Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

Xin Li; Quan Liu; Chong Fu; Mengxun Li; Changchun Li; Xinyun Li; Shuhong Zhao; Zhuqing Zheng

doi:10.1016/j.jgg.2023.11.005

Volume 51 Issue 4

Apr. 2024

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Article Navigation > Journal of Genetics and Genomics > 2024 > 51(4): 394-406

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Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

doi: 10.1016/j.jgg.2023.11.005

a. Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China;
b. Institute of Agricultural Biotechnology, Jingchu University of Technology, Jingmen, Hubei 448000, China;
c. The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China;
d. Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China

Funds:

We would like to thank the staff at our laboratory for their ongoing assistance, and Kevin G. Daly from Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland for language polishing. The computations were run on the bioinformatics computing platform of the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University. This work was supported by Creative Research Team Project of the National Natural Science Foundation of China (32221005 to S. Zhao), grants from the National Natural Science Foundation of China (32202637 to Z. Zheng and 31972536 to X. Li), the earmarked fund for CARS-35, and China Postdoctoral Science Foundation (2020M682446 to Z. Zheng).

Received Date: 2023-07-14
Accepted Date: 2023-11-24
Rev Recd Date: 2023-11-23

Available Online: 2025-06-06

Publish Date: 2023-12-04

Abstract

Abstract

Structural variants (SVs), such as deletions (DELs) and insertions (INSs), contribute substantially to pig genetic diversity and phenotypic variation. Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes, we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes. Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation. Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements. We identify that the genotypes of two DELs (296-bp DEL, chr7: 52,172,101–52,172,397; 278-bp DEL, chr18: 23,840,143–23,840,421) located in muscle-specific enhancers are associated with the expression of target genes related to meat quality (FSD2) and muscle fiber hypertrophy (LMOD2 and WASL) in pigs. Our results highlight the role of SVs in domestic porcine evolution, and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.
- Pigs,
- Structural variation,
- Selection signatures,
- Regulatory elements

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