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Zhang W, Xu C, Zhou M, Liu L, Ni Z, Su S, Wang C. Copy number variants selected during pig domestication inferred from whole genome resequencing. Front Vet Sci 2024; 11:1364267. [PMID: 38505001 PMCID: PMC10950068 DOI: 10.3389/fvets.2024.1364267] [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: 01/02/2024] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
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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Affiliation(s)
- Wei Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, China
| | - Chengliang Xu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, China
| | - Mei Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, China
| | - Linqing Liu
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, China
| | - Zelan Ni
- Anhui Provincial Livestock and Poultry Genetic Resources Conservation Center, Hefei, China
| | - Shiguang Su
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, China
| | - Chonglong Wang
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Anhui Provincial Breeding Pig Genetic Evaluation Center, Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, China
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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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Deng X, Zhang Y, Song G, Fu Y, Chen Y, Gao H, Wang Q, Jin Z, Yin Y, Xu K. Integrative Analysis of Transcriptomic and Lipidomic Profiles Reveals a Differential Subcutaneous Adipose Tissue Mechanism among Ningxiang Pig and Berkshires, and Their Offspring. Animals (Basel) 2023; 13:3321. [PMID: 37958077 PMCID: PMC10647668 DOI: 10.3390/ani13213321] [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: 08/18/2023] [Revised: 09/28/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Adipose tissue composition contributes greatly to the quality and nutritional value of meat. Transcriptomic and lipidomic techniques were used to investigate the molecular mechanisms of the differences in fat deposition in Ningxiang pigs, Berkshires and F1 offspring. Transcriptomic analysis identified 680, 592, and 380 DEGs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. The lipidomic analysis screened 423, 252, and 50 SCLs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. Lycine, serine, and the threonine metabolism pathway, fatty acid biosynthesis and metabolism-related pathways were significantly enriched in comparisons of Berkshires vs. Ningxiang pigs and Berkshires vs. F1 offspring. The DEGs (PHGDH, LOC110256000) and the SCLs (phosphatidylserines) may have a great impact on the glycine, serine, and the threonine metabolism pathway. Moreover, the DEGs (FASN, ACACA, CBR4, SCD, ELOV6, HACD2, CYP3A46, CYP2B22, GPX1, and GPX3) and the SCLs (palmitoleic acid, linoleic acid, arachidonic acid, and icosadienoic acid) play important roles in the fatty acid biosynthesis and metabolism of fatty acids. Thus, the difference in fat deposition among Ningxiang pig, Berkshires, and F1 offspring may be caused by differences in the expression patterns of key genes in multiple enriched KEGG pathways. This research revealed multiple lipids that are potentially available biological indicators and screened key genes that are potential targets for molecular design breeding. The research also explored the molecular mechanisms of the difference in fat deposition among Ningxiang pig, Berkshires, and F1 pigs, and provided an insight into selection for backfat thickness and the fat composition of adipose tissue for future breeding strategies.
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Affiliation(s)
- Xiaoxiao Deng
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Yuebo Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Gang Song
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Yawei Fu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Yue Chen
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Hu Gao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Qian Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Zhao Jin
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Yulong Yin
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Kang Xu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
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Yin S, Li Z, Yang F, Guo H, Zhao Q, Zhang Y, Yin Y, Wu X, He J. A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond. Int J Mol Sci 2023; 24:14550. [PMID: 37833998 PMCID: PMC10572203 DOI: 10.3390/ijms241914550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand for meats from indigenous breeds has grown significantly, fueling the selection and crossbreeding of Ningxiang pigs (NXP). The latter has raised concerns about the conservation and sustainable use of Ningxiang pigs as an important genetic resource. To address these concerns, we conducted a comprehensive genomic study using 2242 geographically identified Ningxiang pigs. The estimated genomic breed composition (GBC) suggested 2077 pigs as purebred Ningxiang pigs based on a ≥94% NXP-GBC cut-off. The remaining 165 pigs were claimed to be crosses, including those between Duroc and Ningxiang pigs and between Ningxiang and Shaziling pigs, and non-Ningxiang pigs. Runs of homozygosity (ROH) were identified in the 2077 purebred Ningxiang pigs. The number and length of ROH varied between individuals, with an average of 32.14 ROH per animal and an average total length of 202.4 Mb per animal. Short ROH (1-5 Mb) was the most abundant, representing 66.5% of all ROH and 32.6% of total ROH coverage. The genomic inbreeding estimate was low (0.089) in purebred Ningxiang pigs compared to imported western pig breeds. Nine ROH islands were identified, pinpointing candidate genes and QTLs associated with economic traits of interest, such as reproduction, carcass and growth traits, lipid metabolism, and fat deposition. Further investigation of these ROH islands and candidate genes is anticipated to better understand the genomics of Ningxiang pigs.
