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ORIGINAL RESEARCH article

Front. Genet.
Sec. Livestock Genomics
Volume 15 - 2024 | doi: 10.3389/fgene.2024.1409335
This article is part of the Research Topic Genetic Regulation of Reproduction Traits in Livestock Species View all 7 articles

Identification of candidate SNP associated with embryo mortality and fertility traits of lactating Holstein Cows

Provisionally accepted
Carolina L. Gonzalez-Berrios Carolina L. Gonzalez-Berrios 1Courtney F. Bowden Courtney F. Bowden 1Hamad M. Saad Hamad M. Saad 2*Jeanette V. Bishop Jeanette V. Bishop 3*Hana Van Campen Hana Van Campen 3*Pablo Pinedo Pablo Pinedo 4*Thomas R. Hansen Thomas R. Hansen 3*Milton G. Thomas Milton G. Thomas 2*
  • 1 Colorado State University, Fort Collins, United States
  • 2 Texas A&M AgriLife Research Station, Beeville, Texas, United States
  • 3 Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States
  • 4 Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, Colorado, United States

The final, formatted version of the article will be published soon.

    Targeted single nucleotide polymorphisms (SNPs) have been used in genomic prediction methodologies to enhance the accuracy of associated genetic transmitting abilities in Holstein cows. The objective of this study was to identify and validate SNP associated with fertility traits impacting early embryo mortality. The mRNA sequencing data from day 16 normal (n=9) and embryo mortality (n=6) conceptuses from lactating multiparous Holstein cows were used to detect SNPs. Selection of specific genes with SNP as preliminary candidates were based on associations with reproductive and fertility traits. Validation of candidate SNP and genotype to phenotype analysis were conducted in a separate cohort of lactating primiparous Holstein cows (n=500). After genotyping, candidate SNP were filtered using a quality control pipeline via PLINK software.Continuous numeric and binary models from reproductive traits were evaluated using the mixed procedure for a generalized linear model-one way ANOVA or logistic regression, respectively.Sixty-nine candidate SNPs were initially identified, but only 23 passed quality control procedures.Ultimately, the study incorporated 466 observations for statistical analysis, after excluding animals with missing genotypes or phenotypes. Significant (P<0.05) associations with fertility traits were identified in seven of the 23 SNP: DSC2 (cows at 1st calving were older with A allele); SREBF1 and UBD (cows took longer to conceive with T or G allele, respectively); DECR1 and FASN (cows were less likely to become pregnant at first artificial insemination with C allele); SREBF1 and BOLA-DMB (cows were less likely to be pregnant at 150 days in milk with T allele). It was also determined that two candidate SNPs within the DSC2 gene were tag SNPs. Only DSC2 SNP had an important allele substitution effect in cows with the G allele by having a decreased age at first calving by 10 days. Candidate SNPs found in this study could be used to develop genetic selection tools to improve fertility traits in dairy production systems.

    Keywords: Cattle, Health traits, Pregnancy, Holstein cows, Early embryo mortality, Single nucleotide polymorphisms, Linkage Disequilibrium

    Received: 29 Mar 2024; Accepted: 16 Jul 2024.

    Copyright: © 2024 Gonzalez-Berrios, Bowden, Saad, Bishop, Van Campen, Pinedo, Hansen and Thomas. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Hamad M. Saad, Texas A&M AgriLife Research Station, Beeville, Texas, United States
    Jeanette V. Bishop, Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States
    Hana Van Campen, Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States
    Pablo Pinedo, Department of Animal Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, 80523-1171, Colorado, United States
    Thomas R. Hansen, Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States
    Milton G. Thomas, Texas A&M AgriLife Research Station, Beeville, Texas, United States

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