Phaseolus acutifolius (tepary bean) is a heat- and drought-tolerant legume adapted to semi-arid environments with emerging genomic resources, yet the genetic architecture of biomass and nitrogen-related traits remains poorly resolved. Here, we aimed to resolve the genetic architecture of cover-crop-relevant traits in tepary bean, anticipating predominantly polygenic control but allowing for a major-effect component of flowering time. We assessed 206 accessions and four commercial checks for biomass, flowering time, leaf amino acids, and a Relative NUE-Index that integrates plant N uptake with seasonal soil N changes. Genotyping-by-sequencing produced 49,384 high-quality SNPs for multi-model genome-wide association studies (GWAS). The results show substantial natural variation across traits, enabling association mapping. Biomass-associated loci on chromosomes 6, 7, and 11 align with candidate genes involved in structural growth and development, including hydroxyproline-rich glycoproteins and carotenoid cleavage dioxygenase 1. Relative NUE-Index loci implicate trehalose-6-phosphate signaling and phosphatase activity, supporting a role for coordinated carbon-nitrogen regulation in NUE-related physiology. Leaf ureide and amino-acid profiles showed pronounced among-accession variation, providing a complementary physiological context for NUE-related trait variation. A major QTL on chromosome 3 for flowering time, near a BTB-domain gene, highlights a candidate region for phenology tuning in tepary bean. Overall, SNP data from GBS and GWAS reveal a largely distinct polygenic structure across traits in tepary bean, providing actionable loci and hypotheses for marker-assisted breeding and introgression toward resilient summer cover crop varieties.
Alla et al. (2026) studied this question.