Genome-wide scans for selection signatures in indigenous pigs revealed candidate genes relating to heat tolerance

Zhong, Zhen; Li, R.; Wang, Zonghua; Tian, Shilin; Xie, Xiaofeng; Wang, Z.Y.; Na, W.; Wang, Qingsong; Pan, Yuchun; Xiao, Qiang

doi:10.1016/j.animal.2023.100882

Cited by 7 publications

(3 citation statements)

References 67 publications

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“…This study aimed to determine the population structure and genetic diversity to provide rational scientific conservation strategies for HX, MX, BM, and HZ pig populations. More and more studies have investigated the genetic diversity and population structure of various species of livestock (e.g., Min pig, Tongcheng pig, Tibetan sheep, Hainan cattle, and BoHuai goat) using whole-genome sequencing or SNP chips [14,[22][23][24][25][26][27]. For instance, Meng et al used a KPS porcine breeding chip v1 50K for SNP to study the genetic diversity of the Min pig-conserved population.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of the Genetic Diversity and Population Structure of Four Native Pig Populations in Gansu Province

Yan,

Song,

Wang

et al. 2023

IJMS

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Indigenous pig populations, including Bamei pigs (BM), Hezuo pigs (HZ), Huixian Qingni Black pigs (HX), and Minxian Black pigs (MX) in Gansu Province, live in a particular climate and a relatively closed geographical environment. These local pig breeds are characterized by excellent characteristics (e.g., cold tolerance, robust disease resistance, and superior meat quality). In the past few years, pig populations in Gansu Province have decreased significantly because of their poor lean meat percentage, high fat content, and slow growth rate. Maintaining the diversity of these four breeds can act as a source of new alleles to be incorporated into commercial breeds which are more susceptible to disease and less adaptable to changing conditions because of inbreeding. Genomic data analysis is adequate for determining the genetic diversity and livestock breeding population structure, even in local pig populations. However, the genetic diversity and population structure of the four native pig populations in Gansu Province are still unknown. Thus, we used “Zhongxin-I” porcine chip for the SNP detection of 102 individuals living on four pig conservation farms. A total of 57,466 SNPs were identified among the four pig breeds. The linkage disequilibrium (LD) plot showed that MX had the highest level of LD, followed by BM, HZ, and HX. The observed heterozygosity (Ho) in all four populations was higher than the expected heterozygosity (He). A principal component analysis (PCA) demonstrated that the four local pig populations were isolated. The identity displayed by the state matrix and G matrix heat map results indicated that small numbers of individuals among the four pig breeds had a high genetic distance and weak genetic relationships. The results of the population genetic structure of BM, HZ, HX, and MX pigs showed a slight genetic diversity loss. Our findings enabled us to better understand the genome characteristics of these four indigenous pig populations, which will provide novel insights for the future germplasm conservation and utilization of these indigenous pig populations.

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Section: Discussionmentioning

confidence: 99%

Evaluation of the Genetic Diversity and Population Structure of Four Native Pig Populations in Gansu Province

Yan,

Song,

Wang

et al. 2023

IJMS

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“…For instance, the coat color trait, a prominent characteristic in pigs, has been the subject of several studies, identifying genes such as MITF, EDNRB, KIT, and MC1R associated with this trait (6)(7)(8)(9). Additionally, genes associated with environmental adaptation traits like cold tolerance (TRPV5) (10), heat tolerance (VPS13A) (11,12), and hypoxia (EPAS1) (13) have been discovered. However, these findings were predominantly based on single nucleotide polymorphism (SNP) detection.…”

Section: Introductionmentioning

confidence: 99%

Copy number variants selected during pig domestication inferred from whole genome resequencing

Zhang,

Xu,

Zhou

et al. 2024

Front. Vet. Sci.

