Identification of photosynthetic pigment contents related genes in peanut (Arachis hypogaea L.) by GWAS and RNA-seq

Photosynthetic pigments are indispensable for light absorption and electron transfer in photosynthesis, which is essential for increasing crop productivity. However, genetic basis of photosynthetic pigment contents in peanuts ( Arachis hypogaea L.) at seedling and flowering stages remains poorly understood. In this study, an association panel of 241 peanut accessions was assayed for four photosynthetic pigment contents, including chlorophyll a (Chl a), chlorophyll b (Chl b), total chlorophyll (Chl a + b) and carotenoids (Car) across five environments. A total of 2,110,659 high-quality single nucleotide polymorphisms (SNPs) were obtained by whole-genome re-sequencing. A genome-wide association study was performed based on the best linear unbiased estimation values of four photosynthetic pigment contents. In total, 23 and 45 quantitative trait loci (QTLs) were associated with four photosynthetic pigment contents at the seedling and flowering stages, respectively, with eight QTLs associated with multiple traits. Thirty-two genes were identified within these QTL regions. Furthermore, through RNA-seq analysis of two peanut accessions with contrasting photosynthetic pigments contents, 3829 and 4972 differentially expressed genes were detected at seedling and flowering stages, respectively. Two candidate genes, Arahy.YWY61J and Arahy.VMJ95M , were differently expressed at flowering stages. Haplotype analysis suggested that Arahy.YWY61J was involved in Chl a and Chl b contents; and Arahy.VMJ95M gene was involved in Chl b and Car synthesis of peanut leaves. 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.