In other species: turkey , horse , indicine cattle (zebu)

Categories: Reproductive system phene , Mortality / aging (incl. embryonic lethal)

Mendelian trait/disorder: unknown

Disease-related: yes

Cross-species summary: Deviation from Mendelian inheritance expectations / transmission ratio distortion (TDR) identified in the analysis of single nucleotide polymorphism data. Identified haplotypes with homozygous deficiency can indicate the presence of (embryonic) recessive lethal or semi-lethal alleles in a population.

Species-specific description: See also various other OMIA phenes called 'Haplotypes with homozygous deficiency' or 'Haplotype with homozygous deficiency, ...'

Mapping: Id-Lahoucine et al. (2023, PMID:37422635 ) investigated "TRD using SNP-by-SNP and sliding windows approaches on 441,802 genotyped Holstein cattle and 132,991 (or 47,910 phased) autosomal SNPs. ... The TRD was characterized using allelic and genotypic parameterizations. Across the whole genome a total of 604 chromosomal regions showed strong significant TRD. Most (85%) of the regions presented an allelic TRD pattern with an under-representation (reduced viability) of carrier (heterozygous) offspring or with the complete or quasi-complete absence (lethality) for homozygous individuals. On the other hand, the remaining regions with genotypic TRD patterns exhibited the classical recessive inheritance or either an excess or deficiency of heterozygote offspring. Among them, the number of most relevant novel regions with strong allelic and recessive TRD patterns were 10 and 5, respectively." Several identified regions overlapped with previously reported haplotypes with homozygous deficiency in dairy cattle. "Potential new candidate regions with lethal alleles identified with transmission ratio distortion (TRD) in Holstein cattle" include: BTA 1 27,285–27,325 BTA 1 102,167–103,035 BTA 1 109,285–109,707 BTA 1 112,498–112,863 BTA 3 20,502–20,970 BTA 6 58,498–58,753 BTA 8 18,087–18,273 BTA 9 71,916 BTA 9 77,576–77,734 BTA 10 42,238 BTA 12 147–742 BTA 19 60,921–60,949 BTA 22 9,621 BTA 24 48,165–48,420 BTA 29 34,677–34,697 Coordinates based on UMD3.1 Bos taurus genome assembly. In a different publication, Id-Lahoucine et al. (2023, PMID:37591956) investigated TRD in Angus cattle: "TRD was evaluated using both SNP-by-SNP and sliding windows of 2-, 4-, 7-, 10- and 20-SNP across 92,942 autosomal SNPs for 258,140 genotyped Angus cattle including 7,486 sires, 72,688 dams and 205,966 offspring. Transmission ratio distortion was characterized using allelic (specific- and unspecific-parent TRD) and genotypic parameterizations (additive- and dominance-TRD). Across the Angus autosomal chromosomes, 851 regions were clearly found with decisive evidence for TRD. Among these findings, 19 haplotypes with recessive patterns (potential lethality for homozygote individuals) and 52 regions with allelic patterns exhibiting complete or quasi-complete absence for homozygous individuals in addition to under-representation (potentially reduced viability) of the carrier (heterozygous) offspring were found. In addition, 64 (12) and 20 (4) regions showed significant influence on the trait heifer pregnancy at p-value < 0.05 (after chromosome-wise false discovery rate) and 0.01, respectively, reducing the pregnancy rate up to 15%, thus, supporting the biological importance of TRD phenomenon in reproduction."

Breeds: Angus (Cattle) (VBO_0000104), Holstein Friesian (Cattle) (VBO_0000239).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).