SNP effects depend on genetic and environmental context

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademic

Abstract

Effects that are estimated for SNP markers depend on LD with the QTL, and interactions of the QTL with other genetic and environmental factors. These factors are often mentioned but rarely studied. Breeding for crossbred performance both brings the need and supplies data for studying these interactions. SNPs with different effects on litter size in pigs between low and high production environments were identified from a genomic reaction norm model. Clustering of these SNPs lead to candidate genes related to bacterial defense that are expressed in reproductive tracts and regulated by the estrous cycle. To study interaction of SNPs with genetic background, a method to determine breed origin of alleles in crossbreds was implemented using long range phasing with AlphaPhase software. With more genotypes and phenotypes on crossbreds, estimation of interactions with genetic background and the environment will become feasible.
LanguageEnglish
Title of host publicationProceedings of the 10th World congress on genetics applied to livestock production
Pages356
Publication statusPublished - 2014
EventWCGALP, Vancouver, Canada -
Duration: 17 Aug 201422 Aug 2014

Conference

ConferenceWCGALP, Vancouver, Canada
Period17/08/1422/08/14

Fingerprint

crossbreds
litter size
estrous cycle
genetic background
quantitative trait loci
alleles
breeds
genomics
phenotype
environmental factors
swine
genotype
breeding
genes
methodology

Cite this

Bastiaansen, J. W. M., Bovenhuis, H., Lopes, M. S., Silva, F., Megens, H. J. W. C., & Calus, M. P. L. (2014). SNP effects depend on genetic and environmental context. In Proceedings of the 10th World congress on genetics applied to livestock production (pp. 356)
Bastiaansen, J.W.M. ; Bovenhuis, H. ; Lopes, M.S. ; Silva, F. ; Megens, H.J.W.C. ; Calus, M.P.L. / SNP effects depend on genetic and environmental context. Proceedings of the 10th World congress on genetics applied to livestock production. 2014. pp. 356
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abstract = "Effects that are estimated for SNP markers depend on LD with the QTL, and interactions of the QTL with other genetic and environmental factors. These factors are often mentioned but rarely studied. Breeding for crossbred performance both brings the need and supplies data for studying these interactions. SNPs with different effects on litter size in pigs between low and high production environments were identified from a genomic reaction norm model. Clustering of these SNPs lead to candidate genes related to bacterial defense that are expressed in reproductive tracts and regulated by the estrous cycle. To study interaction of SNPs with genetic background, a method to determine breed origin of alleles in crossbreds was implemented using long range phasing with AlphaPhase software. With more genotypes and phenotypes on crossbreds, estimation of interactions with genetic background and the environment will become feasible.",
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Bastiaansen, JWM, Bovenhuis, H, Lopes, MS, Silva, F, Megens, HJWC & Calus, MPL 2014, SNP effects depend on genetic and environmental context. in Proceedings of the 10th World congress on genetics applied to livestock production. pp. 356, WCGALP, Vancouver, Canada, 17/08/14.

SNP effects depend on genetic and environmental context. / Bastiaansen, J.W.M.; Bovenhuis, H.; Lopes, M.S.; Silva, F.; Megens, H.J.W.C.; Calus, M.P.L.

Proceedings of the 10th World congress on genetics applied to livestock production. 2014. p. 356.

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademic

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AU - Bastiaansen, J.W.M.

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Bastiaansen JWM, Bovenhuis H, Lopes MS, Silva F, Megens HJWC, Calus MPL. SNP effects depend on genetic and environmental context. In Proceedings of the 10th World congress on genetics applied to livestock production. 2014. p. 356