Genomic evaluation of a relatively small dairy cattle population by combination with a larger population

Abstract

The objectives were to investigate the accuracy of genomic evaluations obtained for a small dairy cattle population (Israeli Holsteins) via joint evaluation with a larger population (Dutch Holsteins), and to evaluate the use of pedigree data from foreign bulls computed by Interbull without daughter records in Israel. The training population included 4,010 Dutch bulls and 713 Israeli bulls. The validation population included 185 Israeli bulls with daughter records for milk production traits and slightly fewer bulls for the nonproduction traits. Milk, fat, and protein yields, somatic cell score, longevity, female fertility, direct and maternal calving ease, direct and maternal stillbirth, and the Israeli breeding index were analyzed. The genomic prediction model was based on the Bayesian multi-QTL model of Meuwissen and Goddard, where the effects of dense single nucleotide polymorphisms across the whole genome are fitted directly, without the use of haplotypes or identical-by-descent probabilities. Correlations of May 2014 estimated breeding values (EBV14) with genomic EBV (GEBV) were higher than the correlations of EBV14 with parent averages (PA) computed from the June 2009 evaluation for all traits. For the Israel selection index, the difference between EBV14 and GEBV correlation on the one hand and EBV14 and PA computed using Interbull data on the other hand was 15 percentage points. For protein, the difference between the corresponding correlations was 14 percentage points. Generally, correlations of EBV14 with PA based on Israeli EBV only were similar to correlations of EBV14 with PA including Interbull evaluations. Relative to EBV14, milk production traits were biased upwards for both GEBV and PA, but the bias was greater for PA. The Y-intercepts of regressions of EBV14 were significantly different from zero for regression on GEBV for all 3 milk production traits and the Israeli selection index. This was not the case for regression of EBV14 on PA. The regression line intersected with the line of unbiased estimation near the EBV of the bulls with highest values. Because only bulls with high evaluations are of interest for selection, GEBV for these bulls were less biased compared with that of bulls with lower evaluations. The difference in mean EBV14 between bulls born during 2007-2008 selected by GEBV and PA was 65 units. If half of all inseminations are by young bulls, then the annual genetic gain obtained by implementation of genomic evaluation will be 8 units per year (65/8). Because annual gain is currently 107 units, this is a gain of 7%.

Effect of genotyped cows in the reference population on the genomic evaluation of Holstein cattle

“…EBV of genotyped animals was then deregressed Mendelian term according to the method which was used in a similar form of deregression procedure described by VanRaden et al (2009), Schopen and Schrooten (2013) and Weller et al (2015) as follows: h 2 , where h 2 is the heritability of the trait. The reliability of all animals in the pedigree was estimated using the method described by Liu et al (2004).…”

“…Alternative approach for the genomic evaluation using small progeny-tested bull populations is to include genotyped foreign bulls (Weller et al, 2015) or genotyped domestic cows with records (Wiggans et al, 2011a) in the reference population (Calus, 2016). When including the latter, it is important to understand how information from additional genotyped cows contributes to the accuracy of GEBV in our population, because the contribution to overall reliability is different between bulls and cows (de Roos, 2011).…”

Invited review: A perspective on the future of genomic selection in dairy cattle

“…Membership in the consortiums is dependent on submission of a quota of bulls with genotypes and genetic evaluations based on daughter records. Smaller countries that are not able to meet this requirement, such as Israel and Ireland, have initiated joint genomic evaluations with larger countries (e.g., Weller et al, 2015;Lund et al, 2016).…”

Optimization of a genomic breeding program for a moderately sized dairy cattle population

“…where r oG 2 is the reliability for offspring with genomic evaluations. Weller et al (2015) obtained the estimate of 0.43 for r oG 2 as follows. For the Israeli index, a correlation of 0.59 was found between young bulls with genomic evaluations, and their evaluations based on daughter records 4 yr later.…”