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Abstract

Genomic prediction is widely used to select candidates for breeding. Size and composition of the reference population are important factors influencing prediction accuracy. In Holstein dairy cattle, large reference populations are used, but this is difficult to achieve in numerically small breeds...

Author(s)
Berg, I. van den; Meuwissen, T. H. E.; MacLeod, I. M.; Goddard, M. E.
Publisher
Elsevier Inc., Philadelphia, USA
Citation
Journal of Dairy Science, 2019, 102, 4, pp 3155-3174
Abstract

Background: The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple individuals (eQTL mapping), or by comparing the expression of the alleles in a...

Author(s)
Khansefid, M.; Pryce, J. E.; Bolormaa, S.; Chen YiZhou; Millen, C. A.; Chamberlain, A. J.; Jagt, C. J. vander; Goddard, M. E.
Publisher
BioMed Central Ltd, London, UK
Citation
BMC Genomics, 2018, 19, 793, pp (3 November 2018)
Abstract

Background: Genomic prediction of breeding values from dense single nucleotide polymorphisms (SNP) genotypes is used for livestock and crop breeding, and can also be used to predict disease risk in humans. For some traits, the most accurate genomic predictions are achieved with non-linear estimates ...

Author(s)
Wang TingTing; Chen YiPing [Chen, Y. P. P. ]; Goddard, M. E.; Meuwissen, T. H. E.; Kemper, K. E.; Hayes, B. J.
Publisher
BioMed Central Ltd, London, UK
Citation
Genetics, Selection, Evolution, 2015, 47, 34, pp (30 April 2015)
Abstract

Background: Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and model species, we used sequence variants to map a type of expression...

Author(s)
Xiang RuiDong; Hayes, B. J.; Jagt, C. J. vander; MacLeod, I. M.; Khansefid, M.; Bowman, P. J.; Yuan, Z.; Prowse-Wilkins, C. P.; Reich, C. M.; Mason, B. A.; Garner, J. B.; Marett, L. C.; Chen YiZhou; Bolormaa, S.; Daetwyler, H. D.; Chamberlain, A. J.; Goddard, M. E.
Publisher
BioMed Central Ltd, London, UK
Citation
BMC Genomics, 2018, 19, 521, pp (4 July 2018)
Abstract

Background: Genomic selection is increasingly widely practised, particularly in dairy cattle. However, the accuracy of current predictions using GBLUP (genomic best linear unbiased prediction) decays rapidly across generations, and also as selection candidates become less related to the reference...

Author(s)
Kemper, K. E.; Reich, C. M.; Bowman, P. J.; Jagt, C. J. vander; Chamberlain, A. J.; Mason, B. A.; Hayes, B. J.; Goddard, M. E.
Publisher
BioMed Central Ltd, London, UK
Citation
Genetics, Selection, Evolution, 2015, 47, 29, pp (17 April 2015)
Abstract

Cost-effective high-density (HD) genotypes of livestock species can be obtained by genotyping a proportion of the population using a HD panel and the remainder using a cheaper low-density panel, and then imputing the missing genotypes that are not directly assayed in the low-density panel. The...

Author(s)
Aliloo, H.; Mrode, R.; Okeyo, A. M.; Ni, G.; Goddard, M. E.; Gibson, J. P.
Publisher
Elsevier Inc., Philadelphia, USA
Citation
Journal of Dairy Science, 2018, 101, 10, pp 9108-9127
Abstract

Background: The increasing availability of whole-genome sequence data is expected to increase the accuracy of genomic prediction. However, results from simulation studies and analysis of real data do not always show an increase in accuracy from sequence data compared to high-density (HD) single...

Author(s)
Berg, I. van den; Bowman, P. J.; MacLeod, I. M.; Hayes, B. J.; Wang TingTing; Bolormaa, S.; Goddard, M. E.
Publisher
BioMed Central Ltd, London, UK
Citation
Genetics, Selection, Evolution, 2017, 49, 70, pp (21 September 2017)
Abstract

Background: The apparent effect of a single nucleotide polymorphism (SNP) on phenotype depends on the linkage disequilibrium (LD) between the SNP and a quantitative trait locus (QTL). However, the phase of LD between a SNP and a QTL may differ between Bos indicus and Bos taurus because they...

Author(s)
Bolormaa, S.; Pryce, J. E.; Kemper, K. E.; Hayes, B. J.; Zhang YuanDan; Tier, B.; Barendse, W.; Reverter, A.; Goddard, M. E.
Publisher
BioMed Central Ltd, London, UK
Citation
Genetics, Selection, Evolution, 2013, 45, 43, pp (29 October 2013)
Abstract

The proportion of genetic variation in complex traits explained by rare variants is a key question for genomic prediction, and for identifying the basis of "missing heritability"-the proportion of additive genetic variation not captured by common variants on SNP arrays. Sequence variants in...

Author(s)
Gonzalez-Recio, O.; Daetwyler, H. D.; MacLeod, I. M.; Pryce, J. E.; Bowman, P. J.; Hayes, B. J.; Goddard, M. E.
Publisher
Public Library of Sciences (PLoS), San Francisco, USA
Citation
PLoS ONE, 2015, 10, 12, pp e0143945
Abstract

The objective of this study was to estimate the value derived from using DNA information to increase the accuracy of beef sire selection in a closed seedstock herd. Breeding objectives for commercial production systems targeting 2 diverse markets were examined using multiple-trait selection indexes ...

Author(s)
Eenennaam, A. L. van; Werf, J. H. J. van der; Goddard, M. E.
Publisher
American Society of Animal Science, Savoy, USA
Citation
Journal of Animal Science, 2011, 89, 2, pp 307-320

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