Genome-Wide Association Analysis Identified Variants Associated with Body Measurement and Reproduction Traits in Shaziling Pigs
Author:
Lan Qun1, Deng Qiuchun1, Qi Shijin1, Zhang Yuebo1, Li Zhi1, Yin Shishu1, Li Yulian2, Tan Hong2, Wu Maisheng2, Yin Yulong13, He Jun1, Liu Mei14ORCID
Affiliation:
1. College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China 2. Xiang Dong Experiment Station, Hunan Provincial Pig Industrial Technology System, Xiangtan 411100, China 3. Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha 410125, China 4. Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
Abstract
With the increasing popularity of genomic sequencing, breeders pay more attention to identifying the crucial molecular markers and quantitative trait loci for improving the body size and reproduction traits that could affect the production efficiency of pig-breeding enterprises. Nevertheless, for the Shaziling pig, a well-known indigenous breed in China, the relationship between phenotypes and their corresponding genetic architecture remains largely unknown. Herein, in the Shaziling population, a total of 190 samples were genotyped using the Geneseek Porcine 50K SNP Chip, obtaining 41857 SNPs for further analysis. For phenotypes, two body measurement traits and four reproduction traits in the first parity from the 190 Shaziling sows were measured and recorded, respectively. Subsequently, a genome-wide association study (GWAS) between the SNPs and the six phenotypes was performed. The correlation between body size and reproduction phenotypes was not statistically significant. A total of 31 SNPs were found to be associated with body length (BL), chest circumference (CC), number of healthy births (NHB), and number of stillborns (NSB). Gene annotation for those candidate SNPs identified 18 functional genes, such as GLP1R, NFYA, NANOG, COX7A2, BMPR1B, FOXP1, SLC29A1, CNTNAP4, and KIT, which exert important roles in skeletal morphogenesis, chondrogenesis, obesity, and embryonic and fetal development. These findings are helpful to better understand the genetic mechanism for body size and reproduction phenotypes, while the phenotype-associated SNPs could be used as the molecular markers for the pig breeding programs.
Funder
Natural Science Foundation of Hunan Province National Natural Science Foundation of China Special Fund for the Construction of Innovative Provinces in Hunan Funding of Major Scientific Research Tasks, Kunpeng Institute of Modern Agriculture at Foshan
Subject
Genetics (clinical),Genetics
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