1
|
Li G, Liu Y, Feng X, Diao S, Zhong Z, Li B, Teng J, Zhang W, Zeng H, Cai X, Gao Y, Liu X, Yuan X, Li J, Zhang Z. Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations. Int J Mol Sci 2024; 25:5689. [PMID: 38891877 PMCID: PMC11171535 DOI: 10.3390/ijms25115689] [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: 04/17/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
The domestic pig (Sus scrofa) and its subfamilies have experienced long-term and extensive gene flow, particularly in Southeast Asia. Here, we analyzed 236 pigs, focusing on Yunnan indigenous, European commercial, East Asian, and Southeast Asian breeds, using the Pig Genomics Reference Panel (PGRP v1) of Pig Genotype-Tissue Expression (PigGTEx) to investigate gene flow and associated complex traits by integrating multiple database resources. In this study, we discovered evidence of admixtures from European pigs into the genome of Yunnan indigenous pigs. Additionally, we hypothesized that a potential conceptual gene flow route that may have contributed to the genetic composition of the Diannan small-ear pig is a gene exchange from the Vietnamese pig. Based on the most stringent gene introgression scan using the fd statistic, we identified three specific loci on chromosome 8, ranging from 51.65 to 52.45 Mb, which exhibited strong signatures of selection and harbored the NAF1, NPY1R, and NPY5R genes. These genes are associated with complex traits, such as fat mass, immunity, and litter weight, in pigs, as supported by multiple bio-functionalization databases. We utilized multiple databases to explore the potential dynamics of genetic exchange in Southeast Asian pig populations and elucidated specific gene functionalities.
Collapse
Affiliation(s)
- Guangzhen Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Yuqiang Liu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xueyan Feng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Shuqi Diao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Zhanming Zhong
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Bolang Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Jinyan Teng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Wenjing Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Haonan Zeng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xiaodian Cai
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Yahui Gao
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Xiaolong Yuan
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Jiaqi Li
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| | - Zhe Zhang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (G.L.); (Y.L.); (X.F.); (S.D.); (Z.Z.); (B.L.); (J.T.); (W.Z.); (H.Z.); (X.C.); (Y.G.); (X.Y.)
| |
Collapse
|
2
|
Zhang W, Jiang Y, Ni Z, Zhou M, Liu L, Li X, Su S, Wang C. Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study. Animals (Basel) 2024; 14:1419. [PMID: 38791637 PMCID: PMC11117326 DOI: 10.3390/ani14101419] [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: 04/07/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A total of 14,161 CNVs were detected in the WSPs, accounting for 0.72% of the porcine genome. The fixation index (Fst) was used to identify the selection signatures, and 195 CNVs with the top 1% of the Fst value were selected. Eighty genes were identified in the selected CNV regions. Functional GO and KEGG analyses revealed that the genes within these selected CNVs are associated with key traits such as reproduction (GAL3ST1 and SETD2), fatty acid composition (PRKG1, ACACA, ACSL3, UGT8), immune system (LYZ), ear size (WIF1), and feed efficiency (VIPR2). The findings of this study contribute novel insights into the genetic CNVs underlying WSP characteristics and provide essential information for the protection and utilization of WSP populations.
Collapse
Affiliation(s)
- Wei Zhang
- 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, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Yao Jiang
- National Animal Husbandry Service, Beijing 100125, China;
| | - Zelan Ni
- Anhui Provincial Livestock and Poultry Genetic Resources Conservation Center, Hefei 231283, China;
| | - Mei Zhou
- 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, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Linqing Liu
- 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, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Xiaoyu Li
- 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, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Shiguang Su
- 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, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| | - Chonglong Wang
- 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, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China; (W.Z.); (M.Z.); (L.L.); (X.L.)
| |
Collapse
|
3
|
Du H, Liu Z, Lu SY, Jiang L, Zhou L, Liu JF. Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed. BMC Genomics 2024; 25:331. [PMID: 38565992 PMCID: PMC10986048 DOI: 10.1186/s12864-024-10259-5] [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: 09/26/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND The pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown. RESULTS Through whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness. CONCLUSIONS Our research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.
Collapse
Affiliation(s)
- Heng Du
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Zhen Liu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Shi-Yu Lu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Li Jiang
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China
| | - Lei Zhou
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China.
| | - Jian-Feng Liu
- State Key Laboratory of Animal Biotech Breeding, Key Laboratory of Animal Genetics and Breeding, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University (West District), No.2 Yuanmingyuan West Road, 100193, Beijing, China.
| |
Collapse
|
4
|
Kuang R, Xu Z, Zhou H, Zhang Z, Peng H, Wang D, Xu X, Zhao S, Zhao Y, Zhu M. H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig. Anim Genet 2024; 55:217-229. [PMID: 38296601 DOI: 10.1111/age.13400] [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: 06/03/2023] [Revised: 12/25/2023] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
The establishment of high-quality pork breeds for improving meat quality in the pig industry is needed. The Chuxiang Black (CX) pig is a new breed developed from Chinese local pigs and Western lean pigs that has a high proportion of lean meat and excellent meat quality. However, the characteristics of cis-regulatory elements in CX pigs are still unknown. In this study, cis-regulatory elements of muscle and adipose tissues in CX pigs were investigated using ChIP-seq and RNA sequencing. Compared with the reported cis-regulatory elements of muscle and adipose tissues, 1768 and 1012 highly activated enhancers and 433 and 275 highly activated promoters in CX muscle and adipose tissues were identified, respectively. Motif analysis showed that transcription factors, such as MEF2A and MEF2C, were core regulators of highly activated enhancers and promoters in muscle. Similarly, the transcription factors JUNB and CUX1 were identified as essential for highly activated enhancers and promoters in CX adipose tissue. These results enrich the resources for the analysis of cis-regulatory elements in the pig genome and provide new basic data for further meat quality improvement through breeding in pigs.
Collapse
Affiliation(s)
- Renzhuo Kuang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Zhixiang Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Honghong Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Zhao Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Hao Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Daoyuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Yunxia Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| |
Collapse
|
5
|
He S, Wang Y, Luo Y, Xue M, Wu M, Tan H, Peng Y, Wang K, Fang M. Integrated analysis strategy of genome-wide functional gene mining reveals DKK2 gene underlying meat quality in Shaziling synthesized pigs. BMC Genomics 2024; 25:30. [PMID: 38178019 PMCID: PMC10765619 DOI: 10.1186/s12864-023-09925-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: 07/09/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Shaziling pig is a well-known indigenous breed in China who has superior meat quality traits. However, the genetic mechanism and genomic evidence underlying meat quality characteristics of Shaziling pigs are still unclear. To explore and investigate the germplasm characteristics of Shaziling pigs, we totally analyzed 67 individual's whole genome sequencing data for the first time (20 Shaziling pigs [S], 20 Dabasha pigs [DBS], 11 Yorkshire pigs [Y], 10 Berkshire pigs [BKX], 5 Basha pigs [BS] and 1 Warthog). RESULTS A total of 2,538,577 SNPs with high quality were detected and 9 candidate genes which was specifically selected in S and shared in S to DBS were precisely mined and screened using an integrated analysis strategy of identity-by-descent (IBD) and selective sweep. Of them, dickkopf WNT signaling pathway inhibitor 2 (DKK2), the antagonist of Wnt signaling pathway, was the most promising candidate gene which was not only identified an association of palmitic acid and palmitoleic acid quantitative trait locus in PigQTLdb, but also specifically selected in S compared to other 48 Chinese local pigs of 12 populations and 39 foreign pigs of 4 populations. Subsequently, a mutation at 12,726-bp of DKK2 intron 1 (g.114874954 A > C) was identified associated with intramuscular fat content using method of PCR-RFLP in 21 different pig populations. We observed DKK2 specifically expressed in adipose tissues. Overexpression of DKK2 decreased the content of triglyceride, fatty acid synthase and expression of relevant genes of adipogenic and Wnt signaling pathway, while interference of DKK2 got contrary effect during adipogenesis differentiation of porcine preadipocytes and 3T3-L1 cells. CONCLUSIONS Our findings provide an analysis strategy for mining functional genes of important economic traits and provide fundamental data and molecular evidence for improving pig meat quality traits and molecular breeding.
