Genetic diversity and population structure of faba bean (Vicia faba) from Turkey

Faba bean (Vicia faba L.) is an important food and feed legume because of the nutritional value of its seed protein and starch content, good biomass, and high efficiency nitrogen fixation.This study analyzed the molecular genetic diversity and population structure of 101 Turkish faba bean accessions using simple sequence repeat (SSR) markers.A total of 32 SSR markers yielded 281 loci of which 277 (98.6%) were polymorphic.Mean dissimilarity between genotypes was 0.355, a relatively high value which was expected given faba bean’s large genome and limited breeding history.According to the results, faba bean individuals grouped into three main clusters based on both distance matrix (neighbor-joining algorithm) and model-based (population structure) clustering analyses.Clustering was not correlated with seed size or origin within Turkey.Six cultivars were included in the analysis and showed high genetic diversity compared with the landraces, as expected, given the fact that at least some of the cultivars were bred by hybridization.A total of 47 individuals were selected for the core collection to represent the diversity of Turkish faba bean germplasm.This core set encompasses material adapted to all growing regions and should be a priority for morphological characterization. © 2016, American Society for Horticultural Science.All rights reserved.Republic of Turkey's Ministry of Science, Industry and Technology (0424.STZ.2013-2

Bakla'da (Vicia faba L.) genetik çeşitlilik ve populasyon yapısının belirlenmesi

Thesis (Master)--Izmir Institute of Technology, Molecular Biology and Genetics, Izmir, 2015Includes bibliographical references (leaves: 46-51)Text in English; Abstract: Turkish and Englishix, 51 leavesFaba bean (Vicia faba L.) is an important legume species because of the high protein and starch content of its seeds. Broad bean can be grown in different climatic conditions and is an ideal rotation crop because of the symbiotic relationship between the plant and nitrogen fixing bacteria in its roots. Broad bean seeds are consumed as fresh vegetables in many countries throughout the world. However, the genetic diversity found in this germplasm has not yet been characterized and has not been systematically used in broad bean breeding programs. In this project, faba bean individuals obtained from International Center for Agricultural Research in the Dry Areas (ICARDA), Centre for Genetic Resources (CGN), Aegean Agricultural Research Institute (AARI), Nordic Gene Bank (NGB) and Australia (The University of Adelaide, Jeffrey Paull) were examined for their genetic diversity and population structure. For this purpose, 259 faba bean germplasm accessions were characterized using 32 SSR primers. A total of 302 polymorphic SSR fragments were analyzed. According the results, faba bean individuals were divided into two main clusters based on Neighbor-joining algorithm (r = 0.9062) with some clustering based on geographical origin as well as seed size. STRUCTURE 2.2.3 program was used to determine population structure. K was determined as 2 subpopulations. Cluster 1 had 87 individuals; cluster 2 had 162 individuals and 10 individuals were intermixed with results generally agreeing with the dendrogram analysis. A total of 45 well-characterized faba bean individuals were selected for the core collection to be used in breeding studies.Bakla (Vicia faba L.), tohumunun yüksek protein ve nişasta içeriğinden dolayı önemli bir baklagil türüdür. Bakla, değişik iklim koşullarında yetiştirilebilmektedir ve kök sisteminin azot bağlayan bakteriler ile oluşturduğu simbiyotik ilişki sayesinde ideal bir rotasyon bitki türüdür. Dünya genelinde pek çok ülkede taze sebze olarak tüketilir. Ancak, bakla germplazmlarının barındırdığı genetik çeşitliliğin karakterizasyonuna ilişkin çalışmalar yetersiz olup, bu baklagil türü için sistematik ıslah programları da oluşturulmuş değildir. Önerilen projenin esas amacı, ETAE, ICARDA, CGN, NGB ve Adelaide Üniversitesi’nden temin edilen bakla germplazmlarının genetik çeşitlilik ve populasyon yapısı bakımından kapsamlı bir şekilde incelemesinin yapılmasıdır. Bu amaçla, 259 bakla germplasmı 32 adet SSR primeri ile karakterize edilmiştir. Toplamda, 302 polimorfik SSR fragmenti analiz edilmiştir. Bakla örnekleri, Neighbor-joining algoritması (r = 0.9062) ile analizi sonucunda coğrafi orijin ve tohum büyüklüğüne göre iki ana kümeye ayrılmıştır. Popülasyon yapısının belirlenmesi için STRUCTURE 2.2.3 programı kullanılmıştır. K, 2 alt popülasyon olarak tespit edilmiştir. Küme 1’de 87, küme 2’de 162 ve hiçbir gruba bağlı olmayan 10 birey vardır. Genetik olarak iyi karakterize edilmiş 45 bakla bireyi çekirdek koleksiyon oluşturmak için seçilmiştir. Bu koleksiyon daha sonraki ıslah çalışmalarında kullanılabilecektir.SAN-TEZ and Polen Seed Compan

