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.

Figure 1

Identification and annotation of 49,817 single nucleotide polymorphisms (SNPs) obtained from the genotyping of 219 common bean accessions. (a) Distribution of SNP density along the common bean genome in a 200 kb sliding window. (b) Annotation of SNPs and proportion of genomic traits. (c) Transversion/transition ratio. Figure produced in R v.4.0.

Figure 2

Genetic differentiation between Andean and Mesoamerican gene pools. (a) Principal component analysis of 219 accessions of Andean and Mesoamerican origin including different commercial groups (black, carioca, cream, red, etc.). (b) Venn diagram of the total set of SNPs and SNPs belonging to the Andean and Mesoamerican groups. (c) Distribution of the Fst values of each SNP (colored according to the population in which they occur). (d) Total number of differentiating SNPs on each chromosome and number of differentiating SNPs located within genes. (e) Distribution of the 11,805 differentiating SNPs of the Andean and Mesoamerican groups along the common bean genome in a 200 kb sliding window. Figures (a), (c), (d) and (e) produced in R v.4.0 and Figure b produced in JVENN (http://jvenn.toulouse.inra.fr).

Figure 3

Analysis of the population structure using 219 accessions belonging to the Brazilian common bean diversity panel with K = 3: (1) corresponds to the group of common beans of Andean origin; (2) mostly formed by Mesoamerican accessions of black, cream, red, and other seed tegument colors; (3) mostly formed by Mesoamerican accessions from the carioca commercial group; and (4) mostly formed by Mesoamerican accessions with membership coefficient < 0.6 for the previous groups. Figure produced in R v.4.0.

Figure 4

Principal component analyses and Venn diagrams. (a) Principal component analysis of 207 accessions of common beans of Mesoamerican origin with different seed tegument colors. (b) Venn diagram for the different sets of SNPs related to seed tegument color. (c) Principal component analysis of 207 accessions of common beans from different research institutions. (d) Venn diagram for the different sets of SNPs related to the institutions of origin. Figure (a) and (c) produced in R v.4.0 and Figures b and d produced in JVENN (http://jvenn.toulouse.inra.fr).

Figure 5

Dendrogram showing the genetic relatedness among 207 common bean accessions belonging to the Brazilian Diversity Panel. The different colors identify the accessions according to the color of the seed tegument. Purple = black tegument, Orange = carioca-type tegument, Green = cream tegument, Pink = red tegument, and Blue = others. Figure produced in FigTree v1.4.4.

Figure 6

Analysis of linkage disequilibrium (LD) decay as a function of physical distance without correction (r²), and after correcting for population structure (r²_s), relatedness (r²_v), and for both population structure and relatedness (r²_vs). Figure produced in R v.4.0.