of the study when compared to colonies that were more genetically diverse (headed by queens with m e  > 7.0). The stark contrast in colony survival based on increased genetic diversity suggests that there are important tangible benefits of increased queen mating number in managed honey bees, although the exact mechanism(s) that govern these benefits have not been fully elucidated. PMID:23728203

  13. Turtle Carapace Anomalies: The Roles of Genetic Diversity and Environment

    PubMed Central

    Velo-Antón, Guillermo; Becker, C. Guilherme; Cordero-Rivera, Adolfo

    2011-01-01

    Background Phenotypic anomalies are common in wild populations and multiple genetic, biotic and abiotic factors might contribute to their formation. Turtles are excellent models for the study of developmental instability because anomalies are easily detected in the form of malformations, additions, or reductions in the number of scutes or scales. Methodology/Principal Findings In this study, we integrated field observations, manipulative experiments, and climatic and genetic approaches to investigate the origin of carapace scute anomalies across Iberian populations of the European pond turtle, Emys orbicularis. The proportion of anomalous individuals varied from 3% to 69% in local populations, with increasing frequency of anomalies in northern regions. We found no significant effect of climatic and soil moisture, or climatic temperature on the occurrence of anomalies. However, lower genetic diversity and inbreeding were good predictors of the prevalence of scute anomalies among populations. Both decreasing genetic diversity and increasing proportion of anomalous individuals in northern parts of the Iberian distribution may be linked to recolonization events from the Southern Pleistocene refugium. Conclusions/Significance Overall, our results suggest that developmental instability in turtle carapace formation might be caused, at least in part, by genetic factors, although the influence of environmental factors affecting the developmental stability of turtle carapace cannot be ruled out. Further studies of the effects of environmental factors, pollutants and heritability of anomalies would be useful to better understand the complex origin of anomalies in natural populations. PMID:21533278

  14. Genetic structure and differentiation in cultivated fig (Ficus carica L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    One hundred ninety-four germplasm accessions of fig representing the four fig types, Common, Smyrna, San Pedro, and Caprifig were analyzed for genetic diversity, structure, and differentiation using genetic polymorphism at 17 microsatellite loci. The collection showed considerable polymorphism with ...

  15. Genetic diversity in Malus × domestica (Rosaceae) through time in response to domestication

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Patterns of genetic diversity in domesticated plants are affected by geographic region of origin and cultivation, intentional artificial selection, and unintentional loss of diversity referred to as genetic bottlenecks. While bottlenecks are mainly associated with the initial domestication process, ...

  16. ASSOCIATIONS BETWEEN GENETIC DIVERSITY AND ANTHROPOGENIC DISTURBANCE IN MIDWESTERN STREAM-DWELLING MINNOWS

    EPA Science Inventory

    Anthropogenic disturbances may leave imprints on patterns of intraspecific genetic diversity through their effects on population size, adaptation, migration, and mutation. We examined patterns of genetic diversity for a stream-dwelling minnow (the central stoneroller, Campostoma...

  17. Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis).

    PubMed

    Ong, P W; Maizura, I; Abdullah, N A P; Rafii, M Y; Ooi, L C L; Low, E T L; Singh, R

    2015-01-01

    The genetic evaluation of oil palm germplasm collections is required for insight into the variability among populations. The information obtained is also useful for incorporating new genetic materials into current breeding programs. Single nucleotide polymorphisms (SNPs) have been widely used in many plant genetic studies due to the availability of large numbers of genomic sequences and expressed sequence tags. The present study examined 219 oil palms collected from two natural Angolan populations, a few hundred kilometers apart. A total of 62 SNPs were designed from oil palm genomic sequences and converted to cleaved amplified polymorphic sequence (CAPS). Of these, nine were found to be informative across the two populations. The nine informative SNPs revealed mean major allele frequency of 0.693. The average expected and observed heterozygosities were 0.398 and 0.400, respectively. The mean polymorphism information content was 0.315 (ranging between 0.223 and 0.375). None of the loci deviated from Hardy-Weinberg equilibrium and no rare alleles were detected. In cluster analysis using unweighted pair group method with arithmetic, the 219 oil palms fell into two clusters. This was further supported by the population structure analysis result (K = 2), suggesting that the samples were divided into two main genetic groups. However, the two groups did not coincide with the geographic populations. Analysis of molecular variance indicated that within-population variation contributed 93% of the total genetic variation. This study showed that SNP-based CAPS markers are useful for studying the genetic diversity of oil palm and have potential application for marker-trait association studies. PMID:26505369

  18. Genetic diversity and maternal origin of Bangladeshi chicken.

    PubMed

    Bhuiyan, M S A; Chen, Shanyuan; Faruque, S; Bhuiyan, A K F H; Beja-Pereira, Albano

