Genome-Wide Association Study of Leaf Chlorophyll Content Using High-Density SNP Array in Peanuts (Arachis hypogaea L.)

The content of chlorophyll, a fundamental component required for photosynthesis in plants, has been widely studied across crop species. In this study, we aimed to evaluate the genetic diversity of 453 peanut accessions. We evaluated the evolutionary relationships using a genome-wide association study (GWAS) of leaf color data based on chlorophyll content analysis using the Axiom_Arachis array containing 58K single-nucleotide polymorphisms (SNPs). We identified seven SNPs as being significantly associated with leaf chlorophyll content on the chromosomes Aradu.A02, Aradu.A08, Araip.B02, Araip.B05, Araip.B06, and Araip.B08 in a GAPIT analysis. The SNP AX-176820297 on Araip.B05 was significantly linked with leaf chlorophyll content across the seasons. The Arahy.SDG4EV gene was detected to be in linkage disequilibrium (LD) with the significant SNPs, and its expression was significantly correlated with leaf chlorophyll content. The results of the current study provide useful and fundamental information with which to assess genetic variations in chlorophyll content and can be utilized for further genetic and genomic studies and breeding programs in peanuts.

Automated summary

This study aimed to evaluate the genetic diversity of peanut accessions and identified several SNPs associated with leaf chlorophyll content. The study also found a significant correlation between a specific SNP and leaf chlorophyll content across seasons. The expression of the Arahy.SDG4EV gene was also significantly correlated with leaf chlorophyll content. These findings provide valuable information for assessing genetic variations in chlorophyll content and can be used for further genetic and genomic studies and breeding programs in peanuts.