Abstract
BackgroundAchieving rapid genetic progress while maintaining adequate genetic diversity is one of the main challenges facing the dairy industry. The increase in inbreeding can be used to monitor the loss of genetic diversity. Inbreeding tends to increase the proportion of homozygous loci, some of which cause homozygosity of recessive alleles that results in reduced performance. This phenomenon is known as inbreeding depression and tends to be most prominent on fitness-related traits, such as male fertility. Traditionally, inbreeding has been monitored using pedigree information, or more recently, genomic data. Alternatively, it can be quantified using runs of homozygosity (ROH), i.e., contiguous lengths of homozygous genotypes observed in an individual’s chromosome.ResultsThe objective of this study was to evaluate the association between ROH and sire conception rate. ROH were evaluated using 268 k genetic markers in 11,790 US Holstein bulls. Interestingly, either the sum, mean, or maximum length of ROH were negatively associated with bull fertility. The association analysis between ROH and sire fertility was performed comparing 300 high-fertility vs. 300 low-fertility bulls. Both the average and sum of ROH length were higher in the low-fertility group. The enrichment of ROH regions in bulls with low fertility was assessed using a Fisher’s exact test. Nine regions were significantly enriched in low-fertility compared to high-fertility bulls. Notably, these regions harbor genes that are closely related to sperm biology and male fertility, including genes exclusively or highly expressed in testis.ConclusionsThe results of this study can help not only to manage inbreeding in genomic selection programs by designing custom mating schemes, but also to better understand the mechanisms underlying male fertility in dairy cattle.
Highlights
Achieving rapid genetic progress while maintaining adequate genetic diversity is one of the main challenges facing the dairy industry
Inbreeding depression can arise from three basic mechanisms: (i) the partial dominance hypothesis refers to the expression of deleterious recessive alleles in homozygous individuals and expressing the deleterious genotype; (ii) the over-dominance hypothesis where the heterozygous alleles expressing the superior genotype are underrepresented in a population with increased inbreeding; and (iii) the epistasis hypothesis where a combination of heterozygous alleles expressing a superior genotype is less frequent as inbreeding arises [10]
This study evaluated the association between runs of homozygosity and male fertility in dairy cattle
Summary
Achieving rapid genetic progress while maintaining adequate genetic diversity is one of the main challenges facing the dairy industry. Inbreeding tends to increase the proportion of homozygous loci, some of which cause homozygosity of recessive alleles that results in reduced performance. This phenomenon is known as inbreeding depression and tends to be most prominent on fitness-related traits, such as male fertility. Inbreeding has been monitored using pedigree information, or more recently, genomic data It can be quantified using runs of homozygosity (ROH), i.e., contiguous lengths of homozygous genotypes observed in an individual’s chromosome. Inbreeding depression is calculated by regressing the individual phenotype on its own pedigree inbreeding coefficient [11], assuming that the inbreeding depression is a linear function of the inbreeding level of the individual. Pedigree inbreeding is based on the expected proportion of the genome that is identical by descent but the true genomic relationship between two individuals deviate as a consequence of Mendelian sampling, leading to underestimated values for inbreeding coefficients [12, 13]
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