Genome-Wide Association Study for Seed Yield of Tepary Bean Using Whole-Genome Resequencing

Area of Science:

• Plant genetics and breeding
• Legume genomics
• Agronomy

Background:

• Tepary bean (Phaseolus acutifolius) is a highly drought- and heat-tolerant legume native to arid regions.
• Limited molecular markers for key agronomic traits like seed weight and yield hinder cultivar development.
• Understanding the genetic basis of these traits is crucial for improving tepary bean's agricultural value.

Purpose of the Study:

• To evaluate tepary bean accessions for 100-seed weight and seed yield.
• To identify single-nucleotide polymorphism (SNP) markers associated with these traits.
• To discover candidate genes influencing seed development in tepary bean.

Main Methods:

• Whole-genome resequencing of 153 tepary bean accessions to identify 230,000 high-quality SNPs.
• Association analysis using mixed linear model (MLM) and compressed mixed linear model (cMLM) for trait-marker identification.
• Candidate gene identification based on SNP associations with 100-seed weight and seed yield.

Main Results:

• Identified 5 (MLM) and 20 (cMLM) SNPs associated with 100-seed weight.
• Identified 1 (MLM) and 8 (cMLM) SNPs associated with seed yield.
• Candidate genes Phacu.CVR.002G320800.13 (SBP domain TF) and Phacu.CVR.009G294200.1 (peroxidase) linked to traits.

Conclusions:

• This study provides valuable SNP markers for marker-assisted selection in tepary bean breeding.
• Identified candidate genes are likely involved in tepary bean seed development.
• These findings contribute to the genetic understanding of seed traits in this important legume.