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

Abstract

Brazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.

Genome-wide association study for grain mineral content in a Brazilian common bean diversity panel

“…The distinction of two groups broadly corresponding to the commercial groups of black and carioca common beans was already used in several studies (Valdisser et al 2016;Gioia et al 2019;Del ni et al 2021). In contrast to conventional QTL mapping, association mapping is based on unstructured populations; consequently, it is fundamental to consider the population structure and relationship between individuals to prevent false associations due to the confounding effects of population mixture (Oraguzie et al 2007).…”

Genetic diversity of Norway spruce ecotypes assessed by GBS-derived SNPs

“…However, optimal settings are not straightforward and vary widely among studies 75 – 78 . The only exception is minor allele frequency (MAF) as in similar studies it is conventionally set to 0.05 79 – 81 . However, settings to different thresholds (0.01 and 0.02) are also reported.…”

Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean

“…In all, 178 Mesoamerican common bean accessions belonging to the BDP were evaluated (Delfini et al, 2021a). This panel consists of accessions that represent a large part of the variability present in Brazil and are adapted to tropical growing conditions.…”

“…The genotyping-by-sequencing (GBS) technique was used to obtain the SNPs. The methodology used, as well as the results 1 https://www.r-project.org/ of the population structure and linkage disequilibrium (LD) analyses, are detailed in a previous work (Delfini et al, 2021a). In summary, GBS was conducted using the restriction enzyme CviAII (Ariani et al, 2016(Ariani et al, , 2017 and the data were imputed using Beagle software version 5 (Browning and Browning, 2016).…”