Comparative transcriptomic analysis of maize ear heterosis during the inflorescence meristem differentiation stage

Abstract

Background: Heterosis is widely used in many crops and is important for global food safety, and maize is one of the most successful crops to take advantage of heterosis. Gene expression patterns control the development of the maize ear, but the mechanisms by which heterosis affects transcriptional-level control are not fully understood.

Results: In this study, we sampled ear inflorescence meristems (IMs) from the single-segment substitution maize (Zea mays) line lx9801^hlEW2b, which contains the heterotic locus hlEW2b associated with ear width, as well as the receptor parent lx9801, the test parent Zheng58, and their corresponding hybrids Zheng58 × lx9801^hlEW2b (HY) and Zheng58 × lx9801 (CK). After RNA sequencing and transcriptomic analysis, 2531 unique differentially expressed genes (DEGs) were identified between the two hybrids (HY vs. CK). Our results showed that approximately 64% and 48% of DEGs exhibited additive expression in HY and CK, whereas the other genes displayed a non-additive expression pattern. The DEGs were significantly enriched in GO functional categories of multiple metabolic processes, plant organ morphogenesis, and hormone regulation. These essential processes are potentially associated with heterosis performance during the maize ear developmental stage. In particular, 125 and 100 DEGs from hybrids with allele-specific expression (ASE) were specifically identified in HY and CK, respectively. Comparison between the two hybrids suggested that ASE genes were involved in different development-related processes that may lead to the hybrid vigor phenotype during maize ear development. In addition, several critical genes involved in auxin metabolism and IM development were differentially expressed between the hybrids and showed various expression patterns (additive, non-additive, and ASE). Changes in the expression levels of these genes may lead to differences in auxin homeostasis in the IM, affecting the transcription of core genes such as WUS that control IM development.

Conclusions: Our research suggests that additive, non-additive, and allele-specific expression patterns may fine-tune the expression of crucial DEGs that modulate carbohydrate and protein metabolic processes, nitrogen assimilation, and auxin metabolism to optimal levels, and these transcriptional changes may play important roles in maize ear heterosis. The results provide new information that increases our understanding of the relationship between transcriptional variation and heterosis during maize ear development, which may be helpful for clarifying the genetic and molecular mechanisms of heterosis.

Keywords: Additive and non-additive gene expression; Allele-specific expression; Heterosis; Inflorescence meristem; Maize (Zea mays L.); Transcriptomics.

Fig. 1

Heterosis performance of mature ear width trait between Zheng58×lx9801^hlEW2b (HY) and Zheng58×lx9801 (CK). Scale bar is 5 cm

Fig. 2

Inflorescence meristem size in hybrids and inbred lines. A Scanning electron micrograph of 2–4-mm immature ears from Zheng58×lx9801^hlEW2b (HY) and Zheng58×lx9801 (CK), Bar = 200 μm. B Scanning electron micrograph of 2–4-mm immature ears from lx9801, lx9801^hlEW2b and Zheng58, Bar = 150 μm. C–D Comparison of inflorescence meristem size between lx9801, lx9801^hlEW2b, Zheng58, Zheng58×lx9801^hlEW2b and Zheng58×lx9801. * and ** indicate significant differences at the 0.05 and 0.01 probability levels. More than 10 individuals were measured for each inbred line, and 30 individuals were measured for the two hybrids

Fig. 3

Expression patterns of differentially expressed genes (DEGs). A Statistical analyses of DEGs between hybrids [Zheng58 × lx9801^hlEW2b (HY), Zheng58 × lx9801 (CK)] and their corresponding inbred lines lx9801^hlEW2b and lx9801. B Expression pattern analysis of specific DEGs between hybrids. C Venn diagram showing the number of additively (HY_additive and CK_additive) and non-additively (HY_Non-additive and CK_Non-additive) expressed genes in each hybrid

Fig. 4

Comparison and functional enrichment of additive genes in hybrids. A Top 20 enriched biological process GO terms in additive genes of the HY hybrid. B All 10 enriched biological process GO terms in the CK hybrid. The Y-axis lists the enriched GO terms, and the X-axis represents the rich factor. The smaller the Q value, the higher the significance level and the closer to the red point. The more genes, the larger the circle

Fig. 5

Comparison and functional enrichment of non-additive genes in hybrids. A Top 20 enriched biological process GO terms in non-additive genes of the HY hybrid. B All 14 enriched biological process GO terms in the CK hybrid. The Y-axis lists the enriched GO terms, and the X-axis represents the rich factor. The smaller the Q value, the higher the significance level and the closer to the red point. The more genes, the larger the circle

Fig. 6

Global allele-specific expression analysis. A: The distribution of ASE genes in hybrids. Green and red represent genes with ASE and no ASE at the genome-wide level in Zheng58 × lx9801^hlEW2b (HY) and Zheng58 × lx9801 (CK). B Comparison of DEGs between hybrids that show an ASE pattern

Fig. 7

Critical DEGs with an ASE expression pattern in HY and CK hybrids that participate in regulation of ear development. Each point on the figure represents an SNP between the two parental genomes of the hybrid, and the size of the point indicates the read number at each SNP. The more reads, the larger the point. The X-axis represents the position of the SNP in the parental genomes, and the Y-axis represents the level of allele-specific expression (P). The lx9801^hlEW2b allele is set to 0 in Zheng58×lx9801^hlEW2b, and the lx9801 allele is set to 0 in Zheng58×lx9801. The test parent Zheng58 is set to 1 in both hybrids

Fig. 8

Predicting the regulatory process of heterosis formation during the inflorescence meristem period. Auxin may contribute to hybrid heterosis during maize ear development. Additive, non-additive, and allele-specific expression patterns may fine-tune the expression of crucial genes that control auxin metabolism and IM development to an optimal level, and this may be responsible for maize ear heterosis formation in hybrids