ArticleG3 (Bethesda, Md.)2026
Genotype-by-sequencing-enabled genome-wide association studies reveal genetic architecture of biomass and nitrogen modulation in tepary bean (Phaseolus acutifolius).
Article in G3 (Bethesda, Md.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Phaseolus acutifolius (tepary bean) is a heat- and drought-tolerant legume adapted to semiarid 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 4 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 multimodel genome-wide association studies. 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 nitrogen uptake efficiency-related physiology. Leaf ureide and amino acid profiles showed pronounced among-accession variation, providing a complementary physiological context for nitrogen uptake efficiency-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 genotyping-by-sequencing and genome-wide association studies 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.
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