Genotypic and multi-environment phenotypic evaluation of the lima bean USDA National Plant Germplasm System collection

Lima bean (Phaseolus lunatus L.) is an economically and agronomically important grain legume. Lima beans (or limas) show a range of climatic adaptations with independent domestications in the Andes (large-seeded) and Mesoamerica (small- or medium-seeded). We generated and integrated genotypic and comprehensive field- and laboratory-based phenotypic information for the available accessions in the USDA National Plant Germplasm System collection across multiple environments to inform germplasm utilization in breeding. A total of 810 accessions were genotyped using short-read, low-coverage sequencing. Accession geographic origin and domestication explained population structure. A partially overlapping subset of the panel (n=141-308) was field-evaluated across two years in each of Davis, CA, Central Ferry, WA, and Coachella Valley, CA (the latter was fall-planted for evaluation of photoperiod-sensitive accessions) to assess trait performance in contrasting environments. Agronomic traits such as determinacy and flowering time, and seed traits such as seed coat color and hundred-seed weight, were scored. Macronutrient traits (protein, starch, fat, and ash content) were measured on dry (mature) harvested grain via near-infrared spectroscopy. Genome-wide association analyses identified loci significantly associated with descriptive, agronomic, and seed traits, including orthologs of known genes in common bean and novel candidate regions. Genomic predictive abilities were moderate to high for key traits. Finally, we established a conditional core collection that was constrained to include 211 extensively phenotyped accessions and for which 91 supplemental accessions were selected to maximize genetic diversity from among the genotyped accessions. Overall, these resources provide a foundation to support genomics-assisted breeding of limas.