Determining Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces from Türkiye Using SSR Markers

Abstract

Assessment of genetic diversity among different varieties helps to improve desired characteristics of crops, including disease resistance, early maturity, high yield, and resistance to drought. Molecular markers are one of the most effective tools for discovering genetic diversity that can increase reproductive efficiency. Simple sequence repeats (SSRs), which are codominant markers, are preferred for the determination of genetic diversity because they are highly polymorphic, multi-allelic, highly reproducible, and have good genome coverage. This study aimed to determine the genetic diversity of 40 common bean (Phaseolus vulgaris L.) landraces collected from the Ispir district located in the Northeast Anatolia region of Türkiye and five commercial varieties using SSR markers. The Twenty-seven SSR markers produced a total of 142 polymorphic bands, ranging from 2 (GATS91 and PVTT001) to 12 (BM153) alleles per marker, with an average number of 5.26 alleles. The gene diversity per marker varied between 0.37 and 0.87 for BM053 and BM153 markers, respectively. When heterozygous individuals are calculated proportional to the population, the heterozygosity ranged from 0.00 to 1.00, with an average of 0.30. The expected heterozygosity of the SSR locus ranged from 0.37 (BM053) to 0.88 (BM153), with an average of 0.69. Nei’s gene diversity scored an average of 0.69. The polymorphic information content (PIC) values of SSR markers varied from 0.33 (BM053) to 0.86 (BM153), with an average of 0.63 per locus. The greatest genetic distance (0.83) was between lines 49, 50, 53, and cultivar Karacaşehir-90, while the shortest (0.08) was between lines 6 and 26. In cluster analysis using Nei’s genetic distance, 45 common bean genotypes were divided into three groups and very little relationship was found between the genotypes and the geographical distances. In genetic structure analysis, three subgroups were formed, including local landraces and commercial varieties. The result confirmed that the rich diversity existing in Ispir bean landraces could be used as a genetic resource in designing breeding programs and may also contribute to Türkiye bean breeding programs.

Genetic Diversity and Population Structure of the Peruvian Andean Legume, tarwi (Lupinus mutabilis), With High Quality SNPs

“…Genetic diversity indices of lupin, based on SNPs, is high among the nine populations sampled across the Peruvian Andes, which is concordant for individuals that are landraces, as reported for other landraces of rye [51], pea [52] , maize [53], rice [54,55], squash [56], bean [57], wheat [58]. The wealth and abundance among tarwi landraces can be explained due to their adaptation to local environments and diversity of grower´s choice [49].…”

Exploring I, bc-12 and bc-3 Gene Locus in Promising Common Bean Lines

“…Türkiye's historical position at the crossroads of the Palearctic region, both culturally and geographically, makes it potentially influential in the dissemination of common bean genotypes from Asia to Europe and Africa. Although Türkiye is not recognized as the primary origin or center of domestication for the common bean, the previous studies indicated a wide diversity in common bean germplasm from Türkiye (Nadeem et al, 2018;Haliloğlu et al, 2022;Özkan et al, 2022;Yeken et al, 2022). These studies revealed that the common landrace collection in Türkiye harbored a substantial amount of genetic diversity.…”

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

“…SSR molecular marker technology involves tandem repeat sequence consisting of 1–6 nucleotides as repeat units, which has excellent characteristics such as co-dominant inheritance, high polymorphism, good reproducibility, and stable and accurate results. It has emerged as a key molecular marker technology for plant genetic diversity analysis, population structure research, variety identification, and molecular ID construction [ 4 , 5 , 6 , 7 , 8 ].…”