Collapse
Affiliation(s)
- Shuaihan He
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yubei Wang
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Yabiao Luo
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xue
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Maisheng Wu
- Xiangtan Bureau of Animal Husbandry and Veterinary Medicine and Aquatic Product, Xiangtan, 411102, China
| | - Hong Tan
- Xiangtan Bureau of Animal Husbandry and Veterinary Medicine and Aquatic Product, Xiangtan, 411102, China
| | - Yinglin Peng
- Hunan Institute of Animal & Veterinary Science, Changsha, 410131, China
| | - Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Meiying Fang
- State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
| |
Collapse
|
6
|
Ren Y, Wang F, Sun R, Zheng X, Liu Y, Lin Y, Hong L, Huang X, Chao Z. The Genetic Selection of HSPD1 and HSPE1 Reduce Inflammation of Liver and Spleen While Restraining the Growth and Development of Skeletal Muscle in Wuzhishan Pigs. Animals (Basel) 2024; 14:174. [PMID: 38200905 PMCID: PMC10777996 DOI: 10.3390/ani14010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Wuzhishan (WZS) pigs, which are minipigs native to Hainan Province in China, are characterized by strong resistance to extreme hot temperatures and humidity. The relationship between their immune response and growth still needs to be clarified. In this study, we used whole genome sequencing (WGS) to detect variations within 37 WZS pigs, 32 Large White (LW) pigs, and 22 Xiangxi black (XXB) pigs, and ~2.49 GB of SNPs were obtained. These data were combined with those of two other pig breeds, and it was found that most of the genes detected (354) were located within the distinct genetic regions between WZS pigs and LW pigs. The network that was constructed using these genes represented a center including 12 hub genes, five of which had structural variations (SVs) within their regulatory regions. Furthermore, RNA-seq and RT-qPCR data for 12 genes were primarily consistent in liver, spleen, and LDM tissues. Notably, the expression of HSPs (HSPD1 and HSPE1) was higher while that of most genes involved in the JAK3-STAT pathway were lower in liver tissue of WZS pigs, compared with LW pigs. This likely not only reduced inflammation-related immune response but also impaired their growth. Our findings demonstrated the role of HSPs in the connection between inflammation and growth rate, while also providing the fundamental genetic selection of the adaptability of WZS pigs.
Collapse
Affiliation(s)
- Yuwei Ren
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Feng Wang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Ruiping Sun
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Xinli Zheng
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Yuanyuan Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yanning Lin
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Lingling Hong
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Xiaoxian Huang
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| | - Zhe Chao
- Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China; (Y.R.)
| |
Collapse
|
7
|
Wang Y, Ma J, Wang J, Zhang L, Hu J, Ma M, Xu L, Chen Y, Zhu B, Wang Z, Gao H, Li J, Gao X. Genetic Origin and Introgression Pattern of Pingliang Red Cattle Revealed Using Genome-Wide SNP Analyses. Genes (Basel) 2023; 14:2198. [PMID: 38137021 PMCID: PMC10743310 DOI: 10.3390/genes14122198] [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: 11/16/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The Pingliang red cattle, an outstanding indigenous resource in China, possesses an exceptional breeding value attributed to its tender meat and superior marbling quality. Currently, research efforts have predominantly concentrated on exploring its maternal origin and conducting conventional phenotypic studies. However, there remains a lack of comprehensive understanding regarding its genetic basis. To address this gap, we conducted a thorough whole-genome analysis to investigate the population structure, phylogenetic relationships, and gene flows of this breed using genomic SNP chip data from 17 bovine breeds. The results demonstrate that Pingliang red cattle have evolved distinct genetic characteristics unique to this breed, clearly distinguishing it from other breeds. Based on the analysis of the population structure and phylogenetic tree, it can be classified as a hybrid lineage between Bos taurus and Bos indicus. Furthermore, Pingliang red cattle display a more prominent B. taurus pedigree in comparison with Jinnan, Qinchuan, Zaosheng, Nanyang, and Luxi cattle. Moreover, this study also revealed closer genetic proximity within the Chinese indigenous cattle breed, particularly Qinchuan cattle, which shares the longest identical by descent (IBD) fragment with Pingliang red cattle. Gene introgression analysis shows that Pingliang red cattle have undergone gene exchange with South Devon and Red Angus cattle from Europe. Admixture analysis revealed that the proportions of East Asian taurine and Chinese indicine in the ancestry of Pingliang red cattle are approximately 52.44% and 21.00%, respectively, while Eurasian taurine, European taurine, and Indian indicine account for approximately 17.55%, 7.27%, and 1.74%. Our findings unveil distinct genetic characteristics in Pingliang red cattle and attribute their origin to B. taurus and B. indicus ancestry, as well as contributions from Qinchuan cattle, South Devon, and Red Angus.
Collapse
Affiliation(s)
- Yuanqing Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Jun Ma
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Jing Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Junwei Hu
- Academy of Pingliang Red Cattle, 492 South Ring Road, Kongtong District, Pingliang 744000, China
| | - Minghao Ma
- Academy of Pingliang Red Cattle, 492 South Ring Road, Kongtong District, Pingliang 744000, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Zezhao Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Y.W.)
| |
Collapse
|
8
|
Liu C, Huang R, Su G, Hou L, Zhou W, Liu Q, Qiu Z, Zhao Q, Li P. Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs. BMC Genomics 2023; 24:733. [PMID: 38049711 PMCID: PMC10694980 DOI: 10.1186/s12864-023-09860-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: 10/05/2023] [Accepted: 11/29/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Eurasian pigs have undergone lineage admixture throughout history. It has been confirmed that the genes of indigenous pig breeds in China have been introduced into Western commercial pigs, providing genetic materials for breeding Western pigs. Pigs in Taihu Lake region (TL), such as the Meishan pig and Erhualian pig, serve as typical representatives of indigenous pig breeds in China due to their high reproductive performances. These pigs have also been imported into European countries in 1970 and 1980 s. They have played a positive role in improving the reproductive performances in European commercial pigs such as French Large White pigs (FLW). However, it is currently unclear if the lineage of TL pigs have been introgressed into the Danish Large White pigs (DLW), which are also known for their high reproductive performances in European pigs. To systematically identify genomic regions in which TL pigs have introgressed into DLW pigs and their physiological functions, we collected the re-sequencing data from 304 Eurasian pigs, to identify shared haplotypes between DLW and TL pigs. RESULTS The findings revealed the presence of introgressed genomic regions from TL pigs in the genome of DLW pigs indeed. The genes annotated within these regions were found to be mainly enriched in neurodevelopmental pathways. Furthermore, we found that the 115 kb region located in SSC16 exhibited highly shared haplotypes between TL and DLW pigs. The major haplotype of TL pigs in this region could significantly improve reproductive performances in various pig populations. Around this genomic region, NDUFS4 gene was highly expressed and showed differential expression in multiple reproductive tissues between extremely high and low farrowing Erhualian pigs. This suggested that NDUFS4 gene could be an important candidate causal gene responsible for affecting the reproductive performances of DLW pigs. CONCLUSIONS Our study has furthered our knowledge of the pattern of introgression from TL into DLW pigs and the potential effects on the fertility of DLW pigs.
Collapse
Affiliation(s)
- Chenxi Liu
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruihua Huang
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing, 210095, China
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, DK-8000, Denmark
| | - Liming Hou
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing, 210095, China
| | - Wuduo Zhou
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Liu
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing, 210095, China
| | - Zijian Qiu
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing, 210095, China
| | - Qingbo Zhao
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing, 210095, China.
| | - Pinghua Li
- Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)), Nanjing Agricultural University, Nanjing, 210095, China.
- Huaian Academy, Nanjing Agricultural University, Huaian, 223001, China.
| |
Collapse
|
9
|
Zhang Y, Lai J, Wang X, Li M, Zhang Y, Ji C, Chen Q, Lu S. Genome-wide single nucleotide polymorphism (SNP) data reveal potential candidate genes for litter traits in a Yorkshire pig population. Arch Anim Breed 2023; 66:357-368. [PMID: 38111388 PMCID: PMC10726026 DOI: 10.5194/aab-66-357-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/10/2023] [Indexed: 12/20/2023] Open
Abstract
The litter trait is one of the most important economic traits, and increasing litter size is of great economic value in the pig industry. However, the molecular mechanisms underlying pig litter traits remain elusive. To identify molecular markers and candidate genes for pig litter traits, a genome-wide association study (GWAS) and selection signature analysis were conducted in a Yorkshire pig population. A total of 518 producing sows were genotyped with Illumina Porcine SNP 50 BeadChip, and 1969 farrowing records for the total number born (TNB), the number born alive (NBA), piglets born dead (PBD), and litter weight born alive (LWB) were collected. Then, a GWAS was performed for the four litter traits using a repeatability model. Based on the estimated breeding values (EBVs) of TNB, 15 high- and 15 low-prolificacy individuals were selected from the 518 sows to implement selection signature analysis. Subsequently, the selection signatures affecting the litter traits of sows were detected by using two methods including the fixation index (FST) and θ π . Combining the results of the GWAS and selection signature analysis, 20 promising candidate genes (NKAIN2, IGF1R, KISS1R, TYRO3, SPINT1, ADGRF5, APC2, PTBP1, CLCN3, CBR4, HPF1, FAM174A, SCP2, CLIC1, ZFYVE9, SPATA33, KIF5C, EPC2, GABRA2, and GABRA4) were identified. These findings provide novel insights into the genetic basis of pig litter traits and will be helpful for improving the reproductive performances of sows in pig breeding.
