Landscape Genomics of Bean Adaptation

The size of some gene banks is now so large that it prevents an effective characterization of its content. To address this issue, we propose an approach that combines the traditional agronomic and molecular characterization with geographic and ecological information (GAMA). This approach promises to identify germplasm adapted to certain biotic and abiotic conditions based on correlations with specific environmental conditions. In this research, we analyzed a set of 279 landraces of common bean (Phaseolus vulgaris) from Brazil with known geographic coordinates of origin. Following the standard agronomic and molecular (74 markers, mainly SSRs) characterization, the diversity of the sample was analyzed by GIS (Geographic Information System). Variables take into account included biome, soil fertility, soil slope, climate parameters (e.g., annual precipitation, cultivation precipitation and temperature). Grouping of landraces included gene pool (Andean vs. Mesoamerican), market types (based primarily on seed type), and Structure grouping (K = 5). Results show that 1) beans are mainly distributed in on average the Andean and Mesoamerican gene pool accessions had similar ecological distributions; 2) among market types, the “mulatinho” type stood out through its cultivation in more arid, hotter environments, whereas the "roxo" category constitutes a mesic control; 3) SAM analyses identified markers correlated with precipitation during the cultivation period (24 markers), mean annual temperature (5 markers), and altitude (1); 4) five markers were confirmed by FDIST2 analysis; and 5) Several regions of the genome showed clustering of significant markers for precipitation, temperature, and/or altitude. These analyses guide germplasm users towards specific accessions with potential tolerance to heat and drought; further research is needed to confirm these assessments but our data sp far represent a potential increase in the efficiency of characterization and utilization of large germplasm collections.