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Ren Y, Wang F, Sun R, Zheng X, Liu Y, Lin Y, Hong L, Huang X, Chao Z. The Genetic Selection of HSPD1 and HSPE1 Reduce Inflammation of Liver and Spleen While Restraining the Growth and Development of Skeletal Muscle in Wuzhishan Pigs. Animals (Basel) 2024; 14:174. [PMID: 38200905 PMCID: PMC10777996 DOI: 10.3390/ani14010174] [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: 11/21/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Wuzhishan (WZS) pigs, which are minipigs native to Hainan Province in China, are characterized by strong resistance to extreme hot temperatures and humidity. The relationship between their immune response and growth still needs to be clarified. In this study, we used whole genome sequencing (WGS) to detect variations within 37 WZS pigs, 32 Large White (LW) pigs, and 22 Xiangxi black (XXB) pigs, and ~2.49 GB of SNPs were obtained. These data were combined with those of two other pig breeds, and it was found that most of the genes detected (354) were located within the distinct genetic regions between WZS pigs and LW pigs. The network that was constructed using these genes represented a center including 12 hub genes, five of which had structural variations (SVs) within their regulatory regions. Furthermore, RNA-seq and RT-qPCR data for 12 genes were primarily consistent in liver, spleen, and LDM tissues. Notably, the expression of HSPs (HSPD1 and HSPE1) was higher while that of most genes involved in the JAK3-STAT pathway were lower in liver tissue of WZS pigs, compared with LW pigs. This likely not only reduced inflammation-related immune response but also impaired their growth. Our findings demonstrated the role of HSPs in the connection between inflammation and growth rate, while also providing the fundamental genetic selection of the adaptability of WZS pigs.
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Affiliation(s)
- Yuwei Ren
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Feng Wang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Ruiping Sun
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Xinli Zheng
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Yuanyuan Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yanning Lin
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Lingling Hong
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Xiaoxian Huang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Zhe Chao
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
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Xu Z, Wu J, Zhang Y, Qiao M, Zhou J, Feng Y, Li Z, Sun H, Lin R, Song Z, Zhao H, Li L, Chen N, Li Y, Oyelami FO, Peng X, Mei S. Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype in EDNRB associated with two-end black coat color. BMC Genomics 2024; 25:23. [PMID: 38166718 PMCID: PMC10763394 DOI: 10.1186/s12864-023-09943-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Jianli pig, a renowned indigenous breed in China, has the characteristics of a two-end black (TEB) coat color, excellent meat quality, strong adaptability and increased prolificacy. However, there is limited information available regarding the genetic diversity, population structure and genomic regions under selection of Jianli pig. On the other hand, the genetic mechanism of TEB coat color has remained largely unknown. RESULTS In this study, the whole genome resequencing of 30 Jianli pigs within a context of 153 individuals representing 13 diverse breeds was performed. The population structure analysis revealed that Jianli pigs have close genetic relationships with the Tongcheng pig breed, their geographical neighbors. Three methods (observed heterozygosity, expected heterozygosity, and runs of homozygosity) implied a relatively high level of genetic diversity and, a low inbreeding coefficient in Jianli compared with other pigs. We used Fst and XP-EHH to detect the selection signatures in Jianli pigs compared with Asian wild boar. A total of 451 candidate genes influencing meat quality (CREBBP, ADCY9, EEPD1 and HDAC9), reproduction (ESR1 and FANCA), and coat color (EDNRB, MITF and MC1R), were detected by gene annotation analysis. Finally, to fine-map the genomic region for the two-end black (TEB) coat color phenotype in Jianli pigs, we performed three signature selection methods between the TEB coat color and no-TEB coat color pig breeds. The current study, further confirmed that the EDNRB gene is a candidate gene for TEB color phenotype found in Chinese pigs, including Jinhua pigs, and the haplotype harboring 25 SNPs in the EDNRB gene may promote the formation of TEB coat color. Further ATAC-seq and luciferase reporter assays of these regions suggest that the 25-SNPs region was a strong candidate causative mutation that regulates the TEB coat color phenotype by altering enhancer function. CONCLUSION Our results advanced the understanding of the genetic mechanism behind artificial selection, and provided further resources for the protection and breeding improvement of Jianli pigs.
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Affiliation(s)
- Zhong Xu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Junjing Wu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Yu Zhang
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Mu Qiao
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Jiawei Zhou
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Yue Feng
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Zipeng Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Hua Sun
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Ruiyi Lin
- (College of Animal Sciences, College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxu Song
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Haizhong Zhao
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Lianghua Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Nanqi Chen
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Yujie Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China
| | | | - Xianwen Peng
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China.
- Hubei Hongshan Laboratory, Wuhan, 430064, China.
| | - Shuqi Mei
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan, 430064, China.
- Hubei Hongshan Laboratory, Wuhan, 430064, China.