Collapse
Affiliation(s)
- Yu Zhang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jinhua Lai
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Yanlin Zhang
- Yunnan Fuyuefa Livestock and Poultry Feeding Company Limited, Kunming, 650300, China
| | - Chunlv Ji
- Yunnan Fuyuefa Livestock and Poultry Feeding Company Limited, Kunming, 650300, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| |
Collapse
|
10
|
Wang C, Lei B, Liu Y. An Analysis of a Transposable Element Expression Atlas during 27 Developmental Stages in Porcine Skeletal Muscle: Unveiling Molecular Insights into Pork Production Traits. Animals (Basel) 2023; 13:3581. [PMID: 38003198 PMCID: PMC10668843 DOI: 10.3390/ani13223581] [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: 09/30/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
The development and growth of porcine skeletal muscle determine pork quality and yield. While genetic regulation of porcine skeletal muscle development has been extensively studied using various omics data, the role of transposable elements (TEs) in this context has been less explored. To bridge this gap, we constructed a comprehensive atlas of TE expression throughout the developmental stages of porcine skeletal muscle. This was achieved by integrating porcine TE genomic coordinates with whole-transcriptome RNA-Seq data from 27 developmental stages. We discovered that in pig skeletal muscle, active Tes are closely associated with active epigenomic marks, including low levels of DNA methylation, high levels of chromatin accessibility, and active histone modifications. Moreover, these TEs include 6074 self-expressed TEs that are significantly enriched in terms of muscle cell development and myofibril assembly. Using the TE expression data, we conducted a weighted gene co-expression network analysis (WGCNA) and identified a module that is significantly associated with muscle tissue development as well as genome-wide association studies (GWAS) of the signals of pig meat and carcass traits. Within this module, we constructed a TE-mediated gene regulatory network by adopting a unique multi-omics integration approach. This network highlighted several established candidate genes associated with muscle-relevant traits, including HES6, CHRNG, ACTC1, CHRND, MAMSTR, and PER2, as well as novel genes like ENSSSCG00000005518, ENSSSCG00000033601, and PIEZO2. These novel genes hold promise for regulating muscle-related traits in pigs. In summary, our research not only enhances the TE-centered dissection of the genetic basis underlying pork production traits, but also offers a general approach for constructing TE-mediated regulatory networks to study complex traits or diseases.
Collapse
Affiliation(s)
- Chao Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.W.); (B.L.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bowen Lei
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.W.); (B.L.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuwen Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (C.W.); (B.L.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan 528226, China
| |
Collapse
|
11
|
Zhang H, Liu Z, Wang J, Zeng T, Ai X, Wu K. An Integrative ATAC-Seq and RNA-Seq Analysis of the Endometrial Tissues of Meishan and Duroc Pigs. Int J Mol Sci 2023; 24:14812. [PMID: 37834260 PMCID: PMC10573446 DOI: 10.3390/ijms241914812] [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: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Meishan pigs are a well-known indigenous pig breed in China characterized by a high fertility. Notably, the number of endometrial grands is significantly higher in Meishan pigs than Duroc pigs. The characteristics of the endometrial tissue are related to litter size. Therefore, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-sequencing (RNA-seq) to analyze the mechanisms underlying the differences in fecundity between the breeds. We detected the key transcription factors, including Double homeobox (Dux), Ladybird-like homeobox gene 2 (LBX2), and LIM homeobox 8 (Lhx8), with potentially pivotal roles in the regulation of the genes related to endometrial development. We identified the differentially expressed genes between the breeds, including SOX17, ANXA4, DLX3, DMRT1, FLNB, IRF6, CBFA2T2, TFCP2L1, EFNA5, SLIT2, and CYFIP2, with roles in epithelial cell differentiation, fertility, and ovulation. Interestingly, ANXA4, CBFA2T2, and TFCP2L1, which were upregulated in the Meishan pigs in the RNA-seq analysis, were identified again by the integration of the ATAC-seq and RNA-seq data. Moreover, we identified genes in the cancer or immune pathways, FoxO signaling, Wnt signaling, and phospholipase D signaling pathways. These ATAC-seq and RNA-seq analyses revealed the accessible chromatin and potential mechanisms underlying the differences in the endometrial tissues between the two types of pigs.
Collapse
Affiliation(s)
| | | | | | | | | | - Keliang Wu
- National Engineering Laboratory for Animal Breeding, Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (H.Z.); (Z.L.); (J.W.); (T.Z.); (X.A.)
| |
Collapse
|
12
|
Feng W, Zhou L, Zhao P, Du H, Diao C, Zhang Y, Liu Z, Jin W, Yu J, Han J, Okoth E, Mrode R, Liu JF. Comparative Genomic Analysis of Warthog and Sus Scrofa Identifies Adaptive Genes Associated with African Swine Fever. BIOLOGY 2023; 12:1001. [PMID: 37508430 PMCID: PMC10376286 DOI: 10.3390/biology12071001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/01/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND As warthogs (Phacochoerus africanus) have innate immunity against African swine fever (ASF), it is critical to understand the evolutionary novelty of warthogs to explain their specific ASF resistance. METHODS Here, we present two completed new genomes of one warthog and one Kenyan domestic pig as fundamental genomic references to elucidate the genetic mechanisms of ASF tolerance. RESULTS Multiple genomic variations, including gene losses, independent contraction, and the expansion of specific gene families, likely molded the warthog genome to adapt to the environment. Importantly, the analysis of the presence and absence of genomic sequences revealed that the DNA sequence of the warthog genome had an absence of the gene lactate dehydrogenase B (LDHB) on chromosome 2 compared with the reference genome. The overexpression and siRNA of LDHB inhibited the replication of the African swine fever virus. Combined with large-scale sequencing data from 42 pigs worldwide, the contraction and expansion of tripartite motif-containing (TRIM) gene families revealed that TRIM family genes in the warthog genome are potentially responsible for its tolerance to ASF. CONCLUSION Our results will help improve the understanding of genetic resistance to ASF in pigs.
Collapse
Affiliation(s)
- Wen Feng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- Shenzhen Kingsino Technology Co., Ltd., Shenzhen 518107, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Pengju Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yu Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhen Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenjiao Jin
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jian Yu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100193, China
| | - Edward Okoth
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Raphael Mrode
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; Frontiers Science Center for Molecular Design Breeding (MOE), College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
13
|
Wang F, Zha Z, He Y, Li J, Zhong Z, Xiao Q, Tan Z. Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China. Animals (Basel) 2023; 13:1835. [PMID: 37889708 PMCID: PMC10252034 DOI: 10.3390/ani13111835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 09/29/2023] Open
Abstract
Tunchang pig is one population of Hainan pig in the Hainan Province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, FST, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (SELENOV, CBR4, TNNT1, TNNT3, VPS13A, PLD3, SRFBP1, and SSPN), immune regulation (CD48, FBL, PTPRH, GNA14, LOX, SLAMF6, CALCOCO1, IRGC, and ZNF667), growth and development (SYT5, PRX, PPP1R12C, and SMG9), reproduction (LGALS13 and EPG5), vision (SLC9A8 and KCNV2), energy metabolism (ATP5G2), cell migration (EPS8L1), and olfaction (GRK3). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.
