RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation. Issue 3 (17th March 2015)

• Record Type: Journal Article
• Authors: Zhan, Junpeng; Thakare, Dhiraj; Ma, Chuang; Lloyd, Alan; Nixon, Neesha M.; Arakaki, Angela M.; Burnett, William J.; Logan, Kyle O.; Wang, Dongfang; Wang, Xiangfeng; Drews, Gary N.; Yadegari, Ramin
• Is Part Of: The Plant Cell. Volume 27:Issue 3(2015)
• Page Start: 513
• Page End: 531
• Publication Date: 2015-03-17
• DOI: 10.1105/tpc.114.135657
• Languages: English
• ISSNs: 1040-4651

Abstract

Abstract : RNA profiling of maize kernel compartments revealed coexpression modules for each major cell type in the endosperm, including a module regulating differentiation of the basal endosperm transfer layer. Abstract: Endosperm is an absorptive structure that supports embryo development or seedling germination in angiosperms. The endosperm of cereals is a main source of food, feed, and industrial raw materials worldwide. However, the genetic networks that regulate endosperm cell differentiation remain largely unclear. As a first step toward characterizing these networks, we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the maize ( Zea mays ) kernel. Comparisons of these mRNA populations revealed the diverged gene expression programs between filial and maternal compartments and an unexpected close correlation between embryo and the aleurone layer of endosperm. Gene coexpression network analysis identified coexpression modules associated with single or multiple kernel compartments including modules for the endosperm cell types, some of which showed enrichment of previously identified temporally activated and/or imprinted genes. Detailed analyses of a coexpression module highly correlated with the basal endosperm transfer layer (BETL ) identified a regulatory module activated by MRP-1, a regulator of BETL differentiation and function. These results provide a high-resolution atlas of gene activity in the compartments of the maize kernel and help to uncover the regulatory modules associated with the differentiation of the major endosperm cell types.