    2013-06-01

    Local domestic chicken populations are of paramount importance as a source of protein in developing countries. Bangladesh possesses a large number of native chicken populations which display a broad range of phenotypes well adapted to the extreme wet and hot environments of this region. This and the fact that wild jungle fowls (JFs) are still available in some regions of the country, it urges to study the present genetic diversity and relationships between Bangladeshi autochthonous chicken populations. Here, we report the results of the mitochondrial DNA (mtDNA) sequence polymorphisms analyses to assess the genetic diversity and possible maternal origin of Bangladeshi indigenous chickens. A 648-bp fragment of mtDNA control region (D-loop) was analyzed in 96 samples from four different chicken populations and one red JF population. Sequence analysis revealed 39 variable sites that defined 25 haplotypes. Estimates of haplotype and nucleotide diversities ranged from 0.745 to 0.901 and from 0.011 to 0.016, respectively. The pairwise differences between populations ranged from 0.091 to 1.459 while most of the PhiST (ΦST) values were significant. Furthermore, AMOVA analysis revealed 89.16 % of the total genetic diversity was accounted for within population variation, indicating little genetic differentiation among the studied populations. The median network analysis from haplotypes of Bangladeshi chickens illustrated five distinct mitochondrial haplogroups (A, D, E, F and I). Individuals from all Bangladeshi chicken populations were represented in the major clades D and E; those maternal origins are presumed to be from Indian Subcontinent and Southeast Asian countries, more particularly from South China, Vietnam, Myanmar and Thailand. Further, phylogenetic analysis between indigenous chicken populations and sub-species of red JFs showed G. g. gallus and G. g. spadiceus shared with almost all haplogroups and had major influence than G. g. murghi in the origin of

  19. Genetic and biological diversity among isolates of Neospora caninum.

    PubMed

    Schock, A; Innes, E A; Yamane, I; Latham, S M; Wastling, J M

    2001-07-01

    Neospora caninum is a protozoan parasite that causes bovine abortion. The epidemiology of N. caninum is poorly understood and little is known about the genetic diversity of the parasite, or whether individual isolates differ in virulence. Such diversity may, among other factors, underlie the range of pathologies seen in cattle. In this study we analysed biological and genetic variation in 6 isolates of N. caninum originating from canine and bovine hosts by measurement of growth rate in vitro, Western blotting and random amplification of polymorphic DNA (RAPD). This comparative analysis of intra-species diversity demonstrated that heterogeneity exists within the species. The relative growth rate in vitro, as assessed by 3[H]uracil uptake, showed significant variation between isolates. However, no significant differences were detected between the antigenic profiles of each isolate by Western blotting. RAPD-PCR was performed on DNA from the 6 Neospora isolates; 3 strains of Toxoplasma gondii, Sarcocystis sp. and Cryptosporidium parvum were also analysed. Twenty-six RAPD primers gave rise to 434 markers of which 222 were conserved between all the Neospora isolates and distinguished them from the other Apicomplexa. An additional 54 markers were unique for Neospora but were polymorphic within the species and able to differentiate between the individual isolates. The RAPD data were subjected to pair-wise similarity and cluster analysis and showed that the Neospora isolates clustered together as a group, with T. gondii as their nearest neighbour. N. caninum isolates showed no clustering with respect either to host or geographical origin. The genetic similarity between Neospora isolates from cattle and dogs suggests that these hosts may be epidemiologically related, although further analysis of bovine and canine field samples are required. The genetic and biological diversity observed in this study may have important implications for our understanding of the pathology and

  20. Genetic diversity of Plasmodium vivax in Kolkata, India

    PubMed Central

    Kim, Jung-Ryong; Imwong, Mallika; Nandy, Amitabha; Chotivanich, Kesinee; Nontprasert, Apichart; Tonomsing, Naowarat; Maji, Ardhendu; Addy, Manjulika; Day, Nick PJ; White, Nicholas J; Pukrittayakamee, Sasithon

    2006-01-01

    Background Plasmodium vivax malaria accounts for approximately 60% of malaria cases in Kolkata, India. There has been limited information on the genotypic polymorphism of P. vivax in this malaria endemic area. Three highly polymorphic and single copy genes were selected for a study of genetic diversity in Kolkata strains. Methods Blood from 151 patients with P. vivax infection diagnosed in Kolkata between April 2003 and September 2004 was genotyped at three polymorphic loci: the P. vivax circumsporozoite protein (pvcs), the merozoite surface protein 1 (pvmsp1) and the merozoite surface protein 3-alpha (pvmsp3-alpha). Results Analysis of these three genetic markers revealed that P. vivax populations in Kolkata are highly diverse. A large number of distinguishable alleles were found from three genetic markers: 11 for pvcs, 35 for pvmsp1 and 37 for pvmsp3-alpha. These were, in general, randomly distributed amongst the isolates. Among the 151 isolates, 142 unique genotypes were detected the commonest genotype at a frequency of less than 2% (3/151). The overall rate of mixed genotype infections was 10.6%. Conclusion These results indicate that the P. vivax parasite population is highly diverse in Kolkata, despite the low level of transmission. The genotyping protocols used in this study may be useful for differentiating re-infection from relapse and recrudescence in studies assessing of malarial drug efficacy in vivax malaria. PMID:16907979

  1. Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India.

    PubMed

    Karuppaiah, R; Viswanathan, R; Kumar, V Ganesh

    2013-06-01

    Sugarcane bacilliform virus (SCBV), which causes leaf freckle in sugarcane, is a member of the genus Badnavirus. Studies were conducted to characterize SCBV in Saccharum officinarum germplasm and cultivated varieties in India by sequencing the complete genomes of five isolates. Genome lengths ranged from 7,553 to 7,884 nucleotides. Duplications in ORF3 and insertions in the RNase H-domain in some of the isolates were found to contribute to the large size of their genomes. The Indian SCBV isolates share identities of 69-85 % for the complete genomic sequence, indicating wide genetic diversity among them, and share 70-82 % identity with Sugarcane bacilliform Ireng Maleng virus (SCBIMV) and Sugarcane bacilliform Morocco virus (SCBMV), as well as 43-46 % identity with Banana streak virus (BSV) and BSV-related SCBV species from Guadeloupe, indicating that the Indian SCBV isolates are distinct from SCBV isolates reported to date. Irrespective of the region compared, SCBV isolates from India, Australia, and Morocco clustered together. BSV and BSV-related SCBV isolates from Guadeloupe formed another cluster. A phylogenetic analysis based on the partial RT/RNase H-sequence separated SCBV and BSV-related SCBV sequences into 11 SCBV groups viz. SCBV-A to -K. Among the 11 groups, the SCBV sequences separated under H, I, J, and K are newly identified in this study, representing three new species and are tentatively named as SCBBBV, SCBBOV, and SCBBRV. Thus, the PASC and phylogenetic analyses evidenced that the symptoms associated with badnaviruses in sugarcane in India are caused by at least three new species, SCBBBV, SCBBOV, and SCBBRV, besides SCBIMV and SCBMV represented by SCBV-BT and SCBV-Iscam, respectively. PMID:23430710

