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- MakaleAçık Erişim2017Scopus SJRQ1Diversity and genetic analysis through DArTseq in common bean (Phaseolus vulgaris L.) germplasm from Turkey
Nemlı, Seda; Kaygisiz Aşçioğul, Tansel; Ateş, Duygu; Eşıyok, Dursun; Tanyolaç, Muhammed Bahattin
The common bean (Phaseolus vulgaris L.) is the most consumed food legume in the world and is a major source of dietary protein, carbohydrates, and valuable micronutrients, especially in developing countries. Diversity Arrays Technology (DArTseq), based on genome reduction with restriction enzymes, provides a rapid, high-throughput, and cost-effective tool capable of generating thousands of genotyped single nucleotide polymorphisms (SNPs) for a genome-wide analysis of genetic diversity. In this study, we aimed to characterize common bean accessions using SNPs detected by a DArTseq approach. A total of 43,018 SNPs were identified from 173 common bean accessions, including Andean and Mesoamerican genotypes. After filtering raw and redundant data, a total of 16,366 SNPs were considered for further analyses. According to population structure analysis, the genotypes were roughly divided into 2 gene pools of Andean and Mesoamerican types. Pairwise fixation index (Fst) values were calculated to resolve the differentiation between populations. This study demonstrated that discovering SNPs from the whole genome is a potential resource for identifying naturally diverse accessions and also the information could be used in breeding programs to develop new common bean varieties.
AtıfScopus19WoS18OpenAlex24TR Dizin3
İncele - MakaleYalnız künye2015Scopus SJRQ3Determination of the population structure of common bean (Phaseolus vulgaris L.) accessions using lipoxygenase and resistance gene analog markers
Nemli, Seda; Kutlu, Burcu; Tanyolac, Bahattin
The common bean (Phaseolus vulgaris L.) is an important food legume throughout the world. Because of the conservation across different plant species, it is possible to evaluate the degree of genetic diversity in the common bean using gene-based marker techniques. The lipoxygenase (LOX) and resistance gene analog (RGA) genes play an important role in the response to biotic and abiotic stresses. Eighty-six common bean accessions were genotyped using gene-based LOX and RGA markers. The total number of polymorphic bands ranged from 193 for LOX to 17 for RGA markers. We detected considerable diversity with a mean of 8.7 alleles per primer for the LOX analysis. For the RGA markers, the number of alleles per polymorphic locus varied from 1 to 4 with an average allele number of 2.8. The genetic similarity between the accessions based on the LOX and RGA markers ranged from 0.12 to 0.55. Using STRUCTURE, 3 groups were revealed among the accessions. The results of this study should provide valuable information for future studies on the genetic diversity of common bean accessions and for association mapping studies examining the relationships between the genotypic and phenotypic traits related to the stress response.
AtıfScopus3WoS3OpenAlex4İncele - MakaleAçık Erişim2015Scopus SJRQ2Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers
Nemli, Seda; Kianoosh, Tala; Tanyolaç, Muhammed Bahattin
The common bean (Phaseolus vulgaris L.) is an important crop throughout the world and is highly recommended for many developing countries due to its nutritional components. A retrotransposon-based DNA marker system, interprimer binding sites (iPBSs), developed from reverse transcriptase primer binding sites, was used to determine genetic diversity in common bean accessions. The genetic polymorphism and effectiveness of the marker system were evaluated. A total of 180 polymorphic bands were detected using 47 iPBS primers among 67 common bean accessions, with an average of 4 polymorphic fragments per primer. The genetic similarity between accessions was calculated using the software NTSYS-pc and ranged from 0.09 to 0.99. The average polymorphism information content value for the iPBS markers was 0.73. A model-based clustering method classified the common bean accessions into 4 populations using STRUCTURE software. The results indicated that the iPBS marker method can successfully determine the genetic diversity level in common bean accessions.
AtıfScopus63WoS60OpenAlex56TR Dizin12İncele