Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu Campus, Chengdu, 611130, China.
Special Key Laboratory of Microbial Resources and Drug Development, Zunyi Medical University, Zunyi, 563000, China.
Mol Genet Genomics. 2021 Mar;296(2):331-339. doi: 10.1007/s00438-020-01744-z. Epub 2021 Jan 6.
Allelic transmission ratio distortion (TRD) is the significant deviation from the expected ratio under Mendelian inheritance theory, which may be resulted from multiple disrupted biological processes, including germline selection, meiotic drive, gametic competition, imprint error, and embryo lethality. However, it is less known that whether or what extent the allelic TRD is present in farm animals. In this study, whole-genome resequencing technology was applied to reveal TRD loci in chicken by constructing a full-sib F hybrid population. Through the whole-genome resequencing data of two parents (30 ×) and 38 offspring (5 ×), we detected a total of 2850 TRD SNPs (p-adj < 0.05) located within 400 genes showing TRD, and all of them were unevenly distributed on macrochromosomes and microchromosomes. Our findings suggested that TRD in the chicken chromosome 16 might play an important role in chicken immunity and disease resistance and the MYH1F with significant TRD and allele-specific expression could play a key role in the fast muscle development. In addition, functional enrichment analyses revealed that many genes (e.g., TGFBR2, TGFBR3, NOTCH1, and NCOA1) with TRD were found in the significantly enriched biological process and InterPro terms in relation to embryonic lethality and germline selection. Our results suggested that TRD is considerably prevalent in the chicken genome and has functional implications.
等位基因传递比失真（TRD）是指与孟德尔遗传理论预期比例的显著偏差，这可能是由于多种生物过程的破坏，包括生殖系选择、减数分裂驱动、配子竞争、印迹错误和胚胎致死。然而，人们对等位基因 TRD 是否存在以及存在的程度知之甚少。在这项研究中，我们应用全基因组重测序技术，通过构建全同胞 F1 杂交群体，揭示鸡中的 TRD 基因座。通过对两个亲本（30×）和 38 个后代（5×）的全基因组重测序数据，我们共检测到 2850 个位于 400 个表现出 TRD 的基因内的 TRD SNPs（p-adj<0.05），它们都不均匀地分布在大染色体和微染色体上。我们的研究结果表明，鸡染色体 16 上的 TRD 可能在鸡的免疫和抗病性中发挥重要作用，具有显著 TRD 和等位基因特异性表达的 MYH1F 可能在快肌发育中发挥关键作用。此外，功能富集分析显示，TRD 基因（如 TGFBR2、TGFBR3、NOTCH1 和 NCOA1）在与胚胎致死和生殖系选择相关的显著富集的生物学过程和 InterPro 术语中被发现。我们的结果表明，TRD 在鸡基因组中相当普遍，并具有功能意义。
