• Associations between the K232A polymorphism in the diacylglycerol-O-transferase 1 (DGAT1) gene and performance in Irish Holstein-Friesian dairy cattle

      Berry, Donagh; Howard, Dawn J.; O'Boyle, Padraig; Waters, Sinead M.; Kearney, J.F.; McCabe, Matthew (Teagasc, Oak Park, Carlow, Ireland, 2010)
      Selection based on genetic polymorphisms requires accurate quantification of the effect or association of the polymorphisms with all traits of economic importance. The objective of this study was to estimate, using progeny performance data on 848 Holstein-Friesian bulls, the association between a non-conservative alanine to lysine amino acid change (K232A) in exon 8 of the diacylglycerol-O-transferase 1 (DGAT1) gene and milk production and functionality in the Irish Holstein-Friesian population. The DGAT1 gene encodes the diacylglycerol-O-transferase microsomal enzyme necessary to catalyze the final step in triglyceride synthesis. Weighted mixed model methodology, accounting for the additive genetic relationships among animals, was used to evaluate the association between performance and the K232A polymorphism. The minor allele frequency (K allele) was 0.32. One copy of the K allele was associated (P < 0.001) with 77 kg less milk yield, 4.22 kg more fat yield, 0.99 kg less protein yield, and 1.30 and 0.28 g/kg greater milk fat and protein concentration, respectively; all traits were based on predicted 305-day production across the first five lactations. The K232A polymorphism explained 4.8%, 10.3% and 1.0% of the genetic variance in milk yield, fat yield and protein yield, respectively. There was no association between the K232A polymorphism and fertility, functional survival, calving performance, carcass traits, or any conformation trait with the exception of rump width and carcass conformation. Using the current economic values for the milk production traits in the Irish total merit index, one copy of the K allele is worth €5.43 in expected profitability of progeny. Results from this study will be useful in quantifying the cost-benefit of including the K232A polymorphism in the Irish national breeding programme.
    • Genetics of reproductive performance in seasonal calving dairy cattle production systems

      Berry, Donagh; Kearney, J.F.; Twomey, K.; Evans, R. D.; Department of Agriculture, Food and the Marine (Teagasc (Agriculture and Food Development Authority), Ireland, 2013)
      Profitable seasonal calving dairy production systems require a cow that will establish pregnancy early in the breeding season implying a quick return to service post-calving and good pregnancy rates. Genetic selection provides an opportunity to achieve this goal so therefore the objective of this study was to estimate the necessary genetic parameters for fertility traits, pertinent to seasonal calving herds, in order to facilitate genetic selection for fertility. The data, following editing, consisted of parity 1 to 3 records on up to 397,373 Holstein-Friesian dairy cows in Ireland. Variance components for the defined interval fertility traits (age at first calving, calving to first service interval, calving interval), binary fertility traits (submission rate in the first 21 days of the breeding season, pregnant to first service, pregnant in the first 42 days of the breeding season, calved in the first 42 days of the calving season) and the count fertility trait (number of services) were estimated using univariate animal models and covariances among traits were estimated using bivariate sire models. Heritability estimates of the nine fertility traits (including age at first calving and survival) varied from 0.01 to 0.07 within parity one to three. The coefficient of genetic variation for the fertility traits varied from 3.3% to 15.3%. Calving to first service interval, within parity, was moderately positively genetically correlated (0.54 to 0.75) with calving interval and was, in general, moderately negatively correlated with both submission rate (-0.68 to -0.29) and pregnant in the first 42 days of the breeding season (-0.36 to -0.14). Calving interval was moderately positively correlated (0.24 to 0.68) with number of services. Irrespective of parity, the genetic correlations between calving interval with calving in the first 42 days of the calving season, and submission rate with pregnant in the first 42 days of the breeding season were all negative. The genetic correlations among calving in the first 42 days of the calving season, submission rate and pregnant in the first 42 days of the breeding season were all positive. All fertility traits were generally antagonistically genetically correlated with lactation milk yield, but most were moderate to strongly favourably correlated with survival to the next lactation. This study provides the necessary genetic parameters to undertake national genetic evaluations for fertility to help achieve the fertility targets in seasonal calving herds.
    • Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection

      Berry, Donagh; Kearney, J.F.; Department of Agriculture, Food and the Marine; European Union; RSF-06-0353; RSF-06-0428 (Cambridge University Press, 2011-02)
      The objective of this study was to quantify the accuracy achievable from imputing genotypes from a commercially available low-density marker panel (2730 single nucleotide polymorphisms (SNPs) following edits) to a commercially available higher density marker panel (51 602 SNPs following edits) in Holstein–Friesian cattle using Beagle, a freely available software package. A population of 764 Holstein–Friesian animals born since 2006 were used as the test group to quantify the accuracy of imputation, all of which had genotypes for the high-density panel; only SNPs on the low-density panel were retained with the remaining SNPs to be imputed. The reference population for imputation consisted of 4732 animals born before 2006 also with genotypes on the higher density marker panel. The concordance between the actual and imputed genotypes in the test group of animals did not vary across chromosomes and was on average 95%; the concordance between actual and imputed alleles was, on average, 97% across all SNPs. Genomic predictions were undertaken across a range of production and functional traits for the 764 test group animals using either their real or imputed genotypes. Little or no mean difference in the genomic predictions was evident when comparing direct genomic values (DGVs) using real or imputed genotypes. The average correlation between the DGVs estimated using the real or imputed genotypes for the 15 traits included in the Irish total merit index was 0.97 (range of 0.92 to 0.99), indicating good concordance between proofs from real or imputed genotypes. Results show that a commercially available high-density marker panel can be imputed from a commercially available lower density marker panel, which will also have a lower cost, thereby facilitating a reduction in the cost of genomic selection. Increased available numbers of genotyped and phenotyped animals also has implications for increasing the accuracy of genomic prediction in the entire population and thus genetic gain using genomic selection.
    • Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes

      Berry, Donagh; McParland, Sinead; Kearney, J.F.; Sargolzaei, Mehdi; Mullen, Michael P.; Department of Agriculture, Food and the Marine, Ireland; Science Foundation Ireland; European Union; RSF-06-0353; RSF-06-0428; et al. (Cambridge University Press, 2014-04-09)
      The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n = 3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n = 5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the withinanimal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, ⩾96% accuracy.