The GAMA Approach for the Analysis of Large Germplasm Collections: Genetic Diversity and Landscape Genomics of Common Bean (Phaseolus Vulgaris) Landraces in Brazil

Abstract Common bean (Phaseolus vulgaris L.) is an essential staple crop in the Brazilian diet, being the major source of dietary protein in this tropical country. In addition, Brazil is also one the biggest producer and consumer of this crop worldwide. Brazil covers a wide and diverse geographical area in South America, where common bean is cultivated both in tropical climates in the North and Central regions, or sub-tropical ones in the South. This climatic diversity in Brazil is reflected in the wide genetic diversity of Brazilian common bean landraces, which could represent an important resource for breeding improvement of this crop. In the current study, we characterized the genetic diversity, population structure and linkage disequilibrium in a collection of 274 georeferenced Brazilian landraces using Single Nucleotide Polymorphisms obtained with Genotype-By-Sequencing. We integrated geographic information system, climatic conditions, agronomic (market class information), and molecular diversity analyses, labeled here GAMA (Geographic Agronomic Molecular Approach), to identify patterns of selection in this collection. This combined landscape genomic analysis allowed the identification of candidate genes or genomic regions related to abiotic stress response in this species, but also possible donor accessions for drought and heat tolerance in this collection. This information can facilitate the pre-selection of smaller samples of Brazilian landraces diversity and identify candidate markers and genes for in-depth evaluation in breeding programs aimed at the improvement of this crop.