Frontiers in Genetics ( IF 3.7 ) Pub Date : 2020-06-16 , DOI: 10.3389/fgene.2020.00733 Fen Wu 1 , Hao Sun 2 , Shaoxiong Lu 3 , Xiao Gou 3 , Dawei Yan 3 , Zhong Xu 2 , Zhenyang Zhang 2 , Qamar Raza Qadri 2 , Zhe Zhang 1 , Zhen Wang 1 , Qiang Chen 3 , Mingli Li 3 , Xiaoyi Wang 3 , Xinxing Dong 3 , Qishan Wang 1 , Yuchun Pan 1
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 (