Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
Anim Genet. 2020 Dec;51(6):876-889. doi: 10.1111/age.13003. Epub 2020 Oct 1.
Deviation from Mendelian inheritance expectations (transmission ratio distortion, TRD) has been observed in several species, including the mouse and humans. In this study, TRD was characterized in the turkey genome using both allelic (specific- and unspecific-parent TRD) and genotypic (additive- and dominance-TRD) parameterizations within a Bayesian framework. In this study, we evaluated TRD for 23 243 genotyped Turkeys across 56 393 autosomal SNPs. The analyses included 500 sires, 2013 dams and 11 047 offspring (trios). Three different haplotype sliding windows of 4, 10 and 20 SNPs were used across the autosomal chromosomes. Based on the genotypic parameterizations, 14 haplotypes showed additive and dominance TRD effects highlighting regions with a recessive TRD pattern. In contrast, the allelic model uncovered 12 haplotype alleles with the allelic TRD pattern which showed an underrepresentation of heterozygous offspring in addition to the absence of homozygous animals. For regions with the allelic pattern, only one particular region showed a parent-specific TRD where the penetrance was high via the dam, but low via the sire. The gene set analysis uncovered several gene ontology functional terms, Reactome pathways and several Medical Subject Headings that showed significant enrichment of genes associated with TRD. Many of these gene ontology functional terms (e.g. mitotic spindle assembly checkpoint, DRM complex and Aneuploidy), Reactome pathways (e.g. Mismatch repair) and Medical Subject Headings (e.g. Adenosine monophosphate) are known to be related to fertility, embryo development and lethality. The results of this study revealed potential novel candidate lethal haplotypes, functional terms and pathways that may enhance breeding programs in Turkeys through reducing mortality and improving reproduction rate.
偏离孟德尔遗传预期（传递率偏差，TRD）已在包括小鼠和人类在内的几个物种中观察到。在这项研究中，我们使用贝叶斯框架中的等位基因（特异性和非特异性亲本 TRD）和基因型（加性和显性 TRD）参数化来描述火鸡基因组中的 TRD。在这项研究中，我们评估了 56393 个常染色体 SNP 上 23243 个土耳其火鸡的 TRD。分析包括 500 个父本、2013 个母本和 11047 个后代（三亲）。在常染色体上使用了三个不同的单倍型滑动窗口，大小分别为 4、10 和 20 SNP。基于基因型参数化，有 14 个单倍型显示出加性和显性 TRD 效应，突出了具有隐性 TRD 模式的区域。相比之下，等位基因模型揭示了 12 个具有等位基因 TRD 模式的单倍型等位基因，这些等位基因除了缺乏纯合动物外，还表现出杂合后代的代表性不足。对于具有等位基因模式的区域，只有一个特定区域表现出母本特异性 TRD，通过母本的外显率较高，但通过父本的外显率较低。基因集分析揭示了几个基因本体论功能术语、反应通路和几个医学主题词，这些术语和词显示了与 TRD 相关的基因的显著富集。这些基因本体论功能术语（例如，有丝分裂纺锤体组装检查点、DRM 复合物和非整倍体）、反应通路（例如，错配修复）和医学主题词（例如，单磷酸腺苷）都与生育力、胚胎发育和致死性有关。这项研究的结果揭示了潜在的新的致死性候选单倍型、功能术语和途径，这可能通过降低死亡率和提高繁殖率来增强火鸡的繁殖计划。
