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Genome-wide association mapping for dominance effects in female fertility using real and simulated data from Danish Holstein cattle.

ABSTRACT: Exploring dominance variance and loci contributing to dominance variation is important to understand the genetic architecture behind quantitative traits. The objectives of this study were i) to estimate dominance variances, ii) to detect quantitative trait loci (QTL) with dominant effects, and iii) to evaluate the power and the precision of identifying loci with dominance effect through post-hoc simulations, with applications for female fertility in Danish Holstein cattle. The female fertility records analyzed were number of inseminations (NINS), days from calving to first insemination (ICF), and days from the first to last insemination (IFL), covering both abilities to recycle and to get pregnant in the female reproductive cycle. There were 3,040 heifers and 4,483 cows with both female fertility records and Illumina BovineSNP50 BeadChip genotypes (35,391 single nucleotide polymorphisms (SNP) after quality control). Genomic best linear unbiased prediction (BLUP) models were used to estimate additive and dominance genetic variances. Linear mixed models were used for association analyses. A post-hoc simulation study was performed using genotyped heifers' data. In heifers, estimates of dominance genetic variances for female fertility traits were larger than additive genetic variances, but had large standard errors. The variance components for fertility traits in cows could not be estimated due to non-convergence of the statistical model. In total, five QTL located on chromosomes 9, 11 (2 QTL), 19, and 28 were identified and all of them showed both additive and dominance genetic effects. Among them, the SNP rs29018921 on chromosome 9 is close to a previously identified QTL in Nordic Holstein for interval between first and last insemination. This SNP is located in the 3' untranslated region of gene peptidylprolyl isomerase like 4 (PPIL4), which was shown to be associated with milk production traits in US Holstein cattle but not known for fertility-related functions. Simulations indicated that the current sample size had limited power to detect QTL with dominance effects for female fertility probably due to low QTL variance. More females need to be genotyped to achieve reliable mapping of QTL with dominance effects for female fertility.

SUBMITTER: Mao X

PROVIDER: S-EPMC7031268 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Genome-wide association mapping for dominance effects in female fertility using real and simulated data from Danish Holstein cattle.

Mao Xiaowei X Sahana Goutam G Johansson Anna Maria AM Liu Aoxing A Ismael Ahmed A Løvendahl Peter P De Koning Dirk-Jan DJ Guldbrandtsen Bernt B

Scientific reports 20200219 1

Exploring dominance variance and loci contributing to dominance variation is important to understand the genetic architecture behind quantitative traits. The objectives of this study were i) to estimate dominance variances, ii) to detect quantitative trait loci (QTL) with dominant effects, and iii) to evaluate the power and the precision of identifying loci with dominance effect through post-hoc simulations, with applications for female fertility in Danish Holstein cattle. The female fertility r ...[more]