Collapse
Affiliation(s)
| | | | | | | | | | - Qian Xiao
- School of Animal Science and Technology, Hainan University, Haikou 570228, China; (F.W.)
| | - Zhen Tan
- School of Animal Science and Technology, Hainan University, Haikou 570228, China; (F.W.)
| |
Collapse
|
14
|
Liu X, Zhang Y, Pu Y, Ma Y, Jiang L. Whole-genome identification of transposable elements reveals the equine repetitive element insertion polymorphism in Chinese horses. Anim Genet 2023; 54:144-154. [PMID: 36464985 DOI: 10.1111/age.13277] [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: 08/13/2022] [Revised: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) are diverse, abundant, and complicated in genomes. They not only can drive the genome evolution process but can also act as special resources for adaptation. However, little is known about the evolutionary processes that shaped horses. In this work, 126 horse assemblages involved in most horse breeds in China were used to investigate the patterns of TE variation for the first time. By using RepeatMasker and melt software, we found that the horse-specific short interspersed repetitive elements family, equine repetitive elements (ERE1), exhibited polymorphisms in horse genomes. Phylogenetic analysis based on these ERE1 loci (minor allele frequency ≥0.05) revealed three major horse groups, namely, those in northern China, southern China, and Qinghai-Tibetan, which mirrors the result determined by SNPs to some extent. The present ERE1 family emerged ~0.26 to 1.77 Mya ago, with an activity peak at ~0.49 Mya, which matches the early stage of the horse lineage and decreases after the divergence of Equus caballus and Equus ferus przewalskii. To detect the functional ERE1(s) associated with adaptation, locus-specific branch length, genome-wide association study, and absolute allele frequency difference analyses were conducted and resulted in two common protein-coding genes annotated by candidate ERE1s. They were clustered into the vascular smooth muscle contraction (p = 0.01, EDNRA) and apelin signalling pathways (p = 0.02, NRF1). Notably, ERE1 insertion into the EDNRA gene showed a higher association with adaptation among southern China horses and other horses in 15 populations and 451 individuals (p = 4.55 e-8). Our results provide a comprehensive understanding of TE variations to analyse the phylogenetic relationships and traits relevant to adaptive evolution in horses.
Collapse
Affiliation(s)
- Xuexue Liu
- National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Yanli Zhang
- National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yabin Pu
- National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yuehui Ma
- National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lin Jiang
- National Germplasm Centre of Domestic Animal Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| |
Collapse
|
15
|
Han Y, Tan T, Li Z, Ma Z, Lan G, Liang J, Li K, Bai L. Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs. Genes (Basel) 2023; 14:genes14030655. [PMID: 36980926 PMCID: PMC10048629 DOI: 10.3390/genes14030655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters’ annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future.
Collapse
Affiliation(s)
- Yachun Han
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Tao Tan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zixin Li
- College of Animal Science & Technology, Guangxi University, Nanning 530003, China
| | - Zheng Ma
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ganqiu Lan
- College of Animal Science & Technology, Guangxi University, Nanning 530003, China
| | - Jing Liang
- College of Animal Science & Technology, Guangxi University, Nanning 530003, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Lijing Bai
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Correspondence: ; Tel./Fax: +86-0755-2325-0160
| |
Collapse
|
16
|
Peng Y, Derks MFL, Groenen MAM, Zhao Y, Bosse M. Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds. Front Genet 2023; 13:1070783. [PMID: 36712875 PMCID: PMC9880450 DOI: 10.3389/fgene.2022.1070783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68-98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.
Collapse
Affiliation(s)
- Yebo Peng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Martijn FL Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands,Topigs Norsvin Research Center, Beuningen, Netherlands
| | - Martien AM Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands,Amsterdam Insitute of Life and Environment (A-Life), VU University Amsterdam, Amsterdam, Netherlands,*Correspondence: Mirte Bosse,
| |
Collapse
|
17
|
Zhang W, Liu L, Zhou M, Su S, Dong L, Meng X, Li X, Wang C. Assessing Population Structure and Signatures of Selection in Wanbei Pigs Using Whole Genome Resequencing Data. Animals (Basel) 2022; 13:ani13010013. [PMID: 36611624 PMCID: PMC9817800 DOI: 10.3390/ani13010013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/10/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Wanbei pig (WBP) is one of the indigenous pig resources in China and has many germplasm characteristics. However, research on its genome is lacking. To assess the genomic variation, population structure, and selection signatures, we resequenced 18 WBP for the first time and performed a comprehensive analysis with resequenced data of 10 Asian wild boars. In total, 590.03 Gb of data and approximately 41 million variants were obtained. Polymorphism level (θπ) ratio and genetic differentiation (fixation index)-based cross approaches were applied, and 539 regions, which harbored 176 genes, were selected. Functional analysis of the selected genes revealed that they were associated with lipid metabolism (SCP2, APOA1, APOA4, APOC3, CD36, BCL6, ADCY8), backfat thickness (PLAG1, CACNA2D1), muscle (MYOG), and reproduction (CABS1). Overall, our results provide a valuable resource for characterizing the uniqueness of WBP and a basis for future breeding.
Collapse
Affiliation(s)
- Wei Zhang
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Linqing Liu
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Mei Zhou
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shiguang Su
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Lin Dong
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xinxin Meng
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xueting Li
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Chonglong Wang
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Correspondence:
| |
Collapse
|
18
|
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.
Collapse
|
19
|
Liu Z, Xu R, Zhang H, Wang D, Wang J, Wu K. A unique 15-bp InDel in the first intron of BMPR1B regulates its expression in Taihu pigs. BMC Genomics 2022; 23:799. [PMID: 36463109 PMCID: PMC9719134 DOI: 10.1186/s12864-022-08988-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/03/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND BMPR1B (Bone morphogenetic protein receptor type-1B) is a receptor in the bone morphogenetic protein (BMP) family and has been identified as a candidate gene for reproductive traits in pigs. Our previous study in Taihu pigs found a specific estrogen response element (ERE) in the first intron of the BMPR1B gene that is associated with the number born alive trait. However, little is known about the mechanism by which the ERE regulates the expression of BMPR1B in the endometrium. RESULTS Here, a 15-bp InDel (insertion/deletion) (AGCCAGAAAGGAGGA) was identified as a unique variation in Taihu pigs, and was shown to be responsible for the binding of the type I receptor of estrogen (ESR1) to the ERE using dual-luciferase assays. Four BMPR1B transcripts (T1, T2, T3, and T4) were identified by 5' RACE in endometrial tissue. Expression of T3 and T4 in the endometrium of Meishan pigs was significantly higher than in Duroc pigs during pregnancy. Luciferase assays showed that three distinct BMPR1B promoters may drive expression of T1, T3, and T4. Interestingly, ERE-mediated enhancement of T4 promoter activity significantly increased expression of Transcript T4 in the endometrium of Taihu pigs (P < 0.05). In contrast, the ERE inhibited activity of the T3 promoter and decreased expression of the T3 transcript in the Duroc background (P < 0.05). In summary, we identified a 15-bp InDel in the Taihu ERE that can be used as a molecular marker for the number born alive trait, characterized the 5' untranslated regions (UTRs) of BMPR1B transcripts in the endometrium, and determined how the transcripts are processed by alternative splicing events. CONCLUSIONS Our results provide a foundation for understanding the transcriptional regulation of BMPR1B and its contributions to the unique breeding prolificacy characteristics of Taihu pigs.
Collapse
Affiliation(s)
- Zhexi Liu
- grid.22935.3f0000 0004 0530 8290Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China ,grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ran Xu
- grid.22935.3f0000 0004 0530 8290Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China ,grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Han Zhang
- grid.22935.3f0000 0004 0530 8290Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China ,grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Depeng Wang
- grid.22935.3f0000 0004 0530 8290Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China ,grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ji Wang
- grid.22935.3f0000 0004 0530 8290Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China ,grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Keliang Wu
- grid.22935.3f0000 0004 0530 8290Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China ,grid.22935.3f0000 0004 0530 8290Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
20
|
Zhang Y, Zhang J, Wang C, Qin X, Zhang Y, Liu J, Pan Z. Effective Quality Breeding Directions-Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds. BIOLOGY 2022; 11:1631. [PMID: 36358332 PMCID: PMC9687233 DOI: 10.3390/biology11111631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 10/24/2023]
Abstract
The transcriptional initiation of genes is closely bound to the functions of cis-regulatory elements, including promoters, typical enhancers (TEs), and recently-identified super-enhancers (SEs). In this study, we identified these cis-regulatory elements in the livers of two Chinese (Meishan and Enshi Black) and two Western (Duroc and Large White) pig breeds using ChIP-seq data, then explored their similarities and differences. In addition, we analyzed the conservation of SEs among different tissues and species (pig, human, and mouse). We observed that SEs were more significantly enriched by transcriptional initiation regions, TF binding sites, and SNPs than other cis-elements. Western breeds included fewer SEs in number, while more growth-related QTLs were associated with these SEs. Additionally, the SEs were highly tissue-specific, and were conserved in the liver among humans, pigs, and mice. We concluded that intense selection could concentrate functional SEs; thus, SEs could be applied as effective detection regions in genomic selection breeding.
