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.
Highlights
While seeds are well established as a major food source for humans around the world, they are important raw materials for industry
Seed morphology showed that ZD1002 and its paternal parent ZH71 exhibited larger seed size and heavier weights than ZD958 and C72, respectively, during the seven seed developmental stages (Figure 1A)
ANOVA and Duncan’s multiple comparisons of fresh kernel weight (FKW), dry kernel weight (DKW), ten-kernel length (TKL), and ten-kernel width (TKW) for DAP8–40 stages further revealed the differences between the seed morphological characteristics of ZH71 and C72 were obvious during the investigation, whereas the differences between Z588 and Z58 were comparatively smaller (Supplementary Figure 1; Supplementary Table 1)
Summary
While seeds are well established as a major food source for humans around the world, they are important raw materials for industry. Seed development, including seed size and weight, is crucial to the life cycle of higher plants, and impacts seed yields. It is important to understand the molecular mechanisms regulating the various aspects of seed development in maize, including their size and weight, to improve seed yields. High-resolution transcriptome technology has been used to monitor variations in gene expression during seed development. Transcriptomes of F1 hybrids and their parents allow the investigation of gene expression patterns and variation in regulation, which have been proposed to play a role in heterosis. Nonadditive patterns in hybrids deviate significantly from the mid-parent values, while additive expression patterns do not. The differences in genetic background, tissues, developmental stages, and methodologies result in nonadditive expression pattern being predominant in many hybrids (Hoecker et al, 2008; Jahnke et al, 2010; Zhao et al, 2019); whereas additive expression is the most common in other known cases (Stupar and Springer, 2006; Paschold et al, 2012; Hu et al, 2016; Zhou et al, 2019)
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