Dataset Information

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection.

ABSTRACT: Seven years after the introduction of genomic selection in the United States, it is now possible to evaluate the impact of this technology on the population. Selection differential(s) (SD) and generation interval(s) (GI) were characterized in a four-path selection model that included sire(s) of bulls (SB), sire(s) of cows (SC), dam(s) of bulls (DB), and dam(s) of cows (DC). Changes in SD over time were estimated for milk, fat, and protein yield; somatic cell score (SCS); productive life (PL); and daughter pregnancy rate (DPR) for the Holstein breed. In the period following implementation of genomic selection, dramatic reductions were seen in GI, especially the SB and SC paths. The SB GI reduced from ?7 y to less than 2.5 y, and the DB GI fell from about 4 y to nearly 2.5 y. SD were relatively stable for yield traits, although modest gains were noted in recent years. The most dramatic response to genomic selection was observed for the lowly heritable traits DPR, PL, and SCS. Genetic trends changed from close to zero to large and favorable, resulting in rapid genetic improvement in fertility, lifespan, and health in a breed where these traits eroded over time. These results clearly demonstrate the positive impact of genomic selection in US dairy cattle, even though this technology has only been in use for a short time. Based on the four-path selection model, rates of genetic gain per year increased from ?50-100% for yield traits and from threefold to fourfold for lowly heritable traits.

SUBMITTER: Garcia-Ruiz A

PROVIDER: S-EPMC4948329 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection.

García-Ruiz Adriana A Cole John B JB VanRaden Paul M PM Wiggans George R GR Ruiz-López Felipe J FJ Van Tassell Curtis P CP

Proceedings of the National Academy of Sciences of the United States of America 20160627 28

Seven years after the introduction of genomic selection in the United States, it is now possible to evaluate the impact of this technology on the population. Selection differential(s) (SD) and generation interval(s) (GI) were characterized in a four-path selection model that included sire(s) of bulls (SB), sire(s) of cows (SC), dam(s) of bulls (DB), and dam(s) of cows (DC). Changes in SD over time were estimated for milk, fat, and protein yield; somatic cell score (SCS); productive life (PL); an ...[more]

PMID: 27354521

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Project description:BackgroundInbreeding depression refers to the decrease in mean performance due to inbreeding. Inbreeding depression is caused by an increase in homozygosity and reduced expression of (on average) favourable dominance effects. Dominance effects and allele frequencies differ across loci, and consequently inbreeding depression is expected to differ along the genome. In this study, we investigated differences in inbreeding depression across the genome of Dutch Holstein Friesian cattle, by estimating dominance effects and effects of regions of homozygosity (ROH).MethodsGenotype (75 k) and phenotype data of 38,792 cows were used. For nine yield, fertility and udder health traits, GREML models were run to estimate genome-wide inbreeding depression and estimate additive, dominance and ROH variance components. For this purpose, we introduced a ROH-based relationship matrix. Additive, dominance and ROH effects per SNP were obtained through back-solving. In addition, a single SNP GWAS was performed to identify significant additive, dominance or ROH associations.ResultsGenome-wide inbreeding depression was observed for all yield, fertility and udder health traits. For example, a 1% increase in genome-wide homozygosity was associated with a decrease in 305-d milk yield of approximately 99 kg. For yield traits only, including dominance and ROH effects in the GREML model resulted in a better fit (P < 0.05) than a model with only additive effects. After correcting for the effect of genome-wide homozygosity, dominance and ROH variance explained less than 1% of the phenotypic variance for all traits. Furthermore, dominance and ROH effects were distributed evenly along the genome. The most notable region with a favourable dominance effect for yield traits was on chromosome 5, but overall few regions with large favourable dominance effects and significant dominance associations were detected. No significant ROH-associations were found.ConclusionsInbreeding depression was distributed quite equally along the genome and was well captured by genome-wide homozygosity. These findings suggest that, based on 75 k SNP data, there is little benefit of accounting for region-specific inbreeding depression in selection schemes.

Project description:Dominance may be an important source of non-additive genetic variance for many traits of dairy cattle. However, nearly all prediction models for dairy cattle have included only additive effects because of the limited number of cows with both genotypes and phenotypes. The role of dominance in the Holstein and Jersey breeds was investigated for eight traits: milk, fat, and protein yields; productive life; daughter pregnancy rate; somatic cell score; fat percent and protein percent. Additive and dominance variance components were estimated and then used to estimate additive and dominance effects of single nucleotide polymorphisms (SNPs). The predictive abilities of three models with both additive and dominance effects and a model with additive effects only were assessed using ten-fold cross-validation. One procedure estimated dominance values, and another estimated dominance deviations; calculation of the dominance relationship matrix was different for the two methods. The third approach enlarged the dataset by including cows with genotype probabilities derived using genotyped ancestors. For yield traits, dominance variance accounted for 5 and 7% of total variance for Holsteins and Jerseys, respectively; using dominance deviations resulted in smaller dominance and larger additive variance estimates. For non-yield traits, dominance variances were very small for both breeds. For yield traits, including additive and dominance effects fit the data better than including only additive effects; average correlations between estimated genetic effects and phenotypes showed that prediction accuracy increased when both effects rather than just additive effects were included. No corresponding gains in prediction ability were found for non-yield traits. Including cows with derived genotype probabilities from genotyped ancestors did not improve prediction accuracy. The largest additive effects were located on chromosome 14 near DGAT1 for yield traits for both breeds; those SNPs also showed the largest dominance effects for fat yield (both breeds) as well as for Holstein milk yield.

Dataset Information

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection.

Publications

Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection.

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