Background: Heterosis, or hybrid vigor, refers to the phenotypic superiority of an F₁hybrid relative to its parents in terms of growth rate, biomass production, grain yield, and stress tolerance. Light is an energy source and main environmental cue with marked impacts on heterosis in plants. Research into the production applications and mechanism of heterosis has been conducted for over a century and a half, but little is known about the effect of light on plant heterosis.Results: In this study, an integrated transcriptome and metabolome analysis was performed using maize (Zea maysL.) inbred parents, B73 and Mo17, and their hybrids, B73 × Mo17 (BM) and Mo17 × B73 (MB), grown in darkness or under far-red, red, or blue light. Most differentially expressed genes (73.72–92.50%) and differentially accumulated metabolites (84.74–94.32%) exhibited non-additive effects in BM and MB hybrids. Gene Ontology analysis revealed that differential genes and metabolites were involved in glutathione transfer, carbohydrate transport, terpenoid biosynthesis, and photosynthesis. The darkness, far-red, red, and blue light treatments were all associated with phenylpropanoid–flavonoid biosynthesis by Weighted Gene Co-expression Network Analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Five genes and seven metabolites related to phenylpropanoid–flavonoid biosynthesis pathway were identified as potential contributors to the interactions between maize heterosis and light conditions. Consistent with the strong mid-parent heterosis observed for metabolites, significant increases in both fresh and dry weights were found in the MB and BM hybrids compared with their inbred parents. Unexpectedly, increasing light intensity resulted in higher biomass heterosis in MB, but lower biomass heterosis in BM.Conclusions: The transcriptomic and metabolomic results provide unique insights into the effects of light quality on gene expression patterns and genotype–environment interactions, and have implications for gene mining of heterotic loci to improve maize production.

Background: Heterosis has successfully enhanced maize productivity and quality. Although significant progress has been made in delineating the genetic basis of heterosis, the molecular mechanisms underlying its genetic components remain less explored. Allele-specific expression (ASE), the imbalanced expression between two parental alleles in hybrids, is increasingly being recognized as a factor contributing to heterosis. ASE is a complex process regulated by both epigenetic and genetic variations in response to developmental and environmental conditions. Results: In this study, we explored the differential characteristics of ASE by analyzing the transcriptome data of two maize hybrids and their parents under four light conditions. On the basis of allele expression patterns in different hybrids under various conditions, ASE genes were divided into three categories: bias-consistent genes involved in basal metabolic processes in a functionally complementary manner, bias-reversal genes adapting to the light environment, and bias-specific genes maintaining cell homeostasis. We observed that 758 ASE genes (ASEGs) were significantly overlapped with heterosis quantitative trait loci (QTLs), and high-frequency variations in the promoter regions of heterosis-related ASEGs were identified between parents. In addition, 10 heterosis-related ASEGs participating in yield heterosis were selected during domestication. Conclusions: The comprehensive analysis of ASEGs offers a distinctive perspective on how light quality influences gene expression patterns and gene-environment interactions, with implications for the identification of heterosis-related ASEGs to enhance maize yield.

