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

Abstract

The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.

Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

“…Polymorphisms were widely distributed across the 11 chromosomes and were highly correlated with the length and number of genes on each chromosome. The transition/transversion rate was consistent with that observed in other studies on common bean and other species 28 , 35 , 52 , 53 . Transitions are usually more frequent than transversions in several species, which indicates that the former are better tolerated during natural selection, which may be due to the fact that they are synonymous mutations in protein-coding sequences 29 , 54 .…”

“…Genetic differentiation between common bean accessions based on the gene pool has been well documented in several previous studies 3 , 34 , 35 , 57 – 60 . The relationship between the genetic similarity of the Mesoamerican accessions and the color of the seed tegument was also observed by Valdisser et al 61 and Gioia et al 62 .…”

“…In the present study, 11% of all the candidate genes for domestication harbored differentiating SNPs. These genes have also been identified in other studies aimed at finding selection signatures between the Andean and Mesoamerican 34 , 35 accessions. The candidate genes for domestication are directly or indirectly associated with the main characteristics that distinguish the two gene pools, such as flowering time, plant size, and seed size.…”

“…Because LD may affect the inference of the population structure, an LD filter was further applied, which resulted in a decrease of the number of SNPs. This is due to the fact that the common bean is an autogamous plant with very long blocks of markers in LD 35 , 55 , 56 .…”

Genetic Diversity, Nitrogen Fixation, and Water Use Efficiency in a Panel of Honduran Common Bean (Phaseolus vulgaris L.) Landraces and Modern Genotypes

“…We identified several regions on chromosomes Pv02, Pv07, Pv09, and Pv11 where F ST values exceeded 0.5. Similarly, in a study of genetic diversity of Italian bean landraces, Lioi et al [ 64 ] reported that genomic regions related to domestication were concentrated on Pv02, Pv07, and Pv09 for Mesoamerican types. For comparisons between wild and domesticated bean landraces, Papa et al [ 65 ] also reported significantly larger levels of F ST differentiation around genomic regions associated with domestication.…”