Genetic variability in local and imported germplasm chicken populations as revealed by analyzing runs of homozygosity

Simple Summary To maintain the uniqueness of conserved chicken populations of local and imported breeds is of great importance. In this study, we genotyped small populations belonging to 14 breeds and 7 crossbreds using an Illumina Chicken 60K SNP (Single Nucleotide Polymorphisms) BeadChip and looked for appropriate methods to characterize their purity/variability. It was not straightforward to identify crossbred individuals, and the best approach was based on calculating the length and number of homozygous regions, or runs of homozygosity (ROH), in the populations studied. The latter enabled most accurate identification of crossbreds and can be served as an effective tool in testing genome-wide purity of chicken breeds. Abstract Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity

Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations

Phenotypic diversity in poultry has been mainly driven by artificial selection and genetic drift. These led to the adaptation to the environment and the development of specific phenotypic traits of chickens in response to their economic use. This study evaluated genetic diversity within and between Russian breeds and populations using Illumina Chicken 60 K SNP iSelect BeadChip by analysing genetic differences between populations with Hudson's fixation index (FST statistic) and heterozygosity. We estimated the effect of rare alleles and linkage disequilibrium (LD) on these measurements. To assess the effect of LD on the genetic diversity population, we carried out the LD-based pruning (LD < 0.5 and LD < 0.1) for seven chicken populations combined (I) or separately (II). LD pruning was specific for different dataset groups. Because of the noticeably large sample size in the RussianWhite RG population, pruningwas substantial for Dataset I, and FST valueswere only positivewhen LD< 0.1 pruning was applied. For Dataset II, the LD pruning results were confirmed by examining heterozygosity and alleles' frequency distribution. LD between single nucleotide polymorphisms was consistent across the seven chicken populations, except the RussianWhite RG populationwith the smallest r2 values and the largest effective population size. Our findings suggest to study variability in each population LD pruning has to be carried separately not after merging to avoid bias in estimates

Risk of sperm disorders and impaired fertility in frozen–thawed bull semen: a genome-wide association study

Simple Summary This study tackles the genetic aspects of the risk of sperm damage and related impaired fertility when handling frozen–thawed bull semen for artificial insemination. To this end, we performed genomic association analysis to identify relevant genetic markers and candidate genes associated with various abnormalities in frozen–thawed Holstein cattle sperm. The results provide important insights into the molecular mechanisms underlying sperm morphology and abnormalities after cryopreservation. Further research is needed to explore causative genetic variants and implement these findings to improve animal reproduction and breeding. Abstract 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