  2. Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction

    PubMed Central

    Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C.; Kuhn, David N.; Glaz, Barry; Gilbert, Robert A.; Comstock, Jack C.; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358

  3. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction.

    PubMed

    Nayak, Spurthi N; Song, Jian; Villa, Andrea; Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C; Kuhn, David N; Glaz, Barry; Gilbert, Robert A; Comstock, Jack C; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358

  4. Genetic diversity of hydrothermal-vent barnacles in Manus Basin

    NASA Astrophysics Data System (ADS)

    Plouviez, Sophie; Schultz, Thomas F.; McGinnis, Gwendolyn; Minshall, Halle; Rudder, Meghan; Van Dover, Cindy L.

    2013-12-01

    We evaluated mitochondrial cytochrome oxidase I genetic diversity of two barnacle species (Eochionelasmus ohtai manusensis, Vulcanolepas cf. parensis) at three sites in Manus Basin (Solwara 1, South Su, Solwara 8). There was no evidence for within-site or between-site genetic differentiation for either species. While E. ohtai manusensis showed limited genetic variation, V. cf. parensis showed greater variation, with sequences distributed between two divergent groups. Assuming the cytochrome oxidase I gene is not under selection, significantly negative Tajima's D in E. ohtai manusensis is consistent with a recent population expansion due to a bottleneck or founder effect, whereas V. cf. parensis (combined groups) did not depart from a stable effective population size. Considering the groups separately, V. cf. parensis Group 1 (but not Group 2) showed a negative Tajima's D, indicating these groups may have encountered different historical demographic conditions. Data reported here are part of a baseline study against which recovery of genetic diversity following mineral extraction at Solwara 1 can be measured.

  5. Inter-Simple Sequence Repeat Data Reveals High Genetic Diversity in Wild Populations of the Narrowly Distributed Endemic Lilium regale in the Minjiang River Valley of China

    PubMed Central

    Wu, Zhu-hua; Shi, Jisen; Xi, Meng-li; Jiang, Fu-xing; Deng, Ming-wen; Dayanandan, Selvadurai

    2015-01-01

    Lilium regale E.H. Wilson is endemic to a narrow geographic area in the Minjiang River valley in southwestern China, and is considered an important germplasm for breeding commercially valuable lily varieties, due to its vigorous growth, resistance to diseases and tolerance for low moisture. We analyzed the genetic diversity of eight populations of L. regale sampled across the entire natural distribution range of the species using Inter-Simple Sequence Repeat markers. The genetic diversity (expected heterozygosity= 0.3356) was higher than those reported for other narrowly distributed endemic plants. The levels of inbreeding (Fst = 0.1897) were low, and most of the genetic variability was found to be within (80.91%) than amongpopulations (19.09%). An indirect estimate of historical levels of gene flow (Nm =1.0678) indicated high levels of gene flow among populations. The eight analyzed populations clustered into three genetically distinct groups. Based on these results, we recommend conservation of large populations representing these three genetically distinct groups. PMID:25799495

  6. 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

  7. 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

  8. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

    PubMed Central

    Goron, Travis L.; Raizada, Manish N.

    2015-01-01

    Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed “orphan cereals.” Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa. PMID:25852710

  9. Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution.

    PubMed

    Goron, Travis L; Raizada, Manish N

    2015-01-01

    Small millets are nutrient-rich food sources traditionally grown and consumed by subsistence farmers in Asia and Africa. They include finger millet (Eleusine coracana), foxtail millet (Setaria italica), kodo millet (Paspalum scrobiculatum), proso millet (Panicum miliaceum), barnyard millet (Echinochloa spp.), and little millet (Panicum sumatrense). Local farmers value the small millets for their nutritional and health benefits, tolerance to extreme stress including drought, and ability to grow under low nutrient input conditions, ideal in an era of climate change and steadily depleting natural resources. Little scientific attention has been paid to these crops, hence they have been termed "orphan cereals." Despite this challenge, an advantageous quality of the small millets is that they continue to be grown in remote regions of the world which has preserved their biodiversity, providing breeders with unique alleles for crop improvement. The purpose of this review, first, is to highlight the diverse traits of each small millet species that are valued by farmers and consumers which hold potential for selection, improvement or mechanistic study. For each species, the germplasm, genetic and genomic resources available will then be described as potential tools to exploit this biodiversity. The review will conclude with noting current trends and gaps in the literature and make recommendations on how to better preserve and utilize diversity within these species to accelerate a New Green Revolution for subsistence farmers in Asia and Africa. PMID:25852710

  10. Genetic diversity for wheat improvement as a conduit to food security

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity is paramount for any crops genetic improvement and this resides in three gene pools of the Triticeae for wheat. Access to the diversity and its exploitation is based upon genetic distance of the species relatives from the wheat genomes. Apart from the conventional genetic base fo...