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Affiliation(s)
- Shishu Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Fang Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Haimin Guo
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Qinghua Zhao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
| | - Yulong Yin
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
- Animal Nutrition Genome and Germplasm Innovation Research Center, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China
| | - Xiaolin Wu
- Council on Dairy Cattle Breeding, Bowie, MD 20716, USA
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (S.Y.); (Z.L.); (F.Y.); (H.G.); (Q.Z.); (Y.Z.)
- Key Laboratory for Evaluation and Utilization of Livestock and Poultry Resources (Pigs) of the Ministry of Agriculture and Rural Affairs, Changsha 410128, China;
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Di Gregorio P, Perna A, Di Trana A, Rando A. Identification of ROH Islands Conserved through Generations in Pigs Belonging to the Nero Lucano Breed. Genes (Basel) 2023; 14:1503. [PMID: 37510406 PMCID: PMC10378754 DOI: 10.3390/genes14071503] [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: 06/30/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
The recovery of Nero Lucano (NL) pigs in the Basilicata region (Southern Italy) started in 2001 with the collaboration of several public authorities in order to preserve native breeds that can play a significant economic role both due to their remarkable ability to adapt to difficult environments and the value of typical products from their area of origin. In this study, by using the Illumina Porcine SNP60 BeadChip, we compared the genetic structures of NL pigs reared in a single farm in two different periods separated by a time interval corresponding to at least three generations. The results showed an increase in the percentage of polymorphic loci, a decrease in the inbreeding coefficient calculated according to ROH genome coverage (FROH), a reduction in the number of ROH longer than 16 Mb and an increase in ROH with a length between 2 and 4 Mb, highlighting a picture of improved genetic variability. In addition, ROH island analysis in the two groups allowed us to identify five conserved regions, located on chromosomes 1, 4, 8, 14 and 15, containing genes involved in biological processes affecting immune response, reproduction and production traits. Only the conserved ROH island on chromosome 14 contains markers which, according to the literature, are associated with QTLs affecting thoracic vertebra number, teat number, gestation length, age at puberty and mean platelet volume.
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Affiliation(s)
- Paola Di Gregorio
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Annamaria Perna
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Adriana Di Trana
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Andrea Rando
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Via dell'Ateneo Lucano 10, 85100 Potenza, Italy
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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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Li C, Han J, Duan D, Liu C, Han X, Wang K, Qiao R, Li XL, Li XJ. Lymphoid enhancer binding factor 1 is associated with nose color in Yunong black pigs. Anim Genet 2023; 54:398-402. [PMID: 36649734 DOI: 10.1111/age.13292] [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: 07/16/2022] [Revised: 11/11/2022] [Accepted: 12/31/2022] [Indexed: 01/19/2023]
Abstract
Yunong black pig is an indigenous black pig breed being cultivated that has a pure black whole body. However, some individuals appear with a white spot on the nose. We performed case-control association studies and FST approaches in 76 animals with nose color records (26 white-nosed pigs vs. 50 black-nosed pigs) by Illumina Porcine SNP50 BeadChip data. In total, 76 SNPs, which included 2 genome-wide significant SNPs and 18 chromosome-wide suggestive SNPs, were identified by association study. The top-ranked 0.1% windows of FST results as signals under selection and 24 windows were selected. The lymphoid enhancer binding factor 1 was identified as candidate gene with strong signal in analyses of genome-wide association study and FST in black- and white-nosed pigs. Overall, our findings provide evidence that nose color is a heritable trait influenced by many loci. The results contribute to expand our understanding of pigmentation in pigs and provide SNP markers for skin color and related traits selection in Yunong black pigs. Additional research on the genetic link between nose pigmentation is needed.