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Over extended periods of natural and artificial selection, China has developed numerous exceptional pig breeds. Deciphering the germplasm characteristics of these breeds is crucial for their preservation and utilization. While many studies have employed single nucleotide polymorphism (SNP) analysis to investigate the local pig germplasm characteristics, copy number variation (CNV), another significant type of genetic variation, has been less explored in understanding pig resources. In this study, we examined the CNVs of 18 Wanbei pigs (WBP) using whole genome resequencing data with an average depth of 12.61. We identified a total of 8,783 CNVs (~30.07 Mb, 1.20% of the pig genome) in WBP, including 8,427 deletions and 356 duplications. Utilizing fixation index (Fst), we determined that 164 CNVs were within the top 1% of the Fst value and defined as under selection. Functional enrichment analyses of the genes associated with these selected CNVs revealed genes linked to reproduction (SPATA6, CFAP43, CFTR, BPTF), growth and development (NR6A1, SMYD3, VIPR2), and immunity (PARD3, FYB2). This study enhances our understanding of the genomic characteristics of the Wanbei pig and offers a theoretical foundation for the future breeding of this breed.

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“…It has a vast territory and a wide distribution of local pig breeds, forming many excellent pig breeds. For example, Meishan pigs [ 2 ] and Erhualian pigs [ 3 ] in East China have large litter sizes, and Erhualian pig breed is one of the famous high-yielding pig breeds in China; Luchuan pigs and Bama pigs in South China have thin skin and excellent heat resistance [ 4 , 5 ]; Min pigs [ 6 ] and Tibetan pigs [ 7 ] have strong cold tolerance; and there are varieties resistant to rough feeding, with strong adaptability and excellent meat quality. These pig breeds play a key role in the Chinese pig industry and contribute to the development of international commercial breeds.…”

Section: Introductionmentioning

confidence: 99%

Unveiling the Genetic Secrets of Chinese Indigenous Pigs from Guizhou Province: Diversity, Evolution and Candidate Genes Affecting Pig Coat Color

Hu,

Su,

Zong

et al. 2024

Animals

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The local pig breeds in Guizhou possess exceptional meat quality, robust adaptability, and resilience to harsh feeding conditions, making them ideal for producing high-quality pork. With over 10 local pig breeds in the region, we focused on 7 specific breeds: Baixi pigs (BX), Congjiang Xiang pigs (CJX), Guanling pigs (GL), Jianhe White Xiang pigs (JHBX), Jiangkou Luobo pigs (JKLB), Kele pigs (KL), and Qiandong Hua pigs (QDH). Unfortunately, these breeds face threats such as introduced species and inbreeding, resulting in a decline in population size and numbers. To better protect and utilize these breeds, we employed genome-wide single-nucleotide polymorphism (SNP) markers to investigate the population structure, genetic diversity, and selection characteristics of 283 pigs across these seven breeds. Our findings revealed distinct ancestral sources between Chinese and Western pig breeds, as demonstrated by principal component analysis, adjacent tree analysis, and ADMIXTURE analysis. Notably, JHBX exhibited a distant genetic relationship from the other six local pig breeds in Guizhou province, showcasing unique genetic characteristics. While the genetic diversity of the six Chinese native pig populations, excluding JHBX, was generally moderate in Guizhou province, the JHBX population displayed low genetic diversity. Therefore, it is imperative to intensify selection efforts to prevent inbreeding decline in JHBX while further enhancing the protection measures for the other six pig populations. Additionally, we identified candidate genes influencing the size disparity among pigs in Guizhou province through signal selection. Our study outcomes serve as a reference for developing effective conservation and utilization plans for pig breeds in Guizhou province and deepen our understanding of the genetic mechanisms underlying pig body size.

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Genome-wide scans for selection signatures in indigenous pigs revealed candidate genes relating to heat tolerance

Cited by 7 publications

References 67 publications

Evaluation of the Genetic Diversity and Population Structure of Four Native Pig Populations in Gansu Province

Evaluation of the Genetic Diversity and Population Structure of Four Native Pig Populations in Gansu Province

Copy number variants selected during pig domestication inferred from whole genome resequencing

Unveiling the Genetic Secrets of Chinese Indigenous Pigs from Guizhou Province: Diversity, Evolution and Candidate Genes Affecting Pig Coat Color

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