  11. A MULTI-LOCUS, MULTI-TAXA PHYLOGEOGRAPHICAL ANALYSIS OF GENETIC DIVERSITY

    EPA Science Inventory

    In addition to measuring spatial patterns of genetic diversity, population genetic measures of biological resources should include temporal data that indicate whether the observed patterns are the result of historical or contemporary processes. In general, genetic measures focus...

  12. Genetic diversity for Russian wheat aphid resistance as determined by genome-wide association mapping and inheritance in progeny

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Russian wheat aphid (RWA) is an increasing problem on barley throughout the world. Genetic resistance has been identified and used to create barley germplasm and cultivars adapted to the US. Several mapping studies have been conducted to identify loci associated with resistance, but questions remain...

  13. Genetic Diversity of Japanese Strawberry Species Based on Microsatellite Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The strawberry collection at the United States Department of Agriculture (USDA) - Agricultural Research Service (ARS) - National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, consists of 1769 accessions from 17 species and 37 countries. Molecular techniques which include DNA-Based methods...

  14. Comparative Assessment of Genetic Diversity in Wild and Primitive Cultivated Barley in a Center of Diversity

    PubMed Central

    Jana, S.; Pietrzak, L. N.

    1988-01-01

    Wild barley (Hordeum spontaneum K.) and indigenous primitive varieties of cultivated barley (Hordeum vulgare L.), collected from 43 locations in four eastern Mediterranean countries, Jordan, Syria, Turkey and Greece, were electrophoretically assayed for genetic diversity at 16 isozyme loci. Contrary to a common impression, cultivated barley populations were found to maintain a level of diversity similar to that in its wild progenitor species. Apportionment of overall diversity in the region showed that in cultivated barley within-populations diversity was of higher magnitude than the between-populations component. Neighboring populations of wild and cultivated barleys showed high degree of genetic identity. Groups of 3 or 4 isozyme loci were analyzed to detect associations among loci. Multilocus associations of varying order were detected for all three groups chosen for the analysis. Some of the association terms differed between the two species in the region. Although there was no clear evidence for decrease in diversity attributable to the domestication of barley in the region, there was an indication of different multilocus organizations in the two closely related species. PMID:17246441

  15. Procedures and best management practices for genetically engineered traits in USDA/ARS germplasm and breeding lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two decades have passed since the commercialization in the U. S. of crops with genetically engineered (GE) traits. Today more than 80% of corn, soybean, canola, sugar beet and cotton acreage in the United States is planted to transgenic cultivars, but concerns exist regarding how best to manage the ...

  16. Genetic marker comparison for the purpose of determining off-type cacao clones within a West African germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellites are co-dominant PCR-based genetic markers, which are commonly used in modern Marker Aided Selection (MAS) breeding programs. Although many MAS breeding programs have and continue to successfully use microsatellites, various issues with analysis, such as comparing results across diff...

  17. Genetic basis of transcriptome diversity in Drosophila melanogaster

    PubMed Central

    Huang, Wen; Carbone, Mary Anna; Magwire, Michael M.; Peiffer, Jason A.; Lyman, Richard F.; Stone, Eric A.; Anholt, Robert R. H.; Mackay, Trudy F. C.

    2015-01-01

    Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive but is essential for predicting adaptive evolution, for selecting agriculturally important animals and crops, and for personalized medicine. Gene expression may provide a link between variation in DNA sequence and organismal phenotypes, and its abundance can be measured efficiently and accurately. Here we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), increasing the annotated Drosophila transcriptome by 11%, including thousands of novel transcribed regions (NTRs). We found that 42% of the Drosophila transcriptome is genetically variable in males and females, including the NTRs, and is organized into modules of genetically correlated transcripts. We found that NTRs often were negatively correlated with the expression of protein-coding genes, which we exploited to annotate NTRs functionally. We identified regulatory variants for the mean and variance of gene expression, which have largely independent genetic control. Expression quantitative trait loci (eQTLs) for the mean, but not for the variance, of gene expression were concentrated near genes. Notably, the variance eQTLs often interacted epistatically with local variants in these genes to regulate gene expression. This comprehensive characterization of population-scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation. PMID:26483487

  18. Ethnohistory, intertribal relationships, and genetic diversity among Amazonian Indians.

    PubMed

    Aguiar, G F

    1991-12-01

    The influence of recent ethnohistorical factors on the microevolution of South American Indians has not been adequately evaluated by population geneticists. This makes difficult a reasonable interpretation of the present genetic structure of these groups. In this article the genetic diversity of 18 tribes of the Amazon and neighboring areas belonging to 3 linguistic groups (Tupi, Carib, and Gê) is analyzed in light of documentary sources about historical events, such as demographic changes, geographic movements, intertribal relationships, and marriage practices, that have taken place since the end of the eighteenth century. The high depopulation rate suffered by the Tupi groups (61.4% on average) is a probable factor conditioning the large intergroup genetic distances in this linguistic stock, for depopulation is a phenomenon associated with random genetic drift caused by a bottleneck effect. On the other hand, the relatively high similarity of the Gê and the Carib shows an association with two main factors: (1) reduced spatial dispersion of the Gê in the recent past, providing adequate conditions for within-stock gene flow, and (2) strong tradition of intergroup contacts among the Carib, frequently followed by genetic admixture and even fusion of groups, as verified for the Wayana and the Aparaí. The patterns of biologic variation of some Tupi tribes (Waiãpi, Emerillon, Parakanã, and Assurini) are better explained by historical and regional contingencies than by linguistic classification. PMID:1959909

