Genome-wide association study of anogenital distance and its (co)variances with fertility in growing and lactating Holstein-Friesian dairy cattle

Stephen, M.A.; Burke, C.R.; Steele, N.; Pryce, J.E.; Meier, S.; Amer, P.R.; Phyn, C.V.C.; Garrick, D.J.

doi:10.3168/jds.2023-23427

Cited by 4 publications

(1 citation statement)

References 43 publications

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“…This indicates that the pubertal classifications are polygenic traits. Other studies that have tried to define regions of interests through GWAS analysis specific to puberty onset used a greater number of females and utilized other traits associated with age at puberty or female fertility such as: anogenital distance ( Stephen et al, 2023b ), antral follicle counts ( Stegemiller et al, 2021 ), age at puberty in dairy ( Lefebvre et al, 2021 ) and beef ( Vargas et al, 1998 ), age at first CL in Bos indicus ( Fortes et al, 2012 ), and age at menarche, ( Perry et al, 2014 ). While other studies have combined RNAseq data and other “omics” from different reproductive tissues obtained at or around puberty ( Cánovas et al, 2014 ; Tahir et al, 2021 ; 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Puberty classifications in beef heifers are moderately to highly heritable and associated with candidate genes related to cyclicity and timing of puberty

Hess,

Mersha,

Ference

et al. 2024

Front. Genet.

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Introduction: Pubertal attainment is critical to reproductive longevity in heifers. Previously, four heifer pubertal classifications were identified according to attainment of blood plasma progesterone concentrations > 1 ng/ml: 1) Early; 2) Typical; 3) Start-Stop; and 4) Non-Cycling. Early and Typical heifers initiated and maintained cyclicity, Start-Stop started and then stopped cyclicity and Non-Cycling never initiated cyclicity. Start-Stop heifers segregated into Start-Stop-Discontinuous (SSD) or Start-Stop-Start (SSS), with SSD having similar phenotypes to Non-Cycling and SSS to Typical heifers. We hypothesized that these pubertal classifications are heritable, and loci associated with pubertal classifications could be identified by genome wide association studies (GWAS).Methods: Heifers (n = 532; 2017 – 2022) genotyped on the Illumina Bovine SNP50 v2 or GGP Bovine 100K SNP panels were used for variant component estimation and GWAS. Heritability was estimated using a univariate Bayesian animal model.Results: When considering pubertal classifications: Early, Typical, SSS, SSD, and Non-Cycling, pubertal class was moderately heritable (0.38 ± 0.08). However, when heifers who initiated and maintained cyclicity were compared to those that did not cycle (Early+Typical vs. SSD+Non-Cycling) heritability was greater (0.59 ± 0.19). A GWAS did not identify single nucleotide polymorphisms (SNPs) significantly associated with pubertal classifications, indicating puberty is a polygenic trait. A candidate gene approach was used, which fitted SNPs within or nearby a set of 71 candidate genes previously associated with puberty, PCOS, cyclicity, regulation of hormone secretion, signal transduction, and methylation. Eight genes/regions were associated with pubertal classifications, and twenty-two genes/regions were associated with whether puberty was attained during the trial. Additionally, whole genome sequencing (WGS) data on 33 heifers were aligned to the reference genome (ARS-UCD1.2) to identify variants in FSHR, a gene critical to pubertal attainment. Fisher’s exact test determined if FSHR SNPs segregated by pubertal classification. Two FSHR SNPs that were not on the bovine SNP panel were selected for additional genotyping and analysis, and one was associated with pubertal classifications and whether they cycled during the trial.Discussion: In summary, these pubertal classifications are moderately to highly heritable and polygenic. Consequently, genomic tools to inform selection/management of replacement heifers would be useful if informed by SNPs associated with cyclicity and early pubertal attainment.

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Section: Discussionmentioning

confidence: 99%

Puberty classifications in beef heifers are moderately to highly heritable and associated with candidate genes related to cyclicity and timing of puberty

Hess,

Mersha,

Ference

et al. 2024

Front. Genet.

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Using expression data to fine map QTL associated with fertility in dairy cattle

van den Berg,

Chamberlain,

MacLeod

et al. 2024

Genet Sel Evol

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Background Female fertility is an important trait in dairy cattle. Identifying putative causal variants associated with fertility may help to improve the accuracy of genomic prediction of fertility. Combining expression data (eQTL) of genes, exons, gene splicing and allele specific expression is a promising approach to fine map QTL to get closer to the causal mutations. Another approach is to identify genomic differences between cows selected for high and low fertility and a selection experiment in New Zealand has created exactly this resource. Our objective was to combine multiple types of expression data, fertility traits and allele frequency in high- (POS) and low-fertility (NEG) cows with a genome-wide association study (GWAS) on calving interval in Australian cows to fine-map QTL associated with fertility in both Australia and New Zealand dairy cattle populations. Results Variants that were significantly associated with calving interval (CI) were strongly enriched for variants associated with gene, exon, gene splicing and allele-specific expression, indicating that there is substantial overlap between QTL associated with CI and eQTL. We identified 671 genes with significant differential expression between POS and NEG cows, with the largest fold change detected for the CCDC196 gene on chromosome 10. Our results provide numerous candidate genes associated with female fertility in dairy cattle, including GYS2 and TIGAR on chromosome 5 and SYT3 and HSD17B14 on chromosome 18. Multiple QTL regions were located in regions with large numbers of copy number variants (CNV). To identify the causal mutations for these variants, long read sequencing may be useful. Conclusions Variants that were significantly associated with CI were highly enriched for eQTL. We detected 671 genes that were differentially expressed between POS and NEG cows. Several QTL detected for CI overlapped with eQTL, providing candidate genes for fertility in dairy cattle.

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Genome-wide association study of age at puberty and its (co)variances with fertility and stature in growing and lactating Holstein-Friesian dairy cattle

Stephen,

Burke,

Steele

et al. 2024

Journal of Dairy Science

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Genome-wide association study of anogenital distance and its (co)variances with fertility in growing and lactating Holstein-Friesian dairy cattle

Cited by 4 publications

References 43 publications

Puberty classifications in beef heifers are moderately to highly heritable and associated with candidate genes related to cyclicity and timing of puberty

Puberty classifications in beef heifers are moderately to highly heritable and associated with candidate genes related to cyclicity and timing of puberty

Using expression data to fine map QTL associated with fertility in dairy cattle

Genome-wide association study of age at puberty and its (co)variances with fertility and stature in growing and lactating Holstein-Friesian dairy cattle

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