Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing

Fen Wu; Hao Sun; Shaoxiong Lu; Xiao Gou; Dawei Yan; Zhong Xu; Zhenyang Zhang; Qamar Raza Qadri; Zhe Zhang; Zhen Wang; Qiang Chen; Mingli Li; Xiaoyi Wang; Xinxing Dong; Qishan Wang; Yuchun Pan

doi:10.3389/fgene.2020.00733

Genetic Diversity and Selection Signatures Within Diannan Small-Ear Pigs Revealed by Next-Generation Sequencing

Front Genet. 2020 Jul 30:11:733. doi: 10.3389/fgene.2020.00733. eCollection 2020.

Authors

Fen Wu¹, Hao Sun², Shaoxiong Lu³, Xiao Gou³, Dawei Yan³, Zhong Xu², Zhenyang Zhang², Qamar Raza Qadri², Zhe Zhang¹, Zhen Wang¹, Qiang Chen³, Mingli Li³, Xiaoyi Wang³, Xinxing Dong³, Qishan Wang¹, Yuchun Pan¹

Affiliations

¹ Department of Animal Breeding and Reproduction, College of Animal Sciences, Zhejiang University, Hangzhou, China.
² Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
³ College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.

Abstract

Genetic characterization of Chinese indigenous pig breeds is essential to promote scientific conservation and sustainable development of pigs. Here, we systematically surveyed the genomes of 75 unrelated Diannan small-ear (DSE) pigs from three diverse regions (Yingjiang County, Jinping County, and Sipsongpanna in Yunnan Province) to describe their population structures, genetic diversity, inbreeding coefficients, and selection signatures. First, these individuals were sequenced and genotyped using the genome reducing and sequencing (GGRS) protocol. A total of 438,038 autosomal single-nucleotide polymorphisms (SNPs) were obtained and used for subsequent statistical analysis. The results showed that these DSE pigs were clearly differentiated into three separate clades revealed by the population structure and principal component analysis, which is consistent with their geographical origins. Diannan small-ear pigs owned lower genetic diversity when compared with some other pig breeds, which demonstrated the need to strengthen the conservation strategies for DSE pigs. In addition, the inbreeding coefficients based on runs of homozygosity (ROH) length (F _ROH) were calculated in each ROH length categories, respectively. And the results indicated that the ancient (up to 50 generations ago) inbreeding had greater impacts than recent (within the last five generations) inbreeding within DSE pigs. Some candidate selection signatures within the DSE pig population were detected through the ROH islands and integrated haplotype homozygosity score (iHS) methods. And genes associated with meat quality (COL15A1, RPL3L, and SLC9A3R2), body size (PALM2-AKAP2, NANS, TRAF7, and PACSIN1), adaptability (CLDN9 and E4F1), and appetite (GRM4) were identified. These findings can help to understand the genetic characteristics and provide insights into the molecular background of special phenotypes of DSE pigs to promote conservation and sustainability of the breed.

Keywords: Diannan small-ear pigs; genetic diversity; inbreeding coefficients; population structure; selection signatures.