1
|
Petretto E, Luigi-Sierra MG, Vacca GM, Martínez A, Delgado JV, Fernández Álvarez J, Castelló A, Pazzola M, Jordana J, Dettori ML, Amills M. The African introgression of Murciano Granadina goats has a Moroccan origin and displays remarkable levels of inter-individual variability. Anim Genet 2024. [PMID: 39291549 DOI: 10.1111/age.13472] [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: 06/27/2023] [Revised: 07/16/2024] [Accepted: 08/06/2024] [Indexed: 09/19/2024]
Abstract
There is evidence that Murciano Granadina (MG), the most important caprine dairy breed in Spain, has been introgressed by African goats, but the precise geographic origin of such introgression has not been identified yet. Moreover, an accurate estimate of the magnitude of this African introgression is lacking, since current estimates are based on small numbers of sampled individuals. The aim of our work was to tackle these two issues by genotyping 500 MG goats with the Goat SNP50 BeadChip and comparing their genotypes with those of reference populations from Spain (Bermeya), France (Saanen), Morocco (Barcha, Draa, Ghazalia, Noire de Atlas, Nord, Moroccan), Egypt (Barki, Oasis, Saidi), Algeria (Arabia, Makatia, M'Zabite, Kabyle), Tunisia (Tunisian native breeds) and Sudan (Desert, Nilotic, Taggar). The population of 500 MG goats was subdivided into 10 datasets of 50 individuals to ensure that sample sizes of the target (MG) and reference populations are balanced. Performance of an unsupervised ADMIXTURE analysis demonstrated that MG goats have a North African ancestry, with an average proportion of 4.4 ± 2.3%. Next, we did a supervised ADMIXTURE analysis that revealed that the Moroccan genetic component reaches a proportion of 4.01 ± 3.9% in MG goats, while the Algerian (0.001 ± 0.001%), Egyptian (0.2 ± 0.1%), Sudanese (0.1 ± 0.1%) and Tunisian (0.3 ± 0.4%) components are present in extremely small proportions. The historical circumstances of this introgression event are currently unknown, but several plausible scenarios are outlined. Moreover, our results show considerable inter-individual heterogeneity regarding the magnitude of the Moroccan introgression of MG goats (0%- 12% depending on the MG data set under analysis). This result implies that reliable estimates about the introgression of autochthonous livestock by exotic breeds can only be obtained by extensively sampling target populations.
Collapse
Affiliation(s)
- E Petretto
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
- Departament de Ciència Animal i Dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M G Luigi-Sierra
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i Dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - G M Vacca
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - A Martínez
- Departamento de Genética, Universidad de Córdoba, Campus Universitario de Rabanales, Córdoba, Spain
| | - J V Delgado
- Departamento de Genética, Universidad de Córdoba, Campus Universitario de Rabanales, Córdoba, Spain
| | - J Fernández Álvarez
- Departamento de Genética, Universidad de Córdoba, Campus Universitario de Rabanales, Córdoba, Spain
| | - A Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i Dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M Pazzola
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - J Jordana
- Departament de Ciència Animal i Dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - M L Dettori
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i Dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| |
Collapse
|
2
|
Lv W, Peng Y, Hu J, Zhu M, Mao Y, Wang L, Wang G, Xu Z, Wu W, Zuo B. Functional SNPs in SYISL promoter significantly affect muscle fiber density and muscle traits in pigs. Anim Genet 2024; 55:66-78. [PMID: 37881102 DOI: 10.1111/age.13370] [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: 05/02/2023] [Revised: 09/06/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023]
Abstract
Our previous studies showed that SYISL is a negative regulator of muscle growth and regeneration in mice, pigs and humans. SYISL knockout resulted in an increase in the density of muscle fibers and muscle growth. However, it is unclear whether there are natural mutations in pig SYNPO2 intron sense-overlapping lncRNA (pSYISL) that affect the expression of pSYISL and muscle growth traits. In this study, three SNPs in exons and six SNPs within the promoter of pSYISL were identified. Association analysis showed that the two SNPs in exons are significantly associated with loin muscle area (p < 0.05); the six SNPs in the promoter that show complete linkage are significantly associated with live backfat thickness and live loin muscle area in American Large White pigs. Bioinformatics and luciferase reporter assays as well as in vitro binding experiments indicated that the mutation of SNP rs702045770 (g.539G>A) leads to the loss of YY1 binding to the promoter, thus affecting the expression level of pSYISL, and we found that Jiangshan Black pigs with genotype GG have a higher expression level of pSYISL than genotype AA individuals, but the muscle fiber density was significantly lower than in genotype AA individuals. Furthermore, the association analysis showed that the carcass backfat thickness of genotype GG of SNP rs702045770 was significantly higher than that of other genotypes in (Pietrain × Duroc) × (Landrace × Yorkshire) crossbred pigs (p < 0.05). The glycolytic potential of genotype GG was significantly higher than that of other genotypes (p < 0.05). These results provide novel insight into the identification of functional SNPs in non-coding genomic regions.