  19. Genetic basis of transcriptome diversity in Drosophila melanogaster.

    PubMed

    Huang, Wen; Carbone, Mary Anna; Magwire, Michael M; Peiffer, Jason A; Lyman, Richard F; Stone, Eric A; Anholt, Robert R H; Mackay, Trudy F C

    2015-11-01

    Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive but is essential for predicting adaptive evolution, for selecting agriculturally important animals and crops, and for personalized medicine. Gene expression may provide a link between variation in DNA sequence and organismal phenotypes, and its abundance can be measured efficiently and accurately. Here we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), increasing the annotated Drosophila transcriptome by 11%, including thousands of novel transcribed regions (NTRs). We found that 42% of the Drosophila transcriptome is genetically variable in males and females, including the NTRs, and is organized into modules of genetically correlated transcripts. We found that NTRs often were negatively correlated with the expression of protein-coding genes, which we exploited to annotate NTRs functionally. We identified regulatory variants for the mean and variance of gene expression, which have largely independent genetic control. Expression quantitative trait loci (eQTLs) for the mean, but not for the variance, of gene expression were concentrated near genes. Notably, the variance eQTLs often interacted epistatically with local variants in these genes to regulate gene expression. This comprehensive characterization of population-scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation. PMID:26483487

  20. Genetics, Genomics and Breeding in Sunflower

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This book is intended to bridge traditional research with modern molecular investigations on sunflower. It begins with basic information about the sunflower plant and germplasm diversity (Chapter 1), followed by classical genetics and traditional breeding (Chapter 2), history and achievement of gen...

  1. Evaluation of high yielding soybean germplasm under water limitation.

    PubMed

    Prince, Silvas J; Murphy, Mackensie; Mutava, Raymond N; Zhang, Zhengzhi; Nguyen, Na; Kim, Yoon Ha; Pathan, Safiullah M; Shannon, Grover J; Valliyodan, Babu; Nguyen, Henry T

    2016-05-01

    Limited information is available for soybean root traits and their plasticity under drought stress. To date, no studies have focused on examining diverse soybean germplasm for regulation of shoot and root response under water limited conditions across varying soil types. In this study, 17 genetically diverse soybean germplasm lines were selected to study root response to water limited conditions in clay (trial 1) and sandy soil (trial 2) in two target environments. Physiological data on shoot traits was measured at multiple crop stages ranging from early vegetative to pod filling. The phenotypic root traits, and biomass accumulation data are collected at pod filling stage. In trial 1, the number of lateral roots and forks were positively correlated with plot yield under water limitation and in trial 2, lateral root thickness was positively correlated with the hill plot yield. Plant Introduction (PI) 578477A and 088444 were found to have higher later root number and forks in clay soil with higher yield under water limitation. In sandy soil, PI458020 was found to have a thicker lateral root system and higher yield under water limitation. The genotypes identified in this study could be used to enhance drought tolerance of elite soybean cultivars through improved root traits specific to target environments. PMID:26172438

  2. LYGUS GENETICS: INTER- AND INTRASPECIFIC MITOCHONDRIAL GENETIC DIVERSITY IN NORTH AMERICA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mitochondrial DNA (mtDNA) was employed to investigate inter- and intraspecific genetic diversity within the Lygus genus. The main emphasis was on L. lineolaris because it is a widely dispersed species occurring in many regions of North America. Part of the mtDNA cox1 and cox2 gene regions were used ...

  3. Analysis of genetic diversity of Lactarius hatsudake in south China.

    PubMed

    He, Li; Liang, Guo; Guoying, Zhou; Jun-ang, Liu

    2011-08-01

    Lactarius hatsudake is a type of ectomycorrhizal fungus that significantly influences the growth of pine trees. It is widely prevalent in Asian countries and has a high economic value. Artificial cultivation of this fungus has not been achieved as yet; therefore, excessive manual harvesting may cause serious damages to the site of its production. In this study, we analyzed 41 samples of L. hatsudake from south China using internal transcribed spacer (ITS) sequences. By comparing the differences among ITS sequences to identify the haplotype diversity within each population, the relationships among local populations, the relationship between the level of genetic differentiation and geographical separation, and the contributions of local and regional geographical separations to the overall ITS haplotype variation were analyzed. Genetic analysis indicates that ITS sequences obtained from these 41 L. hatsudake samples could be identified as 18 haplotypes, of which 13 haplotypes were contained in only a single sample, whereas the remaining sequence types all were contained in two or more samples. The most common sequence type, haplotype 6, was found in 16 samples and was distributed across nearly every region. The Mantel test demonstrated that there is no significant linear relationship between geographical distance and the F(ST) value of genetic difference. Results of this research illustrates that there exists a certain degree of genetic intermixing among natural populations of L. hatsudake. From the group genetic analysis, it appears that there exists genetic differentiation of lower frequencies in natural populations of L. hatsudake; however, the linear relationship between the degree of genetic differentiation and geographical distance is not distinctly apparent. PMID:21815833

  4. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers

    PubMed Central

    Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

    2015-01-01

    Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei’s genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance

