Heterosis is the phenomenon in which hybrid offspring are vigorous than either parent, resulting in superior growth potential, yielding ability, adaptability, and stress resistance traits in hybrids [1]. Heterosis is an important method to improve crop yield and quality, and it plays a critical role in the breeding of several crops, including maize, rice, sorghum, and rape [2–5]. However, the molecular mechanisms of heterosis are still not clear. At present, three classical hypotheses, dominance, overdominance, and epistasis, have been proposed to explain heterosis, and they have been debated for over 100 years [6]. With advances in science and technology, a series of studies on heterosis using genomics, transcriptomics, proteomics, and epigenetics approaches have provided new insights into the molecular mechanisms of heterosis.
At the transcriptional level, gene expression variation causes changes in biological regulatory networks, which are important sources of phenotypic novelties and affect heterosis [7]. Comparing the differences in gene expression between parents and hybrids, multiple models of gene action, including additive, nonadditive, high- or low-parent dominance, and over- or underdominance, might be involved in the formation of heterosis [8]. Several studies in maize (Zea mays) revealed that the additive effects are universal and have positive correlations with yield heterosis. In addition, the dominant and overdominant expression patterns, belonging to the nonadditive category, are also considered important factors of heterosis in hybrids [9–11]. The alterations in gene expression may cause changes in biological regulatory networks, which affect heterosis. By comparing the gene expression levels of hybrids and their parents at the maize ear developmental stage, Huang et al. [12] found that most negative dominant genes are mainly involved in carbohydrate metabolism, lipid metabolism, energy metabolism, and protein degradation, whereas positive dominant genes are mainly involved in DNA replication and repair. In allotetraploid Arabidopsis thaliana, nonadditively expressed genes are significantly enriched in energy, metabolism, stress response, and plant hormone signal transduction [13].
In diploid hybrids, each gene contains two copies, one each from the male and female parents. Theoretically, the alleles from both parents should be equally expressed in the hybrid. However, the transcriptional activities of different alleles in hybrids vary greatly [14, 15]. Allele-specific expression (ASE) refers to the preferential expression of a specific parental allele in its hybrids driven by regulatory factors from the parental genomes [16]. Hybridization produces an extremely large pool of allelic variants, which affect gene expression levels. The expression differences caused by ASE may lead to phenotypic diversity, depending on the gene functions [17]. The ASE phenomenon has been documented in Arabidopsis, rice, maize, and barley [18–21]. ASE patterns may have distinct implications in the genetic basis of heterosis, especially the dominance and overdominance hypotheses, because genetic variations frequently cause the differentially expression of genes, which may lead to phenotypic variations in the hybrids [17, 22–24]. Even though many genes in many species have been identified as exhibiting ASE at the whole-genome level, the potential relationship between ASE and heterosis remains unclear.
The important traits related to maize yield, such as kernel row number, kernel number per ear, ear width, and ear length, are all determined during inflorescence meristem (IM) development. The development of immature maize ears displays strong heterosis in ear architecture traits, which greatly affects grain yield [25]. The size of the IM is significantly positively correlated with ear width and length, and its developmental process directly affects the final morphological characteristics of mature maize ears [26]. The classic pathway of maintaining the IM amplification process is the CLAVATA–WUSCHEL (CLV–WUS) negative feedback loop. This pathway affects IM development by regulating the relationship between the proliferation of stem cells and the differentiation activities of tissues and organs [27]. WUS is a crucial regulator that determines stem cell formation and maintenance [28], and CLV3 is a peptide ligand for the CLV1/CLV2 receptor complex. Its expression may be induced by WUS, and it can move back to the organizing center to inhibit WUS expression. The CLV3/WUS negative feedback loop may affect the IM differentiation process [29]. Additionally, analyses of mutants have established that the BARREN STALK1 (BA1) gene encodes a bHLH transcription factor. Its mutant, ba1, cannot develop normal axillary meristem, and the proteins involved in auxin synthesis and transport do not function normally. It has been inferred that auxin deficiency may cause this mutants inability to complete the reproductive transition [30]. KNOTTED1-like homeobox (KNOX), first isolated from maize, is involved in inflorescence development, as well as the maintenance and initiation of shoot apical meristem (SAM) and IM. KNOX regulates the dynamic conversion of SAM to IM by maintaining the balance of gibberellin and cytokinin, and its mutants may cause SAM malformation and the failure to complete the reproductive transformation process [31]. Thus, hormones play critical roles in the regulation of immature maize ear development.
To eliminate the influence of genetic background and reduce environmental impact, single-segment substitution line populations have been developed to map heterotic loci. Yu et al. [32] used single-segment substitution line test populations to research the heterosis performance of yield-related traits, and they discussed the advantages of single-segment substitution lines in heterosis research. Wang et al. [33] detected 21 yield-related heterotic loci through the comparison of differences between a test cross population and background parents of 66 rice single-segment substitution lines. [34] used the same experimental design to identify 21 heterotic loci related to maize plant architecture traits.
During the development of maize ear inflorescence, the IM stage is critical for ear development and heterosis. In the present study, we collected immature maize ears from single-segment substitution line lx9801hlEW2b (containing the heterotic locus hlEW2b associated with ear width), receptor parent lx9801, test parent Zheng58, and their corresponding hybrids, Zheng58 × lx9801hlEW2b and Zheng58 × lx9801, during the IM stage, and we developed a global gene expression profile using RNA sequencing technology (RNA-seq) to clarify the mechanisms of heterosis involved in transcriptome alterations. Our research provides new insights into the relationship between transcriptomic alterations and heterosis during maize ear development.