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Exploiting genomic information on purebred and crossbred pigs

Hidalgo, André Marubayashi (2015). Exploiting genomic information on purebred and crossbred pigs. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2015:120
ISBN 978-91-576-8438-7
eISBN 978-91-576-8439-4
[Doctoral thesis]

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Abstract

The use of genomic information has become increasingly important in a breeding program. In a pig breeding program, where the final goal is an increased crossbred (CB) performance, the use of genomic information needs to be thoroughly evaluated as it may require a different strategy of what is applied in purebred (PB) breeding programs. In this thesis, I explore the use of genomic information for the genetic improvement of PB and CB pigs. I first focus on the identification of genomic regions affecting traits that are important to breeders. I identified two quantitative trait loci (QTL) regions for gestation length, one for Dutch Landrace on Sus scrofa chromosome (SSC) 2 and the other one for Large White on SSC5. I also fine-mapped and narrowed down the region of a previously detected QTL for androstenone level SSC6 from 3.75 Mbp to 1.94 Mbp. A tag-SNP of this fine-mapped region was further investigated and no unfavorable pleiotropic effects were found; indicating that using the studied marker for selection would not unfavorably affect the other studied traits. After that, the focus was changed to the application of genomic selection in pigs. Within-population predictions showed high accuracies, whereas across-population prediction had accuracies close to zero. Using combinations among Dutch
Landrace and Large White populations plus their cross showed that multi-population prediction was not better than within-population. The exception was when the CB pigs were predicted with records from both parental populations added to the CB training data. When using PB pigs to train CB ones, the predictive ability found indicates that selection in the PB pigs results in response in the CB ones. When assessing the source of information used to estimate the breeding values used as response variable, I showed that a more accurate prediction of CB genetic merit was found when training on PB data with breeding values estimated using CB performance than training on PB data with breeding values estimated using PB performance. I also studied the accuracy of using CB pigs in the training population to select PB for CB performance. Predictive ability when using CB phenotypes for training was observed, however, the accuracy was lower than using PB phenotypes in the training population. Lastly, I evaluate the inclusion of dominance in the model when using a CB training population. Results showed that accounting for dominance effects can be slightly beneficial for genomic prediction compared with a model that accounts only for additive effects.

Authors/Creators:Hidalgo, André Marubayashi
Title:Exploiting genomic information on purebred and crossbred pigs
Series/Journal:Acta Universitatis agriculturae Sueciae (1652-6880)
Year of publishing :2015
Volume:2015:120
Number of Pages:42
Papers/manuscripts:
NumberReferences
IHidalgo, A.M., Lopes, M.S., Harlizius, B. and Bastiaansen, J.W.M. Genome-wide association study reveals regions associated with gestation length in two pig populations. Animal Genetics (accepted).
IIHidalgo, A.M., Bastiaansen, J.W.M., Harlizius, B., Megens, H.J., Madsen, O., Crooijmans, R.P.M.A. and Groenen, M.A.M. (2014). On the relationship between an Asian haplotype on chromosome 6 that reduces androstenone levels in boars and the differential expression of SULT2A1 in the testis. BMC Genetics 15:4.
IIIHidalgo, A.M., Bastiaansen, J.W.M., Harlizius, B., Knol, E.F., Lopes, M.S., De Koning, D.J. and Groenen, M.A.M. (2014). Asian low-androstenone haplotype on pig chromosome 6 does not unfavorably affect production and reproduction traits. Animal Genetics 45(6), pp. 874-877.
IVHidalgo, A.M., Bastiaansen, J.W.M., Lopes, M.S., Harlizius, B., Groenen, M.A.M. and De Koning, D.J. (2015). Accuracy of predicted genomic breeding values in purebred and crossbred pigs. G3: Genes | Genomes | Genetics 5, 1575-1583.
VHidalgo, A.M., Bastiaansen, J.W.M., Lopes, M.S., Veroneze, R., Groenen, M.A.M. and De Koning, D.J. (2015). Accuracy of genomic prediction using deregressed breeding values estimated from purebred and crossbred offspring phenotypes in pigs. Journal of Animal Science 93(7), pp. 3313-3321.
VIHidalgo, A.M., Bastiaansen, J.W.M., Lopes, M.S., Calus, M.P.L. and De Koning, D.J. Accuracy of genomic prediction of purebreds for crossbred performance in pigs (manuscript).
VIIHidalgo, A.M., Zeng, J., Fernando, R.L., Lopes, M.S. and Dekkers, J.C.M. Evaluation of genomic prediction of purebreds for crossbred performance in pigs accounting for dominance effects (manuscript).
Place of Publication:Uppsala
Publisher:Wageningen University, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences
ISBN for printed version:978-91-576-8438-7
ISBN for electronic version:978-91-576-8439-4
ISSN:1652-6880
Language:English
Additional Information:Joint PhD thesis, Swedish University of Agricultural Sciences, Uppsala, Sweden and Wageningen University, Wageningen, the Netherlands
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:L Animal production > L10 Animal genetics and breeding
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 402 Animal and Dairy Science > Animal and Dairy Science.
(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Genetics and Breeding
Agrovoc terms:swine, crossbreds, pure lines, genomes, genetic markers, quantitative trait loci, breeding value, selection, genomics, animal breeding
Keywords:Genomic selection, Pigs, Prediction
URN:NBN:urn:nbn:se:slu:epsilon-e-3060
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-3060
ID Code:12788
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: André M Hidalgo
Deposited On:16 Nov 2015 17:04
Metadata Last Modified:18 Nov 2015 10:41

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