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Buglione M, Rivieccio E, Aceto S, Paturzo V, Biondi C, Fulgione D. The Domestication of Wild Boar Could Result in a Relaxed Selection for Maintaining Olfactory Capacity. Life (Basel) 2024; 14:1045. [PMID: 39202786 PMCID: PMC11355481 DOI: 10.3390/life14081045] [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: 07/23/2024] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
Domesticated animals are artificially selected to exhibit desirable traits, however not all traits of domesticated animals are the result of deliberate selection. Loss of olfactory capacity in the domesticated pig (Sus scrofa domesticus) is one example. We used whole transcriptome analysis (RNA-Seq) to compare patterns of gene expression in the olfactory mucosa of the pig and two subspecies of wild boar (Sus scrofa), and investigate candidate genes that could be responsible for the loss of olfactory capacity. We identified hundreds of genes with reductions in transcript abundance in pig relative to wild boar as well as differences between the two subspecies of wild boar. These differences were detected mainly in genes involved in the formation and motility of villi, cilia and microtubules, functions associated with olfaction. In addition, differences were found in the abundances of transcripts of genes related to immune defenses, with the highest levels in continental wild boar subspecies. Overall, the loss of olfactory capacity in pigs appears to have been accompanied by reductions in the expression of candidate genes for olfaction. These changes could have resulted from unintentional selection for reduced olfactory capacity, relaxed selection for maintaining olfactory capacity, pleiotropic effects of genes under selection, or other non-selective processes. Our findings could be a cornerstone for future researches on wild boars, pigs, feral populations, and their evolutionary trajectories, aimed to provide tools to better calibrate species management as well as guidelines for breeders.
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Affiliation(s)
- Maria Buglione
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Eleonora Rivieccio
- Department of Humanities Studies, University of Naples Federico II, 80133 Naples, Italy;
| | - Serena Aceto
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Vincenzo Paturzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Carla Biondi
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
| | - Domenico Fulgione
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (M.B.); (S.A.); (V.P.); (C.B.)
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Kwon D, Ahn J, Kim H, Kim H, Kim J, Wy S, Ko Y, Kim J. Convergent dwarfism consequences of minipigs under independent artificial selections. BMC Genomics 2024; 25:761. [PMID: 39107730 PMCID: PMC11301983 DOI: 10.1186/s12864-024-10677-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Currently, diverse minipigs have acquired a common dwarfism phenotype through independent artificial selections. Characterizing the population and genetic diversity in minipigs is important to unveil genetic mechanisms regulating their body sizes and effects of independent artificial selections on those genetic mechanisms. However, full understanding for the genetic mechanisms and phenotypic consequences in minipigs still lag behind. RESULTS Here, using whole genome sequencing data of 41 pig breeds, including eight minipigs, we identified a large genomic diversity in a minipig population compared to other pig populations in terms of population structure, demographic signatures, and selective signatures. Selective signatures reveal diverse biological mechanisms related to body size in minipigs. We also found evidence for neural development mechanism as a minipig-specific body size regulator. Interestingly, selection signatures within those mechanisms containing neural development are also highly different among minipig breeds. Despite those large genetic variances, PLAG1, CHM, and ESR1 are candidate key genes regulating body size which experience different differentiation directions in different pig populations. CONCLUSIONS These findings present large variances of genetic structures, demographic signatures, and selective signatures in the minipig population. They also highlight how different artificial selections with large genomic diversity have shaped the convergent dwarfism.