Collapse
Affiliation(s)
- Wei Lv
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yaxin Peng
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Hu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Mingfei Zhu
- The Tianpeng Group Co. Ltd, Jiangshan, China
| | | | - Litong Wang
- The Tianpeng Group Co. Ltd, Jiangshan, China
| | | | - Zaiyan Xu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Li Z, Liu X, Wang C, Li Z, Jiang B, Zhang R, Tong L, Qu Y, He S, Chen H, Mao Y, Li Q, Pook T, Wu Y, Zan Y, Zhang H, Li L, Wen K, Chen Y. The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation. Genome Res 2023; 33:1833-1847. [PMID: 37914227 PMCID: PMC10691484 DOI: 10.1101/gr.277638.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 09/12/2023] [Indexed: 11/03/2023]
Abstract
Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.
Collapse
Affiliation(s)
- Zhengcao Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China;
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Chen Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Zhenyang Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Bo Jiang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Ruifeng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Lu Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Youping Qu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Sheng He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Haifan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Yafei Mao
- Bio-X Institutes, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Qingnan Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Torsten Pook
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6700 AH, The Netherlands
| | - Yu Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Yanjun Zan
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266000, China
| | - Hui Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Lu Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Keying Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China;
| |
Collapse
|
5
|
Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [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: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
Collapse
Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| |
Collapse
|
6
|
Zhang M, Zhang C, Hu P, Shi L, Ju M, Zhang B, Li X, Han X, Wang K, Li X, Qiao R. Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds. Anim Genet 2022; 53:803-813. [PMID: 36071602 DOI: 10.1111/age.13261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/27/2022]
Abstract
Mitochondria follow non-Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.
Collapse
Affiliation(s)
- Menghao Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chen Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shanxi, China
| | - Panyang Hu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Lidan Shi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Mingming Ju
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ben Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xinjian Li
- 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
| | - Xiuling Li
- 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
| |
Collapse
|
7
|
Zhang Q, Zhang Q, Jensen J. Association Studies and Genomic Prediction for Genetic Improvements in Agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:904230. [PMID: 35720549 PMCID: PMC9201771 DOI: 10.3389/fpls.2022.904230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
To feed the fast growing global population with sufficient food using limited global resources, it is urgent to develop and utilize cutting-edge technologies and improve efficiency of agricultural production. In this review, we specifically introduce the concepts, theories, methods, applications and future implications of association studies and predicting unknown genetic value or future phenotypic events using genomics in the area of breeding in agriculture. Genome wide association studies can identify the quantitative genetic loci associated with phenotypes of importance in agriculture, while genomic prediction utilizes individual genetic value to rank selection candidates to improve the next generation of plants or animals. These technologies and methods have improved the efficiency of genetic improvement programs for agricultural production via elite animal breeds and plant varieties. With the development of new data acquisition technologies, there will be more and more data collected from high-through-put technologies to assist agricultural breeding. It will be crucial to extract useful information among these large amounts of data and to face this challenge, more efficient algorithms need to be developed and utilized for analyzing these data. Such development will require knowledge from multiple disciplines of research.