Genetic diversity and population structure of faba bean (Vicia faba) from Turkey

Faba bean (Vicia faba L.) is an important food and feed legume because of the nutritional value of its seed protein and starch content, good biomass, and high efficiency nitrogen fixation.This study analyzed the molecular genetic diversity and population structure of 101 Turkish faba bean accessions using simple sequence repeat (SSR) markers.A total of 32 SSR markers yielded 281 loci of which 277 (98.6%) were polymorphic.Mean dissimilarity between genotypes was 0.355, a relatively high value which was expected given faba bean’s large genome and limited breeding history.According to the results, faba bean individuals grouped into three main clusters based on both distance matrix (neighbor-joining algorithm) and model-based (population structure) clustering analyses.Clustering was not correlated with seed size or origin within Turkey.Six cultivars were included in the analysis and showed high genetic diversity compared with the landraces, as expected, given the fact that at least some of the cultivars were bred by hybridization.A total of 47 individuals were selected for the core collection to represent the diversity of Turkish faba bean germplasm.This core set encompasses material adapted to all growing regions and should be a priority for morphological characterization. © 2016, American Society for Horticultural Science.All rights reserved.Republic of Turkey's Ministry of Science, Industry and Technology (0424.STZ.2013-2

Relationship between geographical origin, seed size and genetic diversity in faba bean (Vicia faba L.) as revealed by SSR markers

Faba bean (Vicia faba L.) is an important legume species because of its high protein and starch content. Broad bean can be grown in different climatic conditions and is an ideal rotation crop because of the nitrogen fixing bacteria in its roots. In this work, 255 faba bean germplasm accessions were characterized using 32 SSR primers which yielded 302 polymorphic fragments. According to the results, faba bean individuals were divided into two main groups based on the neighbor-joining algorithm (r = 0.91) with some clustering based on geographical origin as well as seed size. Population structure was also determined and agreed with the dendrogram analysis in splitting the accessions into two subpopulations. Analysis of molecular variance (AMOVA) revealed high levels of within population genetic variation. Genetic similarity and geographical proximity were related with separation of European accessions from African and Asian ones. Interestingly, there was no significant difference between landrace (38%) and cultivar (40%) diversity indicating that genetic variability has not yet been lost due to breeding. A total of 44 genetically well-characterized faba bean individuals were selected for a core collection to be further examined for yield and nutritional traits.Republic of Turkey's Ministry of Science, Industry and Technology (0424.STZ.2013-2

Newly developed SSR markers reveal genetic diversity and geographical clustering in spinach (Spinacia oleracea)

Spinach is a popular leafy green vegetable due to its nutritional composition. It contains high concentrations of vitamins A, E, C, and K, and folic acid. Development of genetic markers for spinach is important for diversity and breeding studies. In this work, Next Generation Sequencing (NGS) technology was used to develop genomic simple sequence repeat (SSR) markers. After cleaning and contig assembly, the sequence encompassed 2.5% of the 980 Mb spinach genome. The contigs were mined for SSRs. A total of 3852 SSRs were detected. Of these, 100 primer pairs were tested and 85% were found to yield clear, reproducible amplicons. These 85 markers were then applied to 48 spinach accessions from worldwide origins, resulting in 389 alleles with 89% polymorphism. The average gene diversity (GD) value of the markers (based on a GD calculation that ranges from 0 to 0.5) was 0.25. Our results demonstrated that the newly developed SSR markers are suitable for assessing genetic diversity and population structure of spinach germplasm. The markers also revealed clustering of the accessions based on geographical origin with clear separation of Far Eastern accessions which had the overall highest genetic diversity when compared with accessions from Persia, Turkey, Europe, and the USA. Thus, the SSR markers have good potential to provide valuable information for spinach breeding and germplasm management. Also they will be helpful for genome mapping and core collection establishment.Izmir Institute of Technology Scientific Research Project, IYTE-BA