Genome wide association study and genomic prediction for fatty acid composition in Chinese Simmental beef cattle using high density SNP array
Autor: | Huijiang Gao, Wengang Zhang, Long Guan, Lingyang Xu, Zezhao Wang, Bo Zhu, Heming Ni, Peng Guo, Junya Li, Hong Niu, Yan Chen, Xue Gao, Yonghu Liang, Lupei Zhang, Yong Guo |
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Rok vydání: | 2017 |
Předmět: |
0301 basic medicine
Candidate gene Genome-wide association study lcsh:QH426-470 lcsh:Biotechnology Single-nucleotide polymorphism Beef cattle Polymorphism Single Nucleotide Linkage Disequilibrium High-density genotypes 03 medical and health sciences food lcsh:TP248.13-248.65 Simmental cattle Genetics Animals Oligonucleotide Array Sequence Analysis chemistry.chemical_classification Genomic prediction biology Fatty Acids Fatty acid food.cheese_milk_source Genomics lcsh:Genetics Fatty acid synthase Red Meat 030104 developmental biology Phenotype chemistry biology.protein Cattle Biotechnology SNP array Research Article |
Zdroj: | BMC Genomics BMC Genomics, Vol 18, Iss 1, Pp 1-15 (2017) |
ISSN: | 1471-2164 |
Popis: | Background Fatty acid composition of muscle is an important trait contributing to meat quality. Recently, genome-wide association study (GWAS) has been extensively used to explore the molecular mechanism underlying important traits in cattle. In this study, we performed GWAS using high density SNP array to analyze the association between SNPs and fatty acids and evaluated the accuracy of genomic prediction for fatty acids in Chinese Simmental cattle. Results Using the BayesB method, we identified 35 and 7 regions in Chinese Simmental cattle that displayed significant associations with individual fatty acids and fatty acid groups, respectively. We further obtained several candidate genes which may be involved in fatty acid biosynthesis including elongation of very long chain fatty acids protein 5 (ELOVL5), fatty acid synthase (FASN), caspase 2 (CASP2) and thyroglobulin (TG). Specifically, we obtained strong evidence of association signals for one SNP located at 51.3 Mb for FASN using Genome-wide Rapid Association Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approaches. Also, region-based association test identified multiple SNPs within FASN and ELOVL5 for C14:0. In addition, our result revealed that the effectiveness of genomic prediction for fatty acid composition using BayesB was slightly superior over GBLUP in Chinese Simmental cattle. Conclusions We identified several significantly associated regions and loci which can be considered as potential candidate markers for genomics-assisted breeding programs. Using multiple methods, our results revealed that FASN and ELOVL5 are associated with fatty acids with strong evidence. Our finding also suggested that it is feasible to perform genomic selection for fatty acids in Chinese Simmental cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3847-7) contains supplementary material, which is available to authorized users. |
Databáze: | OpenAIRE |
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