RNA Sequencing of Laser-Capture Microdissected Compartments of the Maize Kernel Identifies Regulatory Modules Associated with Endosperm Cell Differentiation

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.

OPAQUE11 Is a Central Hub of the Regulatory Network for Maize Endosperm Development and Nutrient Metabolism

“…Second, expression of AtZOU is restricted to the ESR region 473 , but according to our immunofluorescence analysis, O11 474 accumulates in both the ESR and the SE ( Figure 6A). LCM RNA-Seq data 475 (Zhan et al, 2015) (Supplemental Table 3) and quantitative PCR (qPCR) 476 results from another study (Grimault et al, 2015) support our observations. were determined by ChIP-Seq analysis in developing maize kernels ( Figure 7B 486 to 7E).…”

“…Yang 337 et al (2008) showed that zou endosperm fails to separate from the embryo, preferential ESR expression were identified (Zhan et al, 2015). We overlapped 344 the reported ESR-specific genes with the 259 high-confidence potential targets 345 of O11, revealing five ESR-specific genes regulated by O11 ( floral organ development (Ambrose et al, 2000) and AtWOX2, the ortholog of 376 ZmWOX2 in Arabidopsis, is involved in embryo apical patterning and 377 cotyledon development (Wu et al, 2007;Breuninger et al, 2008;Lie et al, 378 2012).…”

“…The yeast transactivation assay was performed as previously described 862 (Qiao et al, 2016 Dual-LUC assays using N. benthamiana plants were performed as described 871 previously (Hellens et al, 2005;Liu et al, 2008). The luciferase activity of the LCM RNA-Seq data (Zhan et al, 2015). …”

NKD Transcription Factors Are Central Regulators of Maize Endosperm Development

“…Maize endosperm consists of seven cell types as defined by histology and 39 gene expression patterns (Leroux et al, 2014;Zhan et al, 2015). In mature kernels, the 40 major cell types include starchy endosperm (SE), basal endosperm transfer (BET) cells 41 and aleurone (AL) .…”

PPIM: A Protein-Protein Interaction Database for Maize

“…The metabolic network MaizeCyc , containing enzyme catalysts, proteins, and other metabolites, has also been constructed. Focusing on maize kernel development, the expression quantitative trait loci have been investigated with RNA sequencing data (Fu et al, 2013), and the gene regulations underlying endosperm cell differentiation have been identified (Zhan et al, 2015).…”