College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, China.
Int J Mol Sci. 2023 Mar 1;24(5):4766. doi: 10.3390/ijms24054766.
Heterosis or hybrid vigor refers to the superior phenotypic traits of hybrids relative to their parental inbred lines. An imbalance between the expression levels of two parental alleles in the F1 hybrid has been suggested as a mechanism of heterosis. Here, based on genome-wide allele-specific expression analysis using RNA sequencing technology, 1689 genes exhibiting genotype-dependent allele-specific expression (genotype-dependent ASEGs) were identified in the embryos, and 1390 genotype-dependent ASEGs in the endosperm, of three maize F1 hybrids. Of these ASEGs, most were consistent in different tissues from one hybrid cross, but nearly 50% showed allele-specific expression from some genotypes but not others. These genotype-dependent ASEGs were mostly enriched in metabolic pathways of substances and energy, including the tricarboxylic acid cycle, aerobic respiration, and energy derivation by oxidation of organic compounds and ADP binding. Mutation and overexpression of one ASEG affected kernel size, which indicates that these genotype-dependent ASEGs may make important contributions to kernel development. Finally, the allele-specific methylation pattern on genotype-dependent ASEGs indicated that DNA methylation plays a potential role in the regulation of allelic expression for some ASEGs. In this study, a detailed analysis of genotype-dependent ASEGs in the embryo and endosperm of three different maize F1 hybrids will provide an index of genes for future research on the genetic and molecular mechanism of heterosis.
杂种优势或杂种优势是指杂种相对于其亲本自交系的优越表型特征。杂种 F1 中两个亲本等位基因表达水平的不平衡被认为是杂种优势的一种机制。在这里，基于使用 RNA 测序技术的全基因组等位基因特异性表达分析，在三个玉米 F1 杂种的胚胎和胚乳中鉴定出了 1689 个表现出基因型依赖性等位基因特异性表达（基因型依赖性 ASEGs）的基因。在这些 ASEGs 中，大多数在一个杂种杂交的不同组织中是一致的，但近 50%的基因表现出从一些基因型而非其他基因型的等位基因特异性表达。这些基因型依赖性 ASEGs 主要富集在物质和能量的代谢途径中，包括三羧酸循环、有氧呼吸以及有机化合物氧化和 ADP 结合的能量衍生。一个 ASEG 的突变和过表达影响了核仁大小，这表明这些基因型依赖性 ASEGs 可能对核仁发育有重要贡献。最后，基因型依赖性 ASEGs 上的等位基因特异性甲基化模式表明，DNA 甲基化可能在一些 ASEGs 的等位基因表达调控中发挥作用。在这项研究中，对三个不同玉米 F1 杂种的胚胎和胚乳中基因型依赖性 ASEGs 的详细分析将为杂种优势的遗传和分子机制的未来研究提供基因指标。
