Abstract
SummaryDeviation 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.
Highlights
Owing to its considerable economic impact, reproduction has drawn the attention of turkey breeders and producers (Saif & Nestor 2002; Huff et al 2005; Emamgholi Begli et al 2019)
The initial numbers of haplotype alleles detected with decisive significant evidence (BF ≥ 100) of transmission ratio distortion (TRD), according to Jeffreys’ scale (Jeffreys 1984), were 48 951, 52 896 and 54 287 for 4, 10 and 20 SNP haplotype windows respectively
The terms NELF complex (GO:0032021) and two similar Gene Ontology (GO) terms, methylosome (GO:0034709) and cytoplasmic part (GO:0044444), are classified under the cellular component domain and show a significant overrepresentation of genes statistically associated with TRD (Table 4)
Summary
Owing to its considerable economic impact, reproduction has drawn the attention of turkey breeders and producers (Saif & Nestor 2002; Huff et al 2005; Emamgholi Begli et al 2019). Lethal alleles may cause mortality before, during or after the embryonic stage, and reduce reproductive performance. Dong et al 2019; Guarini et al 2019) and the correct mate allocation is expected to reduce the economic losses (Cole et al 2016). Several methods, such as screening for the absence of homozygous haplotypes TRD is a process whereby the transmission of alleles from heterozygous parents to offspring deviates from Mendelian ratios, regardless of the cause (Crow 1999; Pardo-Manuel De Villena et al 2000; Huang et al 2013). TRD reveals locus-specific signals that provide insight into genetics and evolutionary processes of individual fitness variation, population divergence and speciation (Fishman & McIntosh 2019)
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