Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu 611130, China.
Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, China; Sichuan Animal Science Academy, Chengdu 610066, China.
Gene. 2020 Jul 15;747:144671. doi: 10.1016/j.gene.2020.144671. Epub 2020 Apr 15.
In diploid organisms, each gene locus is composed of two parental alleles, which would interact with each other for determining the phenotypic variation. Better understanding of the allele-specific expression (ASE) in farm animals is much important to explore the genetic basis underlying economically important traits, which have been poorly understood yet. In this study, genome-wide analysis was applied to explore the spatiotemporal pattern of ASE in the F1 hybrids of chicken. First, meat- and egg-type chickens were selected for producing a full-sib F1 hybrid population (n = 57). Then, genome resequencing of two parents and 38 offspring were performed and liver and breast muscle samples (n = 38) were subjected to strand-specific RNA sequencing (ssRNA-seq) for ASE detection at 1, 28, and 56 days of age, respectively. The results accurately identified a total of 465 informative genes that could be distinguished with respect to their parental origins. There were 0.4% - 4.1% of informative genes showing ASE, and 57 of them were found across different tissues and time points. Besides, most ASE genes in chickens were tissue-specific, and no matter what the time-point pattern of one ASE gene, the same parental allele of this gene almost showed consistently higher or lower expression across all time points in the same type tissue. In conclusion, this study indicated that most of ASE genes were tissue-specific and time-dependent.
在二倍体生物中，每个基因座由两个亲本等位基因组成，这些等位基因相互作用决定表型变异。更好地理解家畜中的等位基因特异性表达（ASE）对于探索经济重要性状的遗传基础非常重要，但目前对此了解甚少。在这项研究中，应用全基因组分析方法来探索鸡 F1 杂种中 ASE 的时空模式。首先，选择肉用型和蛋用型鸡来产生全同胞 F1 杂种群体（n=57）。然后，对两个亲本和 38 个后代进行基因组重测序，并对 1、28 和 56 日龄的肝脏和胸肌样本（n=38）进行链特异性 RNA 测序（ssRNA-seq），以检测 ASE。结果准确地鉴定出总共 465 个可根据其亲本来源区分的信息性基因。有 0.4%-4.1%的信息性基因表现出 ASE，其中 57 个基因在不同组织和时间点都有发现。此外，鸡中的大多数 ASE 基因是组织特异性的，无论一个 ASE 基因的时间点模式如何，同一基因的相同亲本等位基因在同一组织的所有时间点几乎都表现出一致的高或低表达。总之，本研究表明，大多数 ASE 基因是组织特异性和时间依赖性的。
