Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows

Selecting sequence variants to improve genomic predictions for dairy cattle

Background

Millions of genetic variants have been identified by population-scale sequencing projects, but subsets of these variants are needed for routine genomic predictions or genotyping arrays. Methods for selecting sequence variants were compared using simulated sequence genotypes and real July 2015 data from the 1000 Bull Genomes Project.

Methods

Candidate sequence variants for 444 Holstein animals were combined with high-density (HD) imputed genotypes for 26,970 progeny-tested Holstein bulls. Test 1 included single nucleotide polymorphisms (SNPs) for 481,904 candidate sequence variants. Test 2 also included 249,966 insertions-deletions (InDels). After merging sequence variants with 312,614 HD SNPs and editing steps, Tests 1 and 2 included 762,588 and 1,003,453 variants, respectively. Imputation quality from findhap software was assessed with 404 of the sequenced animals in the reference population and 40 randomly chosen animals for validation. Their sequence genotypes were reduced to the subset of genotypes that were in common with HD genotypes and then imputed back to sequence. Predictions were tested for 33 traits using 2015 data of 3983 US validation bulls with daughters that were first phenotyped after August 2011.

Results

The average percentage of correctly imputed variants across all chromosomes was 97.2 for Test 1 and 97.0 for Test 2. Total time required to prepare, edit, impute, and estimate the effects of sequence variants for 27,235 bulls was about 1 week using less than 33 threads. Many sequence variants had larger estimated effects than nearby HD SNPs, but prediction reliability improved only by 0.6 percentage points in Test 1 when sequence SNPs were added to HD SNPs and by 0.4 percentage points in Test 2 when sequence SNPs and InDels were included. However, selecting the 16,648 candidate SNPs with the largest estimated effects and adding them to the 60,671 SNPs used in routine evaluations improved reliabilities by 2.7 percentage points.

Conclusions

Reliabilities for genomic predictions improved when selected sequence variants were added; gains were similar for simulated and real data for the same population, and larger than previous gains obtained by adding HD SNPs. With many genotyped animals, many data sources, and millions of variants, computing strategies must efficiently balance costs of imputation, selection, and prediction to obtain subsets of markers that provide the highest accuracy.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0307-4) contains supplementary material, which is available to authorized users.

Association of single nucleotide polymorphisms in candidate genes previously related to genetic variation in fertility with phenotypic measurements of reproductive function in Holstein cows

Many genetic markers related to health or production traits are not evaluated in populations independent of the discovery population or related to phenotype. Here we evaluated 68 single nucleotide polymorphisms (SNP) in candidate genes previously associated with genetic merit for fertility and production traits for association with phenotypic measurements of fertility in a population of Holstein cows that was selected based on predicted transmitting ability (PTA) for daughter pregnancy rate (DPR; high, ≥1, n = 989; low, ≤ -1.0, n = 1,285). Cows with a high PTA for DPR had higher pregnancy rate at first service, fewer services per conception, and fewer days open than cows with a low PTA for DPR. Of the 68 SNP, 11 were associated with pregnancy rate at first service, 16 with services per conception, and 19 with days open. Single nucleotide polymorphisms in 12 genes (BDH2, BSP3, CAST, CD2, CD14, FUT1, FYB, GCNT3, HSD17B7, IBSP, OCLN, and PCCB) had significant associations with 2 fertility traits, and SNP in 4 genes (CSPP1, FCER1G, PMM2, and TBC1D24) had significant associations with each of the 3 traits. Results from this experiment were compared with results from 2 earlier studies in which the SNP were associated with genetic estimates of fertility. One study involved the same animals as used here, and the other study was of an independent population of bulls. A total of 13 SNP associated with 1 or more phenotypic estimates of fertility were directionally associated with genetic estimates of fertility in the same cow population. Moreover, 14 SNP associated with reproductive phenotype were directionally associated with genetic estimates of fertility in the bull population. Nine SNP (located in BCAS, BSP3, CAST, FUT1, HSD17B7, OCLN, PCCB, PMM2, and TBC1D24) had a directional association with fertility in all 3 studies. Examination of the function of the genes with SNP associated with reproduction in more than one study indicates the importance of steroid hormones and immune function as determinants of reproductive function. All but 1 of the 68 evaluated SNP were variable in 11 breeds besides Holstein, indicating the potential effects of these SNP on reproductive function across breeds of cattle.

Modification of embryonic resistance to heat shock in cattle by melatonin and genetic variation in HSPA1L

The objectives were to test whether (1) melatonin blocks inhibition of embryonic development caused by heat shock at the zygote stage, and (2) the frequency of a thermoprotective allele for HSPA1L is increased in blastocysts formed from heat-shocked zygotes as compared with blastocysts from control zygotes. It was hypothesized that melatonin prevents effects of heat shock on development by reducing accumulation of reactive oxygen species (ROS) and that embryos inheriting the thermoprotective allele of HSPA1L would be more likely to survive heat shock. Effects of 1 µM melatonin on ROS were determined in experiments 1 and 2. Zygotes were cultured at 38.5 or 40°C for 3 h in the presence of CellROX reagent (ThermoFisher Scientific, Waltham, MA). Culture was in a low [5% (vol/vol)] oxygen (experiment 1) or low or high [21% (vol/vol)] oxygen environment (experiment 2). Heat shock and high oxygen increased ROS; melatonin decreased ROS. Development was assessed in experiments 3 and 4. In experiment 3, zygotes were cultured in low oxygen ± 1 µM melatonin and exposed to 38.5 or 40°C for 12 h (experiment 1) beginning 8 h after fertilization. Melatonin did not protect the embryo from heat shock. Experiment 4 was performed similarly except that temperature treatments (38.5 or 40°C, 24 h) were performed in a low or high oxygen environment (2×2 × 2 factorial design with temperature, melatonin, and oxygen concentration as main effects), and blastocysts were genotyped for a deletion (D) mutation (C→D) in the promoter region of HSPA1L associated with thermotolerance. Heat shock decreased percent of zygotes developing to the blastocyst stage independent of melatonin or oxygen concentration. Frequency of genotypes for HSPA1L was affected by oxygen concentration and temperature, with an increase in the D allele for blastocysts that developed in high oxygen and following heat shock. It was concluded that (1) lack of effect of melatonin or oxygen concentration on embryonic development means that the negative effects of heat shock on the zygote are not mediated by ROS, (2) previously reported effect of melatonin on fertility of heat-stressed cows might involve actions independent of the antioxidant properties of melatonin, and (3) the deletion mutation in the promoter of HSPA1L confers protection to the zygote from heat shock and high oxygen. Perhaps, embryonic survival during heat stress could be improved by selecting for thermotolerant genotypes.