Collapse
Affiliation(s)
- Yi Zhang
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinbi Zhang
- College of Animal Science and Technology, Jinling Institute of Technology, Nanjing 211169, China
| | - Caixia Wang
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinxin Qin
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuge Zhang
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingge Liu
- College of Animal Science and Technology, Jinling Institute of Technology, Nanjing 211169, China
| | - Zengxiang Pan
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
21
|
Population Structure and Selection Signatures Underlying Domestication Inferred from Genome-Wide Copy Number Variations in Chinese Indigenous Pigs. Genes (Basel) 2022; 13:genes13112026. [PMID: 36360263 PMCID: PMC9690591 DOI: 10.3390/genes13112026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Single nucleotide polymorphism was widely used to perform genetic and evolution research in pigs. However, little is known about the effect of copy number variation (CNV) on characteristics in pigs. This study performed a genome-wide comparison of CNVs between Wannan black pigs (WBP) and Asian wild boars (AWB), using whole genome resequencing data. By using Manta, we detected in total 28,720 CNVs that covered approximately 1.98% of the pig genome length. We identified 288 selected CNVs (top 1%) by performing Fst statistics. Functional enrichment analyses for genes located in selected CNVs were found to be muscle related (NDN, TMOD4, SFRP1, and SMYD3), reproduction related (GJA1, CYP26B1, WNT5A, SRD5A2, PTPN11, SPEF2, and CCNB1), residual feed intake (RFI) related (MAP3K5), and ear size related (WIF1). This study provides essential information on selected CNVs in Wannan black pigs for further research on the genetic basis of the complex phenotypic and provides essential information for direction in the protection and utilization of Wannan black pig.
Collapse
|
22
|
Zheng S, Xu P, Wu Z, Zhang H, Li D, Liu S, Liu B, Ren J, Chen H, Huang M. Genetic structure and domestication footprints of the tusk, coat color, and ear morphology in East Chinese pigs. J Genet Genomics 2022; 49:1053-1063. [PMID: 35413463 DOI: 10.1016/j.jgg.2022.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/29/2022]
Abstract
The domestication and artificial selection of wild boars have led to dramatic morphological and behavioral changes, especially in East Chinese (ECN) pigs. Here, we provide insights into the population structure and current genetic diversity of representative ECN pig breeds. We identify a 500-kb region containing six tooth development-relevant genes with almost completely different haplotypes between ECN pigs and Chinese wild boars or European domestic pigs. Notably, the c.195A>G missense mutation in exon 2 of AMBN may cause alterations in its protein structure associated with tusk degradation in ECN pigs. In addition, ESR1 may play an important role in the reproductive performance of ECN pigs. A major haplotype of the large lop ear-related MSRB3 gene and eight alleles in the deafness-related GRM7 gene may affect ear morphology and hearing in ECN pigs. Interestingly, we find that the two-end black (TEB) coat color in Jinhua pigs is most likely caused by EDNRB with genetic mechanisms different from other Chinese TEB pigs. This study identifies key loci that may be artificially selected in Chinese native pigs related to the tusk, coat color, and ear morphology, thus providing new insights into the genetic mechanisms of domesticated pigs.
Collapse
Affiliation(s)
- Sumei Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Pan Xu
- School of Animal Science and Technology, Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu 225300, China
| | - Zhongping Wu
- Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong 510225, China
| | - Hui Zhang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Desen Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Shaojuan Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Bingbing Liu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Jun Ren
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Hao Chen
- College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang, Jiangxi 330013, China.
| | - Min Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, Guangdong 510642, China.
| |
Collapse
|
23
|
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.
Collapse
|
24
|
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.
Collapse
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.
| |
Collapse
|
25
|
Chen Z, Zhang Z, Wang Z, Zhang Z, Wang Q, Pan Y. Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: a case study with litter traits in pigs. Comput Struct Biotechnol J 2022; 20:4060-4071. [PMID: 35983229 PMCID: PMC9364102 DOI: 10.1016/j.csbj.2022.07.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/23/2022] Open
Abstract
Runs of heterozygosity (ROHet) and homozygosity (ROH) harbor useful information related to traits of interest. There is a lack of investigating the effect of ROHet and ROH on reproductive success and the loss of reproduction in mammals. Here, we detected and characterized the ROHet and ROH patterns in the genomes of Chinese indigenous pigs (i.e., Jinhua, Chun’an, Longyou Black, and Shengxian Spotted pigs), revealing the similar genetic characteristics of indigenous pigs. Later, we highlighted the underlying litter traits-related ROHet and ROH using association analysis with linear model in these four indigenous pig breeds. To pinpoint the promising candidate genes associated with litter traits, we further in-depth explore the selection patterns of other five pig breeds (i.e., Erhualian, Meishan, Minzhu, Rongchang, and Diqing pigs) with different levels of reproduction performance at the underlying litter traits-related ROHet and ROH using FST and genetic diversity ratio. Then, we identified a set of known and novel candidate genes associated with reproductive performance in pigs. For the novel candidate genes (i.e., CCDC91, SASH1, SAMD5, MACF1, MFSD2A, EPC2, and MBD5), we obtained public available datasets and performed multi-omics analyses integrating transcriptome-wide association studies and comparative single-cell RNA-seq analyses to uncover the roles of them in mammalian reproductive performance. The genes have not been widely reported to be fertility-related genes and can be complementally considered as prior biological information to modify genomic selections models that benefits pig genetic improvement of litter traits. Besides, our findings provide new insights into the function of ROHet and ROH in mammals.
Collapse
|
26
|
Yang W, Liu Z, Zhao Q, Du H, Yu J, Wang H, Liu X, Liu H, Jing X, Yang H, Shi G, Zhou L, Liu J. Population Genetic Structure and Selection Signature Analysis of Beijing Black Pig. Front Genet 2022; 13:860669. [PMID: 35401688 PMCID: PMC8987279 DOI: 10.3389/fgene.2022.860669] [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: 01/23/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022] Open
Abstract
Beijing Black pig is an excellent cultivated black pig breed in China, with desirable body shape, tender meat quality and robust disease resistance. To explore the level of admixture and selection signatures of Beijing Black pigs, a total number of 90 individuals covering nine pig breeds were used in our study, including Beijing Black pig, Large White, Landrace, Duroc, Lantang pig, Luchuan pig, Mashen pig, Huainan pig and Min pig. These animals were resequenced with 18.19 folds mapped read depth on average. Generally, we found that Beijing Black pig was genetically closer to commercial pig breeds by population genetic structure and genetic diversity analysis, and was also affected by Chinese domestic breeds Huainan pig and Min pig. These results are consistent with the cross-breeding history of Beijing Black pig. Selection signal detections were performed on three pig breeds, Beijing Black pig, Duroc and Large White, using three complementary methods (FST, θπ, and XP-EHH). In total, 1,167 significant selected regions and 392 candidate genes were identified. Functional annotations were enriched to pathways related to immune processes and meat and lipid metabolism. Finally, potential candidate genes, influencing meat quality (GPHA2, EHD1, HNF1A, C12orf43, GLTP, TRPV4, MVK, and MMAB), reproduction (PPP2R5B and MAP9), and disease resistance (OASL, ANKRD13A, and GIT2), were further detected by gene annotation analysis. Our results advanced the understanding of the genetic mechanism behind artificial selection of Beijing Black pigs, and provided theoretical basis for the subsequent breeding and genetic research of this breed.
Collapse
Affiliation(s)
- Wenjing Yang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhen Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qiqi Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Heng Du
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongwei Wang
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Xiance Liu
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Hai Liu
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Xitao Jing
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Hongping Yang
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Guohua Shi
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Lei Zhou
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Lei Zhou, ; Jianfeng Liu,
| | - Jianfeng Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Lei Zhou, ; Jianfeng Liu,
| |
Collapse
|
27
|
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 pigs 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] [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 Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Chunyuan Zhang
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Yebo Peng
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Xinyu Cai
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Mirte Bosse
- Animal Breeding and Genomics Centre Wageningen University Wageningen 6708 WD The Netherlands
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| |
Collapse
|
28
|
Ma J, Gao X, Li J, Gao H, Wang Z, Zhang L, Xu L, Gao H, Li H, Wang Y, Zhu B, Cai W, Wang C, Chen Y. Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array. Animals (Basel) 2021; 11:ani11123469. [PMID: 34944246 PMCID: PMC8698132 DOI: 10.3390/ani11123469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.
