DArTseq Analysis of Cypriot Common Bean Germplasm Unveils an Assortment of Unexplored Genetic Variability

TL;DR

This study explores the genetic diversity of Cypriot common bean varieties using SNP genotyping, revealing unique genetic traits useful for breeding and conservation.

Contribution

The first whole-genome genetic characterization of Cypriot common bean landraces using DArTseq-based SNP genotyping.

Findings

Cypriot bean varieties show moderate linkage disequilibrium and high private alleles.

Dry and green bean varieties form genetically distinct clusters.

Some varieties like 'Gliastro' exhibit high genetic diversity or inbreeding.

Abstract

The common bean (Phaseolus vulgaris L.) is a globally significant crop with a well-documented domestication history and a critical role in food security. Here, we present the first whole-genome genetic characterization of Cypriot common bean landraces and heirloom varieties, originated from remote mountainous areas, using DArTseq-based SNP genotyping. A total of 13,215 high-quality SNPs were investigated from 50 genotypes, indicating a moderate linkage disequilibrium, high incidences of private and fixed alleles, and an overall low heterozygosity. The comparison of varieties indicated that dry and green bean varieties consisted of genetically distinct clusters, reinforced by phylogenetic and Bayesian structure analyses. A few of the varieties, such as “Gliastro” and “Stringless Blue Lake,” demonstrated an intense genetic diversity and/or inbreeding, whereas others showed evidence of admixture. The outcomes highlight the unique genetic make-up of the Cypriot bean germplasm and its worth as a tool for breeding, conservation, and upcoming genomic-assisted improvement programs.

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