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. 2023 Aug 9;18(8):e0289066.
doi: 10.1371/journal.pone.0289066. eCollection 2023.

Genomic screening of allelic and genotypic transmission ratio distortion in horse

Nora Laseca  1 , Ángela Cánovas  2 , Mercedes Valera  3 , Samir Id-Lahoucine  4 , Davinia I Perdomo-González  3 , Pablo A S Fonseca  5 , Sebastián Demyda-Peyrás  1 , Antonio Molina  1
Affiliations

Genomic screening of allelic and genotypic transmission ratio distortion in horse

Nora Laseca et al. PLoS One. .

Abstract

The phenomenon in which the expected Mendelian inheritance is altered is known as transmission ratio distortion (TRD). The TRD analysis relies on the study of the transmission of one of the two alleles from a heterozygous parent to the offspring. These distortions are due to biological mechanisms affecting gametogenesis, embryo development and/or postnatal viability, among others. In this study, TRD phenomenon was characterized in horses using SNP-by-SNP model by TRDscan v.2.0 software. A total of 1,041 Pura Raza Español breed horses were genotyped with 554,634 SNPs. Among them, 277 horses genotyped in trios (stallion-mare-offspring) were used to perform the TRD analysis. Our results revealed 140 and 42 SNPs with allelic and genotypic patterns, respectively. Among them, 63 displayed stallion-TRD and 41 exhibited mare-TRD, while 36 SNPs showed overall TRD. In addition, 42 SNPs exhibited heterosis pattern. Functional analyses revealed that the annotated genes located within the TRD regions identified were associated with biological processes and molecular functions related to spermatogenesis, oocyte division, embryonic development, and hormonal activity. A total of 10 functional candidate genes related to fertility were found. To our knowledge, this is the most extensive study performed to evaluate the presence of alleles and functional candidate genes with transmission ratio distortion affecting reproductive performance in the domestic horse.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Manhattan plot of SNPs with allelic and genotypic transmission ratio distortion across the horse genome.
A) Bayes Factor of SNPs with TRD. B) Magnitude of TRD. Overall-TRD (Yellow); stallion-TRD (Green); mare-TRD (Purple); genotypic-TRD (Blue). Suggestive line (red) in log10(BF) = 2 (decisive evidence).
Fig 2
Fig 2. Gene Ontology (GO) analysis using the list of genes with TRD effect in horse using AmiGO and PANTHER GO-Slim.
A) Biological Process sector diagram of the list of genes with allelic TRD. B) Biological Process sector diagram of the list of genes with genotypic TRD.
See this image and copyright information in PMC

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