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 (FROH) 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.
Highlights
In China, there were more than 80 indigenous pig breeds registered according to the second national census of local pig breeds (2004)
The population sizes of Diannan small-ear (DSE) pigs were decreased within years because of the increased introduction of Western pigs and inappropriate management
The researches focused on the genetic information of DSE pigs were limited, which was disadvantageous to scientific conservation and commercial development for DSE pigs
Summary
In China, there were more than 80 indigenous pig breeds registered according to the second national census of local pig breeds (2004). Diannan small-ear (DSE) pigs, a specific Chinese native pig breed, are raised in the southern areas of Yunnan province with subtropical climate. The indigenous animals under subtropical climate exhibit heritable adaptations to high temperature and humidity due to natural selection. DSE pigs might be the ideal animal models for the research on the diseases related to human. DSE pigs are well-known for their better meat quality and more fat deposition than Western pigs (Wang et al, 2015). During the long-term breeding process, DSE pigs have been naturally differentiated into mini type and large type (Liu, 2010). Diannan small-ear pigs own the abundant phenotypic traits and superior commercial traits so that it is regarded as a valuable genetic resource, which deserves to be efficiently utilized for scientific conservation and commercial exploitation
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