Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, PR China.
Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
Poult Sci. 2020 May;99(5):2349-2361. doi: 10.1016/j.psj.2020.01.009. Epub 2020 Mar 26.
There have been several genome-wide association study (GWAS) reported for carcass, growth, and meat traits in chickens. Most of these studies have been based on single SNPs GWAS. In contrast, haplotype-based GWAS reports have been limited. In the present study, 2 Northeast Agricultural University broiler lines divergently selected for abdominal fat content (NEAUHLF) and genotyped with the chicken 60K SNP chip were used to perform a haplotype-based GWAS. The lean and fat chicken lines were selected for abdominal fat content for 11 yr. Abdominal fat weight was significantly different between the 2 lines; however, there was no difference for body weight between the lean and fat lines. A total of 132 haplotype windows were significantly associated with abdominal fat weight. These significantly associated haplotype windows were primarily located on chromosomes 2, 4, 8, 10, and 26. Seven candidate genes, including SHH, LMBR1, FGF7, IL16, PLIN1, IGF1R, and SLC16A1, were located within these associated regions. These genes may play important roles in the control of abdominal fat content. Two regions on chromosomes 3 and 10 were significantly associated with testis weight. These 2 regions were previously detected by the single SNP GWAS using this same resource population. TCF21 on chromosome 3 was identified as a potentially important candidate gene for testis growth and development based on gene expression analysis and the reported function of this gene. TCF12, which was previously detected in our SNP by SNP interaction analysis, was located in a region on chromosome 10 that was significantly associated with testis weight. Six candidate genes, including TNFRSF1B, PLOD1, NPPC, MTHFR, EPHB2, and SLC35A3, on chromosome 21 may play important roles in bone development based on the known function of these genes. In addition, several regions were significantly associated with other carcass and growth traits, but no candidate genes were identified. The results of the present study may be helpful in understanding the genetic mechanisms of carcass and growth traits in chickens.
已经有几项全基因组关联研究（GWAS）报道了鸡的胴体、生长和肉质性状。这些研究大多基于单核苷酸多态性（SNP）GWAS。相比之下，基于单倍型的 GWAS 报道较为有限。在本研究中，我们使用东北农业大学两个肉鸡系进行了基于单倍型的 GWAS，这两个系是为了腹脂含量（NEAUHLF）而进行了 11 年的选择，这些系被基因分型为鸡 60K SNP 芯片。瘦肉鸡和脂肪鸡系在腹脂含量上有显著差异；然而，在体重方面，瘦鸡和肥鸡之间没有差异。共发现 132 个与腹脂重量显著相关的单倍型窗口。这些显著相关的单倍型窗口主要位于第 2、4、8、10 和 26 号染色体上。7 个候选基因，包括 SHH、LMBR1、FGF7、IL16、PLIN1、IGF1R 和 SLC16A1，位于这些相关区域内。这些基因可能在控制腹脂含量方面发挥重要作用。第 3 和第 10 号染色体上的两个区域与睾丸重量显著相关。这两个区域在使用相同资源群体的单 SNP GWAS 中也被检测到。基于基因表达分析和该基因的报道功能，第 3 号染色体上的 TCF21 被确定为睾丸生长和发育的一个潜在重要候选基因。在 SNP 互作分析中，我们之前在 SNP 中检测到的 TCF12 位于与睾丸重量显著相关的第 10 号染色体区域。第 21 号染色体上的 6 个候选基因，包括 TNFRSF1B、PLOD1、NPPC、MTHFR、EPHB2 和 SLC35A3，根据这些基因的已知功能，可能在骨骼发育中发挥重要作用。此外，还有几个区域与其他胴体和生长性状显著相关，但没有鉴定出候选基因。本研究的结果可能有助于理解鸡胴体和生长性状的遗传机制。
