GWAS for genotype by lactation stage interaction in dairy cattle.

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

Abstract

Most Genome Wide Association Studies (GWAS) identified quantitative traits locus (QTLs) based on their average effect over the lactation. However, it is known that additive genetic variance changes during lactation and genetic correlations among milk production traits during different lactation stages deviates from unity. We conducted a GWAS specifically for SNPs whose effects on milk protein content change during lactation, i.e. those that show significant SNP by lactation stage interaction. Significance thresholds for SNP by lactation stage interaction cannot be based on standard distributions but requires permutation of the data. We detected regions on BTA 10 and 14 with significant SNP effects as well as significant SNP by lactation stage effects. Regions on BTA 3 and 27 only showed significant SNP by lactation stage effects. Regions on BTA 6, 15, 16, 20 and 26 only showed significant effects in a traditional GWAS. These results show that a GWAS accounting for a SNP by lactation stage interaction effect can help elucidate the genetic background of milk protein content. Keywords: GWAS, genotype by lactation stage interaction, permutation, milk protein content.
Original languageEnglish
Title of host publicationProceedings of the World Congress on Genetics Applied to Livestock Production
Number of pages6
Volume11.469
Publication statusPublished - Feb 2018
Event11th World Congress on Genetics Applied to Livestock Production - Auckland, New Zealand
Duration: 11 Feb 201816 Feb 2018

Conference

Conference11th World Congress on Genetics Applied to Livestock Production
CountryNew Zealand
CityAuckland
Period11/02/1816/02/18

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lactation stage
dairy cattle
genotype
dairy protein
lactation
genetic variance
genome-wide association study
genetic background
genetic correlation
quantitative trait loci
milk production

Cite this

Lu, H., & Bovenhuis, H. (2018). GWAS for genotype by lactation stage interaction in dairy cattle. In Proceedings of the World Congress on Genetics Applied to Livestock Production (Vol. 11.469)
Lu, Haibo ; Bovenhuis, H. / GWAS for genotype by lactation stage interaction in dairy cattle. Proceedings of the World Congress on Genetics Applied to Livestock Production. Vol. 11.469 2018.
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abstract = "Most Genome Wide Association Studies (GWAS) identified quantitative traits locus (QTLs) based on their average effect over the lactation. However, it is known that additive genetic variance changes during lactation and genetic correlations among milk production traits during different lactation stages deviates from unity. We conducted a GWAS specifically for SNPs whose effects on milk protein content change during lactation, i.e. those that show significant SNP by lactation stage interaction. Significance thresholds for SNP by lactation stage interaction cannot be based on standard distributions but requires permutation of the data. We detected regions on BTA 10 and 14 with significant SNP effects as well as significant SNP by lactation stage effects. Regions on BTA 3 and 27 only showed significant SNP by lactation stage effects. Regions on BTA 6, 15, 16, 20 and 26 only showed significant effects in a traditional GWAS. These results show that a GWAS accounting for a SNP by lactation stage interaction effect can help elucidate the genetic background of milk protein content. Keywords: GWAS, genotype by lactation stage interaction, permutation, milk protein content.",
author = "Haibo Lu and H. Bovenhuis",
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Lu, H & Bovenhuis, H 2018, GWAS for genotype by lactation stage interaction in dairy cattle. in Proceedings of the World Congress on Genetics Applied to Livestock Production. vol. 11.469, 11th World Congress on Genetics Applied to Livestock Production, Auckland, New Zealand, 11/02/18.

GWAS for genotype by lactation stage interaction in dairy cattle. / Lu, Haibo; Bovenhuis, H.

Proceedings of the World Congress on Genetics Applied to Livestock Production. Vol. 11.469 2018.

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

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AU - Bovenhuis, H.

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AB - Most Genome Wide Association Studies (GWAS) identified quantitative traits locus (QTLs) based on their average effect over the lactation. However, it is known that additive genetic variance changes during lactation and genetic correlations among milk production traits during different lactation stages deviates from unity. We conducted a GWAS specifically for SNPs whose effects on milk protein content change during lactation, i.e. those that show significant SNP by lactation stage interaction. Significance thresholds for SNP by lactation stage interaction cannot be based on standard distributions but requires permutation of the data. We detected regions on BTA 10 and 14 with significant SNP effects as well as significant SNP by lactation stage effects. Regions on BTA 3 and 27 only showed significant SNP by lactation stage effects. Regions on BTA 6, 15, 16, 20 and 26 only showed significant effects in a traditional GWAS. These results show that a GWAS accounting for a SNP by lactation stage interaction effect can help elucidate the genetic background of milk protein content. Keywords: GWAS, genotype by lactation stage interaction, permutation, milk protein content.

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Lu H, Bovenhuis H. GWAS for genotype by lactation stage interaction in dairy cattle. In Proceedings of the World Congress on Genetics Applied to Livestock Production. Vol. 11.469. 2018