Transcriptomic Variations and Network Hubs Controlling Seed Size and Weight During Maize Seed Development

Abstract

To elucidate the mechanisms underlying seed development in maize, comprehensive RNA-seq analyses were conducted on Zhengdan1002 (ZD1002), Zhengdan958 (ZD958), and their parental lines during seven seed developmental stages. We found that gene expression levels were largely nonadditive in hybrids and that cis-only or trans × cis pattern played a large role in hybrid gene regulation during seed developmental stage. Weighted gene co-expression network (WGCNA) analysis showed that 36 modules were highly correlated (r = −0.90–0.92, p < 0.05) with kernel weight, length, and width during seed development. Forty-five transcription factors and 38 ribosomal protein genes were identified as major hub genes determining seed size/weight. We also described a network hub, Auxin Response Factor 12 of maize (ZmARF12), a member of a family of transcription factor that mediate gene expression in response to auxin, potentially links auxin signal pathways, cell division, and the size of the seeds. The ZmARF12 mutant exhibited larger seed size and higher grain weight. ZmARF12 transcription was negatively associated with cell division during seed development, which was confirmed by evaluating the yield of protoplasts that isolated from the kernels of the mutant and other inbred lines. Transient knock-down of ZmARF12 in maize plants facilitated cell expansion and division, whereas transient silencing of its potential interactor ZmIAA8 impaired cell division. ZmIAA8 expression was repressed in the ZmARF12 over-expressed protoplasts. The mutant phenotype and the genetics studies presented here illustrated evidence that ZmARF12 is a cell division repressor, and potentially determines the final seed size.

Genome-wide identification of ZmMYC2 binding sites and target genes in maize

“…Auxin biosynthesis genes, ZmYucca6 and ZmYucca9 were reported to participate into root geotropism and lodging resistance [ 37 ]. Auxin signaling genes, ZmIAA8 , ZmGH3.2 , ZmGH3.8 and ZmIAA8 were involved in drought resistance and seed development, and ZmGH3.2 and ZmGH3.8 with roles in seed aging or leaf senescence, respectively [ 38 – 41 ]. ABA synthesis gene ZmNCED3 was also identified in drought response and regulated by ZmMYC2 directly here (Fig.…”

Transcriptome and co-expression network revealed molecular mechanism underlying selenium response of foxtail millet (Setaria italica)

“…The soft threshold power β was set at five, and mergeCutHeight = 0.4 was used to merge similar modules. If the p-value of the module-trait association is 0.05, then the module is defined as significant ( Wang et al., 2022 ). The OmicShare tool2 ( https://www.omicshare.com/ ) was used to map the network visualization of genes within the module.…”

New insights into light spectral quality inhibits the plasticity elongation of maize mesocotyl and coleoptile during seed germination

“…The maize cv. Zheng58 is a representative inbred line, derives from the Reid heterotic group, with superior drought tolerance ( Wang et al., 2022 ). The seeds of cv.…”

“…For which the soft threshold power β was set as nine, and mergeCutHeight = 0.4 was used to merge similar modules. A module was defined as significant if the p -value for module-trait association was 0.05 ( Wang et al., 2022 ). The OmicShare tool2 ( https://www.omicshare.com/ ) was used to map the network visualization of genes within the module, and genes with high co-expression connection within the module were filtered, and Cytoscape v.3.7.1 (Seattle, WA, USA) was used to visualize co-expression network.…”