National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5653-5658. doi: 10.1073/pnas.1820513116. Epub 2019 Mar 4.
Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.
杂种优势的利用极大地提高了全球许多作物的生产力。尽管利用基因组技术在表征杂种优势的遗传基础方面取得了巨大进展，但对遗传成分的分子机制了解甚少。等位基因特异性表达（ASE），即在杂种中两个亲本等位基因的表达水平之间的不平衡，被认为是杂种优势的一种机制。在这里，我们通过比较在四种条件下生长的植物的三个组织中的 RNA-seq 数据中亲本等位基因的读取比例，对杂种优势的全基因组 ASE 进行了分析。该分析总共鉴定出了 3270 个表现出 ASE（ASEGs）的基因，这些基因以不同的方式存在，可以分为两种模式：一致的 ASEGs，即 ASE 在所有组织/条件下偏向于一个亲本等位基因；不一致的 ASEGs，即 ASE 仅在某些组织/条件下发现，而不是所有组织/条件下都发现，包括方向转换的 ASEGs，其中 ASE 在某些组织/条件下偏向于一个亲本等位基因，而在其他组织/条件下偏向于另一个亲本等位基因。结果表明，这些模式可能在杂种优势的遗传基础中具有不同的含义：一致的 ASEGs 可能对其调控的性状产生部分到完全的显性效应，而方向转换的 ASEGs 可能产生超显性效应。我们还表明，ASEGs 在水稻育种过程中差异选择的基因组区域中显著富集。这些 ASEGs 为未来探索杂种优势的遗传和分子机制提供了基因指标。
