Genome-Environment Association Analysis for Bio-Climatic Variables in Common Bean (Phaseolus vulgaris L.) from Brazil

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.

Genetic structure and first genome‐wide insights into the adaptation of a wild relative of grapevine, Vitis berlandieri

“…GEA studies have detected associations between genetic factors and specific environmental conditions in nature, revealing markers responsible for driving local adaptation or “ecoclines” (Huxley, 1938). This method led to the detection of QTL associated with broad environmental traits in Arabidopsis (Frachon et al, 2018), barley (Chang et al, 2022), sorghum (Lasky et al, 2015; Menamo et al, 2021), sunflower (Todesco et al, 2020), bean (Ariani & Gepts, 2019; Elias et al, 2021), five alpine Brassicaceae species (Zulliger et al, 2013), and strawberry (Hu et al, 2022). Moreover, these markers can be genotyped in germplasm collections to improve estimates of the genetic diversity present in the collection and to select the best candidates for breeding programs.…”