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

An integrated GWAS and transcriptome analysis revealed the genetic basis of photosynthetic pigment contents in peanuts and identified two candidate genes, Arahy. YWY61J and Arahy. VMJ95M, that play a role in the natural variation in chlorophyll and carotenoid accumulation. Photosynthetic pigments are indispensable for light absorption and electron transfer in photosynthesis, which directly impacts crop productivity. However, the genetic basis of photosynthetic pigment content in peanuts (Arachis hypogaea L.) at the seedling and flowering stages remains poorly understood. In this study, an association panel of 241 peanut accessions was assayed to identify genes related to four photosynthetic pigment contents, namely, 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 resequencing. A genome-wide association study (GWAS) was performed on the basis of the best linear unbiased estimation values of the contents of the four photosynthetic pigments. In total, 23 and 45 quantitative trait loci (QTLs) were associated with the four photosynthetic pigment contents at the seedling and flowering stages, respectively. Furthermore, through RNA-seq analysis of two peanut accessions whose photosynthetic pigment contents differed, 3829 and 4972 differentially expressed genes were detected at the seedling and flowering stages, respectively. Seventeen differentially expressed genes were identified through the integration of the QTL-associated genes and RNA-seq data. Subsequent haplotype analysis revealed that Arahy. YWY61J was involved in Chl a and Chl b synthesis and that Arahy.VMJ95M was involved in Chl b and Car synthesis in peanut leaves. Overall, this study provides new insights into the genetic and physiological regulation of photosynthetic pigment accumulation and offers valuable candidate genes for improving photosynthetic efficiency through marker-assisted breeding of peanuts.