Genome-wide association study revealed candidate genes associated with leaf size in alfalfa (Medicago sativa L.)

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial leguminous forages globally, known for its high yield and quality. Leaf size plays a crucial role in influencing its photosynthetic capacity, forage yield, and quality. Therefore, understanding the genetic factors regulating leaf size is of great importance for breeding new alfalfa varieties with improved yield and quality. In this study, we performed a genome-wide association study on four leaf size-related traits in 176 alfalfa germplasm resources to identify candidate genes associated with leaf size.

Phenotypic analysis revealed varying degrees of variation among the four traits, with coefficients of variation ranging from 3.43 to 36.84%. The broad sense heritability of these traits was found to be between 38.30% and 53.23%. Correlation analysis showed a significant positive correlation among the four traits (P < 0.01). The GWAS identified 39 SNPs associated with leaf size, distributed across eight chromosomes, of which 9 SNPs were linked to multiple traits. Haplotype analysis further confirmed that the number of superior alleles in each material was positively correlated with leaf area. Finally, we identified five genes near these 39 significant SNPs that are associated with leaf size or development.

Our findings provide new molecular markers for marker-assisted selection in alfalfa breeding programs. Moreover, this study provides a solid foundation for subsequent functional verification and genetic improvement in alfalfa.