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Background/Objectives: The dairy industry relies on reproductive efficiency to maintain efficient milk production. Spontaneous abortion (SA), defined as pregnancy loss between gestation days 42 and 260, occurred in 4.5% of the artificially inseminated (AI) Holstein heifers and 31.6% of the embryo transfer (ET) recipient Holstein heifers that received in vitro-produced frozen embryos on a single dairy farm in Idaho. Methods: A genome-wide association analysis (GWAA) was performed to identify the associations (FDR p < 0.05) with SA in heifers that were bred by AI (1351 controls that delivered at term and 63 cases that aborted) that conceived following the first insemination, as well as in 59 controls and 273 cases of ET recipient heifers pregnant from the first ET. Results: There were 216 loci and 413 positional candidate genes associated (FDR p < 0.05) with SA in the heifers bred by AI in a recessive model and no loci associated with SA in the ET recipients. Conclusions: The identification of loci associated with SA in the heifers bred by AI may be used to reduce fetal loss through genomic selection. [ABSTRACT FROM AUTHOR]

Introduction: Reproductive efficiency in dairy cattle bred by artificial insemination (AI) or via embryo transfer (ET) is important as a means of facilitating the rate of genetic improvement by utilizing superior genetics from sires and donor dams. Fertility is especially challenging in primiparous cows as they have recently calved, are still growing, and are lactating. Fertility, measured by the conception rate from the first service (CCR1), is the number of cows that become pregnant as a result of the first AI or ET compared to all cows serviced, whereas times bred (TBRD) is the number of inseminations cows bred by AI needed to achieve a successful pregnancy. Methods: This study aimed to identify the loci associated with and gene sets enriched for the CCR1 in primiparous cows that were bred by AI (n = 882) or were ET recipients (n = 353), and to identify the loci associated with the TBRD (n = 1,851) in primiparous cows. A genome-wide association analysis and gene set enrichment analysis were performed using single-nucleotide polymorphism (SNP) data for the CCR1 and TBRD in primiparous cows. In cows bred by AI, two loci containing five positional candidate genes were associated with the CCR1 (p < 1 × 10−5) and one gene set with 18 leading-edge genes was enriched (NES ≥3) for the CCR1. Results and discussion: In cows that were ET recipients, five loci were associated with the CCR1, but no gene sets were enriched for the CCR1. For the second phenotype, five loci with nine positional candidate genes were associated with the TBRD and two gene sets with eight leading-edge genes were enriched for the TBRD. Identifying the loci associated with or gene sets enriched for the CCR1 and TBRD provides an opportunity to better understand embryonic loss in AI-bred and ET-recipient cows and to use this information to select for higher reproductive efficiency. [ABSTRACT FROM AUTHOR]

BackgroundBovine respiratory disease complex (BRDC) is an infectious disease of cattle that is caused by a combination of viral and/or bacterial pathogens. Selection for cattle with reduced susceptibility to respiratory disease would provide a permanent tool for reducing the prevalence of BRDC. The objective of this study was to identify BRDC susceptibility loci in pre-weaned Holstein calves as a prerequisite to using genetic improvement as a tool for decreasing the prevalence of BRDC. High density SNP genotyping with the Illumina BovineHD BeadChip was conducted on 1257 male and 757 female Holstein calves from California (CA), and 767 calves identified as female from New Mexico (NM). Of these, 1382 were classified as BRDC cases, and 1396 were classified as controls, with all phenotypes assigned using the McGuirk health scoring system. During the acquisition of blood for DNA isolation, two deep pharyngeal and one mid-nasal diagnostic swab were obtained from each calf for the identification of bacterial and viral pathogens. Genome-wide association analyses were conducted using four analytical approaches (EIGENSTRAT, EMMAX-GRM, GBLUP and FvR). The most strongly associated SNPs from each individual analysis were ranked and evaluated for concordance. The heritability of susceptibility to BRDC in pre-weaned Holstein calves was estimated.ResultsThe four statistical approaches produced highly concordant results for 373 top ranked SNPs that defined 126 chromosomal regions for the CA population. Similarly, in NM, 370 SNPs defined 138 genomic regions that were identified by all four approaches. When the two populations were combined (i.e., CA + NM) and analyzed, 324 SNPs defined 116 genomic regions that were associated with BRDC across all analytical methods. Heritability estimates for BRDC were 21% for both CA and NM as individual populations, but declined to 13% when the populations were combined.ConclusionsFour analytical approaches utilizing both single and multi-marker association methods revealed common genomic regions associated with BRDC susceptibility that can be further characterized and used for genomic selection. Moderate heritability estimates were observed for BRDC susceptibility in pre-weaned Holstein calves, thereby supporting the application of genomic selection to reduce the prevalence of BRDC in U.S. Holsteins.

