Single Nucleotide Polymorphisms of Porcine lncMGPF Regulate Meat Production Traits by Affecting RNA Stability

Wei Lv; Shiyu Zhao; Yunqing Hou; Qian Tong; Yaxin Peng; Jianan Li; Zaiyan Xu; Bo Zuo

doi:10.3389/fcell.2021.731712

Single Nucleotide Polymorphisms of Porcine lncMGPF Regulate Meat Production Traits by Affecting RNA Stability

Front Cell Dev Biol. 2021 Oct 22:9:731712. doi: 10.3389/fcell.2021.731712. eCollection 2021.

Authors

Wei Lv^{1

2}, Shiyu Zhao^{1

2}, Yunqing Hou^{1

2}, Qian Tong^{1

2}, Yaxin Peng^{1

2}, Jianan Li^{1

2}, Zaiyan Xu^{1

3}, Bo Zuo^{1

2

4

5

6

7}

Affiliations

¹ Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.
² Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.
³ Department of Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
⁴ Hubei Hongshan Laboratory, Wuhan, China.
⁵ The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.
⁶ Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China.
⁷ Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

Abstract

lncMGPF is a novel positive regulator of myogenic differentiation, muscle growth and regeneration in mouse, pig, and human. But whether natural mutations within lncMGPF gene regulate animal meat production traits is unclear. In this study, ten single nucleotide polymorphisms (SNPs) of pig lncMGPF (plncMGPF) gene were identified among commercial pig breeds and Chinese local pig breeds. These SNPs are highly linked and constructed into multiple haplotypes, and haplotype ATTCATGTTC (H1) mainly exists in commercial pig breeds while haplotype GCCTGCACCT (H3) is more frequent in Chinese local pig breeds. Association analysis indicated that all SNPs are significantly associated with the backfat thickness and loin muscle area (P < 0.05), respectively, and homologous H1 individuals have higher loin muscle area and lower backfat thickness than H3 pigs. Bioinformatics and functional analysis showed that haplotype H1 has a longer half-life and more stable RNA secondary structure than haplotype H3. plncMGPF haplotype H1 has stronger effects on pig primary myogenic progenitor cells differentiation and muscle growth than haplotype H3. Further experiments showed that two SNPs (rs81403974 and rs325492834) function together to confer plncMGPF stability and function. Our observation suggested that the SNPs in lncMGPF can change the RNA stabilities and lncMGPF function, thereby affecting the porcine meat production traits.

Keywords: RNA stability; SNPs; lncMGPF; meat production traits; pig.