Lignin, the second most abundant terrestrial biopolymer, represents a significant renewable natural biomaterial. Cinnamoyl-CoA reductase (CCR) catalyzes the conversion of various hydroxycinnamoyl-CoA esters into their corresponding aldehydes, utilizing NADPH as a cofactor. CCR functions as a regulatory point that controls the overall carbon flux towards lignin and constitutes the initial committed step in the lignin biosynthesis pathway. Additionally, CCR plays a crucial role in plant development and in resistance to biotic and abiotic stresses. Bread wheat (Triticum aestivum L.), a hexaploid crop, serves as a staple food for much of the global population. However, the copy number variation and expression characteristics of wheat CCR genes remain to be elucidated. This study identified 115 unique members of the CCR gene family through a comprehensive search of the wheat genome database. Subsequent analyses included the physicochemical properties, chromosomal localizations, gene duplication events, and structures of these genes. Wheat CCRs were categorized into TaCCR and TaCCR-like genes based on phylogenetic comparison, sequence alignment, and protein three-dimensional structure analysis. Twenty TaCCR proteins, characterized by key amino acid residues at the protein catalytic and NADPH-binding sites, were identified as genuine TaCCRs, potentially playing significant roles in lignin biosynthesis. The expression patterns of these 20 TaCCR genes were investigated in various wheat tissues and seedlings subjected to biotic and abiotic stresses. These genes may significantly influence stem development and responses to heat, drought, salt, and pathogen stresses. Additionally, degradome data analysis suggested that the expression of TaCCR6D-1 was regulated by miRNAs. Virus-induced gene silencing experiments demonstrated the involvement of TaCCR5-5 and TaCCR6-1 in wheat lignin synthesis. This study presents the first comprehensive identification and analysis of wheat CCR genes. Our findings establish a foundation for further elucidation of TaCCR functions and offer a significant genetic resource for future wheat improvement efforts.

The light environment significantly influences crop growth, development, quality, and yield, particularly in controlled-environment agriculture. Recent advances in artificial lighting technology have allowed growers to precisely control the light environment in terms of duration, spectrum, and intensity. Starch and protein are the most significant nutritional constituents of maize kernels. However, little is known about the effects of the light environment on starch and protein content in maize kernels. Therefore, we investigated the effects of natural light and supplemental exposure to blue (B), far-red (FR), and red (R) light on starch and protein content in kernels of the inbred maize line B73. Exposure to supplemental B, FR, or R light resulted in significant increases in starch content but decreases in protein content. Notably, protein content was lowest under B light. Substantial proportions of genes (5.03–75.23%) and metabolites (46.89–85.64%) were regulated by different wavelengths of light. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, as well as weighted gene co-expression network analysis (WGCNA), revealed that differentially expressed genes (DEGs) under B, FR, and R light were involved in pathways related to starch and protein synthesis. KEGG metabolomic analysis showed that differentially abundant metabolites (DAMs) were primarily associated with histidine, D-amino acid, cysteine, and methionine metabolism. Nine DEGs related to starch synthesis were identified as potential candidates for investigating the effects of light quality on starch synthesis, and 14 DEGs related to protein synthesis provided evidence for the influence of light quality on protein synthesis in maize. This study identified the regulatory network governing starch and protein content in B73 maize kernels under different light conditions, contributing to a deeper understanding of how light quality affects the nutritional components of maize kernels.

SPAs (suppressors of phyA-105) are key modulators of photomorphogenesis that regulate diverse aspects of plant growth. While the role of SPA proteins in Arabidopsis photomorphogenesis is well-characterized, the functions of their maize (Zea mays L.) homologs (ZmSPAs) remain largely unexplored. Here, we show that ZmSPAs have the typical conserved domains of the SPA family and respond to different light qualities and photoperiodic treatments. Further analysis of the subcellular localization of ZmSPAs showed that ZmSPA1 and ZmSPA2 were localized to the nucleus, while ZmSPA3 and ZmSPA4 were localized to both the nucleus and the plasma membrane. The results of tissue-specific expression showed that ZmSPA1 and ZmSPA2 had the highest relative expression level in silks, while ZmSPA3 and ZmSPA4 were mainly expressed in leaves. Interestingly, overexpression of ZmSPAs in Arabidopsis promoted hypocotyl elongation in seedlings, inhibited cotyledon expansion in seedlings, and increased plant height in mature plants. The Y2H and LCI results indicate that ZmSPAs have physical interactions with ZmCOP1a, ZmCOP1b, and AtCOP1. These findings reveal the roles of ZmSPAs in regulating photomorphogenesis in Arabidopsis seedlings and plant height development in mature plants, laying a foundation for future investigations into their endogenous functions in maize.