  5. Assessment of Genetic Diversity and Population Genetic Structure of Corylus mandshurica in China Using SSR Markers.

    PubMed

    Zong, Jian-Wei; Zhao, Tian-Tian; Ma, Qing-Hua; Liang, Li-Song; Wang, Gui-Xi

    2015-01-01

    Corylus mandshurica, also known as pilose hazelnut, is an economically and ecologically important species in China. In this study, ten polymorphic simple sequence repeat (SSR) markers were applied to evaluate the genetic diversity and population structure of 348 C. mandshurica individuals among 12 populations in China. The SSR markers expressed a relatively high level of genetic diversity (Na = 15.3, Ne = 5.6604, I = 1.8853, Ho = 0.6668, and He = 0.7777). According to the coefficient of genetic differentiation (Fst = 0.1215), genetic variation within the populations (87.85%) were remarkably higher than among populations (12.15%). The average gene flow (Nm = 1.8080) significantly impacts the genetic structure of C. mandshurica populations. The relatively high gene flow (Nm = 1.8080) among wild C. mandshurica may be caused by wind-pollinated flowers, highly nutritious seeds and self-incompatible mating system. The UPGMA (unweighted pair group method of arithmetic averages) dendrogram was divided into two main clusters. Moreover, the results of STRUCTURE analysis suggested that C. mandshurica populations fell into two main clusters. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among populations of C. mandshurica. Group I accessions were located in Northeast China, while Group II accessions were in North China. It is worth noting that a number of genetically similar populations were located in the same geographic region. The results further showed that there was obvious genetic differentiation among populations from Northeast China to North China. Results from the Mantel test showed a weak but still significant positive correlation between Nei's genetic distance and geographic distance (km) among populations (r = 0.419, P = 0.005), suggesting that genetic differentiation in the 12 C. mandshurica populations might be related to geographic distance. These

  6. Limited genetic diversity preceded extinction of the Tasmanian tiger.

    PubMed

    Menzies, Brandon R; Renfree, Marilyn B; Heider, Thomas; Mayer, Frieder; Hildebrandt, Thomas B; Pask, Andrew J

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago. PMID:22530022

  7. Limited Genetic Diversity Preceded Extinction of the Tasmanian Tiger

    PubMed Central

    Menzies, Brandon R.; Renfree, Marilyn B.; Heider, Thomas; Mayer, Frieder; Hildebrandt, Thomas B.; Pask, Andrew J.

    2012-01-01

    The Tasmanian tiger or thylacine was the largest carnivorous marsupial when Europeans first reached Australia. Sadly, the last known thylacine died in captivity in 1936. A recent analysis of the genome of the closely related and extant Tasmanian devil demonstrated limited genetic diversity between individuals. While a similar lack of diversity has been reported for the thylacine, this analysis was based on just two individuals. Here we report the sequencing of an additional 12 museum-archived specimens collected between 102 and 159 years ago. We examined a portion of the mitochondrial DNA hyper-variable control region and determined that all sequences were on average 99.5% identical at the nucleotide level. As a measure of accuracy we also sequenced mitochondrial DNA from a mother and two offspring. As expected, these samples were found to be 100% identical, validating our methods. We also used 454 sequencing to reconstruct 2.1 kilobases of the mitochondrial genome, which shared 99.91% identity with the two complete thylacine mitochondrial genomes published previously. Our thylacine genomic data also contained three highly divergent putative nuclear mitochondrial sequences, which grouped phylogenetically with the published thylacine mitochondrial homologs but contained 100-fold more polymorphisms than the conserved fragments. Together, our data suggest that the thylacine population in Tasmania had limited genetic diversity prior to its extinction, possibly as a result of their geographic isolation from mainland Australia approximately 10,000 years ago. PMID:22530022

  8. REGISTRATION OF BIRDSFOOT TREFOIL GERMPLASM ARS-2622

    Technology Transfer Automated Retrieval System (TEKTRAN)

    ARS-2622 broadleafed birdsfoot trefoil (Lotus corniculatus L.) germplasm was released by the USDA-ARS in cooperation with the Missouri Agricultural Experiment Station in August 2002. The merit of ARS-2622 is that it is a rhizome producing population with a broad genetic base. ARS-2622 was developed ...

  9. In Vitro Maintenance of Bermudagrass Germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are currently 213 accessions of bermudagrass (Cynodon sp.) maintained clonally by the Plant Genetic Resources Conservation Unit located in Griffin, Georgia as part of the National Plant Germplasm System. These accessions have been traditionally maintained as potted plants in the greenhouse. ...

  10. Shoot tip cryopreservation of Solanum tuberosum germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Liquid nitrogen storage of vegetatively-propagated germplasm collections is the most economic and reliable long-term preservation method for many of these collections. Over the past 11 years, the USDA-ARS National Center for Genetic Resources Preservation (NCGRP) cryopreserved over 100 different pot...

  11. Rice blast evaluation of newly introduced germplasm

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic resistance to the rice blast fungus, Magnaporthe oryzae (anamorph Pyricularia grisea oryzae) was identified in newly introduced rice germplasm through quarantine when tested in artificially inoculated greenhouse and field nursery tests during the 2007 growing season. Of 229 accessions, 31 we...

  12. Phylogeography, genetic structure, and diversity in the dhole (Cuon alpinus).

    PubMed

    Iyengar, A; Babu, V N; Hedges, S; Venkataraman, A B; Maclean, N; Morin, P A

    2005-07-01

    The Asiatic wild dog or dhole was once very widely distributed across Asia but now has a very fragmented range. In this first genetic study of this little-known species, we obtained information on genetic diversity, phylogeography, and social structure using both mitochondrial control region sequencing and microsatellite genotyping of noninvasive faecal samples from wild populations, as well as from museum and captive samples. A pattern largely consistent with isolation by distance across the Asian mainland was observed, with no clear subspecies distinctions. However, two major phylogeographical groupings were found across the mainland, one extending from South, Central, and North India (south of the Ganges) into Myanmar, and the other extending from India north of the Ganges into northeastern India, Myanmar, Thailand and the Malaysian Peninsula. We propose a scenario involving glaciation events that could explain this pattern. The origin of the dhole populations in Sumatra and Java is enigmatic and requires further study. Very low levels of genetic diversity were observed among wild dholes from Baluran National Park in Java, Indonesia, but in contrast, high levels were observed in Mudumalai Wildlife Sanctuary in South India. PMID:15969714

