Transmission ratio distortion detection by neutral genetic markers in the Pura Raza Española horse breed.

Transmission Ratio Distortion (TRD) is a genetic phenomenon widely demonstrated in several livestock species, but barely in equine species. The TRD occurs when certain genotypes are over- or under-represented in the offspring of a particular mating and can be caused by a variety of factors during gamete formation or during embryonic development. For this study, 126 394 trios consisting of a stallion, mare, and offspring were genotyped using a panel of 17 neutral microsatellite markers recommended by the International Society for Animal Genetics for paternity tests and individual identification.

Unravelling transmission ratio distortion across the bovine genome: identification of candidate regions for reproduction defects.

Background: Biological mechanisms affecting gametogenesis, embryo development and postnatal viability have the potential to alter Mendelian inheritance expectations resulting in observable transmission ratio distortion (TRD). Although the discovery of TRD cases have been around for a long time, the current widespread and growing use of DNA technologies in the livestock industry provides a valuable resource of large genomic data with parent-offspring genotyped trios, enabling the implementation of TRD approach. In this research, the objective is to investigate TRD using SNP-by-SNP and sliding windows approaches on 441,802 genotyped Holstein cattle and 132,991 (or 47,910 phased) autosomal SNPs.

Transmission ratio distortion regions in the context of genomic evaluation and their effects on reproductive traits in cattle.

Transmission ratio distortion (TRD), which is a deviation from Mendelian expectations, has been associated with basic mechanisms of life such as sperm and ova fertility and viability at developmental stages of the reproductive cycle. In this study different models including TRD regions were tested for different reproductive traits [days from first service to conception (FSTC), number of services, first service nonreturn rate (NRR), and stillbirth (SB)]. Thus, in addition to a basic model with systematic and random effects, including genetic effects modeled through a genomic relationship matrix, we developed 2 additional models, including a second genomic relationship matrix based on TRD regions, and TRD regions as a random effect assuming heterogeneous variances.

Parent-offspring genotyped trios unravelling genomic regions with gametic and genotypic epistatic transmission bias on the cattle genome.

Several biological mechanisms affecting the sperm and ova fertility and viability at developmental stages of the reproductive cycle resulted in observable transmission ratio distortion (i.e., deviation from Mendelian expectations).

Unravelling the genetics of non-random fertilization associated with gametic incompatibility.

In the dairy industry, mate allocation is dependent on the producer's breeding goals and the parents' breeding values. The probability of pregnancy differs among sire-dam combinations, and the compatibility of a pair may vary due to the combination of gametic haplotypes. Under the hypothesis that incomplete incompatibility would reduce the odds of fertilization, and complete incompatibility would lead to a non-fertilizing or lethal combination, deviation from Mendelian inheritance expectations would be observed for incompatible pairs.

Deviations from Mendelian Inheritance on Bovine X-Chromosome Revealing Recombination, Sex-of-Offspring Effects and Fertility-Related Candidate Genes.

Transmission ratio distortion (TRD), or significant deviations from Mendelian inheritance, is a well-studied phenomenon on autosomal chromosomes, but has not yet received attention on sex chromosomes. TRD was analyzed on 3832 heterosomal single nucleotide polymorphisms (SNPs) and 400 pseudoautosomal SNPs spanning the length of the X-chromosome using 436,651 genotyped Holstein cattle. On the pseudoautosomal region, an opposite sire-TRD pattern between male and female offspring was identified for 149 SNPs.

Analyses of lambing dates in sheep breeds using von Mises distribution.

Regular changes in the environment and biological responses generate seasonal patterns in the reproduction in small ruminants. Breeding seasonality is a significant constraint impacting efficiency of lamb production. However, seasonality-related traits present a special peculiarity from a statistical point of view being circular data (day of year running 1:365).

Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach.

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.

Discriminating between allele- and genotype-specific transmission ratio distortion.

Transmission ratio distortion (TRD) is defined as the observed deviation from the expected Mendelian inheritance of alleles from heterozygous parents. This phenomenon is attributed to various biological mechanisms acting on germ cells, embryos or fetuses, or even in early postnatal life. Current statistical approaches typically use two independent parametrizations assuming that TRD relies on allele- or genotype-related mechanisms, although they have never been tested and compared.

Analysis of lambing distribution in the Ripollesa sheep breed. I. Development and comparison of circular von Mises models.

Circular data originates in a wide range of scientific fields and can be analyzed on the basis of directional statistics and special distributions wrapped around the circumference. However, both propensity to transform non-linear to linear data and complexity of directional statistics limited the generalization of the circular paradigm in the animal breeding framework, among others. Here, we generalized a circular mixed (CM) model within the context of Bayesian inference.

Analysis of lambing distribution in the Ripollesa sheep breed. II. Environmental and genetic sources of variation.

Seasonal reproduction patterns are typically observed in small ruminants and are a major limitation for production efficiency in most meat- and dairy-type production systems. Indeed, selection for reduced seasonality could be an appealing strategy for the small ruminant industry worldwide, although its genetic background has been poorly analyzed. One of the main limitations relied on the availability of appropriate analytical tools to cope with the circular (i.

Implementation of Bayesian methods to identify SNP and haplotype regions with transmission ratio distortion across the whole genome: TRDscan v.1.0.

Realized deviations from the expected Mendelian inheritance of alleles from heterozygous parents have been previously reported in a broad range of organisms (i.e., transmission ratio distortion; TRD).

Screening for epistatic selection signatures: A simulation study.

Detecting combinations of alleles that diverged between subpopulations via selection signature statistics can contribute to decipher the phenomenon of epistasis. This research focused on the simulation of genomic data from subpopulations under divergent epistatic selection (ES). We used D' and F statistics in pairs of loci to scan the whole-genome.

Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle.

The identification of biological processes related to the regulation of complex traits is a difficult task. Commonly, complex traits are regulated through a multitude of genes contributing each to a small part of the total genetic variance. Additionally, some loci can simultaneously regulate several complex traits, a phenomenon defined as pleiotropy.

Genetic mechanisms underlying spermatic and testicular traits within and among cattle breeds: systematic review and prioritization of GWAS results.

Reduced bull fertility imposes economic losses in bovine herds. Specifically, testicular and spermatic traits are important indicators of reproductive efficiency. Several genome-wide association studies (GWAS) have identified genomic regions associated with these fertility traits.

Reducing cryptic relatedness in genomic data sets via a central node exclusion algorithm.

Cryptic relatedness is a confounding factor in genetic diversity and genetic association studies. Development of strategies to reduce cryptic relatedness in a sample is a crucial step for downstream genetic analyses. This study uses a node selection algorithm, based on network degrees of centrality, to evaluate its applicability and impact on evaluation of genetic diversity and population stratification.