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Affiliation(s)
- Cong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jinyi Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Dongdong Duan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chuang Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuelei Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruimin Qiao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiu-Ling Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xin-Jian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
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Cao C, Kang Y, Zhou Q, Nanaei HA, Bo D, Liu P, Bai Y, Li R, Jiang Y, Lan X, Pan C. Whole-genome resequencing reveals the genomic diversity and signatures of selection in Romanov sheep. J Anim Sci 2023; 101:skad291. [PMID: 37680132 PMCID: PMC10516466 DOI: 10.1093/jas/skad291] [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] [Received: 05/01/2023] [Accepted: 08/26/2023] [Indexed: 09/09/2023] Open
Abstract
Romanov sheep are adapted to the extremely cold and harsh environment and display a distinctive grey color. Herein, we analyzed the population structure, genetic diversity, and selection signatures of Romanov sheep based on whole-genome sequencing data of 17 Romanov sheep, 114 individuals from other 10 European breeds. The results of PCA, ADMIXTURE, and NJ-tree showed that the Romanov sheep was closely related to other northern European breeds. A relative high level of genetic diversity, low inbreeding coefficient, and large effective population size was observed in Romanov sheep when compared with other European breeds. We then screened the genomic selection signatures of Romanov sheep using FST, XP-XLP, and XP-EHH methods. The most significant region under selection (CHR14:14.2 to 14.3 Mb) harbored a haplotype that contained MC1R gene. Furthermore, this haplotype was also found in other grey-body breeds including Gotland sheep, Grey Tronder Sheep, and German grey heath sheep, suggesting that it was associated with the unique coat color of these breeds. We also found one region (CHR10:40.8Mb- 41.0Mb) harboring PCDH9 gene which was potentially associated with cold environmental adaptation. In summary, this study identified candidate genes that were associated with the unique grey color and environmental adaptation in Romanov sheep, which provided a basis for understanding the genetic background and utilization of this breed.
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Affiliation(s)
- Chunna Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuxin Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | | | - Didi Bo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peiyao Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yangyang Bai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
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9
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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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10
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Zhang W, Li X, Jiang Y, Zhou M, Liu L, Su S, Xu C, Li X, Wang C. Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing. Front Genet 2022; 13:1022261. [PMID: 36324508 PMCID: PMC9618877 DOI: 10.3389/fgene.2022.1022261] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
The genetic resources among pigs in Anhui Province are diverse, but their value and potential have yet to be discovered. To illustrate the genetic diversity and population structure of the Anhui pigs population, we resequenced the genome of 150 pigs from six representative Anhui pigs populations and analyzed this data together with the sequencing data from 40 Asian wild boars and commercial pigs. Our results showed that Anhui pigs were divided into two distinct types based on ancestral descent: Wannan Spotted pig (WSP) and Wannan Black pig (WBP) origins from the same ancestor and the other four populations origins from another ancestor. We also identified several potential selective sweep regions associated with domestication characteristics among Anhui pigs, including reproduction-associated genes (CABS1, INSL6, MAP3K12, IGF1R, INSR, LIMK2, PATZ1, MAPK1), lipid- and meat-related genes (SNX19, MSTN, MC5R, PRKG1, CREBBP, ADCY9), and ear size genes (MSRB3 and SOX5). Therefore, these findings expand the catalogue and how these genetic differences among pigs and this newly generated data will be a valuable resource for future genetic studies and for improving genome-assisted breeding of pigs and other domesticated animals.