Collapse
Affiliation(s)
- Qianqian Zhang
- Institute of Biotechnology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Qin Zhang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, China
- College of Animal Science and Technology, China Agricultural University, BeijingChina
| | - Just Jensen
- Centre for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| |
Collapse
|
8
|
Wang Y, Zhang C, Peng Y, Cai X, Hu X, Bosse M, Zhao Y. Whole-genome analysis reveals the hybrid formation of Chinese indigenous DHB pig following human migration. Evol Appl 2022; 15:501-514. [PMID: 35386394 PMCID: PMC8965386 DOI: 10.1111/eva.13366] [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: 05/06/2021] [Revised: 12/07/2021] [Accepted: 02/20/2022] [Indexed: 12/01/2022] Open
Abstract
Hybridization is widespread in nature and is a valuable tool in domestic breeding. The DHB (DaHuaBai) pig in South China is the product of such a breeding strategy, resulting in increased body weight compared with other pigs in the surrounding area. We analyzed genomic data from 20 Chinese pig breeds and investigated the genomic architecture after breed formation of DHB. The breed showed inconsistency in genotype and body weight phenotype, in line with selection after hybridization. By quantifying introgression with a haplotype-based approach, we proposed a two-step introgression from large-sized pigs into small-sized pigs to produce DHB, consistent with the human migration events in Chinese history. Combining with gene prioritization and allele frequency analysis, we identify candidate genes that showed selection after introgression and that may affect body weight, such as IGF1R, SRC, and PCM1. Our research provides an example of a hybrid formation of domestic breeds along with human migration patterns.
Collapse
Affiliation(s)
- Yuzhan Wang
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Chunyuan Zhang
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yebo Peng
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xinyu Cai
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xiaoxiang Hu
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Mirte Bosse
- Animal Breeding and Genomics CentreWageningen UniversityWageningenThe Netherlands
| | - Yiqiang Zhao
- State Key Laboratory of AgrobiotechnologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| |
Collapse
|
9
|
Petrelli S, Buglione M, Maselli V, Troiano C, Larson G, Frantz L, Manin A, Ricca E, Baccigalupi L, Wright D, Pietri C, Fulgione D. Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs. Mol Ecol 2021; 31:220-237. [PMID: 34676935 DOI: 10.1111/mec.16238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/31/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of FST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised FST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.
Collapse
Affiliation(s)
- Simona Petrelli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Buglione
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Maselli
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Claudia Troiano
- Department of Humanities, University of Naples Federico II, Naples, Italy
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Aurelie Manin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Ezio Ricca
- Department of Biology, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
| | - Loredana Baccigalupi
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy.,Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Dominic Wright
- IFM Biology, AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Christian Pietri
- Fédération Départementale des Chasseurs de Haute-Corse (FDCHC), Résidence Nouvelle-Corniche, St Joseph, Bastia, France
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Napoli, Italy
| |
Collapse
|
10
|
Yang R, Guo X, Zhu D, Tan C, Bian C, Ren J, Huang Z, Zhao Y, Cai G, Liu D, Wu Z, Wang Y, Li N, Hu X. Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy. Gigascience 2021; 10:giab048. [PMID: 34282453 PMCID: PMC8290195 DOI: 10.1093/gigascience/giab048] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/21/2021] [Accepted: 06/15/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Uncovering the genetic architecture of economic traits in pigs is important for agricultural breeding. However, high-density haplotype reference panels are unavailable in most agricultural species, limiting accurate genotype imputation in large populations. Moreover, the infinitesimal model of quantitative traits implies that weak association signals tend to be spread across most of the genome, further complicating the genetic analysis. Hence, there is a need to develop new methods for sequencing large cohorts without large reference panels. RESULTS We describe a Tn5-based highly accurate, cost- and time-efficient, low-coverage sequencing method to obtain 11.3 million whole-genome single-nucleotide polymorphisms in 2,869 Duroc boars at a mean depth of 0.73×. On the basis of these single-nucleotide polymorphisms, a genome-wide association study was performed, resulting in 14 quantitative trait loci (QTLs) for 7 of 21 important agricultural traits in pigs. These QTLs harbour genes, such as ABCD4 for total teat number and HMGA1 for back fat thickness, and provided a starting point for further investigation. The inheritance models of the different traits varied greatly. Most follow the minor-polygene model, but this can be attributed to different reasons, such as the shaping of genetic architecture by artificial selection for this population and sufficiently interconnected minor gene regulatory networks. CONCLUSIONS Genome-wide association study results for 21 important agricultural traits identified 14 QTLs/genes and showed their genetic architectures, providing guidance for genetic improvement harnessing genomic features. The Tn5-based low-coverage sequencing method can be applied to large-scale genome studies for any species without a good reference panel and can be used for agricultural breeding.
