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Wang Z, Zhong Z, Xie X, Wang F, Pan D, Wang Q, Pan Y, Xiao Q, Tan Z. Detection of Runs of Homozygosity and Identification of Candidate Genes in the Whole Genome of Tunchang Pigs. Animals (Basel) 2024; 14:201. [PMID: 38254370 PMCID: PMC10812771 DOI: 10.3390/ani14020201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Tunchang pigs are an indigenous pig population in China known for their high tolerance to roughage, delicious meat, and fecundity. However, the number of Tunchang pigs has been declining due to the influence of commercial breeds and African swine fever, which could potentially lead to inbreeding. To assess the inbreeding level and the genetic basis of important traits in Tunchang pigs, our research investigated the patterns in "runs of homozygosity" (ROHs) using whole genome resequencing data from 32 Tunchang pigs. The study aimed to determine the length, number, coverage, and distribution model of ROHs in Tunchang pigs, as well as genomic regions with high ROH frequencies. The results of the study revealed that a total of 20,499,374 single-nucleotide polymorphisms (SNPs) and 1953 ROH fragments were recognized in 32 individuals. The ROH fragments in Tunchang pigs were predominantly short, ranging from 0.5 to 1 megabases (Mb) in length. Furthermore, the coverage of ROHs varied across chromosomes, with chromosome 3 having the highest coverage and chromosome 11 having the lowest coverage. The genetic diversity of Tunchang pigs was found to be relatively high based on the values of HE (expected heterozygosity), HO (observed heterozygosity), pi (nucleotide diversity), Ne (effective population size), and MAF (minor allele frequency). The average inbreeding coefficients of Tunchang pigs, as determined by three different methods (FHOM, FGRM, and FROH), were 0.019, 0.0138, and 0.0304, respectively. These values indicate that the level of inbreeding in Tunchang pigs is currently low. Additionally, the study identified a total of 13 ROH islands on all chromosomes, which in total contained 38,913 SNPs and 120 genes. These ROH islands included genes associated with economically important traits, including meat quality (GYS1, PHLPP1, SLC27A5, and CRTC1), growth and development (ANKS1A, TAF11, SPDEF, LHB, and PACSIN1), and environmental adaptation (SLC26A7). The findings of this research offer valuable perspectives on the present status of Tunchang pig resources and offer a reference for breeding conservation plans and the efficient utilization of Tunchang pigs in the future. By understanding the inbreeding level and genetic basis of important traits in Tunchang pigs, conservation efforts can be targeted towards maintaining genetic diversity and promoting the sustainable development of this indigenous pig population.
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Affiliation(s)
- Ziyi Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Xinfeng Xie
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Feifan Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Deyou Pan
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Qishan Wang
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Yuchun Pan
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Qian Xiao
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
| | - Zhen Tan
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (Z.W.)
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Zhong Z, Wang Z, Xie X, Tian S, Wang F, Wang Q, Ni S, Pan Y, Xiao Q. Evaluation of the Genetic Diversity, Population Structure and Selection Signatures of Three Native Chinese Pig Populations. Animals (Basel) 2023; 13:2010. [PMID: 37370521 DOI: 10.3390/ani13122010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Indigenous pig populations in Hainan Province live in tropical climate conditions and a relatively closed geographical environment, which has contributed to the formation of some excellent characteristics, such as heat tolerance, strong disease resistance and excellent meat quality. Over the past few decades, the number of these pig populations has decreased sharply, largely due to a decrease in growth rate and poor lean meat percentage. For effective conservation of these genetic resources (such as heat tolerance, meat quality and disease resistance), the whole-genome sequencing data of 78 individuals from 3 native Chinese pig populations, including Wuzhishan (WZS), Tunchang (TC) and Dingan (DA), were obtained using a 150 bp paired-end platform, and 25 individuals from two foreign breeds, including Landrace (LR) and Large White (LW), were downloaded from a public database. A total of 28,384,282 SNPs were identified, of which 27,134,233 SNPs were identified in native Chinese pig populations. Both genetic diversity statistics and linkage disequilibrium (LD) analysis indicated that indigenous pig populations displayed high genetic diversity. The result of population structure implied the uniqueness of each native Chinese pig population. The selection signatures were detected between indigenous pig populations and foreign breeds by using the population differentiation index (FST) method. A total of 359 candidate genes were identified, and some genes may affect characteristics such as immunity (IL-2, IL-21 and ZFYVE16), adaptability (APBA1), reproduction (FGF2, RNF17, ADAD1 and HIPK4), meat quality (ABCA1, ADIG, TLE4 and IRX5), and heat tolerance (VPS13A, HSPA4). Overall, the findings of this study will provide some valuable insights for the future breeding, conservation and utilization of these three Chinese indigenous pig populations.
