Abstract
Abiotic stress is a limiting factor for common bean (Phaseolus vulgaris L.) production globally. The study of the genotypic, phenotypic, and bio-climatic variables in a broad set of accessions may assist the identification of genomic regions involved in the climatic adaptation of the common bean. We conducted a genotyping-by-sequencing analysis using 28,823 SNPs on 110 georeferenced common bean accessions from Brazil to discover associations between SNPs and bio-climatic indexes. The population structure analysis clustered the accessions into two groups corresponding to the Andean and Mesoamerican gene pools. Of the 19 bioclimatic variables, 17 exhibited a significant association with SNPs on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, Pv09, Pv10, and Pv11 of common bean. Ten candidate genes were associated with specific bio-climatic variables related to temperature and precipitation. The candidate genes associated with this significant Pv09 region encode a Platz transcription factor family protein previously reported to be an essential regulator of drought stress. The SNP markers and candidate genes associated with the bio-climatic variables should be validated in segregating populations for water stress, which could further be used for marker-assisted selection. As a result, bean breeding programs may be able to provide advances in obtaining drought-tolerant cultivars.
Highlights
Common bean (Phaseolus vulgaris L.) is one of the most important legume crops, providing 15% of the total daily calories and 36% of the complete daily protein in parts of Africa and the Americas [1,2,3,4]
A total of 180,515 single nucleotide polymorphisms (SNPs) identified in 175 common bean accessions were used for imputation, and were processed and analyzed using Next Generation Sequencing Eclipse Plugin (NGSEP) software
Genome–environment association studies were performed to identify genomic loci that are associated with climatic traits and to define the potential genetic architecture of these associations, assuming that it is the result of genetic adaptation to the respective climatic traits of the locations or regions of origin
Summary
Common bean (Phaseolus vulgaris L.) is one of the most important legume crops, providing 15% of the total daily calories and 36% of the complete daily protein in parts of Africa and the Americas [1,2,3,4]. The assumption is that genome–environment associations reflect the adaptation of common bean to abiotic stresses at the sampling sites This approach can be used to efficiently identify loci that control drought tolerance in bean germplasm [28,29]. Ariani et al [30] evaluated 246 accessions of wild Phaseolus vulgaris that were related to distribution and associated environmental changes These authors identified five subpopulations distributed in different dry forests and observed distinct distributions of temperature and rainfall, resulting in decreased local potential evapotranspiration. We evaluated common bean accessions from smallholder farmers settled in different Brazilian regions These accessions are cultivated annually and are exposed to adverse climatic conditions, such as high temperature and rainfall shortages during the critical growth phase, such as flowering and pod fill. Plants 2021, 10, 1572 structure, and identified QTLs associated with 19 bio-climatic variables obtained from the WorldClim database
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