两个杜洛克猪群体平均日增重和瘦肉率全基因组关联研究的荟萃分析。
A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations.
作者信息
Zhou Shenping, Ding Rongrong, Meng Fanming, Wang Xingwang, Zhuang Zhanwei, Quan Jianping, Geng Qian, Wu Jie, Zheng Enqin, Wu Zhenfang, Yang Jianhui, Yang Jie
机构信息
College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
State Key Laboratory of Livestock and Poultry Breeding / Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China.
出版信息
BMC Genomics. 2021 Jan 6;22(1):12. doi: 10.1186/s12864-020-07288-1.
BACKGROUND
Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs.
RESULTS
In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development.
CONCLUSIONS
We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.
背景
平均日增重（ADG）和瘦肉率（LMP）是猪的主要生产性能指标。然而，ADG和LMP的遗传结构仍不清楚。在此，我们对3770头美国杜洛克猪和2090头加拿大杜洛克猪的ADG和LMP进行了全基因组关联研究（GWAS）和荟萃分析。
结果
在美国杜洛克猪中，在猪1号染色体（SSC1）上鉴定出一个新的多效性数量性状位点（QTL）与ADG和LMP相关，其跨度为2.53 Mb（从159.66至162.19 Mb）。在加拿大杜洛克猪中，在SSC1上检测到两个与LMP相关的新QTL，分别位于3.86 Mb（从157.99至161.85 Mb）和555 kb（从37.63至38.19 Mb）区域。荟萃分析分别为ADG和LMP鉴定出另外10个和20个单核苷酸多态性（SNP）。最后，检测到四个基因（PHLPP1、STC1、DYRK1B和PIK3C2A）与ADG和/或LMP相关。进一步的生物信息学分析表明，ADG的候选基因主要参与骨骼生长发育，而LMP的候选基因主要参与脂肪组织和肌肉组织的生长发育。
结论
我们基于由两个杜洛克猪群体组成的大样本量对ADG和LMP进行了GWAS和荟萃分析。发现在SSC1上一个从159.66至161.85 Mb共享2.19 Mb单倍型块的多效性QTL影响两个杜洛克猪群体的ADG和LMP。此外，GWAS的单群体分析和荟萃分析相结合提高了检测所分析性状的额外SNP的效率。我们的结果为猪ADG和LMP性状的遗传结构提供了新的见解。此外，本研究中一些与ADG和/或LMP相关的显著SNP可能有助于猪育种中的标记辅助选择。
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