Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing

Abstract

A common bean (Phaseolus vulgaris) diversity panel of 308 lines was established from local Spanish germplasm, as well as old and elite cultivars mainly used for snap consumption. Most of the landraces included derived from the Spanish common bean core collection, so this panel can be considered to be representative of the Spanish diversity for this species. The panel was characterized by 3099 single-nucleotide polymorphism markers obtained through genotyping-by-sequencing, which revealed a wide genetic diversity and a low level of redundant material within the panel. Structure, cluster, and principal component analyses revealed the presence of two main subpopulations corresponding to the two main gene pools identified in common bean, the Andean and Mesoamerican pools, although most lines (70%) were associated with the Andean gene pool. Lines showing recombination between the two gene pools were also observed, most of them showing useful for snap bean consumption, which suggests that both gene pools were probably used in the breeding of snap bean cultivars. The usefulness of this panel for genome-wide association studies was tested by conducting association mapping for determinacy. Significant marker–trait associations were found on chromosome Pv01, involving the gene Phvul.001G189200, which was identified as a candidate gene for determinacy in the common bean.

Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

“…The population structure of our accessions reflected the two independent domestication events that occurred, separating the common beans into Mesoamerican genotypes, characterized by a type S phaseolin, and Andean material, with a C or T phaseolin pattern [63]. In fact, the most probable number of groups in our structure analysis was K = 2, dividing these two sets of accessions, as already observed in other common bean germplasm collections [20,42]. Some admixed accessions between the two groups might have derived from hybridization events.…”

“…Therefore, the landrace´´Locale di Accettura´´, which was admixed in all the structure plots and isolated in the phylogenetic tree, could have been derived from a hybridization event. Hybridizations between Andean and Mesoamerican genepools are quite diffuse in the European common bean germplasm (> 40%), but with a lower frequency in Spain and Italy [28,42].…”

“…Prior to analysis, the SVS software v8.4.0 was used to trim the SNP dataset based on pairwise linkage disequilibrium (LD) between adjacent markers. The threshold was set at r 2 > 0.5, as reported in previous SNP analyses in the common bean [42,47].…”

“…The digestion of genomic DNA is performed using a single restriction enzyme [35,36], a combination of a single enzyme with random shearing [34,37], or two restriction enzymes [38,39]. The GBS technique was successfully optimized and used in the common bean for various purposes [40][41][42].…”

Uncovering Phenotypic Diversity and DArTseq Marker Loci Associated with Antioxidant Activity in Common Bean

“…This shows a rough estimation of extent of LD, however, highly significant threshold LD values (r 2 ≥ 0.2) are used for more precise LD calculation. Our results are in a disagreement with the findings of Campa et al [67], who stated that chromosome 9 shows maximum LD. Linkage disequilibrium measured r 2 plotted vs. p-value between pairs of DArTseq markers the studied germplasm showed a relatively bigger LD decay on LG6 ( Figure S3).…”