Genome-wide association study of photosynthetic pigment content in peanut (Arachis hypogaea L.)

Abstract Improving the photosynthetic capacity could increase crop yields but is particularly challenging in C3 crops. Photosynthetic pigments are important for photosynthesis; however, their genetic basis at the seedling and flowering stages in peanuts (Arachis hypogaea L.) is unclear. In the present study, 241 peanut accessions were genotyped using whole-genome re-sequencing and phenotyped for 4 photosynthetic pigment-related traits across 5 environments. A genome-wide association study of 2,110,659 single nucleotide polymorphisms (SNPs) was performed, and 149 and 426 SNPs were associated with photosynthetic pigment-related traits based on the best linear unbiased estimation values, including 93 and 242 quantitative trait loci identified at the seedling and flowering stages, respectively. Furthermore, 19 genes were screened using gene-based association analysis, and two novel candidate genes (Arahy.VMJ95M and Arahy.YWY61J) were identified using RNA sequencing. Arahy.VMJ95M, encoding the photosystem I P700 chlorophyll A-binding protein, was linked to the leading SNP 04-121558770, which was associated with Chl b and Car content. Meanwhile, Arahy.YWY61J encoding the terpene synthase 14, was linked to the leading SNP 20-6416174, which was associated with Chl a and Chl b content. Two haplotypes of the two genes encoded distinct phenotypes considering photosynthetic pigment content in the peanut accessions. These findings will contribute to the understanding of genetic and molecular mechanisms underlying variations in photosynthetic pigments and benefits the improvement of photosynthetic efficiency using marker-assisted breeding in peanuts.