A genome-wide association study of mare fertility in the Pura Raza Español horse

Laseca, Nora; Demyda-Peyrás, S.; Valera, M.; Ramón, Manuel; Escribano, Begoña M.; Perdomo-González, Davinia I.; Molina, A.

doi:10.1016/j.animal.2022.100476

Cited by 11 publications

(9 citation statements)

References 57 publications

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“…However, none of these employed Re as a fertility estimator for the cows. Likewise, similar h 2 values (near 0.25) were recently reported in goats and horses [13,47]. In addition, it was also noticeable that the permanent environmental effect of the cow accounted for nearly 35% of the total variance and the contemporary group (HYS) for only 9%.…”

Section: Modeling the Genetic Influence On Re Using A Repeatability M...supporting

confidence: 85%

“…However, at the same time, it is one of the most neglected from a genetic point of view, since it is difficult to study models in such production conditions. For this reason, the use of indirect traits obtained from pedigree records is becoming an interesting alternative to evaluating fertility at the population level since it allows us to obtain large phenotypic datasets, which are crucial for making reliable estimations [13,47]. Using such an approach, we were able to determine the genetic and environmental effects in a large cohort of beef cows bred in extensive conditions.…”

Section: Resultsmentioning

confidence: 99%

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Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle

Jiménez¹,

Morales

Menéndez-Buxadera

et al. 2023

Animals

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In this study, we analyzed the variation of reproductive efficiency, estimated as the deviation between the optimal and real parity number of females at each stage of the cow’s life, in 12,554 cows belonging to the Retinta Spanish cattle breed, using classical repeatability and random regression models. The results of the analyses using repeatability model and the random regression model suggest that reproductive efficiency is not homogeneous throughout the cow’s life. The h2 estimate for this model was 0.30, while for the random regression model it increased across the parities, from 0.24 at the first calving to 0.51 at calving number 9. Additionally, we performed a preliminary genome-wide association study for this trait in a population of 252 Retinta cows genotyped using the Axiom Bovine Genotyping v3 Array. The results showed 5 SNPs significantly associated with reproductive efficiency, located in two genomic regions (BTA4 and BTA28). The functional analysis revealed the presence of 5 candidate genes located within these regions, which were previously involved in different aspects related to fertility in cattle and mice models. This new information could give us a better understanding of the genetic architecture of reproductive traits in this species, as well as allow us to accurately select more fertile cows.

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Section: Modeling the Genetic Influence On Re Using A Repeatability M...supporting

confidence: 85%

Section: Resultsmentioning

confidence: 99%

Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle

Jiménez¹,

Morales

Menéndez-Buxadera

et al. 2023

Animals

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“…Joint Analysis of NAT10-Depleted and OGA-Depleted Transcriptomes the expression of Rsph6a, Gm7788, and Gm41780 was downregulated in both NAT10-depleted and OGA-depleted oocytes. Among them, Rsph6a is associated with mammalian fertility and is recognized as a potential marker for fertility (37).…”

Section: Expression Profiling Of Oocytes With Oga Knockdownmentioning

confidence: 99%

NAT10 Maintains OGA mRNA Stability Through ac4C Modification in Regulating Oocyte Maturation

et al. 2022

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In vitro maturation (IVM) refers to the process of developing immature oocytes into the mature in vitro under the microenvironment analogous to follicle fluid. It is an important technique for patients with polycystic ovary syndrome and, especially, those young patients with the need of fertility preservation. However, as the mechanisms of oocyte maturation have not been fully understood yet, the cultivation efficiency of IVM is not satisfactory. It was confirmed in our previous study that oocyte maturation was impaired after N-acetyltransferase 10 (NAT10) knockdown (KD). In the present study, we further explored the transcriptome alteration of NAT10-depleted oocytes and found that O-GlcNAcase(OGA) was an important target gene for NAT10-mediated ac4C modification in oocyte maturation. NAT10 might regulate OGA stability and expression by suppressing its degradation. To find out whether the influence of NAT10-mediated ac4C on oocyte maturation was mediated by OGA, we further explored the role of OGA in IVM. After knocking down OGA of oocytes, oocyte maturation was inhibited. In addition, as oocytes matured, OGA expression increased and, conversely, O-linked N-acetylglucosamine (O-GlcNAc) level decreased. On the basis of NAT10 KD transcriptome and OGA KD transcriptome data, NAT10-mediated ac4C modification of OGA might play a role through G protein–coupled receptors, molecular transduction, nucleosome DNA binding, and other mechanisms in oocyte maturation. Rsph6a, Gm7788, Gm41780, Trpc7, Gm29036, and Gm47144 were potential downstream genes. In conclusion, NAT10 maintained the stability of OGA transcript by ac4C modification on it, thus positively regulating IVM. Moreover, our study revealed the regulation mechanisms of oocytes maturation and provided reference for improving IVM outcomes. At the same time, the interaction between mRNA ac4C modification and protein O-GlcNAc modification was found for the first time, which enriched the regulation network of oocyte maturation.

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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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A genome-wide association study of mare fertility in the Pura Raza Español horse

Cited by 11 publications

References 57 publications

Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle

Estimation of the Genetic Components of (Co)variance and Preliminary Genome-Wide Association Study for Reproductive Efficiency in Retinta Beef Cattle

NAT10 Maintains OGA mRNA Stability Through ac4C Modification in Regulating Oocyte Maturation

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

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