Collapse
Affiliation(s)
- Jun Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Zezhao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Han Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Hongwei Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Yahui Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Bo Zhu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Congyong Wang
- Beijing Lianyu Beef Cattle Breeding Technology Limited Company, Beijing 100193, China;
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
- Correspondence:
| |
Collapse
|
29
|
Xiaoli L, Fengbin H, Shihui H, Xi N, Sheng L, Zhou W, Xueqin R, Jiafu W. Detection of genomic structure variants associated with wrinkled skin in Xiang pig by next generation sequencing. Aging (Albany NY) 2021; 13:24710-24739. [PMID: 34837693 PMCID: PMC8660620 DOI: 10.18632/aging.203711] [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: 12/30/2020] [Accepted: 08/02/2021] [Indexed: 11/25/2022]
Abstract
Wrinkling is prominent manifestation of aging skin. A mutant phenotype characterized by systemic wrinkles and thickened skin was discovered in Xiang pig populations with incidence about 1-3%. The feature in histological structure was epidermal hyperplasia and thickening, collagen fibers disorder. To uncover genetic mechanisms for the mutant phenotype of Xiang pigs with systemic wrinkle (WXP), a genome-wide of structural variations (SVs) in WXP was described by next generation resequencing, taking Xiang pigs (XP) and European pigs (EUP) as compares. Total of 32,308 SVs were detected from three pig groups and 965 SVs were identified specifically from WXP, involving 481 protein-coding genes. These genes were mainly enriched in nuclear structure, ECM components and immunomodulatory pathways. According to gene function and enrichment analysis, we found that 65 candidate SVs in 59 protein genes were probably related with the systemic wrinkle of WXP. Of these, several genes are reported to be associate with aging, such as EIF4G2, NOLC1, XYLT1, FUT8, MDM2 and so on. The insertion/deletion and duplication variations of SVs in these genes resulted in the loss of stop-codon or frameshift mutation, and aberrant alternative splicing of transcripts. These genes are involved in cell lamin filament, intermediate filament cytoskeleton, supramolecular complex, cell differentiation and regulation of macromolecule metabolic process etc. Our study suggested that the loss of function or aberrant expression of these genes lead to structural disorder of nuclear and the extracellular matrix (ECM) in skin cells, which probably was the genetic mechanisms for the mutant phenotype of systemic skin wrinkle of Xiang pig.
Collapse
Affiliation(s)
- Liu Xiaoli
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Hu Fengbin
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Huang Shihui
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Niu Xi
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Li Sheng
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Wang Zhou
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Ran Xueqin
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Wang Jiafu
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| |
Collapse
|
30
|
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: 15] [Impact Index Per Article: 5.0] [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
|
31
|
A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome. Nat Commun 2021; 12:2217. [PMID: 33850120 PMCID: PMC8044108 DOI: 10.1038/s41467-021-22448-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Although major advances in genomics have initiated an exciting new era of research, a lack of information regarding cis-regulatory elements has limited the genetic improvement or manipulation of pigs as a meat source and biomedical model. Here, we systematically characterize cis-regulatory elements and their functions in 12 diverse tissues from four pig breeds by adopting similar strategies as the ENCODE and Roadmap Epigenomics projects, which include RNA-seq, ATAC-seq, and ChIP-seq. In total, we generate 199 datasets and identify more than 220,000 cis-regulatory elements in the pig genome. Surprisingly, we find higher conservation of cis-regulatory elements between human and pig genomes than those between human and mouse genomes. Furthermore, the differences of topologically associating domains between the pig and human genomes are associated with morphological evolution of the head and face. Beyond generating a major new benchmark resource for pig epigenetics, our study provides basic comparative epigenetic data relevant to using pigs as models in human biomedical research.
Collapse
|
32
|
Arora D, Srikanth K, Lee J, Lee D, Park N, Wy S, Kim H, Park JE, Chai HH, Lim D, Cho IC, Kim J, Park W. Integration of multi-omics approaches for functional characterization of muscle related selective sweep genes in Nanchukmacdon. Sci Rep 2021; 11:7219. [PMID: 33785872 PMCID: PMC8009959 DOI: 10.1038/s41598-021-86683-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/12/2021] [Indexed: 02/01/2023] Open
Abstract
Pig as a food source serves daily dietary demand to a wide population around the world. Preference of meat depends on various factors with muscle play the central role. In this regards, selective breeding abled us to develop "Nanchukmacdon" a pig breeds with an enhanced variety of meat and high fertility rate. To identify genomic regions under selection we performed whole-genome resequencing, transcriptome, and whole-genome bisulfite sequencing from Nanchukmacdon muscles samples and used published data for three other breeds such as Landrace, Duroc, Jeju native pig and analyzed the functional characterization of candidate genes. In this study, we present a comprehensive approach to identify candidate genes by using multi-omics approaches. We performed two different methods XP-EHH, XP-CLR to identify traces of artificial selection for traits of economic importance. Moreover, RNAseq analysis was done to identify differentially expressed genes in the crossed breed population. Several genes (UGT8, ZGRF1, NDUFA10, EBF3, ELN, UBE2L6, NCALD, MELK, SERP2, GDPD5, and FHL2) were identified as selective sweep and differentially expressed in muscles related pathways. Furthermore, nucleotide diversity analysis revealed low genetic diversity in Nanchukmacdon for identified genes in comparison to related breeds and whole-genome bisulfite sequencing data shows the critical role of DNA methylation pattern in identified genes that leads to enhanced variety of meat. This work demonstrates a way to identify the molecular signature and lays a foundation for future genomic enabled pig breeding.
Collapse
Affiliation(s)
- Devender Arora
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Krishnamoorthy Srikanth
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea ,grid.5386.8000000041936877XDepartment of Animal Science, Cornell University, Ithaca, NY 14853 USA
| | - Jongin Lee
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Daehwan Lee
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Nayoung Park
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Suyeon Wy
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Hyeonji Kim
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Jong-Eun Park
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Han-Ha Chai
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - Dajeong Lim
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| | - In-Cheol Cho
- grid.484502.f0000 0004 5935 1171Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju, 63242 Korea
| | - Jaebum Kim
- grid.258676.80000 0004 0532 8339Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029 Republic of Korea
| | - Woncheoul Park
- grid.484502.f0000 0004 5935 1171Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365 Republic of Korea
| |
Collapse
|
33
|
Zhao QB, Oyelami FO, Qadri QR, Sun H, Xu Z, Wang QS, Pan YC. Identifying the unique characteristics of the Chinese indigenous pig breeds in the Yangtze River Delta region for precise conservation. BMC Genomics 2021; 22:151. [PMID: 33653278 PMCID: PMC7927379 DOI: 10.1186/s12864-021-07476-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 02/24/2021] [Indexed: 02/08/2023] Open
Abstract
Background China is the country with the most abundant swine genetic resources in the world. Through thousands of years of domestication and natural selection, most of pigs in China have developed unique genetic characteristics. Finding the unique genetic characteristics and modules of each breed is an essential part of their precise conservation. Results In this study, we used the partial least squares method to identify the significant specific SNPs of 19 local Chinese pig breeds and 5 Western pig breeds. A total of 37,514 significant specific SNPs (p < 0.01) were obtained from these breeds, and the Chinese local pig breed with the most significant SNPs was Hongdenglong (HD), followed by Jiaxing black (JX), Huaibei (HB), Bihu (BH), small Meishan (SMS), Shengxian Hua (SH), Jiangquhai (JQ), Mi (MI), Chunan (CA), Chalu (CL), Jinhualiangtouwu (JHL), Fengjing (FJ), middle Meishan (MMS), Shanzhu (SZ), Pudong white (PD), Dongchuan (DC), Erhualian (EH), Shawutou (SW) and Lanxi Hua (LX) pig. Furthermore, we identified the breeds with the most significant genes, GO terms, pathways, and networks using KOBAS and IPA and then ranked them separately. The results showed that the breeds with the highest number of interaction networks were Hongdenglong (12) and Huaibei (12) pigs. In contrast, the breeds with the lowest interaction networks were Shawutou (4) and Lanxi Hua pigs (3), indicating that Hongdenglong and Huaibei pigs might have the most significant genetic modules in their genome, whereas Shawutou and Lanxi Hua pigs may have the least unique characteristics. To some degree, the identified specific pathways and networks are related to the number of genes and SNPs linked to the specific breeds, but they do not appear to be the same. Most importantly, more significant modules were found to be related to the development and function of the digestive system, regulation of diseases, and metabolism of amino acids in the local Chinese pig breeds, whereas more significant modules were found to be related to the growth rate in the Western pig breeds. Conclusion Our results show that each breed has some relatively unique structural modules and functional characteristics. These modules allow us to better understand the genetic differences among local Chinese and Western pig breeds and therefore implement precise conservation methods. This study could provide a basis for formulating more effective strategies for managing and protecting these genetic resources in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07476-7.
