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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. This finding revealed unique SNPs linked to a specific-sex (Y- or X-) chromosome and describes the accumulation of recombination events across the pseudoautosomal region. On the heterosomal region, 13 SNPs and 69 haplotype windows were identified with dam-TRD. Functional analyses for TRD regions highlighted relevant biological functions responsible to regulate spermatogenesis, development of Sertoli cells, homeostasis of endometrium tissue and embryonic development. This study uncovered the prevalence of different TRD patterns across both heterosomal and pseudoautosomal regions of the X-chromosome and revealed functional candidate genes for bovine reproduction. [ABSTRACT FROM AUTHOR]

Simple Summary: Heterozygosity-rich regions (HRRs) are regions of high heterozygosity, which can harbor important genes associated with key functional traits such as immune response and disease resilience. Runs of homozygosity (ROH) are contiguous homozygous segments of the genome, which can be informative of the population's history, structure, demography events, and overall genetic diversity. We first detected factors impacting the identification of ROH and HRR in worldwide sheep populations, which were artificially selected for specific purposes or under natural conditions. We also identified common regions of high homozygosity or heterozygosity among these populations, where a diversity of candidate genes with distinct functions might indicate differential selection pressure on these regions in breeds with different trait expression. Moreover, we evaluated a tool commonly used in the corporate environment, making use of the business intelligence (BI) concept to support managers in the decision-making process, which allowed us to combine results from multiple analyses and create visualization schemes integrating different information. Our findings and proposed tools contribute to the development of more efficient breeding strategies and conservation of genetic resources in sheep and other livestock species. In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions. [ABSTRACT FROM AUTHOR]

Simple Summary: The Guzerá breed is one of the most relevant animal genetic resources for tropical and extreme environments, that is, low and high temperatures, and dry or humid environments. These animals were selected for beef, milk, or dual-purpose (beef and milk), and were extensively used to produce crossbred animals. Consequently, subjecting the breed to intense genetic bottlenecks in Brazil. The local scientific community and breeders have pursued a sustainable management and conservation program over the last 50 years. To evaluate the efficacy of these efforts, we characterized genetic diversity and structure in a Guzerá meta-population. DNA samples of 744 animals from one dairy, nine dual-purpose, and five beef herds were genotyped for 21 microsatellite loci. The genetic diversity estimates suggested a low fixation index, revealing a large genetic diversity in Guzerá herds. The dual-purpose herds/selection lines are the most uniform subpopulation, while the beef one preserved larger amounts of genetic diversity, representing a genetic diversity reservoir for the breed. In addition, the dairy herd showed to be genetically distant from other herds. Taken together, these results suggest that this Guzerá meta-population has higher genetic diversity, a lower degree of population subdivision, and a lower inbreeding level. The Brazilian Guzerá population originated from a few founders introduced from India. These animals adapted well to the harsh environments in Brazil, were selected for beef, milk, or dual-purpose (beef and milk), and were extensively used to produce crossbred animals. Here, the impact of these historical events with regard to the population structure and genetic diversity in a Guzerá meta-population was evaluated. DNA samples of 744 animals (one dairy, nine dual-purpose, and five beef herds) were genotyped for 21 microsatellite loci. Ho, He, PIC, Fis, Fit, and Fst estimates were obtained considering either farms or lineages as subpopulations. Mean Ho (0.73) and PIC (0.75) suggest that genetic diversity was efficiently conserved. Fit, Fis and Fst values (95% CI) pointed to a low fixation index, and large genetic diversity: Fit (Farms = 0.021–0.100; lineages = 0.021–0.100), Fis (Farms = –0.007–0.076; lineages = −0.014–0.070), and Fst (Farms = 0.0237–0.032; lineages = 0.029–0.038). The dual-purpose herds/selection lines are the most uniform subpopulation, while the beef one preserved larger amounts of genetic diversity among herds. In addition, the dairy herd showed to be genetically distant from other herds. Taken together, these results suggest that this Guzerá meta-population has high genetic diversity, a low degree of population subdivision, and a low inbreeding level. [ABSTRACT FROM AUTHOR]

Improved reproductive efficiency could lead to economic benefits for the beef industry, once the intensive selection pressure has led to a decreased fertility. However, several factors limit our understanding of fertility traits, including genetic differences between populations and statistical limitations. In the present study, the RNA-sequencing data from uterine samples of high-fertile (HF) and sub-fertile (SF) animals was integrated using co-expression network meta-analysis, weighted gene correlation network analysis, identification of upstream regulators, variant calling, and network topology approaches. Using this pipeline, top hub-genes harboring fixed variants (HF × SF) were identified in differentially co-expressed gene modules (DcoExp). The functional prioritization analysis identified the genes with highest potential to be key-regulators of the DcoExp modules between HF and SF animals. Consequently, 32 functional candidate genes (10 upstream regulators and 22 top hub-genes of DcoExp modules) were identified. These genes were associated with the regulation of relevant biological processes for fertility, such as embryonic development, germ cell proliferation, and ovarian hormone regulation. Additionally, 100 candidate variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs)) were identified within those genes. In the long-term, the results obtained here may help to reduce the frequency of subfertility in beef herds, reducing the associated economic losses caused by this condition. [ABSTRACT FROM AUTHOR]