Collapse
Affiliation(s)
- Ruifei Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| | - Xiaoli Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| | - Di Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| | - Cheng Tan
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, No. 483 Wushan road, Tianhe district, Guangdong 510640, China
| | - Cheng Bian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| | - Jiangli Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| | - Zhuolin Huang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, No. 483 Wushan road, Tianhe district, Guangdong 510640, China
| | - Dewu Liu
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, No. 483 Wushan road, Tianhe district, Guangdong 510640, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, No. 483 Wushan road, Tianhe district, Guangdong 510640, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
- National Research Facility for Phenotypic and Genotypic Analysis of Model Animals (Beijing), China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| | - Ning Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan west road, Haidian district, Beijing 100193, China
| |
Collapse
|
11
|
Zhou R, Li ST, Yao WY, Xie CD, Chen Z, Zeng ZJ, Wang D, Xu K, Shen ZJ, Mu Y, Bao W, Jiang W, Li R, Liang Q, Li K. The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication. Mol Ecol Resour 2021; 21:2077-2092. [PMID: 33825319 DOI: 10.1111/1755-0998.13396] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/17/2021] [Accepted: 03/29/2021] [Indexed: 01/27/2023]
Abstract
There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.
Collapse
Affiliation(s)
- Rong Zhou
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shang-Tong Li
- National Institute of Biological Sciences (NIBS, Beijing, China
| | - Wen-Ye Yao
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chun-Di Xie
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Zhi-Jie Zeng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Di Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Kui Xu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhao-Ji Shen
- Guangdong Provincial key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,Fulcrum gene science and technology (Beijing) Ltd, Beijing, China
| | - Yulian Mu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
12
|
Bovo S, Ribani A, Muñoz M, Alves E, Araujo JP, Bozzi R, Čandek-Potokar M, Charneca R, Di Palma F, Etherington G, Fernandez AI, García F, García-Casco J, Karolyi D, Gallo M, Margeta V, Martins JM, Mercat MJ, Moscatelli G, Núñez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Schiavo G, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems. Genet Sel Evol 2020; 52:33. [PMID: 32591011 PMCID: PMC7318759 DOI: 10.1186/s12711-020-00553-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
Background Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.
Collapse
Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Maria Muñoz
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Estefania Alves
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Jose P Araujo
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, 4990-706, Ponte de Lima, Portugal
| | - Riccardo Bozzi
- DAGRI - Animal Science Section, Università di Firenze, Via delle Cascine 5, 50144, Florence, Italy
| | | | - Rui Charneca
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Polo da Mitra, Apartado 94, 7006-554, Évora, Portugal
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
| | - Graham Etherington
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
| | - Ana I Fernandez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Fabián García
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Juan García-Casco
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Danijel Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Rome, Italy
| | - Vladimir Margeta
- Faculty of Agrobiotechnical Sciences, University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia
| | - José Manuel Martins
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Polo da Mitra, Apartado 94, 7006-554, Évora, Portugal
| | - Marie J Mercat
- IFIP Institut du porc, La Motte au Vicomte, BP 35104, 35651, Le Rheu Cedex, France
| | - Giulia Moscatelli
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Yolanda Núñez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Raquel Quintanilla
- Programa de Genética y Mejora Animal, IRTA, Torre Marimon, 08140, Caldes de Montbui, Barcelona, Spain
| | - Čedomir Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, Belgrade-Zemun, 11080, Serbia
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania
| | - Juliette Riquet
- GenPhySE, INRAE, Université de Toulouse, Chemin de Borde-Rouge 24, Auzeville Tolosane, 31326, Castanet Tolosan, France
| | - Radomir Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, Belgrade-Zemun, 11080, Serbia
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Graziano Usai
- AGRIS SARDEGNA, Loc. Bonassai, 07100, Sassari, Italy
| | - Valerio J Utzeri
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Christoph Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Schwäbisch Hall, Germany
| | - Cristina Ovilo
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña km. 7,5, 28040, Madrid, Spain
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy.
| |
Collapse
|
13
|
Abstract
The domestication of animals led to a major shift in human subsistence patterns, from a hunter-gatherer to a sedentary agricultural lifestyle, which ultimately resulted in the development of complex societies. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent methodological innovations, such as improved ancient DNA extraction methods and next-generation sequencing, have enabled the sequencing of whole ancient genomes. These genomes have helped reconstruct the process by which animals entered into domestic relationships with humans and were subjected to novel selection pressures. Here, we discuss and update key concepts in animal domestication in light of recent contributions from ancient genomics.
Collapse
|
14
|
McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019; 17:98. [PMID: 31791340 PMCID: PMC6889691 DOI: 10.1186/s12915-019-0724-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.