Collapse
Affiliation(s)
- Qing-Bo Zhao
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Favour Oluwapelumi Oyelami
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Qamar Raza Qadri
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Hao Sun
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Zhong Xu
- School of Agriculture and Biology, Department of Animal Science, Shanghai Jiao Tong University, Shanghai, 200240, P.R. China
| | - Qi-Shan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, 310030, P.R. China.
| | - Yu-Chun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, Hangzhou, 310030, P.R. China.
| |
Collapse
|
34
|
Du H, Zheng X, Zhao Q, Hu Z, Wang H, Zhou L, Liu JF. Analysis of Structural Variants Reveal Novel Selective Regions in the Genome of Meishan Pigs by Whole Genome Sequencing. Front Genet 2021; 12:550676. [PMID: 33613628 PMCID: PMC7890942 DOI: 10.3389/fgene.2021.550676] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 01/15/2021] [Indexed: 12/17/2022] Open
Abstract
Structural variants (SVs) represent essential forms of genetic variation, and they are associated with various phenotypic traits in a wide range of important livestock species. However, the distribution of SVs in the pig genome has not been fully characterized, and the function of SVs in the economic traits of pig has rarely been studied, especially for most domestic pig breeds. Meishan pig is one of the most famous Chinese domestic pig breeds, with excellent reproductive performance. Here, to explore the genome characters of Meishan pig, we construct an SV map of porcine using whole-genome sequencing data and report 33,698 SVs in 305 individuals of 55 globally distributed pig breeds. We perform selective signature analysis using these SVs, and a number of candidate variants are successfully identified. Especially for the Meishan pig, 64 novel significant selection regions are detected in its genome. A 140-bp deletion in the Indoleamine 2,3-Dioxygenase 2 (IDO2) gene, is shown to be associated with reproduction traits in Meishan pig. In addition, we detect two duplications only existing in Meishan pig. Moreover, the two duplications are separately located in cytochrome P450 family 2 subfamily J member 2 (CYP2J2) gene and phospholipase A2 group IVA (PLA2G4A) gene, which are related to the reproduction trait. Our study provides new insights into the role of selection in SVs' evolution and how SVs contribute to phenotypic variation in pigs.
Collapse
Affiliation(s)
- Heng Du
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qiqi Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengzheng Hu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haifei Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
35
|
Zhang S, Zhang K, Peng X, Zhan H, Lu J, Xie S, Zhao S, Li X, Ma Y. Selective sweep analysis reveals extensive parallel selection traits between large white and Duroc pigs. Evol Appl 2020; 13:2807-2820. [PMID: 33294024 PMCID: PMC7691457 DOI: 10.1111/eva.13085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
In the process of pig genetic improvement, different commercial breeds have been bred for the same purpose, improving meat production. Most of the economic traits, such as growth and fertility, have been selected similarly despite the discrepant selection pressure, which is known as parallel selection. Here, 28 whole-genome sequencing data of Danish large white pigs with an approximately 25-fold depth each were generated, resulting in about 12 million high-quality SNPs for each individual. Combined with the sequencing data of 27 Duroc and 23 European wild boars, we investigated the parallel selection of Danish large white and Duroc pigs using two complementary methods, Fst and iHS. In total, 67 candidate regions were identified as the signatures of parallel selection. The genes in candidate regions of parallel selection were mainly associated with sensory perception, growth rate, and body size. Further functional annotation suggested that the striking consistency of the terms may be caused by the polygenetic basis of quantitative traits, and revealing the complex genetic basis of parallel selection. Besides, some unique terms were enriched in population-specific selection regions, such as the limb development-related terms enriched in Duroc-specific selection regions, suggesting unique selections of breed-specific selected traits. These results will help us better understand the parallel selection process of different breeds. Moreover, we identified several potential causal SNPs that may contribute to the pig genetic breeding process.
Collapse
Affiliation(s)
- Saixian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Kaili Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Xia Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Huiwen Zhan
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Jiahui Lu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of AgricultureHuazhong Agricultural UniversityWuhanChina
| |
Collapse
|
36
|
Genome-Wide Detection of Selection Signatures in Duroc Revealed Candidate Genes Relating to Growth and Meat Quality. G3-GENES GENOMES GENETICS 2020; 10:3765-3773. [PMID: 32859686 PMCID: PMC7534417 DOI: 10.1534/g3.120.401628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
With the development of high-throughput genotyping techniques, selection signatures in the genome of domestic pigs have been extensively interrogated in the last decade. The Duroc, a major commercial pig breed famous for its fast growth rate and high lean ratio, has not been extensively studied focusing on footprints of intensively artificial selection in their genomes by a lot of re-sequencing data. The goal of this study was to investigate genomic regions under artificial selection and their contribution to the unique phenotypic traits of the Duroc using whole-genome resequencing data from 97 pigs. Three complementary methods (di, CLR, and iHH12) were implemented for selection signature detection. In Total, 464 significant candidate regions were identified, which covered 46.4 Mb of the pig genome. Within the identified regions, 709 genes were annotated, including 600 candidate protein-coding genes (486 functionally annotated genes) and 109 lncRNA genes. Genes undergoing selective pressure were significantly enriched in the insulin resistance signaling pathway, which may partly explain the difference between the Duroc and other breeds in terms of growth rate. The selection signatures identified in the Duroc population demonstrated positive pressures on a set of important genes with potential functions that are involved in many biological processes. The results provide new insights into the genetic mechanisms of fast growth rate and high lean mass, and further facilitate follow-up studies on functional genes that contribute to the Duroc's excellent phenotypic traits.
Collapse
|
37
|
Zhang W, Yang M, Zhou M, Wang Y, Wu X, Zhang X, Ding Y, Zhao G, Yin Z, Wang C. Identification of Signatures of Selection by Whole-Genome Resequencing of a Chinese Native Pig. Front Genet 2020; 11:566255. [PMID: 33093844 PMCID: PMC7527633 DOI: 10.3389/fgene.2020.566255] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/20/2020] [Indexed: 12/03/2022] Open
Abstract
Identification of genomic signatures of selection that help reveal genetic mechanisms underlying traits in domesticated pigs is of importance. Anqing six-end-white pig (ASP), a representative of the native breeds in China, has many distinguishing phenotypic characteristics. To identify the genomic signatures of selection of the ASP, whole-genome sequencing of 20 ASPs produced 469.01 Gb of sequence data and more than 26 million single-nucleotide polymorphisms. Combining these data with the available whole genomes of 13 Chinese wild boars, 157 selected regions harboring 48 protein-coding genes were identified by applying the polymorphism levels (θπ) and genetic differentiation (FST) based cross approaches. The genes found to be positively selected in ASP are involved in crucial biological processes such as coat color (MC1R), salivary secretion (STATH), reproduction (SPIRE2, OSBP2, LIMK2, FANCA, and CABS1), olfactory transduction (OR5K4), and growth (NPY1R, NPY5R, and SELENOM). Our research increased the knowledge of ASP phenotype-related genes and help to improve our understanding of the underlying biological mechanisms and provide valuable genetic resources that enable effective use of pigs in agricultural production.
Collapse
Affiliation(s)
- 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, China
| | - Min Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 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, China
| | - Yuanlang Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xudong Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiaodong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yueyun Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Guiying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 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, China
| |
Collapse
|
38
|
Li D, Sun G, Zhang M, Cao Y, Zhang C, Fu Y, Li F, Li G, Jiang R, Han R, Li Z, Wang Y, Tian Y, Liu X, Li W, Kang X. Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken. BMC Genomics 2020; 21:511. [PMID: 32703156 PMCID: PMC7376702 DOI: 10.1186/s12864-020-06900-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
Background Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype. Results Principal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds. Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds. The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago. Fst analysis identified a selective sweep that contains genes related to melanogenesis. This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection. A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis. Conclusions These findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals.
