Domestication has altered gene expression in pea seed coat. 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. Overall design: 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).

被子植物（angiosperms）的成熟种子由胚（embryo，缩写E）、种皮（seed coat，缩写SC）以及多数类群中存在的胚乳（endosperm）组成。相较于对胚与胚乳的已有认知，目前学界对种皮的了解仍较为匮乏，尤其是在基因组学（genomics）层面。本研究利用栽培与野生豌豆基因型（pea genotype）群体，解析了种子发育过程中的基因表达（gene expression）特征，报道了与种子发育进程及驯化状态均相关的全面基因表达变化。对种子发育阶段的比较分析显示，野生豌豆祖先种与栽培豌豆之间的基因表达模式存在广泛重塑。野生豌豆基因型的早期发育阶段（D1、D2）与晚期发育阶段（D3、D4、D5）之间的基因表达动态存在显著差异：前者基因表达量上调3~5倍，后者上调5~10倍。本研究拓展了人们对豌豆种子发育过程中种皮功能的认知，揭示了与特定代谢谱相关的基因表达动态，为豌豆驯化研究提供了全新视角。实验设计概述：为获取种子发育的时空表达图谱，本研究对5个发育阶段（D1~D5）下分离得到的种子组织（种皮SC与胚E）开展了RNA测序（RNA sequencing）分析。本次实验共设置3类豌豆基因型：3份野生豌豆基因型（均为P. elatius，编号JI64、JI261、JI1794）、2份栽培豌豆（P. sativum的JI92地方品种与Cameor栽培品种，cv. Cameor）以及埃塞俄比亚豌豆P. abyssinicum（编号PI358617）。所有样本的测序reads均比对至豌豆参考基因组（Cameor v1.0）。