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Genome-wide association study in Brown Swiss for udder traits based on sequence data

Frischknecht, M.; Flury, C.; Bapst, B.; Seefried, F.R.; Signer-Hasler, H.; Garrick, D.; Stricker, C.; Intergenomics, Consortium; Bagnato, A.; Bieber, A.; Fries, R.; Russ, I.; Sölkner, J. and Gredler, B. (2016) Genome-wide association study in Brown Swiss for udder traits based on sequence data. In: Book of Abstracts of the 67th Annual Meeting of the European Federation of Animal Science, 29 August - 2 September 2016, Belfast, UK, p. 109.

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Summary

Identification of QTL, especially of causative variants within QTL is still challenging. Higher SNP densities aid the identification and fine-mapping of QTL. Based on imputed sequence data we performed GWAS for udder traits in Brown Swiss cattle. The GWAS was performed using a mixed-model approach with deregressed breeding values as phenotypes. The traits investigated included: udder depth (UD), fore udder attachment (FUA), rear udder width (RUW), rear udder height (RUH), fore udder length (FUL), and central ligament (CL). We found significant associations on BTA 3 (UD, FUA), BTA 5 (UD), BTA 17 (FUL, RUW, CL) and BTA 20 (FUA). A single gene was located in the significantly associated regions on BTA 5 (ABCC9) and BTA 20 (HCN1). The region on BTA 17 spans almost 3 Mb and includes 74 genes (maximal region for all the traits combined) and the region on BTA 3 includes 91 genes across 3 Mb. We also looked for associated missense variants in these intervals. Neither for ABCC9 nor for HCN1 we could identify such a variant. On BTA 17 we identified 2 missense variants that were significantly associated with CL. On BTA 3, 11 missense variants were significantly associated with UD and/or FUA. The advantages of using imputed sequence data compared to SNP chip genotypes are mainly through the inclusion of potential causative variants.


EPrint Type:Conference paper, poster, etc.
Type of presentation:Poster
Keywords:dairy cattle, animal breeding
Agrovoc keywords:
LanguageValueURI
Englishdairy cattlehttp://aims.fao.org/aos/agrovoc/c_2108
Englishanimal breedinghttp://aims.fao.org/aos/agrovoc/c_423
Subjects: Animal husbandry > Production systems > Beef cattle
Animal husbandry > Breeding and genetics
Animal husbandry > Health and welfare
Research affiliation: Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Animal > Animal breeding
Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Animal > Cattle
Deposited By: Bieber, Anna
ID Code:38681
Deposited On:02 Dec 2020 10:07
Last Modified:02 Dec 2020 10:08
Document Language:English
Status:Published
Refereed:Peer-reviewed and accepted

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