Collapse
Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
| |
Collapse
|
15
|
Chen M, Su G, Fu J, Wang A, Liu J, Lund MS, Guldbrandtsen B. Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs. Evol Appl 2019; 12:292-300. [PMID: 30697340 PMCID: PMC6346729 DOI: 10.1111/eva.12716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 11/26/2022] Open
Abstract
The distribution of Asian ancestry in the genome of Danish Duroc pigs was investigated using whole-genome sequencing data from European wild boars, Danish Duroc, Chinese Meishan and Bamaxiang pigs. Asian haplotypes deriving from Meishan and Bamaxiang occur widely across the genome. Signatures of selection on Asian haplotypes are common in the genome, but few of these haplotypes have been fixed. By defining 50-kb windows with more than 50% Chinese ancestry, which did not exhibit extreme genetic differentiation between Meishan and Bamaxiang as candidate regions, the enrichment of quantitative trait loci in candidate regions supports that Asian haplotypes under selection play an important role in contributing genetic variation underlying production, reproduction, meat and carcass, and exterior traits. Gene annotation of regions with the highest proportion of Chinese ancestry revealed genes of biological interest, such as NR6A1. Further haplotype clustering analysis suggested that a haplotype of Chinese origin around the NR6A1 gene was introduced to Europe and then underwent a selective sweep in European pigs. Besides, functional genes in candidate regions, such as AHR and PGRMC2, associated with fertility, and SAL1, associated with meat quality, were identified. Our results demonstrate the contribution of Asian haplotypes to the genomes of European pigs. Findings herein facilitate further genomic studies such as genomewide association study and genomic prediction by providing ancestry information of variants.
Collapse
Affiliation(s)
- Minhui Chen
- Department of Molecular Biology and Genetics, Centre for Quantitative Genetics and GenomicsAarhus UniversityTjeleDenmark
- Department of Animal Genetics, Breeding and ReproductionChina Agricultural UniversityBeijingChina
| | - Guosheng Su
- Department of Molecular Biology and Genetics, Centre for Quantitative Genetics and GenomicsAarhus UniversityTjeleDenmark
| | - Jinluan Fu
- Department of Animal Genetics, Breeding and ReproductionChina Agricultural UniversityBeijingChina
| | - Aiguo Wang
- Department of Animal Genetics, Breeding and ReproductionChina Agricultural UniversityBeijingChina
| | - Jian‐Feng Liu
- Department of Animal Genetics, Breeding and ReproductionChina Agricultural UniversityBeijingChina
| | - Mogens S. Lund
- Department of Molecular Biology and Genetics, Centre for Quantitative Genetics and GenomicsAarhus UniversityTjeleDenmark
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Centre for Quantitative Genetics and GenomicsAarhus UniversityTjeleDenmark
| |
Collapse
|
16
|
Hudson NJ, Naval-Sánchez M, Porto-Neto L, Pérez-Enciso M, Reverter A. RAPID COMMUNICATION: A haplotype information theory method reveals genes of evolutionary interest in European vs. Asian pigs. J Anim Sci 2018; 96:3064-3069. [PMID: 29873754 DOI: 10.1093/jas/sky225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/04/2018] [Indexed: 01/01/2023] Open
Abstract
Asian and European wild boars were independently domesticated ca. 10,000 yr ago. Since the 17th century, Chinese breeds have been imported to Europe to improve the genetics of European animals by introgression of favorable alleles, resulting in a complex mosaic of haplotypes. To interrogate the structure of these haplotypes further, we have run a new haplotype segregation analysis based on information theory, namely compression efficiency (CE). We applied the approach to sequence data from individuals from each phylogeographic region (n = 23 from Asia and Europe) including a number of major pig breeds. Our genome-wide CE is able to discriminate the breeds in a manner reflecting phylogeography. Furthermore, 24,956 nonoverlapping sliding windows (each comprising 1,000 consecutive SNP) were quantified for extent of haplotype sharing within and between Asia and Europe. The genome-wide distribution of extent of haplotype sharing was quite different between groups. Unlike European pigs, Asian pigs haplotype sharing approximates a normal distribution. In line with this, we found the European breeds possessed a number of genomic windows of dramatically higher haplotype sharing than the Asian breeds. Our CE analysis of sliding windows captures some of the genomic regions reported to contain signatures of selection in domestic pigs. Prominent among these regions, we highlight the role of a gene encoding the mitochondrial enzyme LACTB which has been associated with obesity, and the gene encoding MYOG a fundamental transcriptional regulator of myogenesis. The origin of these regions likely reflects either a population bottleneck in European animals, or selective targets on commercial phenotypes reducing allelic diversity in particular genes and/or regulatory regions.