Collapse
Affiliation(s)
- Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Meng Zhang
- The First Hospital, Jilin University, Changchun, 130062, Jilin, China
| | - Yanfang Cao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenxi Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yawei Fu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Fang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Yanbin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China. .,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China.
| |
Collapse
|
39
|
Identification of Ovarian Circular RNAs and Differential Expression Analysis between MeiShan and Large White Pigs. Animals (Basel) 2020; 10:ani10071114. [PMID: 32610571 PMCID: PMC7401585 DOI: 10.3390/ani10071114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 12/16/2022] Open
Abstract
MeiShan and Large White pigs differ in their female fecundity. However, the mechanisms behind the gene expression and regulation that cause these differences remain unclear. In this study, we profiled circRNAs and identified 5,879 circRNAs from the ovaries of MeiShan and Large White pigs. Eighty-five circRNAs were differentially expressed between the two pig breeds. Of these, 37 were up-regulated and 48 were down-regulated in MeiShan pigs. Gene ontology enrichment analysis suggested that the differentially expressed circRNA were involved in the hormone-mediated signaling pathway. We verified that circSCIN and its parent gene, scinderin (SCIN), were differentially expressed by reverse transcription and quantitative PCR (RT-qPCR). Luciferase assays demonstrated that circSCIN can target and sponge miR-133 and miR-148a/b. The identification of differentially expressed circRNAs (DECs) and their regulatory functions increased our understanding of the differences in reproductive efficiency between MeiShan and Large White pigs.
Collapse
|
40
|
Zhang Q, Huang R, Ma X, Jiang N, Zhou W, Gao C, Zhao M, Niu P, Zhang Z, Li Q, Zhou J, Li P. Association of Rs339939442 in the AHR Gene with Litter Size are Inconsistent among Chinese Indigenous Pigs and Western Commercial Pigs. Animals (Basel) 2019; 10:ani10010011. [PMID: 31861561 PMCID: PMC7023200 DOI: 10.3390/ani10010011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/08/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022] Open
Abstract
Eastern and Southern Chinese pigs have been imported to Western countries to improve economic traits including fertility in Western pig breeds by intensive selecting Chinese advantage genes. It was reported that the selected Asian-derived non-synonymous mutations including rs339939442 (G > T) in the aryl hydrocarbon receptor (AHR) gene could increase litter size in multiple European commercial lines. The objective of this study is to identify whether rs339939442 in the AHR gene is polymorphic and has an influence on the litter size in 10 pig populations including five Chinese indigenous breeds, one cultivated breed, one lean-type breed, two North American lean-type breeds, and one European lean-type breed. We found that rs339939442 had polymorphism in all 10 populations, whereas rs339939442 was associated with litter size only in French Yorkshire (FRA-Y) and Chinese cultivated Suhuai (SH) pigs containing approximately 75% British Yorkshire pigs ancestry. Our results indicated that rs339939442 in the AHR gene was a potential marker to improve litter size in European commercial lines and the pigs containing ancestries of European commercial lines, whereas this locus maybe not a causal mutation affecting the litter size but only in linkage disequilibrium with the causal mutation for litter size.
Collapse
Affiliation(s)
- Qian Zhang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Ruihua Huang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Xiang Ma
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Nengjing Jiang
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Wuduo Zhou
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Chen Gao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Moran Zhao
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Peipei Niu
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Zongping Zhang
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
| | - Qiang Li
- Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China; (Q.L.); (J.Z.)
| | - Juan Zhou
- Huaiyin Pig Breeding Farm of Huaian City, Huaian 223322, China; (Q.L.); (J.Z.)
| | - Pinghua Li
- Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China; (Q.Z.); (R.H.); (X.M.); (N.J.); (W.Z.); (C.G.); (M.Z.)
- Huaian Academy, Nanjing Agricultural University, Huaian 223005, China; (P.N.); (Z.Z.)
- Correspondence:
| |
Collapse
|
41
|
Zhang W, Yang M, Wang Y, Wu X, Zhang X, Ding Y, Yin Z. Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:712-721. [PMID: 31480149 PMCID: PMC7206397 DOI: 10.5713/ajas.19.0289] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 08/01/2019] [Indexed: 12/31/2022]
Abstract
Objective The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding. Methods We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (FST) and π ratios. Results Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions. Conclusion Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs.
Collapse
Affiliation(s)
- Wei Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Min Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yuanlang Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xudong Wu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xiaodong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yueyun Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| |
Collapse
|
42
|
Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array. Animals (Basel) 2019; 9:ani9060361. [PMID: 31208134 PMCID: PMC6616596 DOI: 10.3390/ani9060361] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The pig is one of the most important livestock animals, providing the majority of protein for humans. The population genetics analysis of pigs not only helps humans understand the domestication of the pig but also helps breeders in the genetic improvement of pigs. In this study, the population genetics of 11 pig breeds of South China were analyzed with the help of single nucleotide polymorphism (SNP) chips. The results showed that the genetic diversity of South China indigenous pigs is declining rapidly, and gene introgression from commercial pigs to indigenous pigs was detected. Selection signature analysis showed differences among South China indigenous pig breeds, commercial pig breeds, and wild pig breeds were present for meat quality and growth. Our study deepened understanding of the conservation status and selection mechanisms of Chinese indigenous pigs. Abstract To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.
Collapse
|
43
|
Liang Z, Bu L, Qin Y, Peng Y, Yang R, Zhao Y. Selection of Optimal Ancestry Informative Markers for Classification and Ancestry Proportion Estimation in Pigs. Front Genet 2019; 10:183. [PMID: 30915106 PMCID: PMC6421339 DOI: 10.3389/fgene.2019.00183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/19/2019] [Indexed: 12/26/2022] Open
Abstract
Using small sets of ancestry informative markers (AIMs) constitutes a cost-effective method to accurately estimate the ancestry proportions of individuals. This study aimed to generate a small and effective number of AIMs from ∼60 K single nucleotide polymorphism (SNP) data of porcine and estimate three ancestry proportions [East China pig (ECHP), South China pig (SCHP), and European commercial pig (EUCP)] from Asian breeds and European domestic breeds. A total of 186 samples of 10 pure breeds were divided into three groups: ECHP, SCHP, and EUCP. Using these samples and a one-vs.-rest SVM classifier, we found that using only seven AIMs could completely separate the three groups. Subsequently, we utilized supervised ADMIXTURE to calculate ancestry proportions and found that the 129 AIMs performed well on ancestry estimates when pseudo admixed individuals were used. Furthermore, another 969 samples of 61 populations were applied to evaluate the performance of the 129 AIMs. We also observed that the 129 AIMs were highly correlated with estimates using ∼60 K SNP data for three ancestry components: ECHP (Pearson correlation coefficient (r) = 0.94), SCHP (r = 0.94), and EUCP (r = 0.99). Our results provided an example of using a small number of pig AIMs for classifications and estimating ancestry proportions with high accuracy and in a cost-effective manner.
Collapse
Affiliation(s)
- Zuoxiang Liang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lina Bu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yidi Qin
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yebo Peng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ruifei Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yiqiang Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, China.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| |
Collapse
|
44
|
Zhao P, Yu Y, Feng W, Du H, Yu J, Kang H, Zheng X, Wang Z, Liu GE, Ernst CW, Ran X, Wang J, Liu JF. Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization. Gigascience 2018; 7:5001425. [PMID: 29790964 PMCID: PMC6007440 DOI: 10.1093/gigascience/giy058] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
Background Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with its unique features is still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to the phenotypic traits of Meishan via large-scale sequencing. Results We found that the unique domestication of Meishan pigs occurred in the Taihu Basin area between the Majiabang and Liangzhu Cultures, during which 300 protein-coding genes have underwent positive selection. Notably, enrichment of the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with the high fertility of Meishan pigs. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of NF-kB signaling, which may have resulted in the wrinkled skin and face of Meishan pigs. Particularly, three population-specific synonymous single-nucleotide variants occurred in PYROXD1, MC1R, and FAM83G genes; the T305C substitution in the MCIR gene explained the black coat of the Meishan pigs well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs. Conclusions These findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs and offer a plausible method for their utilization of Meishan pigs as valuable genetic resources in pig breeding and as an animal model for human wrinkled skin disease research.
Collapse
Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jian Yu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Huimin Kang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhiquan Wang
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, T6G 2C8, Canada
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705-2350, USA
| | | | - Xueqin Ran
- School of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jiafu Wang
- School of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| |
Collapse
|