  13. Genetic variation in biomass traits among 20 diverse rice varieties.

    PubMed

    Jahn, Courtney E; Mckay, John K; Mauleon, Ramil; Stephens, Janice; McNally, Kenneth L; Bush, Daniel R; Leung, Hei; Leach, Jan E

    2011-01-01

    Biofuels provide a promising route of producing energy while reducing reliance on petroleum. Developing sustainable liquid fuel production from cellulosic feedstock is a major challenge and will require significant breeding efforts to maximize plant biomass production. Our approach to elucidating genes and genetic pathways that can be targeted for improving biomass production is to exploit the combination of genomic tools and genetic diversity in rice (Oryza sativa). In this study, we analyzed a diverse set of 20 recently resequenced rice varieties for variation in biomass traits at several different developmental stages. The traits included plant size and architecture, aboveground biomass, and underlying physiological processes. We found significant genetic variation among the 20 lines in all morphological and physiological traits. Although heritability estimates were significant for all traits, heritabilities were higher in traits relating to plant size and architecture than for physiological traits. Trait variation was largely explained by variety and breeding history (advanced versus landrace) but not by varietal groupings (indica, japonica, and aus). In the context of cellulosic biofuels development, cell wall composition varied significantly among varieties. Surprisingly, photosynthetic rates among the varieties were inversely correlated with biomass accumulation. Examining these data in an evolutionary context reveals that rice varieties have achieved high biomass production via independent developmental and physiological pathways, suggesting that there are multiple targets for biomass improvement. Future efforts to identify loci and networks underlying this functional variation will facilitate the improvement of biomass traits in other grasses being developed as energy crops. PMID:21062890

  14. Functional consequences of genetic diversity in Strongyloides ratti infections.

    PubMed Central

    Paterson, S; Viney, M E

    2003-01-01

    Parasitic nematodes show levels of genetic diversity comparable to other taxa, but the functional consequences of this are not understood. Thus, a large body of theoretical work highlights the potential consequences of parasite genetic diversity for the epidemiology of parasite infections and its possible implications for the evolution of host and parasite populations. However, few relevant empirical data are available from parasites in general and none from parasitic nematodes in particular. Here, we test two hypotheses. First, that different parasitic nematode genotypes vary in life-history traits, such as survivorship and fecundity, which may cause variation in infection dynamics. Second, that different parasitic nematode genotypes interact within the host (either directly or via the host immune system) to increase the mean reproductive output of mixed-genotype infections compared with single-genotype infections. We test these hypotheses in laboratory infections using genetically homogeneous lines of Strongyloides ratti. We find that nematode genotypes do vary in their survivorship and fecundity and, consequently, in their dynamics of infection. However, we find little evidence of interactions between genotypes within hosts under a variety of trickle- and single-infected infection regimes. PMID:12803891

  15. Genetic diversity of coronaviruses in Miniopterus fuliginosus bats.

    PubMed

    Du, Jiang; Yang, Li; Ren, Xianwen; Zhang, Junpeng; Dong, Jie; Sun, Lilian; Zhu, Yafang; Yang, Fan; Zhang, Shuyi; Wu, Zhiqiang; Jin, Qi

    2016-06-01

    Coronaviruses, such as severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, pose significant public health threats. Bats have been suggested to act as natural reservoirs for both these viruses, and periodic monitoring of coronaviruses in bats may thus provide important clues about emergent infectious viruses. The Eastern bent-wing bat Miniopterus fuliginosus is distributed extensively throughout China. We therefore analyzed the genetic diversity of coronaviruses in samples of M. fuliginosus collected from nine Chinese provinces during 2011-2013. The only coronavirus genus found was Alphacoronavirus. We established six complete and five partial genomic sequences of alphacoronaviruses, which revealed that they could be divided into two distinct lineages, with close relationships to coronaviruses in Miniopterus magnater and Miniopterus pusillus. Recombination was confirmed by detecting putative breakpoints of Lineage 1 coronaviruses in M. fuliginosus and M. pusillus (Wu et al., 2015), which supported the results of topological and phylogenetic analyses. The established alphacoronavirus genome sequences showed high similarity to other alphacoronaviruses found in other Miniopterus species, suggesting that their transmission in different Miniopterus species may provide opportunities for recombination with different alphacoronaviruses. The genetic information for these novel alphacoronaviruses will improve our understanding of the evolution and genetic diversity of coronaviruses, with potentially important implications for the transmission of human diseases. PMID:27125516

  16. Sézary Syndrome: Translating Genetic Diversity into Personalized Medicine.

    PubMed

    Chevret, Edith; Merlio, Jean-Philippe

    2016-07-01

    Sézary syndrome is probably the most studied cutaneous T-cell lymphoma subtype. Beyond the consensus criteria for Sézary syndrome diagnosis, Sézary cells display heterogeneous phenotypes and differentiation profiles. In the face of SS diversity, the great hope is to develop targeted therapies based on next-generation sequencing to define the genetic landscape of Sézary syndrome. Prasad et al. report on the use of exome sequencing and RNA sequencing to study selected CD4(+) blood cells from 15 patients with erythroderma Sézary syndrome, 14 of whom fulfilled the conventional criteria for diagnosis. The most common genetic abnormality, TP53 gene deletion on chromosome arm 17p and/or mutation, was observed in 58% of patients. However, mutations affecting PLCG1, STAT5B, GLI3, and CARD11 each were detected in only one individual. Nevertheless, Prasad et al. report single point mutations or copy number alterations in several new genes and in new fusion genes, with predicted biological relevance. This information underscores the diversity of genetic alterations and of the mechanisms of alterations of single genes. At the individual level, Sézary cells may combine alterations of genes involved in T-cell signaling, NF-kB and JAK-signal transducer and activator of transcription pathways, apoptosis control, chromatin remodeling, and DNA damage response. The therapeutic relevance of these potential targets needs to be evaluated with tests of function. PMID:27342034

  17. Range-edge genetic diversity: locally poor extant southern patches maintain a regionally diverse hotspot in the seagrass Zostera marina.