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Affiliation(s)
- Ziqi Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Ziyi Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Xinfeng Xie
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Shuaishuai Tian
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Feifan Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Qishan Wang
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Shiheng Ni
- Animal Husbandry Technology Extending Stations of Hainan Province, Haikou 570203, China
| | - Yuchun Pan
- Hainan Yazhou Bay Seed Laboratory, Yongyou Industrial Park, Yazhou Bay Sci-Tech City, Sanya 572025, China
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Qian Xiao
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
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Mo J, Lu Y, GangYan, Wang Y, Zhang K, Zhang S, Wang M, Chen X, Lan G, Liang J. Identifying selection signatures for litter size in Guangxi Bama Xiang pigs. Reprod Domest Anim 2022; 57:1536-1543. [PMID: 35989556 DOI: 10.1111/rda.14230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/18/2022] [Indexed: 11/26/2022]
Abstract
Litter size is an important economic trait in pig production. However, the genetic mechanisms underlying varying litter size in Guangxi Bama Xiang pigs remain unknown. To identify selection signatures for litter size in Guangxi Bama Xiang pigs, we obtained 297 Illumina PorcineSNP50 BeadChip array data and the average born number (ABN) from parity one to nine in Guangxi Bama Xiang pigs. Fixation index (Fst) methods were used to identify the selection signature of the litter size, and three phenotypic gradient differential population pairs (according to the ABN) in individuals were used to reduce the false positives of signature selections. Single nucleotide polymorphisms (SNPs) were identified in the VEGFA promoter and exons. The general linear model was used to analyse the differences in distinct genotypes after they were typed using three-round multiplex PCR technology. Finally, the transcriptome factor and CpG island in the VEGFA promoter were predicted. A total of 328, 328 and 317 significant loci were identified in the 1st, 2nd and 3rd population pairs, respectively. After removing the false positives, 25 SNPs were defined as the selection signatures in relation to litter size. Ten (VEGFA, USP49, USP25, SRPK1, SLC26A8, RPL10A, PPARD, MAPK14, HMGA1 and CHRDL2) out of 52 genes in the selection regions were annotated as the candidate genes of litter size, respectively, VEGFA. There were no SNPs in the VEGFA exon region, but we obtained three SNPs (rs786889605, rs343769603 and rs323942424) in the VEGFA promoter regions. The ABN in CC was significantly higher than that in TT in rs786889605, and the ABN in TT was significantly lower than that in GG in rs323942424. Meanwhile, the mutation of the VEGFA promoter result in the loss of Sp1 and NF-1 and the formation of Oct-1. In summary, we obtained ten candidate genes, and two mutations in the VEGFA promoter that could be important potential molecular biomarkers for litter size in Bama Xiang pigs.
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Affiliation(s)
- Jiayuan Mo
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Yujie Lu
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - GangYan
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Yubing Wang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Kun Zhang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Shuai Zhang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Mengying Wang
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Xingfa Chen
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning, China
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Jiayuan M, Yujie L, Kuirong C, Siran Z, Wenjing Q, Lingli F, Xiaoxiao L, Liang L, Ganqiu L, Jing L. Identifying selection signatures and runs of homozygosity for spine curvature in Chinese indigenous pigs. Anim Genet 2022; 53:513-517. [PMID: 35634679 DOI: 10.1111/age.13224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/03/2022] [Accepted: 05/17/2022] [Indexed: 11/28/2022]
Abstract
In China there are approximately 100 pig breeds, which show great diversity in their appearance. However, information on genome selection signatures, such as spine curvature, is scarce. Therefore, we used the fixation index (FST ) and cross-population extended haplotype homozygosity (XPEHH) methods to explore the genome selection signatures of spine curvature in six breeds of Chinese indigenous pig. We identified 396 and 389 single nucleotide polymorphisms using the FST and XPEHH methods, respectively. We detected 19 selection signatures and 28 genes located in the selected regions. Five candidate genes (MAP3K7, CUX1, GRIN2B, ALPL and MACF1) were identified in the selection signatures. Additionally, 719 high-frequency runs of homozygosity regions, 17 unique runs of homozygosity regions, 78 genes and 27 pathways were identified in the runs of homozygosity analysis. The TGF-beta signaling pathway and eight genes related to the spine formation, spine defects and intervertebral disk degeneration were identified, comprising ACVR1, FMOD, ITGA4, MAPK8, PDGF, RPL3, SULF1 and UBE2D1. In summary, we identified 13 candidate genes related to spine curvature in Chinese indigenous pigs.
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Affiliation(s)
- Mo Jiayuan
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lu Yujie
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Chen Kuirong
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zhu Siran
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qi Wenjing
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Feng Lingli
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liu Xiaoxiao
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liang Liang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lan Ganqiu
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liang Jing
- College of Animal Science and Technology, Guangxi University, Nanning, China
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