Heifer conception rate to the first service (HCR1) is defined as the number of heifers that become pregnant to the first breeding service compared to the heifers bred. This study aimed to identify loci associated and gene sets enriched for HCR1 for heifers that were bred by artificial insemination (AI, n = 2829) or were embryo transfer (ET, n = 2086) recipients, by completing a genome-wide association analysis and gene set enrichment analysis using SNP data (GSEA-SNP). Three unique loci, containing four positional candidate genes, were associated (p < 1 × 10−5) with HCR1 for ET recipients, while the GSEA-SNP identified four gene sets (NES ≥ 3) and sixty-two leading edge genes (LEGs) enriched for HCR1. While no loci were associated with HCR1 bred by AI, one gene set and twelve LEGs were enriched (NES ≥ 3) for HCR1 with the GSEA-SNP. This included one gene (PKD2) shared between HCR1 AI and ET services. Identifying loci associated or enriched for HCR1 provides an opportunity to use them as genomic selection tools to facilitate the selection of cattle with higher reproductive efficiency, and to better understand embryonic loss. [ABSTRACT FROM AUTHOR]

Genomic selection is a tool available to the dairy industry, capable of increasing economic returns through improved efficiencies and selection of superior animals. However, these tools are underutilized within the commercial sector, mostly due to a lack of information on how to effectively use them. The objective of this work was to provide producers and veterinarians with educational workshops that included information about genomic selection and evaluate the impact of these workshops on participant receptivity towards using genomic selection tools. Three workshops were held in both Washington and Idaho for industry personnel and veterinarians. Thirty-six individuals attended the workshops and completed a pre-workshop survey to capture their understanding of genomic selection and its uses, as well as information regarding their current usage or interest in the technology. After attending a discussion on the basics of genomic selection, various uses and benefits, and then applying the information to an example herd, participants were asked to complete the same survey. In addition to the initial questions, participants were polled to determine if their opinions surrounding genomic selection had changed and if the workshop was beneficial. A third survey on skills gained and applicability of information was also completed. Before the workshop, 59% reported that they have used genomic selection, 54% stated they would use genomics to select replacement heifers, and 73% would use genomics to make breeding decisions. When comparing pre- and post-workshop survey responses using a t-test, the mean score increased (P = 0.0027) from 83% to 94%. When gauging the success of the workshop, 87% stated they found the workshop helpful and 80% said they would like more information. All individuals stated they will either be using genomic selection in the future (57%) or would consider the technology (43%). Producers in attendance manage over 20,600 cows and 6,600 replacement heifers. Attending veterinarians provided consultations for > 56,000 cows and 30,800 heifers. Moreover, attendees estimated they would discuss the workshop with approximately 240 other individuals. These workshops provide a basis for establishing hands-on learning for industry members to gain information on technologies that can be used to improve their respective businesses. The use of genomic selection could grow exponentially if producers and supporting individuals are given access to educational events and materials to allow for better understanding of how to use the technology to its maximum ability. Funding for this project (# SW21-925) was provided by the Western Sustainable Agriculture Research and Education. [ABSTRACT FROM AUTHOR]

Background: The objectives of this study were to identify loci, positional candidate genes, gene-sets, and pathways associated with spontaneous abortion (SA) in cattle and compare these results with previous human SA studies to determine if cattle are a good SA model for humans. Pregnancy was determined at gestation day 35 for Holstein heifers and cows. Genotypes from 43,984 SNPs of 499 pregnant heifers and 498 pregnant cows that calved at full term (FT) were compared to 62 heifers and 28 cows experiencing SA. A genome-wide association analysis, gene-set enrichment analysis–single nucleotide polymorphism, and ingenuity pathway analysis were used to identify regions, pathways, and master regulators associated with SA in heifers, cows, and a combined population. Results: Twenty-three loci and 21 positional candidate genes were associated (p < 1 × 10−5) with SA and one of these (KIR3DS1) has been associated with SA in humans. Eight gene-sets (NES > 3.0) were enriched in SA and one was previously reported as enriched in human SA. Four master regulators (p < 0.01) were associated with SA within two populations. Conclusions: One locus associated with SA was validated and 39 positional candidate and leading-edge genes and 2 gene-sets were enriched in SA in cattle and in humans. [ABSTRACT FROM AUTHOR]