Diversity and genetic analysis through DArTseq in common bean(Phaseolus vulgaris L.) germplasm from Turkey

Abstract

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.

Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information

“…On average, 1,076.27 (6.89%) markers were identified per chromosome. These results are supported by earlier studies [ 32 – 56 – 58 ] reporting relatively more silicoDArT markers on common bean chromosome 2 and less number of markers on chromosome 6 [ 58 ]. However, our results made strong disagreement with Schroder et al [ 59 ], as they found maximum SNP markers on chromosome 8.…”

“…According to Singh et al [ 12 ], genotypes having seed size above 40g belongs to Andean gene pool and those with seed size below 40g are called Mesoamerican gene pool accessions. The occurrence of two gene pools in Turkish bean pool were confirmed in previous studies by the Nemli et al [ 32 ]. Similarly, Nemli et al [ 32 ] along with other scientific groups also came across the prevalence of Andean gene pool in Turkey and in Europe [ 9 – 53 ], which strongly supports the findings in the present work.…”

“…Valdisser et al [ 56 ] found PIC values from 0.23 to 0.5 using DArTseq markers, Blair et al [ 60 ] found 0.32 using SNPs, Wani et al [ 61 ] obtained 0.22–0.49 with SSR and Kumar et al [ 62 ] achieved 0.22–0.30 using AFLP markers. Mean PIC value (0.4) obtained in our study was much higher than obtained by the Nemli, et al [ 32 ] in their recent work on the characterization of Turkish common bean germplasm with DArTseq-generated SNP markers. The wider PIC range obtained in this work suggests a greater level of variation deriving probably from the use of larger number of high quality markers in a larger and diverse population.…”

“…The overall gene diversity over the entire germplasm was lower than in Gioia et al [ 19 ] working on the 256 European and 56 American landraces using chloroplast microsatellite (cpSSRs) and nuclear markers (phaseolin and Pv-shatterproof1). However gene diversity in the population B was higher than obtained by Nemli, et al [ 32 ] using DArTseq generated SNP markers in 173 accessions mainly from Turkey. The results in this study are in good agreement with previous findings [ 9 – 63 – 64 ] in terms of relative importance of the gene diversity of common bean accessions.…”

“…Northeast Anatolian region. Another study reported genetic diversity of 30 genotypes from two districts of Van province i.e., Ercis and Gevas [ 30 ], while Nemli et al [ 31 ] used iPBS markers for the characterization of the 67 Turkish common bean landraces, and, in their recent work, Nemli et al [ 32 ] used SNP markers for the determination of diversity in the Turkish common bean.…”