Genome-wide association study for frozen-thawed sperm motility in stallions across various horse breeds

Nikitkina, Elena; Дементьева, Н. В.; Shcherbakov, Yuri S.; Atroshchenko, Mikhail; Kudinov, Andrei A.; Samoylov, Oleg I.; Pozovnikova, Marina V.; Dysin, Artem P.; Krutikova, Anna; Musidray, Artem; Митрофанова, О.В.; Plemyashov, Kirill; Griffin, Darren K.; Romanov, Michael N

doi:10.5713/ab.21.0504

Cited by 7 publications

(8 citation statements)

References 43 publications

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“…Herewith, breed may have very little effect on sperm morphology, possibly due to high inbreeding in small breeds. For example, our previous study [3] also showed little influence of breed on sperm morphology. Abnormal sperm morphology can reduce the chances of fertilization [12] and embryo development; it can also increase the risk of transmitting genetic defects [13].…”

Section: Introductionmentioning

confidence: 76%

“…Sperm disorders in frozen-thawed bull semen, widely used in artificial insemination (AI) technology, confer a risk of impaired fertility in cattle (Bos taurus; BTA). Semen cryopreservation is nonetheless a valuable and effective method for disseminating and preserving superior genetics in livestock production (e.g., [1][2][3][4][5]). It allows the use of AI to increase reproductive efficiency and genetic gain in livestock [6].…”

Section: Introductionmentioning

confidence: 99%

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

Dementieva,

Dysin,

Shcherbakov

et al. 2024

Animals

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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.

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Section: Introductionmentioning

confidence: 76%

Section: Introductionmentioning

confidence: 99%

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

Dementieva,

Dysin,

Shcherbakov

et al. 2024

Animals

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“…On a longer term, these databases may lead to the annotation of genes for multifactorial/polygenic traits or disorders and additionally enable future ranking of embryos for traits based on polygenic risk analysis. While the initiation of human embryo selection based on PGT-P poses several ethical and technical problems 78 – 82 , the development of PGT-P in horses can be valuable for assessing important equine polygenic disorders like osteochondrosis dissecans 83 – 85 or insect bite hypersensitivity 86 and traits like performance 87 , 88 , parasite susceptibility 89 or fertility 90 , 91 , for which genome-wide association studies in horses are increasing the knowledge on the heritability and associated SNPs. On the other hand, obtaining materials from family members is straightforward in humans but poses a hurdle for the application of haplotyping-based PGT in the horse industry.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection

De Coster,

Zhao,

Tšuiko

et al. 2024

Sci Rep

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In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.

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“…On a longer term, these databases may lead to the annotation of genes for multifactorial/polygenic traits or disorders and additionally enable future ranking of embryos for traits based on polygenic risk analysis. While the initiation of human embryo selection based on PGT-P poses several ethical and technical problems [79][80][81][82][83] , the development of PGT-P in horses can be valuable for assessing important equine polygenic disorders like osteochondrosis dissecans [84][85][86] or insect bite hypersensitivity 87 and traits like performance 88,89 , parasite susceptibility 90 or fertility 91,92 , for which genome-wide association studies in horses are increasing the knowledge on the heritability and associated SNPs. On the other hand, obtaining materials from family members is straightforward in humans but poses a hurdle for the application of haplotyping-based PGT in the horse industry.…”

Section: Discussionmentioning

confidence: 99%

Simultaneous genome-wide haplotyping and copy number detection enables universal equine preimplantation genetic testing

Coster

Zhao

Tšuiko

et al. 2023

Preprint

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In different species, embryonic chromosomal aneuploidies are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explore the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A), monogenic (PGT-M) and polygenic (PGT-P) traits and diseases in the horse. To this end, over 70,000 single nucleotide polymorphism positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual cells from six arrested embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were determined and compared in biopsy-blastocyst combinations. The inherited parental haplotypes for loci of interest and the euploid (n = 12) or aneuploid (n = 2) state of the biopsied whole embryos were predicted by the biopsy samples in all successfully analyzed embryos. Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their cells, demonstrating the contribution of aneuploidy to equine embryonic arrest in vitro. The application of universal PGT would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.

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Genome-wide association study for frozen-thawed sperm motility in stallions across various horse breeds

Cited by 7 publications

References 43 publications

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

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

Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection

Simultaneous genome-wide haplotyping and copy number detection enables universal equine preimplantation genetic testing

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