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Affiliation(s)
- Daehong Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jiyeong Ahn
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyeonji Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Junyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Suyeon Wy
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin, Gyeonggi-Do, 17035, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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Popowics TE, Hwang I, Lu J, Nguyen T, Sample M, Sangster A, Tang D, Dennison CR, Romanyk DL, Rafferty K, Greenlee G. In vivo measurement of strain in the periodontal space of pig (Sus scrofa) incisors using in-fiber Bragg sensors. J Morphol 2024; 285:e21738. [PMID: 38783683 DOI: 10.1002/jmor.21738] [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: 12/20/2023] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
The incisor teeth in pigs, Sus scrofa, function in association with a disc-shaped snout to explore the environment for potential food. Understanding how mechanical loading applied to the tooth deforms the periodontal ligament (PDL) is important to determining the role of periodontal mechanoreceptors during food exploration and feeding. The objective of this study was to use fiber Bragg (FBG) sensors to measure strain in vivo within the PDL space of pig incisors. The central mandibular incisors of pigs underwent spring loaded lingual tipping during FBG strain recording within the labial periodontal space. FBG sensors were placed within the periodontal space of the central mandibular incisors of ~2-3-month-old farm pigs. The magnitude and orientation of spring loads are expected to mimic incisor contact with food. During incisor tipping with load calibrated springs, FBG strains in vitro (N = 6) and in vivo (N = 6) recorded at comparable load levels overlapped in range (-10-20 με). Linear regressions between peak FBG strains, that is, the highest recorded strain value, and baseline strains, that is, strain without applied spring load, were significant across all in vivo experiments (peak strain at 200 g vs. baseline, p = .04; peak strain at 2000 g vs. baseline p = .03; peak strain at 2000 g vs. 200 g, p = .004). These linear relationships indicate that on a per experiment basis, the maximum measured strain at different spring loads showed predictable differences. A Friedman test of the absolute value of peak strain confirmed the significant increase in strain between baseline, 200 g, and 2000 g spring activation (p = .02). Mainly compressive strains were recorded in the labial PDL space and increases in spring load applied in vivo generated increases in FBG strain measurements. These results demonstrate the capacity for FBG sensors to be used in vivo to assess transmission of occlusal loads through the periodontium. PDL strain is associated with mechanoreceptor stimulation and is expected to affect the functional morphology of the incisors. The overall low levels of strain observed may correspond with the robust functional morphology of pig incisors and the tendency for pigs to encounter diverse foods and substrates during food exploration.
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Affiliation(s)
- Tracy E Popowics
- Department of Oral Health Sciences, University of Washington, Seattle, Washington, USA
| | - Isabelle Hwang
- Department of Oral Health Sciences, University of Washington School of Dentistry, University of Washington, Seattle, Washington, USA
| | - Jason Lu
- Department of Oral Health Sciences, University of Washington School of Dentistry, University of Washington, Seattle, Washington, USA
| | - Tammy Nguyen
- Department of Oral Health Sciences, University of Washington School of Dentistry, University of Washington, Seattle, Washington, USA
| | - Morgan Sample
- Department of Oral Health Sciences, University of Washington School of Dentistry, University of Washington, Seattle, Washington, USA
| | - Anissa Sangster
- Department of Oral Health Sciences, University of Washington School of Dentistry, University of Washington, Seattle, Washington, USA
| | - Derrick Tang
- Department of Oral Health Sciences, University of Washington, Seattle, Washington, USA
| | | | - Dan L Romanyk
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Katherine Rafferty
- Department of Orthodontics, University of Washington, Seattle, Washington, USA
| | - Geoffrey Greenlee
- Department of Orthodontics, University of Washington, Seattle, Washington, USA
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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.
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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.)
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5
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Tan X, Liu L, Dong J, Huang M, Zhang J, Li Q, Wang H, Bai L, Cui M, Zhou Z, Wu D, Xiang Y, Li W, Wang D. Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens. BMC Genomics 2024; 25:485. [PMID: 38755540 PMCID: PMC11097469 DOI: 10.1186/s12864-024-10349-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding. RESULTS To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima's D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively. CONCLUSION Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.
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Affiliation(s)
- Xiaodong Tan
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Lu Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Jinhua Jinfan Feed Co., Ltd, Jinhua, Zhejiang, 321000, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Minjie Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jiawen Zhang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qinghai Li
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Huanhuan Wang
- Animal Husbandry Institute, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Lijuan Bai
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Ming Cui
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock and Poultry Monitoring Station, Hangzhou, 310020, China
| | - Zhenzhen Zhou
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - De Wu
- Postdoctoral Research Station, Jinhua Development Zone, Jinhua, Zhejiang, 321000, China
| | - Yun Xiang
- Jinhua Jinfan Feed Co., Ltd, Jinhua, Zhejiang, 321000, China.
| | - Weifen Li
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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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.
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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.
