Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

Abstract

Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans’ yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r2sv), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.

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

“…Based on these initial studies, several GWAS have further been conducted for different traits of interest, such as yield, plant architecture, nutritional content of grains, cooking time, resistance to diseases, and tolerance to abiotic factors 7 , 32 , 37 – 47 . Some GWAS have been conducted in Brazil 37 , 40 , 48 , however, panels consisting of different genotypes, can contribute to a better understanding about the genetic diversity and relationships of the germplasm available for genetic breeding.…”

Genetic Mapping for Agronomic Traits in IAPAR 81/LP97-28 Population of Common Bean (Phaseolus vulgaris L.) under Drought Conditions

“…The phenotypic correlation coefficients for GY and other variables were higher in the NS experiment than in the DS experiment ( Table 3 ). Positive correlations between SYD and the yield components have previously been reported under drought conditions [ 8 , 33 , 34 , 35 ]. The GY was positively correlated with SYD (r = 0.73), NP (r = 0.65), and SW (r = 0.42).…”

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

“…Although several studies already identified QTNs associated with morpho-agronomic traits in common beans using GWAS (Nemli et al, 2014;Kamfwa et al, 2015;Moghaddam et al, 2016;Soltani et al, 2016;Nascimento et al, 2018;Resende et al, 2018;Lei et al, 2020;Wu et al, 2020), panels composed exclusively of common beans of Mesoamerican origin and adapted to environmental conditions in Brazil had not been sufficiently explored (Valdisser et al, 2020). Moreover, few studies using the GWAS multilocus approach have been conducted in common bean.…”