Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis
Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis
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DOI：
10.1073/pnas.1820513116
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发表时间：
2019-03-19
影响因子：
11.1
通讯作者：
Zhang, Qifa
中科院分区：
文献类型：
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作者：
Shao, Lin;Xing, Feng;Zhang, Qifa
杂种优势的利用极大地提高了世界范围内许多作物的生产力。尽管在利用基因组技术表征杂种优势的遗传基础方面取得了巨大进展，但遗传成分背后的分子机制却知之甚少。等位基因特异性表达（ASE），或两个亲本等位基因表达水平之间的不平衡，被认为是杂种优势的机制。在此，我们利用生长在四种条件下的三种植物组织，通过比较一个优秀水稻杂种及其亲本的rna测序数据中亲本等位基因的读取率，对ASE进行了全基因组分析。分析发现3270基因显示ASE (ASEGs)以不同的方式,可分为两种模式:一致ASEGs这样ASE是偏向一个父母等位基因在所有组织/条件,和不一致的ASEGs这样ASE被发现在一些但不是全部组织/条件,包括direction-shifting ASEGs ASE是偏向一个父母的等位基因在某些组织/条件而向其他父母等位基因在其他组织/条件。结果表明，这些模式可能对杂种优势的遗传基础有不同的影响：一致的ASEGs可能对其调节的性状产生部分或完全显性效应，而方向变化的ASEGs可能导致显性效应。我们还发现ASEGs在水稻育种过程中被差异选择的基因组区域中显著富集。这些ASEGs为今后研究杂种优势的遗传和分子机制提供了基因的索引。
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.