Collapse
Affiliation(s)
- Nicholas J Hudson
- School of Agriculture and Food Sciences, University of Queensland, Gatton, Queensland Australia
| | | | | | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain.,Institut Català de Recerca i Estudis Avançats (ICREA), Carrer de Lluís Companys 23, Barcelona, Spain
| | | |
Collapse
|
17
|
|
18
|
Genome-wide association studies and meta-analysis uncovers new candidate genes for growth and carcass traits in pigs. PLoS One 2018; 13:e0205576. [PMID: 30308042 PMCID: PMC6181390 DOI: 10.1371/journal.pone.0205576] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/27/2018] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have been widely used in the genetic dissection of complex traits. As more genomic data is being generated within different commercial or resource pig populations, the challenge which arises is how to collectively investigate the data with the purpose to increase sample size and implicitly the statistical power. This study performs an individual population GWAS, a joint population GWAS and a meta-analysis in three pig F2 populations. D1 is derived from European type breeds (Piétrain, Large White and Landrace), D2 is obtained from an Asian breed (Meishan) and Piétrain, and D3 stems from a European Wild Boar and Piétrain, which is the common founder breed. The traits investigated are average daily gain, backfat thickness, meat to fat ratio and carcass length. The joint and the meta-analysis did not identify additional genomic clusters besides the ones discovered via the individual population GWAS. However, the benefit was an increased mapping resolution which pinpointed to narrower clusters harboring causative variants. The joint analysis identified a higher number of clusters as compared to the meta-analysis; nevertheless, the significance levels and the number of significant variants in the meta-analysis were generally higher. Both types of analysis had similar outputs suggesting that the two strategies can complement each other and that the meta-analysis approach can be a valuable tool whenever access to raw datasets is limited. Overall, a total of 20 genomic clusters that predominantly overlapped at various extents, were identified on chromosomes 2, 7 and 17, many confirming previously identified quantitative trait loci. Several new candidate genes are being proposed and, among them, a strong candidate gene to be taken into account for subsequent analysis is BMP2 (bone morphogenetic protein 2).
Collapse
|
19
|
Genomic analysis reveals genes affecting distinct phenotypes among different Chinese and western pig breeds. Sci Rep 2018; 8:13352. [PMID: 30190566 PMCID: PMC6127261 DOI: 10.1038/s41598-018-31802-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 08/21/2018] [Indexed: 01/04/2023] Open
Abstract
The differences in artificial and natural selection have been some of the factors contributing to phenotypic diversity between Chinese and western pigs. Here, 830 individuals from western and Chinese pig breeds were genotyped using the reduced-representation genotyping method. First, we identified the selection signatures for different pig breeds. By comparing Chinese pigs and western pigs along the first principal component, the growth gene IGF1R; the immune genes IL1R1, IL1RL1, DUSP10, RAC3 and SWAP70; the meat quality-related gene SNORA50 and the olfactory gene OR1F1 were identified as candidate differentiated targets. Further, along a principal component separating Pudong White pigs from others, a potential causal gene for coat colour (EDNRB) was discovered. In addition, the divergent signatures evaluated by Fst within Chinese pig breeds found genes associated with the phenotypic features of coat colour, meat quality and feed efficiency among these indigenous pigs. Second, admixture and genomic introgression analysis were performed. Shan pigs have introgressed genes from Berkshire, Yorkshire and Hongdenglong pigs. The results of introgression mapping showed that this introgression conferred adaption to the local environment and coat colour of Chinese pigs and the superior productivity of western pigs.
