Domestication has altered gene expression in pea seed coat

In angiosperms, the mature seed consists of an embryo (E), a seed coat (SC), and, in many cases, an endosperm. In contrast to knowledge about embryo and endosperm, we have relatively little knowledge of SC, especially at the genomics level. In this study, we analyzed the gene expression during seed development using the panel of cultivated and wild pea genotypes. We report the comprehensive gene expression changes related both to development as well as domestication status. Analysis of seed developmental stages revealed extensive modification of gene expression between wild pea progenitor and cultivated pea crop. A significant difference in gene expression dynamics appeared between early and late developmental stages D1, D2, and D3, D4, D5 in wild pea genotypes, where the expression was increased 3-5-fold and 5-10-fold, respectively. Our work extends knowledge about the role of the seed coat during pea seed development. We described gene expression dynamic resulting in specific metabolic profiles providing new insight into pea domestication. To obtain spatial and temporal representation, we performed RNA sequencing analysis of isolated seed tissues (SC and E) at 5 developmental stages (D1-5). There were three genotypes representing wild (P. elatius, JI64, JI261, JI1794), two domesticated (P. sativum, JI92 landrace and cv. Cameor) and Ethiopian pea P. abyssinicum (PI358617). Reads from each sample were mapped to the pea reference genome (Cameor v1.0).