Transport and Resources and Dairy Futures Cooperative Research Center

Bundoora, Australia

Transport and Resources and Dairy Futures Cooperative Research Center

Bundoora, Australia
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Pryce J.E.,Transport and Resources and Dairy Futures Cooperative Research Center | Pryce J.E.,La Trobe University | Gonzalez-Recio O.,Transport and Resources and Dairy Futures Cooperative Research Center | Nieuwhof G.,Transport and Resources and Dairy Futures Cooperative Research Center | And 6 more authors.
Journal of Dairy Science | Year: 2015

A new breeding value that combines the amount of feed saved through improved metabolic efficiency with predicted maintenance requirements is described. The breeding value includes a genomic component for residual feed intake (RFI) combined with maintenance requirements calculated from either a genomic or pedigree estimated breeding value (EBV) for body weight (BW) predicted using conformation traits. Residual feed intake is only available for genotyped Holsteins; however, BW is available for all breeds. The RFI component of the "feed saved" EBV has 2 parts: Australian calf RFI and Australian lactating cow RFI. Genomic breeding values for RFI were estimated from a reference population of 2,036 individuals in a multi-trait analysis including Australian calf RFI (n = 843), Australian lactating cow RFI (n = 234), and UK and Dutch lactating cow RFI (n = 958). In all cases, the RFI phenotypes were deviations from a mean of 0, calculated by correcting dry matter intake for BW, growth, and milk yield (in the case of lactating cows). Single nucleotide polymorphism effects were calculated from the output of genomic BLUP and used to predict breeding values of 4,106 Holstein sires that were genotyped but did not have RFI phenotypes themselves. These bulls already had BW breeding values calculated from type traits, from which maintenance requirements in kilograms of feed per year were inferred. Finally, RFI and the feed required for maintenance (through BW) were used to calculate a feed saved breeding value and expressed as the predicted amount of feed saved per year. Animals that were 1 standard deviation above the mean were predicted to eat 66 kg dry matter less per year at the same level of milk production. In a data set of genotyped Holstein sires, the mean reliability of the feed saved breeding value was 0.37. For Holsteins that are not genotyped and for breeds other than Holsteins, feed saved is calculated using BW only. From April 2015, feed saved has been included as part of the Australian national selection index, the Balanced Performance Index (BPI). Selection on the BPI is expected to lead to modest gains in feed efficiency. © 2015 American Dairy Science Association.


PubMed | North Carolina State University and Transport and Resources and Dairy Futures Cooperative Research Center
Type: | Journal: BMC genomics | Year: 2015

Variation in environment, management practices, nutrition or selection objectives has led to a variety of different choices being made in the use of genetic material between countries. Differences in genome-level homozygosity between countries may give rise to regions that result in inbreeding depression to differ. The objective of this study was to characterize regions that have an impact on a runs of homozygosity (ROH) metric and estimate their association with the additive genetic effect of milk (MY), fat (FY) and protein yield (PY) and calving interval (CI) using Australia (AU) and United States (US) Jersey cows.Genotyped cows with phenotypes on MY, FY and PY (n=6751 US; n=3974 AU) and CI (n=5816 US; n=3905 AU) were used in a two-stage analysis. A ROH statistic (ROH4Mb), which counts the frequency of a SNP being in a ROH of at least 4 Mb was calculated across the genome. In the first stage, residuals were obtained from a model that accounted for the portion explained by the estimated breeding value. In the second stage, these residuals were regressed on ROH4Mb using a single marker regression model and a gradient boosted machine (GBM) algorithm. The relationship between the additive and ROH4Mb of a region was characterized based on the (co)variance of 500 kb estimated genomic breeding values derived from a Bayesian LASSO analysis. Phenotypes to determine ROH4Mb and additive effects were residuals from the two-stage approach and yield deviations, respectively.Associations between yield traits and ROH4Mb were found for regions on BTA13, BTA23 and BTA25 for the US population and BTA3, BTA7, BTA17 for the AU population. Only one association (BTA7) was found for CI and ROH4Mb for the US population. Multiple potential epistatic interactions were characterized based on the GBM analysis. Lastly, the covariance sign between ROH4Mb and additive SNP effect of a region was heterogeneous across the genome.We identified multiple genomic regions associated with ROH4Mb in US and AU Jersey females. The covariance of regions impacting ROH4Mb and the additive genetic effect were positive and negative, which provides evidence that the homozygosity effect is location dependent.


PubMed | La Trobe University, SRUC, Jobs, University of Melbourne and Transport and Resources and Dairy Futures Cooperative Research Center
Type: Journal Article | Journal: Journal of dairy science | Year: 2015

A new breeding value that combines the amount of feed saved through improved metabolic efficiency with predicted maintenance requirements is described. The breeding value includes a genomic component for residual feed intake (RFI) combined with maintenance requirements calculated from either a genomic or pedigree estimated breeding value (EBV) for body weight (BW) predicted using conformation traits. Residual feed intake is only available for genotyped Holsteins; however, BW is available for all breeds. The RFI component of the feed saved EBV has 2 parts: Australian calf RFI and Australian lactating cow RFI. Genomic breeding values for RFI were estimated from a reference population of 2,036 individuals in a multi-trait analysis including Australian calf RFI (n=843), Australian lactating cow RFI (n=234), and UK and Dutch lactating cow RFI (n=958). In all cases, the RFI phenotypes were deviations from a mean of 0, calculated by correcting dry matter intake for BW, growth, and milk yield (in the case of lactating cows). Single nucleotide polymorphism effects were calculated from the output of genomic BLUP and used to predict breeding values of 4,106 Holstein sires that were genotyped but did not have RFI phenotypes themselves. These bulls already had BW breeding values calculated from type traits, from which maintenance requirements in kilograms of feed per year were inferred. Finally, RFI and the feed required for maintenance (through BW) were used to calculate a feed saved breeding value and expressed as the predicted amount of feed saved per year. Animals that were 1 standard deviation above the mean were predicted to eat 66 kg dry matter less per year at the same level of milk production. In a data set of genotyped Holstein sires, the mean reliability of the feed saved breeding value was 0.37. For Holsteins that are not genotyped and for breeds other than Holsteins, feed saved is calculated using BW only. From April 2015, feed saved has been included as part of the Australian national selection index, the Balanced Performance Index (BPI). Selection on the BPI is expected to lead to modest gains in feed efficiency.

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