Collapse
|
20
|
A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing. Animal 2018; 13:683-693. [PMID: 29987993 DOI: 10.1017/s1751731118001714] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Taihu pig breeds are the most prolific breeds of swine in the world, and they also have superior economic traits, including high resistance to disease, superior meat quality, high resistance to crude feed and a docile temperament. The formation of these phenotypic characteristics is largely a result of long-term artificial or natural selection. Therefore, exploring selection signatures in the genomes of the Taihu pigs will help us to identify porcine genes related to productivity traits, disease and behaviour. In this study, we used both intra-population (Relative Extend Haplotype Homozygosity Test (REHH)) and inter-population (the Cross-Population Extend Haplotype Homozygosity Test (XPEHH); F-STATISTICS, F ST ) methods to detect genomic regions that might be under selection process in Taihu pig breeds. As a result, we found 282 (REHH) and 112 (XPEHH) selection signature candidate regions corresponding to 159.78 Mb (6.15%) and 62.29 Mb (2.40%) genomic regions, respectively. Further investigations of the selection candidate regions revealed that many genes under these genomic regions were related to reproductive traits (such as the TLR9 gene), coat colour (such as the KIT gene) and fat metabolism (such as the CPT1A and MAML3 genes). Furthermore, gene enrichment analyses showed that genes under the selection candidate regions were significantly over-represented in pathways related to diseases, such as autoimmune thyroid and asthma diseases. In conclusion, several candidate genes potentially under positive selection were involved in characteristics of Taihu pig. These results will further allow us to better understand the mechanisms of selection in pig breeding.
Collapse
|
21
|
Stratz P, Schmid M, Wellmann R, Preuß S, Blaj I, Tetens J, Thaller G, Bennewitz J. Linkage disequilibrium pattern and genome-wide association mapping for meat traits in multiple porcine F 2 crosses. Anim Genet 2018; 49:403-412. [PMID: 29978910 DOI: 10.1111/age.12684] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2018] [Indexed: 12/13/2022]
Abstract
In the present study, data from four F2 crosses were analysed and used to study the linkage disequilibrium (LD) structure within and across the crosses. Genome-wide association analyses (GWASes) for conductivity and dressing out meat traits were conducted using single-marker and Bayesian multi-marker models using the pooled data from all F2 crosses. Porcine F2 crosses generated from the distantly related founder breeds Wild Boar, Piétrain and Meishan, as well as from a porcine F2 cross from the closely related founder breed Piétrain and an F1 Large White × Landrace cross were pooled. A total of 2572 F2 animals were genotyped using a 62K SNP chip. The positions of the SNPs were based on genome assembly Sscrofa11.1. After post-alignment and genotype filtering, approximately 50K SNPs were usable for LD studies and GWASes. The main findings of the present study are that the breakdown of LD was faster in crosses from closely related founder breeds compared to crosses from distantly related founders. The fastest breakdown of LD was observed by pooling the data. Based on the single-marker results and LD structure, clusters and windows were built for 1-Mb intervals. For conductivity and dressing out, 183 and 191 nominal significant associations respectively and six and five clusters respectively were found. Dominance was important for conductivity, and considering dominance in GWASes improved the mapping signals. Most clear signals were found for conductivity on SSC6, 8 and 15 and for dressing out on SSC2 and 7. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. However, further research is needed to investigate if dominance is also important in crossbreed pig breeding schemes.
Collapse
Affiliation(s)
- P Stratz
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
| | - M Schmid
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
| | - R Wellmann
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
| | - S Preuß
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
| | - I Blaj
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 6, 24118, Kiel, Germany
| | - J Tetens
- Functional Breeding Group, Department of Animal Science, Georg-August-University Göttingen, Burckhardtweg 2, 37077, Göttingen, Germany
| | - G Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, Hermann-Rodewald-Straße 6, 24118, Kiel, Germany
| | - J Bennewitz
- Institute of Animal Science, University of Hohenheim, Garbenstraße 17, 70599, Stuttgart, Germany
| |
Collapse
|
22
|
Human-Mediated Introgression of Haplotypes in a Modern Dairy Cattle Breed. Genetics 2018; 209:1305-1317. [PMID: 29848486 PMCID: PMC6063242 DOI: 10.1534/genetics.118.301143] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022] Open
Abstract
Domestic animals can serve as model systems of adaptive introgression and their genomic signatures. In part, their usefulness as model systems is due to their well-known histories. Different breeding strategies such as introgression and artificial selection have generated numerous desirable phenotypes and superior performance in domestic animals. The modern Danish Red Dairy Cattle is studied as an example of an introgressed population. It originates from crossing the traditional Danish Red Dairy Cattle with the Holstein and Brown Swiss breeds, both known for high milk production. This crossing happened, among other things due to changes in the production system, to raise milk production and overall performance. The genomes of modern Danish Red Dairy Cattle are heavily influenced by regions introgressed from the Holstein and Brown Swiss breeds and under subsequent selection in the admixed population. The introgressed proportion of the genome was found to be highly variable across the genome. Haplotypes introgressed from Holstein and Brown Swiss contained or overlapped known genes affecting milk production, as well as protein and fat content (CD14, ZNF215, BCL2L12, and THRSP for Holstein origin and ITPR2, BCAT1, LAP3, and MED28 for Brown Swiss origin). Genomic regions with high introgression signals also contained genes and enriched QTL associated with calving traits, body confirmation, feed efficiency, carcass, and fertility traits. These introgressed signals with relative identity-by-descent scores larger than the median showing Holstein or Brown Swiss introgression are mostly significantly correlated with the corresponding test statistics from signatures of selection analyses in modern Danish Red Dairy Cattle. Meanwhile, the putative significant introgressed signals have a significant dependency with the putative significant signals from signatures of selection analyses. Artificial selection has played an important role in the genomic footprints of introgression in the genome of modern Danish Red Dairy Cattle. Our study on a modern cattle breed contributes to an understanding of genomic consequences of selective introgression by demonstrating the extent to which adaptive effects contribute to shape the specific genomic consequences of introgression.
