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Using genome-wide association analysis to characterize environmental sensitivity of milk traits in dairy cattle.

ABSTRACT: Genotype-by-environment interaction (GxE) has been widely reported in dairy cattle. One way to analyze GxE is to apply reaction norm models. The first derivative of a reaction norm is the environmental sensitivity (ES). In the present study we conducted a large-scale, genome-wide association analysis to identify single-nucleotide polymorphisms (SNPs) that affect general production (GP) and ES of milk traits in the German Holstein population. Sire estimates for GP and for ES were calculated from approximately 13 million daughter records by the use of linear reaction norm models. The daughters were offspring from 2297 sires. Sires were genotyped for 54k SNPs. The environment was defined as the average milk energy yield performance of the herds at the time during which the daughter observations were recorded. The sire estimates were used as observations in a genome-wide association analysis, using 1797 sires. Significant SNPs were confirmed in an independent validation set (500 sires of the same population). To separate GxE scaling and other GxE effects, the observations were log-transformed in some analyses. Results from the reaction norm model revealed GxE effects. Numerous significant SNPs were validated for both GP and ES. Many SNPs that affect GP also affect ES. We showed that ES of milk traits is a typical quantitative trait, genetically controlled by many genes with small effects and few genes with larger effect. A log-transformation of the observation resulted in a reduced number of validated SNPs for ES, pointing to genes that not only caused scaling GxE effects. The results will have implications for breeding for robustness in dairy cattle.

SUBMITTER: Streit M

PROVIDER: S-EPMC3704237 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

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Using genome-wide association analysis to characterize environmental sensitivity of milk traits in dairy cattle.

Streit Melanie M Wellmann Robin R Reinhardt Friedrich F Thaller Georg G Piepho Hans-Peter HP Bennewitz Jörn J

G3 (Bethesda, Md.) 20130708 7

Genotype-by-environment interaction (GxE) has been widely reported in dairy cattle. One way to analyze GxE is to apply reaction norm models. The first derivative of a reaction norm is the environmental sensitivity (ES). In the present study we conducted a large-scale, genome-wide association analysis to identify single-nucleotide polymorphisms (SNPs) that affect general production (GP) and ES of milk traits in the German Holstein population. Sire estimates for GP and for ES were calculated from ...[more]

PMID: 23637124

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Project description:BACKGROUND:Dual-purpose cattle are more adaptive to environmental challenges than single-purpose dairy or beef cattle. Balance among milk, reproductive, and mastitis resistance traits in breeding programs is therefore more critical for dual-purpose cattle to increase net income and maintain well-being. With dual-purpose Xinjiang Brown cattle adapted to the Xinjiang Region in northwestern China, we conducted genome-wide association studies (GWAS) to dissect the genetic architecture related to milk, reproductive, and mastitis resistance traits. Phenotypic data were collected for 2410 individuals measured during 1995-2017. By adding another 445 ancestors, a total of 2855 related individuals were used to derive estimated breeding values for all individuals, including the 2410 individuals with phenotypes. Among phenotyped individuals, we genotyped 403 cows with the Illumina 150?K Bovine BeadChip. RESULTS:GWAS were conducted with the FarmCPU (Fixed and random model circulating probability unification) method. We identified 12 markers significantly associated with six of the 10 traits under the threshold of 5% after a Bonferroni multiple test correction. Seven of these SNPs were in QTL regions previously identified to be associated with related traits. One identified SNP, BovineHD1600006691, was significantly associated with both age at first service and age at first calving. This SNP directly overlapped a QTL previously reported to be associated with calving ease. Within 160 Kb upstream and downstream of each significant SNP identified, we speculated candidate genes based on functionality. Four of the SNPs were located within four candidate genes, including CDH2, which is linked to milk fat percentage, and GABRG2, which is associated with milk protein yield. CONCLUSIONS:These findings are beneficial not only for breeding through marker-assisted selection, but also for genome editing underlying the related traits to enhance the overall performance of dual-purpose cattle.

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Using genome-wide association analysis to characterize environmental sensitivity of milk traits in dairy cattle.

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Using genome-wide association analysis to characterize environmental sensitivity of milk traits in dairy cattle.

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