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11
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Wu X, Zhou R, Wang Y, Zhang W, Zheng X, Zhao G, Zhang X, Yin Z, Ding Y. Genome‐wide scan for runs of homozygosity in Asian wild boars and Anqing six‐end‐white pigs. Anim Genet 2022; 53:867-871. [DOI: 10.1111/age.13250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/26/2022] [Accepted: 08/02/2022] [Indexed: 01/28/2023]
Affiliation(s)
- Xudong Wu
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences Hefei China
| | - Ren Zhou
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Yuanlang Wang
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences Hefei China
| | - Wei Zhang
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences Hefei China
| | - Xianrui Zheng
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Guiying Zhao
- College of Animal Science and Technology Yunnan Agricultural University Kunming China
| | - Xiaodong Zhang
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Zongjun Yin
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
| | - Yueyun Ding
- Anhui Provincial Laboratory of Local Animal Genetic Resource Conservation and Bio‐Breeding, College of Animal Science and Technology Anhui Agricultural University Hefei Anhui China
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12
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Yuan J, Zhou X, Xu G, Xu S, Liu B. Genetic diversity and population structure of Tongcheng pigs in China using whole-genome SNP chip. Front Genet 2022; 13:910521. [PMID: 36092902 PMCID: PMC9455598 DOI: 10.3389/fgene.2022.910521] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Tongcheng (TC) pigs, distinguished by their superior meat quality, are a Chinese indigenous pig breed. Recently, the genetic resources of TC pigs are under tremendous threat due to the introduction of cosmopolitan pig breeds and African swine fever disease. To promote their management and conservation, the present study assessed genetic diversity and population structure of TC pigs using single nucleotide polymorphism (SNP) markers. A total of 26, 999 SNPs were screened from 51, 315 SNPs in 68 TC pigs. The multi-dimensional scaling (MDS) analysis and neighbor-joining tree revealed that all 68 pigs were from a purebred population. The effective population size decreased over time, and it was 96 prior to generation 20. Both linkage disequilibrium (LD) and neutrality test indicated a low selection of TC pigs with average LD value of 0.15 ± 0.23. Genetic diversity results exhibited a minor allele frequency (MAF) of 0.23, observed heterozygosity (HO) of 0.32, expected heterozygosity (He) of 0.31, and nucleotide diversity (Pi) of 0.31. All these parameters indicated a remarkably high genetic diversity of TC pigs. Additionally, 184 runs of homozygosity (ROH) segments were detected from the whole genome of TC pigs with an average ROH length of 23.71Mb, ranging from 11.26Mb to 69.02 Mb. The highest ROH coverage was found on chromosome 1 (10.12%), while the lowest was on chromosome 18 (1.49%). The average inbreeding coefficients based on ROH (FROH) was 0.04%. Fourteen ROH islands containing 240 genes were detected on 9 different autosomes. Some of these 240 genes were overlapped with the genes related to biological processes such as immune function, reproduction, muscular development, and fat deposition, including FFAR2, FFAR4, MAPK8, NPY5R, KISS1, and these genes might be associated with such traits as meat quality and disease resistance in TC pigs. Taken together, population structure and genetic diversity results suggested that the TC pig represented a valuable genetic resource. However, TC pig breed conservation program remains to be further optimized to ensure adequate genetic diversity and avoid inbreeding depression. Our findings provide theoretical basis for formulating management and conservation strategies for TC pigs.
