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A genome‐wide association study suggests several novel candidate genes for carcass traits in Chinese Simmental beef cattle

Chang, T., Xia, J., Xu, L., Wang, X., Zhu, B., Zhang, L., Gao, X., Chen, Y., Li, J., Gao, H.
Animal genetics 2018 v.49 no.4 pp. 312-316
Simmental, beef cattle, carcass weight, chromosome mapping, genes, genome-wide association study, genotyping, models, phenotype, quality control, single nucleotide polymorphism, China
A genome‐wide association study (GWAS) was conducted for two carcass traits in Chinese Simmental beef cattle. The experimental population consisted of 1301 individuals genotyped with the Illumina BovineHD SNP BeadChip (770K). After quality control, 671 990 SNPs and 1217 individuals were retained for the GWAS. The phenotypic traits included carcass weight and bone weight, which were measured after the cattle were slaughtered at 16 to 18 months of age. Three statistical models—a fixed polygene model, a random polygene model and a composite interval mapping polygene model—were used for the GWAS. The genome‐wide significance threshold after Bonferroni correction was 7.44E‐08 (= 0.05/671 990). In this study, we detected eight and seven SNPs significantly associated with carcass weight and bone weight respectively. In total, 11 candidate genes were identified within or close to these significant SNPs. Of these, we found several novel candidate genes, including PBX1, GCNT4, ALDH1A2, LCORL and WDFY3, to be associated with carcass weight and bone weight in Chinese Simmental beef cattle, and their functional roles need to be verified in further studies.