Genome-wide association study reveals candidate markers related to field fertility and semen quality traits in Holstein-Friesian bulls

Investigation of cosmopolitan and local Italian beef cattle breeds uncover common patterns of heterozygosity

The analysis of livestock heterozygosity is less common compared to the study of homozygous patterns. Heterozygous-Rich Regions (HRRs) may harbor significant loci for functional traits such as immune response, survival rate, and fertility. For this reason, this study was conducted to investigate and characterize the heterozygosity patterns of four beef cattle breeds, which included two cosmopolitan breeds (Limousine and Charolaise) and two local breeds (Sarda and Sardo Bruna). Our analysis identified regions with a high degree of heterozygosity using a consecutive runs approach, the Tajima D test, nucleotide diversity estimation, and Hardy Weinberg equilibrium test. These regions exhibited recurrent heterozygosity peaks and were consistently found on specific chromosomes across all breeds, specifically autosomes 15, 16, 20, and 23. The cosmopolitan and Sardo Bruna breeds also displayed peaks on autosomes 2 and 21, respectively. Thirty-five top runs shared by more than 25% of the populations were identified. These genomic fragments encompassed 18 genes, two of which are directly linked to male fertility, while four are associated with lactation. Two other genes play roles in survival and immune response. Our study also detected a region related to growth and carcass traits in Limousine breed. Our analysis of heterozygosity-rich regions revealed particular segments of the cattle genome linked to various functional traits. It appears that balancing selection is occurring in specific regions within the four examined breeds, and unexpectedly, they are common across cosmopolitan and local breeds. The genes identified hold potential for applications in breeding programs and conservation studies to investigate the phenotypes associated with these heterozygous genotypes. In addition, Tajima D test, Nucleotide diversity, and Hardy Weinberg equilibrium test confirmed the presence of heterozygous fragments found with Heterozygous-Rich Regions analysis.

Factors affecting the success of laparoscopic artificial insemination in sheep

Successful artificial breeding underpins rapid genetic and production gains in animal agriculture. In sheep, artificial insemination with frozen semen is performed via intrauterine laparoscopy as frozen-thawed spermatozoa do not traverse the cervix in sufficient numbers for high fertility and transcervical insemination is anatomically impossible in most ewes. Historically, laparoscopic artificial insemination has always been considered reasonably successful, but recent anecdotal reports of poor fertility place it at risk of warning adoption. Understanding the male, female and environmental factors that influence the fertility of sheep is warranted if the success of artificial insemination is to be improved and genetic progress maximised for the sheep industry. This review details the current practice of laparoscopic AI in sheep. It explores the effects of semen quantity and quality, the ewe, her preparation, and environmental conditions, on the fertility obtained following laparoscopic artificial insemination.

Risk of Sperm Disorders and Impaired Fertility in Frozen-Thawed Bull Semen: A Genome-Wide Association Study

Cryopreservation is a widely used method of semen conservation in animal breeding programs. This process, however, can have a detrimental effect on sperm quality, especially in terms of its morphology. The resultant sperm disorders raise the risk of reduced sperm fertilizing ability, which poses a serious threat to the long-term efficacy of livestock reproduction and breeding. Understanding the genetic factors underlying these effects is critical for maintaining sperm quality during cryopreservation, and for animal fertility in general. In this regard, we performed a genome-wide association study to identify genomic regions associated with various cryopreservation sperm abnormalities in Holstein cattle, using single nucleotide polymorphism (SNP) markers via a high-density genotyping assay. Our analysis revealed a significant association of specific SNPs and candidate genes with absence of acrosomes, damaged cell necks and tails, as well as wrinkled acrosomes and decreased motility of cryopreserved sperm. As a result, we identified candidate genes such as POU6F2, LPCAT4, DPYD, SLC39A12 and CACNB2, as well as microRNAs (bta-mir-137 and bta-mir-2420) that may play a critical role in sperm morphology and disorders. These findings provide crucial information on the molecular mechanisms underlying acrosome integrity, motility, head abnormalities and damaged cell necks and tails of sperm after cryopreservation. Further studies with larger sample sizes, genome-wide coverage and functional validation are needed to explore causal variants in more detail, thereby elucidating the mechanisms mediating these effects. Overall, our results contribute to the understanding of genetic architecture in cryopreserved semen quality and disorders in bulls, laying the foundation for improved animal reproduction and breeding.

A Single-Step Genome-Wide Association Study for Semen Traits of Egyptian Buffalo Bulls

The present study aimed to contribute to the limited research on buffalo (Bubalus bubalis) semen traits by incorporating genomic data. A total of 8465 ejaculates were collected. The genotyping procedure was conducted using the Axiom® Buffalo Genotyping 90 K array designed by the Affymetrix Expert Design Program. After conducting a quality assessment, we utilized 67,282 SNPs genotyped in 192 animals. We identified several genomic loci explaining high genetic variance by employing single-step genomic evaluation. The aforementioned regions were located on buffalo chromosomes no. 3, 4, 6, 7, 14, 16, 20, 22, and the X-chromosome. The X-chromosome exhibited substantial influence, accounting for 4.18, 4.59, 5.16, 5.19, and 4.31% of the genomic variance for ejaculate volume, mass motility, livability, abnormality, and concentration, respectively. In the examined genomic regions, we identified five novel candidate genes linked to male fertility and spermatogenesis, four in the X-chromosome and one in chromosome no. 16. Additional extensive research with larger sample sizes and datasets is imperative to validate these findings and evaluate their applicability for genomic selection.

Sperm head morphometry and chromatin alterations in bulls with different conception rates

The objective of this investigation was to analyze timed-AI conception rates (CRs) of different sires in light of their conventional semen quality parameters, sperm head morphometry, and chromatin alterations. Semen was collected in the field from six Angus bulls and used for the timed-AI of 890 suckled multiparous Nellore cows at a single farm. Semen batches were evaluated on the following in vitro parameters: sperm motility, concentration, and morphology, sperm head morphometry, and chromatin alteration types. The overall CR was 49% and Bulls 1 (43%) and 2 (40%) presented reduced (P < 0.05) pregnancies per AI compared to Bull 6 (61%), even though no differences were observed between their conventional semen quality parameters. Bull 1, however, presented higher (P = 0.0001) shape factor, smaller (P = 0.0025) antero-posterior symmetry, and elevated (P = 0.0141) Fourier 1 parameter, whereas Bull 2 exhibited a higher (P = 0.0023) percentage of chromatin alteration along the central axis of the sperm head. In conclusion, bulls with varying CRs may present sperm head morphometric differences and/or chromatin alterations while not presenting differences in conventional in vitro semen quality parameters. Although further studies are needed to elucidate the concrete implications of chromatin alterations on field fertility, sperm morphometric differences and chromatin alterations may be at least partially causative of the lower pregnancies per timed-AI of certain sires.