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Affiliation(s)
- Jiao Yuan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- The Engineering Technology Research Center of Local Pig Breed Improvement of Hubei Province, Wuhan, China
| | - Guoqiang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sanping Xu
- Department of Agricultural and Rural Bureau, Xianning, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- The Engineering Technology Research Center of Local Pig Breed Improvement of Hubei Province, Wuhan, China
- *Correspondence: Bang Liu,
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13
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Wang X, Ran X, Niu X, Huang S, Li S, Wang J. Whole-genome sequence analysis reveals selection signatures for important economic traits in Xiang pigs. Sci Rep 2022; 12:11823. [PMID: 35821031 PMCID: PMC9276726 DOI: 10.1038/s41598-022-14686-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/10/2022] [Indexed: 11/30/2022] Open
Abstract
Xiang pig (XP) is one of the best-known indigenous pig breeds in China, which is characterized by its small body size, strong disease resistance, high adaptability, favorite meat quality, small litter sizes, and early sexual maturity. However, the genomic evidence that links these unique traits of XP is still poorly understood. To identify the genomic signatures of selection in XP, we performed whole-genome resequencing on 25 unrelated individual XPs. We obtained 876.70 Gb of raw data from the genomic libraries. The LD analysis showed that the lowest level of linkage disequilibrium was observed in Xiang pig. Comparative genomic analysis between XPs and other breeds including Tibetan, Meishan, Duroc and Landrace revealed 3062, 1228, 907 and 1519 selected regions, respectively. The genes identified in selected regions of XPs were associated with growth and development processes (IGF1R, PROP1, TBX19, STAC3, RLF, SELENOM, MSTN), immunity and disease resistance (ZCCHC2, SERPINB2, ADGRE5, CYP7B1, STAT6, IL2, CD80, RHBDD3, PIK3IP1), environmental adaptation (NR2E1, SERPINB8, SERPINB10, SLC26A7, MYO1A, SDR9C7, UVSSA, EXPH5, VEGFC, PDE1A), reproduction (CCNB2, TRPM6, EYA3, CYP7B1, LIMK2, RSPO1, ADAM32, SPAG16), meat quality traits (DECR1, EWSR1), and early sexual maturity (TAC3). Through the absolute allele frequency difference (ΔAF) analysis, we explored two population-specific missense mutations occurred in NR6A1 and LTBP2 genes, which well explained that the vertebrae numbers of Xiang pigs were less than that of the European pig breeds. Our results indicated that Xiang pigs were less affected by artificial selection than the European and Meishan pig breeds. The selected candidate genes were mainly involved in growth and development, disease resistance, reproduction, meat quality, and early sexual maturity. This study provided a list of functional candidate genes, as well as a number of genetic variants, which would provide insight into the molecular basis for the unique traits of Xiang pig.
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Affiliation(s)
- Xiying Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.,Tongren University, Tongren, 554300, China
| | - Xueqin Ran
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
| | - Xi Niu
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Shihui Huang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Sheng Li
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jiafu Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang, 550025, China.
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14
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Jiang Y, Li X, Liu J, Zhang W, Zhou M, Wang J, Liu L, Su S, Zhao F, Chen H, Wang C. Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data. BMC Genomics 2022; 23:373. [PMID: 35581549 PMCID: PMC9115978 DOI: 10.1186/s12864-022-08583-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
Background Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight into the genetic architecture of complex traits. Here, we systematically investigated the population genetic structure of five Anhui indigenous pig breeds (AHIPs), and compared them to those of five Western commercial pig breeds (WECPs). Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (FROH) and homozygosity (FHOM). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein. Results The WECPs and AHIPs were clearly differentiated into two separate clades consistent with their geographical origins, as revealed by the population structure and principal component analysis. We identified 13,530 ROHs across all individuals, of which 4,555 and 8,975 ROHs were unique to AHIPs and WECPs, respectively. Most ROHs identified in our study were short (< 10 Mb) or medium (10–20 Mb) in length. WECPs had significantly higher numbers of short ROHs, and AHIPs generally had longer ROHs. FROH values were significantly lower in AHIPs than in WECPs, indicating that breed improvement and conservation programmes were successful in AHIPs. On average, FROH and FHOM values were highly correlated (0.952–0.991) in AHIPs and WECPs. A total of 27 regions had a high frequency of ROHs and contained 17 key candidate genes associated with economically important traits in pigs. Among these, nine candidate genes (CCNT2, EGR2, MYL3, CDH13, PROX1, FLVCR1, SETD2, FGF18, and FGF20) found in WECPs were related to muscular and skeletal development, whereas eight candidate genes (CSN1S1, SULT1E1, TJP1, ZNF366, LIPC, MCEE, STAP1, and DUSP) found in AHIPs were associated with health, reproduction, and fatness traits. Conclusion Our findings provide a useful reference for the selection and assortative mating of pig breeds, laying the groundwork for future research on the population genetic structures of AHIPs, ultimately helping protect these local varieties. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08583-9.