PMID: 32076041

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Project description:BackgroundThe Nordic Red Cattle (NRC) consists of animls belonging to the Danish Red, Finnish Ayrshire, and Swedish Red breeds. Compared to the Holstein breed, NRC animals are smaller, have a shorter calving interval, lower mastitis incidence and lower rates of stillborn calves, however they produce less milk, fat and protein. Female fertility is an important trait for the dairy cattle farmer. Selection decisions in female fertilty in NRC are based on the female fertility index (FTI). FTI is a composite index including a number of sub-indices describing aspects of female fertility in dairy cattle. The sub-traits of FTI are: number of inseminations per conception (AIS) in cows (C) and heifers (H), the length in days of the interval from calving to first insemination (ICF) in cows, days from first to last insemination (IFL) in cows and heifers, and 56-day non-return rate (NRR) in cows and heifers. The aim of this study was first to identify QTL for FTI by conducting a genome scan for variants associated with fertility index using imputed whole genome sequence data based on 4207 Nordic Red sires, and subsequently analyzing which of the sub-traits were affected by each FTI QTL by associating them with the sub-traits.ResultsA total 17,388 significant SNP markers (-log10(P) > 8.25) were detected for FTI distributed over 25 chromosomes. The chromosomes with the most significant markers were tested for associations with the underlying sub-traits: BTA1 (822 SNP), BTA2 (220 SNP), BTA3 (83 SNP), BTA5 (195 SNP), two regions on BTA6 (503 SNP), BTA13 (980 SNP), BTA15 (23 SNP), BTA20 (345 SNP), and BTA24 (104 SNP). The fertility traits underlying the FTI peak area were: BTA1 (IFLC, IFLH), BTA2 (AISH, IFLH, NRRH), BTA3 (AISH, NRRH), BTA5 (AISC, AISH, IFLH), BTA6 (region 1: AISH, NRRH; region 2: AISH, IFLH), BTA13 (IFLH, IFLC), BTA15 (IFLC, NRRH), and BTA24 (AISH, IFLH). For BTA20 all sub-traits had SNP markers with a -log10(P) > 10. Furthermore the genes assigned to the most significant SNP for FTI were located on BTA6 (GPR125), BTA13 (ANKRD60), BTA15 (GRAMD1B), and BTA24 (ZNF521).ConclusionThis study 1) shows that many markers within FTI QTL regions were significantly associated with both AISH and IFLH, and 2) identified candidate genes for FTI located on BTA6 (GPR125), BTA13 (ANKRD60), BTA15 (GRAMD1B), and BTA24 (ZNF521). It is not known how the genes/variants identified in this study regulate female fertility, however the majority of these genes were involved in protein binding, 3) a SNP in a QTL region for FTI on BTA20 was previously validated in three cattle breeds.

Project description:BackgroundCrossover localization during meiotic recombination is mediated by the fast-evolving zinc-finger (ZnF) domain of gene PRDM9. To study its impact on dairy cattle performance, we compared its genetic variation between the relatively small Israeli (IL) Holsteins and the North American (US) Holsteins that count millions.ResultsInitially, we analyzed the major BTA1 haplotypes present in IL Holsteins based on the 10 most telomeric SNPs of the BovineSNP50 BeadChip. Sequencing of representative haplotype carriers indicated that for all frequent haplotypes (> 6%), the variable PRDM9 ZnF array consisted of seven tandem ZnF repeats. Two rare haplotypes (frequency < 4%) carried an indicine PRDM9, whereas all others were variants of the taurine type. These two haplotypes included the minor SNP allele, which was perfectly linked with a previously described PRDM9 allele known to induce unique localization of recombination hotspots. One of them had a significant (p = 0.03) negative effect on IL sire fertility. This haplotype combined the rare minor alleles of the only SNPs with significant (p < 0.05) negative substitution effects on US sire fertility (SCR). Analysis of telomeric SNPs indicated general agreement of allele frequencies (R = 0.95) and of the substitution effects on sire fertility (SCR, R = 0.6) between the US and IL samples. Surprisingly, the alleles that had a negative impact on male fertility had the most positive substitution effects on female fertility traits (DPR, CCR and HCR).ConclusionsA negative genetic correlation between male and female fertility is encoded within the BTA1 telomere. Cloning the taurine PRDM9 gene, which is the common form carried by Holsteins, we encountered the infiltration of an indicine PRDM9 variant into this population. During meiosis, in heterozygous males, the indicine PRDM9 variant may induce incompatibility of recombination hotspots and male infertility. However, this variant is associated with favorable female fertility, which would explain its survival and the general negative correlation (R = - 0.3) observed between male and female fertility in US Holsteins. Further research is needed to explain the mechanism underlying this positive effect and to devise a methodology to unlink it from the negative effect on male fertility during breeding.

Dataset Information

Genome-wide association mapping for dominance effects in female fertility using real and simulated data from Danish Holstein cattle.

Publications

Genome-wide association mapping for dominance effects in female fertility using real and simulated data from Danish Holstein cattle.

Similar Datasets

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