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Liu LL, Meng J, Ma HY, Cao H, Liu WJ. Candidate genes for litter size in Xinjiang sheep identified by Specific Locus Amplified Fragment (SLAF) sequencing. Anim Biotechnol 2023; 34:3053-3062. [PMID: 36244020 DOI: 10.1080/10495398.2022.2131561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The aim of this study was to investigate the selection signatures at a genome-wide level in 'Pishan' sheep using Specific Locus Amplified Fragment (SLAF)-seq. Blood samples from 126 ewes were sequenced using SLAF tags, and the ovarian tissues from 8 ewes (Bashbay sheep, a single litter size group (SG group); 'Pishan' sheep, double litter size group (DG group)) were collected to detect expression levels by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Selection signature analysis was performed using global fixation index (Fst) and nucleotide diversity (π) ratio. A total of 1,192,168 high-quality SLAFs were identified. Notably, 2380 candidate regions under selection using two approaches were identified. A total of 2069 genes were identified, which were involved in dopaminergic synapses, thyroid hormone synthesis, ovarian steroidogenesis and thyroid hormone signalling pathways. Furthermore, Growth Differentiation Factor 9 (GDF9), Period Circadian Regulator 2 (PER2), Thyroid Stimulating Hormone Receptor (TSHR), and Nuclear Receptor Coactivator 1 (NCOA1) reside within these regions and pathways. The expression levels of GDF9 and PER2 genes in sheep tissue of the DG group were significantly higher than those in the SG group. These genes are interesting candidates for litter size and provide a starting point for further identification of conservation strategies for 'Pishan' sheep.
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Affiliation(s)
- Ling-Ling Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jun Meng
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hai-Yu Ma
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hang Cao
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wu-Jun Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
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Panda S, Kumar A, Gaur GK, Ahmad SF, Chauhan A, Mehrotra A, Dutt T. Genome wide copy number variations using Porcine 60K SNP Beadchip in Landlly pigs. Anim Biotechnol 2023; 34:1891-1899. [PMID: 35369845 DOI: 10.1080/10495398.2022.2056047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
In the present study, Porcine 60K SNP genotype data from 69 Landlly pigs were used to explore Copy Number Variations (CNVs) across the autosomes. A total of 386 CNVs were identified using Hidden Markov Model (HMM) in PennCNV software, which were subsequently aggregated to 115 CNV regions (CNVRs). Among the total detected CNVRs, 58 gain, 49 were loss type while remaining 8 events were both gain and loss types. Identified CNVRs covered 12.5 Mb (0.55%) of Sus scrofa reference 11.1 genome. Comparison of our results with previous investigations on pigs revealed that approximately 75% CNVRs were novel, which may be due to differences in genetic background, environment and implementation of artificial selection in Landlly pigs. Functional annotation and pathway analysis showed the significant enrichment of 267 well-annotated Sus scrofa genes in CNVRs. These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity. Additionally, KIT and FUT1 were two major genes detected on CNVR in our population. This investigation provided a comprehensive overview of CNV distribution in the Indian porcine genome for the first time, which may be useful for further investigating the association of important quantitative traits in Landlly pigs.Highlights115 CNVRs were identified in 69 Landlly pig population.Approximately 75% detected CNVRs were novel for Landlly population.Significant enrichment of 267 well-annotated Sus scrofa genes observed in these CNVRs.These genes were involved in different biological functions like sensory perception, meat quality traits, back fat thickness and immunity.Comprehensive CNV map in the Indian porcine genome developed for the first time.
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Affiliation(s)
- Snehasmita Panda
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Amit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Gyanendra Kumar Gaur
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Anuj Chauhan
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
| | - Arnav Mehrotra
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
- Animal Genomics, ETH Zürich, Zürich, Switzerland
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India
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Zhong ZQ, Li R, Wang Z, Tian SS, Xie XF, Wang ZY, Na W, Wang QS, Pan YC, Xiao Q. Genome-wide scans for selection signatures in indigenous pigs revealed candidate genes relating to heat tolerance. Animal 2023; 17:100882. [PMID: 37406393 DOI: 10.1016/j.animal.2023.100882] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 07/07/2023] Open
Abstract
Heat stress is a major problem that constrains pig productivity. Understanding and identifying adaptation to heat stress has been the focus of recent studies, and the identification of genome-wide selection signatures can provide insights into the mechanisms of environmental adaptation. Here, we generated whole-genome re-sequencing data from six Chinese indigenous pig populations to identify genomic regions with selection signatures related to heat tolerance using multiple methods: three methods for intra-population analyses (Integrated Haplotype Score, Runs of Homozygosity and Nucleotide diversity Analysis) and three methods for inter-population analyses (Fixation index (FST), Cross-population Composite Likelihood Ratio and Cross-population Extended Haplotype Homozygosity). In total, 1 966 796 single nucleotide polymorphisms were identified in this study. Genetic structure analyses and FST indicated differentiation among these breeds. Based on information on the location environment, the six breeds were divided into heat and cold groups. By combining two or more approaches for selection signatures, outlier signals in overlapping regions were identified as candidate selection regions. A total of 163 candidate genes were identified, of which, 29 were associated with heat stress injury and anti-inflammatory effects. These candidate genes were further associated with 78 Gene Ontology functional terms and 30 Kyoto Encyclopedia of Genes and Genomes pathways in enrichment analysis (P < 0.05). Some of these have clear relevance to heat resistance, such as the AMPK signalling pathway and the mTOR signalling pathway. The results improve our understanding of the selection mechanisms responsible for heat resistance in pigs and provide new insights of introgression in heat adaptation.