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Affiliation(s)
- Yao Jiang
- 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, 230031, China
| | - Xiaojin Li
- 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, 230031, China
| | - Jiali Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei Zhang
- 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, 230031, China
| | - Mei Zhou
- 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, 230031, China
| | - Jieru Wang
- 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, 230031, China
| | - Linqing Liu
- 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, 230031, China
| | - Shiguang Su
- 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, 230031, China
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongquan Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Chonglong Wang
- 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, 230031, China.
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15
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Ma X, Cheng H, Liu Y, Sun L, Chen N, Jiang F, You W, Yang Z, Zhang B, Song E, Lei C. Assessing Genomic Diversity and Selective Pressures in Bohai Black Cattle Using Whole-Genome Sequencing Data. Animals (Basel) 2022; 12:ani12050665. [PMID: 35268233 PMCID: PMC8909316 DOI: 10.3390/ani12050665] [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: 12/10/2021] [Revised: 02/16/2022] [Accepted: 03/05/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Bohai Black cattle are one of the indigenous black coat cattle breeds in China, which are famous for their excellent meat quality. Whole-genome sequencing technology has been extensively developed to study species genome genetic diversity, population structure, selection pressure, demographic events, etc. However, a limited number of studies have reported genomic diversity and selection pressures in Bohai Black cattle. The purpose of this study is to analyze population structure and genomic differences between Bohai Black cattle and five “core” cattle populations from all over the world, mainly oriented on the identification of selection signatures using whole-genome sequencing data. In addition, we identify a series of candidate genes that can potentially be related to black coat color, meat quality, immunity, and reproduction in this breed. This study provides valuable genomic resources and theoretical basis for the future breeding of Bohai Black cattle. Abstract Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five “core” cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (HE) and the observed heterozygosity (HO), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the “ECM-receptor interaction” pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, FST, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (MC1R), muscle development (ITGA9, ENAH, CAPG, ABI2, and ISLR), fat deposition (TBC1D1, CYB5R4, TUSC3, and EPS8), reproduction traits (SPIRE2, KHDRBS2, and FANCA), and immune system response (CD84, SLAMF1, SLAMF6, and CDK10). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle.
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Affiliation(s)
- Xiaohui Ma
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
| | - Haijian Cheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
| | - Yangkai Liu
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
| | - Luyang Sun
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
| | - Fugui Jiang
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
| | - Wei You
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
| | - Zhangang Yang
- HuaXing Bohai Black Cattle Co., Ltd., Binzhou 256600, China;
| | - Baoheng Zhang
- Wudi Animal Husbandry and Veterinary Service Management Center of Binzhou City, Binzhou 256600, China;
| | - Enliang Song
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China; (X.M.); (H.C.); (F.J.); (W.Y.)
- Correspondence: (E.S.); (C.L.); Tel.: +86-138-6415-6955 (E.S.); +86-135-7299-2159 (C.L.)
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (Y.L.); (L.S.); (N.C.)
- Correspondence: (E.S.); (C.L.); Tel.: +86-138-6415-6955 (E.S.); +86-135-7299-2159 (C.L.)
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16
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Hou H, Wang X, Ding W, Xiao C, Cai X, Lv W, Tu Y, Zhao W, Yao J, Yang C. Whole‐genome sequencing reveals the artificial selection and local environmental adaptability of pigeons (
Columba livia
). Evol Appl 2021; 15:603-617. [PMID: 35505885 PMCID: PMC9046921 DOI: 10.1111/eva.13284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 06/17/2021] [Accepted: 07/12/2021] [Indexed: 12/16/2022] Open
Abstract
To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro‐pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.
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Affiliation(s)
- Haobin Hou
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Xiaoliang Wang
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Weixing Ding
- Shanghai Academy of Agricultural Sciences Shanghai China
| | - Changfeng Xiao
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Xia Cai
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Wenwei Lv
- National Poultry Engineer Research Center Shanghai China
| | - Yingying Tu
- National Poultry Engineer Research Center Shanghai China
| | - Weimin Zhao
- Shanghai Jinhuang Pigeon Company Shanghai China
| | - Junfeng Yao
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
| | - Changsuo Yang
- Shanghai Academy of Agricultural Sciences Shanghai China
- National Poultry Engineer Research Center Shanghai China
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