    PubMed

    Diekmann, Onno E; Serrão, Ester A

    2012-04-01

    Refugial populations at the rear edge are predicted to contain higher genetic diversity than those resulting from expansion, such as in post-glacial recolonizations. However, peripheral populations are also predicted to have decreased diversity compared to the centre of a species' distribution. We aim to test these predictions by comparing genetic diversity in populations at the limits of distribution of the seagrass Zostera marina, with populations in the species' previously described central diversity 'hotspot'. Zostera marina populations show decreased allelic richness, heterozygosity and genotypic richness in both the 'rear' edge and the 'leading' edge compared to the diversity 'hotspot' in the North Sea/Baltic region. However, when populations are pooled, genetic diversity at the southern range is as high as in the North Sea/Baltic region while the 'leading edge' remains low in genetic diversity. The decreased genetic diversity in these southern Iberian populations compared to more central populations is possibly the effect of drift because of small effective population size, as a result of reduced habitat, low sexual reproduction and low gene flow. However, when considering the whole southern edge of distribution rather than per population, diversity is as high as in the central 'hotspot' in the North Sea/Baltic region. We conclude that diversity patterns assessed per population can mask the real regional richness that is typical of rear edge populations, which have played a key role in the species biogeographical history and as marginal diversity hotspots have very high conservation value. PMID:22369278

  18. Host range, prevalence, and genetic diversity of adenoviruses in bats.

    PubMed

    Li, Yan; Ge, Xingyi; Zhang, Huajun; Zhou, Peng; Zhu, Yan; Zhang, Yunzhi; Yuan, Junfa; Wang, Lin-Fa; Shi, Zhengli

    2010-04-01

    Bats are the second largest group of mammals on earth and act as reservoirs of many emerging viruses. In this study, a novel bat adenovirus (AdV) (BtAdV-TJM) was isolated from bat fecal samples by using a bat primary kidney cell line. Infection studies indicated that most animal and human cell lines are susceptible to BtAdV-TJM, suggesting a possible wide host range. Genome analysis revealed 30 putative genes encoding proteins homologous to their counterparts in most known AdVs. Phylogenetic analysis placed BtAdV-TJM within the genus Mastadenovirus, most closely related to tree shrew and canine AdVs. PCR analysis of 350 bat fecal samples, collected from 19 species in five Chinese provinces during 2007 and 2008, indicated that 28 (or 8%) samples were positive for AdVs. The samples were from five bat species, Hipposideros armiger, Myotis horsfieldii, M. ricketti, Myotis spp., and Scotophilus kuhlii. The prevalence ranged from 6.25% (H. armiger in 2007) to 40% (M. ricketti in 2007). Comparison studies based on available partial sequences of the pol gene demonstrated a great genetic diversity among bat AdVs infecting different bat species as well as those infecting the same bat species. This is the first report of a genetically diverse group of DNA viruses in bats. Our results support the notion, derived from previous studies based on RNA viruses (especially coronaviruses and astroviruses), that bats seem to have the unusual ability to harbor a large number of genetically diverse viruses within a geographic location and/or within a taxonomic group. PMID:20089640

  19. Origin and Genetic Diversity of Diploid Parthenogenetic Artemia in Eurasia

    PubMed Central

    Maccari, Marta; Amat, Francisco; Gómez, Africa

    2013-01-01

    There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages. PMID:24376692

  20. Genetics, Genomics and Evolution of Ergot Alkaloid Diversity

    PubMed Central

    Young, Carolyn A.; Schardl, Christopher L.; Panaccione, Daniel G.; Florea, Simona; Takach, Johanna E.; Charlton, Nikki D.; Moore, Neil; Webb, Jennifer S.; Jaromczyk, Jolanta

    2015-01-01

    The ergot alkaloid biosynthesis system has become an excellent model to study evolutionary diversification of specialized (secondary) metabolites. This is a very diverse class of alkaloids with various neurotropic activities, produced by fungi in several orders of the phylum Ascomycota, including plant pathogens and protective plant symbionts in the family Clavicipitaceae. Results of comparative genomics and phylogenomic analyses reveal multiple examples of three evolutionary processes that have generated ergot-alkaloid diversity: gene gains, gene losses, and gene sequence changes that have led to altered substrates or product specificities of the enzymes that they encode (neofunctionalization). The chromosome ends appear to be particularly effective engines for gene gains, losses and rearrangements, but not necessarily for neofunctionalization. Changes in gene expression could lead to accumulation of various pathway intermediates and affect levels of different ergot alkaloids. Genetic alterations associated with interspecific hybrids of Epichloë species suggest that such variation is also selectively favored. The huge structural diversity of ergot alkaloids probably represents adaptations to a wide variety of ecological situations by affecting the biological spectra and mechanisms of defense against herbivores, as evidenced by the diverse pharmacological effects of ergot alkaloids used in medicine. PMID:25875294