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Affiliation(s)
- Z Q Zhong
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - R Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Z Wang
- Department of Animal Science, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - S S Tian
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - X F Xie
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Z Y Wang
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - W Na
- Hainan Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Q S 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
| | - Y C 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
| | - Q 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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Peng Y, Derks MFL, Groenen MAM, Zhao Y, Bosse M. Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds. Front Genet 2023; 13:1070783. [PMID: 36712875 PMCID: PMC9880450 DOI: 10.3389/fgene.2022.1070783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68-98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.
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Affiliation(s)
- Yebo Peng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Martijn FL Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands,Topigs Norsvin Research Center, Beuningen, Netherlands
| | - Martien AM Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands,Amsterdam Insitute of Life and Environment (A-Life), VU University Amsterdam, Amsterdam, Netherlands,*Correspondence: Mirte Bosse,
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Detection of Selection Signatures in Anqing Six-End-White Pigs Based on Resequencing Data. Genes (Basel) 2022; 13:genes13122310. [PMID: 36553577 PMCID: PMC9777694 DOI: 10.3390/genes13122310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
As a distinguished Chinese indigenous pig breed that exhibits disease resistance and high meat quality, the Anqing six-end-white (AQ) pig represents a valuable germplasm resource for improving the quality of the pig breeding industry. In this study, 24 AQ pigs that were distantly blood-related and 6 Asian Wild Boar (AWB) were selected for 10× deep-genome resequencing. The signatures of the selection were analyzed to explore the genetic basis of their germplasm characteristics and to identify excellent germplasm-related functional genes based on NGS data. A total of 49,289,052 SNPs and 6,186,123 indels were detected across the genome in 30 pigs. Most of the genetic variations were synonym mutations and existed in the intergenic region. We identified 275 selected regions (top 1%) harboring 85 genes by applying a crossover approach based on genetic differentiation (FST) and polymorphism levels (π ratio). Some genes were found to be positively selected in AQ pigs' breeding. The SMPD4 and DDX18 genes were involved in the immune response to pseudorabies virus (PRV) and porcine reproductive and respiratory syndrome virus (PRRSV). The BCL6 and P2RX6 genes were involved in biological regulation of immune T cells and phagocytes. The SLC7A4 and SPACA4 genes were related to reproductive performance. The MSTN and HIF1A genes were related to fat deposition and muscle development. Moreover, 138 overlapping regions were detected in selected regions and ROH islands of AQ pigs. Additionally, we found that the QTLs with the most overlapping regions were related to back fat thickness, meat color, pH value, fatty acid content, immune cells, parasitic immunity, and bacterial immunity. Based on functional enrichment analysis and QTLs mapping, we conducted further research on the molecular genetic basis of germplasm traits (disease resistance and excellent meat quality). These results are a reliable resource for conserving germplasm resources and exploiting molecular markers of AQ pigs.
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Yuan Y, Yang B, He Y, Zhang W, E G. Genome-Wide Selection Signal Analysis of Australian Boer Goat by Insertion/Deletion Variants. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs. Genes (Basel) 2022; 13:genes13112026. [PMID: 36360263 PMCID: PMC9690591 DOI: 10.3390/genes13112026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Single nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CNVs between Wannan black pigs (WBP) and Asian wild boars (AWB), using whole genome resequencing data. By using Manta, we detected in total 28,720 CNVs that covered approximately 1.98% of the pig genome length. We identified 288 selected CNVs (top 1%) by performing Fst statistics. Functional enrichment analyses for genes located in selected CNVs were found to be muscle related (NDN, TMOD4, SFRP1, and SMYD3), reproduction related (GJA1, CYP26B1, WNT5A, SRD5A2, PTPN11, SPEF2, and CCNB1), residual feed intake (RFI) related (MAP3K5), and ear size related (WIF1). This study provides essential information on selected CNVs in Wannan black pigs for further research on the genetic basis of the complex phenotypic and provides essential information for direction in the protection and utilization of Wannan black pig.
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Wu X, Zhou R, Zhang W, Cao B, Xia J, Caiyun W, Zhang X, Chu M, Yin Z, Ding Y. Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs. Anim Biosci 2021; 34:1895-1902. [PMID: 33705632 PMCID: PMC8563231 DOI: 10.5713/ab.20.0679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/07/2021] [Indexed: 11/27/2022] Open
Abstract
Objective Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency. Methods In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies. Results In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (FROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits. Conclusion This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.
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Affiliation(s)
- Xudong Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Ren Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Wei Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, P.R. China
| | - Bangji Cao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Jing Xia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Wang Caiyun
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Xiaodong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Mingxing Chu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing,100193, P. R. China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
| | - Yueyun Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, P. R. China.,Anhui province key laboratory of local livestock and poultry genetic resource conservation and bio-breeding, Anhui Agricultural University, Hefei, 230036, P.R. China
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