RNA-Seq-based gene expression analysis of seed protein and sulfur amino acid accumulation in developing pea seeds

This research aims at identifying candidate genes associated with the accumulation of seed protein and sulfur amino acids (SAAs) by comparing the expression profile of genes in developing seeds of pea (Pisum sativum L.) lines. Lines were selected from PR-25, a recombinant inbred line population, derived from a cross between CDC Amarillo and CDC Limerick. The selected lines were high seed protein concentration (SPC) line PR-25-69, high SAA line PR-25-53, and low SPC and low SAA line PR-25-6. These lines were grown in a phytotron chamber, and developing seeds collected from three biological replicates of each line at 7, 14, 21, and 28 days after anthesis were used for RNA sequencing. By comparison of the gene expression profiles between SPC contrasting lines (PR-25-69 vs. PR-25-6) and SAAs contrasting lines (PR-25-53 vs. PR-25-6), 4920 differentially expressed genes (DEGs) were identified over the four time points. Of these, 2798 DEGs were downregulated and 2122 DEGs were upregulated compared to control (PR-25-6). The expression levels of the identified DEGs varied from log₂ twofold to log₂ 10-fold. Extensive transmembrane activities, including transportation of amino acids and proteins, were seen in the results of GO analyses. Downregulated DEGs represented 78 significant GO terms, while upregulated DEGs represented 52 significant GO terms. Some distinct biological processes were exclusively present in upregulated DEGs, for instance, reproduction and nutrient reservoir activities. Future studies will involve genetic variant analyses and the development of genetic markers based on the candidate genes.