Collapse
|
23
|
Adeola AC, Oluwole OO, Oladele BM, Olorungbounmi TO, Boladuro B, Olaogun SC, Nneji LM, Sanke OJ, Dawuda PM, Omitogun OG, Frantz L, Murphy RW, Xie HB, Peng MS, Zhang YP. Analysis of the genetic variation in mitochondrial DNA, Y-chromosome sequences, and MC1R sheds light on the ancestry of Nigerian indigenous pigs. Genet Sel Evol 2017. [PMID: 28651519 PMCID: PMC5485568 DOI: 10.1186/s12711-017-0326-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved in the determination of coat color. We investigated the genetic diversity of Nigerian indigenous pigs (NIP) by simultaneously analyzing variation in mitochondrial DNA (mtDNA), Y-chromosome sequence and the melanocortin receptor 1 (MC1R) gene. Results Median-joining network analysis of mtDNA D-loop sequences from 201 NIP and previously characterized loci clustered NIP with populations from the West (Europe/North Africa) and East/Southeast Asia. Analysis of partial sequences of the Y-chromosome in 57 Nigerian boars clustered NIP into lineage HY1. Finally, analysis of MC1R in 90 NIP resulted in seven haplotypes, among which the European wild boar haplotype was carried by one individual and the European dominant black by most of the other individuals (93%). The five remaining unique haplotypes differed by a single synonymous substitution from European wild type, European dominant black and Asian dominant black haplotypes. Conclusions Our results demonstrate a European and East/Southeast Asian ancestry for NIP. Analyses of MC1R provide further evidence. Additional genetic analyses and archaeological studies may provide further insights into the history of African pig breeds. Our findings provide a valuable resource for future studies on whole-genome analyses of African pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0326-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Olufunke O Oluwole
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Bukola M Oladele
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | | | - Bamidele Boladuro
- Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria
| | - Sunday C Olaogun
- Department of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Lotanna M Nneji
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria
| | - Philip M Dawuda
- Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi, Nigeria
| | - Ofelia G Omitogun
- Department of Animal Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Laurent Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, University of Oxford, Oxford, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Hai-Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China. .,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
| |
Collapse
|
24
|
Groenen MAM. A decade of pig genome sequencing: a window on pig domestication and evolution. Genet Sel Evol 2016; 48:23. [PMID: 27025270 PMCID: PMC4812630 DOI: 10.1186/s12711-016-0204-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/16/2016] [Indexed: 12/02/2022] Open
Abstract
Insight into how genomes change and adapt due to selection addresses key questions in evolutionary biology and in domestication of animals and plants by humans. In that regard, the pig and its close relatives found in Africa and Eurasia represent an excellent group of species that enables studies of the effect of both natural and human-mediated selection on the genome. The recent completion of the draft genome sequence of a domestic pig and the development of next-generation sequencing technology during the past decade have created unprecedented possibilities to address these questions in great detail. In this paper, I review recent whole-genome sequencing studies in the pig and closely-related species that provide insight into the demography, admixture and selection of these species and, in particular, how domestication and subsequent selection of Sus scrofa have shaped the genomes of these animals.
Collapse
Affiliation(s)
- Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| |
Collapse
|