Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China

Abstract

Tunchang pigs are one of the unique black pig breeds in the Hainan province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, FST, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (SELENOV, CBR4, TNNT1, TNNT3, VPS13A, PLD3, SRFBP1, and SSPN), immune regulation (CD48, FBL, PTPRH, GNA14, LOX, SLAMF6, CALCOCO1, IRGC, and ZNF667), growth and development (SYT5, PRX, PPP1R12C, and SMG9), reproduction (LGALS13 and EPG5), vision (SLC9A8 and KCNV2), energy metabolism (ATP5G2), cell migration (EPS8L1), and olfaction (GRK3). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.

Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness

“…[ 44 , 46 , 47 ]. FST, θπ Ratio, and XP-EHH methods all capture selection signals in different contexts, and for the filtered regions with stronger predicted impacts, the validation experiments can be repeated on them to increase the credibility of the selection signals and reduce the number of occurrences of false positives and false negatives [ 31 , 49 , 53 , 55 ]. Thus, the combination of the three methods in this study can cover a wider and more comprehensive genomic region and improve the efficiency and reliability of selection signal screening.…”

“…Three methods were used in this study to validate each other: the θπ Ratio method to provide information on gene diversity, the Fst method to provide information on the degree of gene differentiation, and the XP-EHH method to provide information on natural selection events, which together can provide more comprehensive and accurate information on genetic evolution [ 48 , 49 ].…”

Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep

“…Each method has its own unique information and limitations, so joint analysis can combine the strengths of different methods and increase the sensitivity and accuracy of detection of genetic signals [55][56][57]. In addition to increasing detection power, the combined analysis of three methods can be independently validated, providing complementary information [40,53,58,59]. Consistent results from multiple methods can increase confidence in the signal.…”

Study on the Characteristics of Coarse Feeding Tolerance of Ding’an Pigs: Phenotypic and Candidate Genes Identification

“…This breed is characterized by its small body size (approximate weight of 66 kg at seven months of age), black back and white belly, inverted eight-fold facial wrinkles, and a hanging upside-down white triangular star on the middle of the forehead [2]. The Ding'an pig is known for its advantageous properties, such as coarse feeding tolerance, tolerance to high temperature, tender meat quality, and lower susceptibility to diseases [3,4]. However, in recent years, Ding'an pigs have been affected by foreign pig breeds, African swine fever, and other factors, resulting in a continuous decline in their population and even endangering their survival.…”