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Yang R, Jin S, Fang S, Yan D, Zhang H, Nie J, Liu J, Lv M, Zhang B, Dong X. Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes. Genet Sel Evol 2024; 56:24. [PMID: 38566006 PMCID: PMC10985947 DOI: 10.1186/s12711-024-00893-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Gene flow is crucial for enhancing economic traits of livestock. In China, breeders have used hybridization strategies for decades to improve livestock performance. Here, we performed whole-genome sequencing of a native Chinese Lijiang pig (LJP) breed. By integrating previously published data, we explored the genetic structure and introgression of genetic components from commercial European pigs (EP) into the LJP, and examined the impact of this introgression on phenotypic traits. RESULTS Our analysis revealed significant introgression of EP breeds into the LJP and other domestic pig breeds in China. Using a haplotype-based approach, we quantified introgression levels and compared EP to LJP and other Chinese domestic pigs. The results show that EP introgression is widely prevalent in Chinese domestic pigs, although there are significant differences between breeds. We propose that LJP could potentially act as a mediator for the transmission of EP haplotypes. We also examined the correlation between EP introgression and the number of thoracic vertebrae in LJP and identified VRTN and STUM as candidate genes for this trait. CONCLUSIONS Our study provides evidence of introgressed European haplotypes in the LJP breed and describes the potential role of EP introgression on phenotypic changes of this indigenous breed.
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Affiliation(s)
- Ruifei Yang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Siqi Jin
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Suyun Fang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Dawei Yan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Hao Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingru Nie
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinqiao Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Minjuan Lv
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Bo Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
| | - Xinxing Dong
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
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Zhao X, Wen J, Zhang X, Zhang J, Zhu T, Wang H, Yang W, Cao G, Xiong W, Liu Y, Qu C, Ning Z, Qu L. Significant genomic introgression from grey junglefowl (Gallus sonneratii) to domestic chickens (Gallus gallus domesticus). J Anim Sci Biotechnol 2024; 15:45. [PMID: 38556896 PMCID: PMC10983685 DOI: 10.1186/s40104-024-01006-7] [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: 11/06/2023] [Accepted: 01/31/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Chicken is one of the most numerous and widely distributed species around the world, and many studies support the multiple ancestral origins of domestic chickens. The research regarding the yellow skin phenotype in domestic chickens (regulated by BCO2) likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens. However, beyond the BCO2 gene region, much remains unknown about the introgression from the grey junglefowl into domestic chickens. Therefore, in this study, based on whole-genome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds, we explored the introgression events from the grey junglefowl to domestic chickens. RESULTS We successfully detected introgression regions besides BCO2, including two associated with growth trait (IGFBP2 and TKT), one associated with angiogenesis (TIMP3) and two members of the heat shock protein family (HSPB2 and CRYAB). Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens. Furthermore, we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds, indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained. Additionally, our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens, possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens. CONCLUSIONS In summary, our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens, laying the foundation for a deeper understanding of the genetic composition within domestic chickens, and offering new perspectives on the impact of introgression on domestic chickens.
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Affiliation(s)
- Xiurong Zhao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junhui Wen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xinye Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinxin Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Tao Zhu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Huie Wang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Corps, Tarim University, Alar, 843300, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Guomin Cao
- Animal husbandry station of Fangchenggang, Fangchenggang, Guangxi Province, 538001, China
| | - Wenjie Xiong
- Animal Disease Prevention and Control Center of Fangchenggang, Fangchenggang, Guangxi Province, 538001, China
| | - Yong Liu
- Beijing Agricultural Effect Poultry Industry Co., Ltd., Beijing, 101100, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, Anhui, 236037, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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9
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Alfieri JM, Hingoranee R, Athrey GN, Blackmon H. Domestication is associated with increased interspecific hybrid compatibility in landfowl (order: Galliformes). J Hered 2024; 115:1-10. [PMID: 37769441 PMCID: PMC10838130 DOI: 10.1093/jhered/esad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/15/2023] [Accepted: 09/26/2023] [Indexed: 09/30/2023] Open
Abstract
Some species are able to hybridize despite being exceptionally diverged. The causes of this variation in accumulation of reproductive isolation remain poorly understood, and domestication as an impetus or hindrance to reproductive isolation remains to be characterized. In this study, we investigated the role of divergence time, domestication, and mismatches in morphology, habitat, and clutch size among hybridizing species on reproductive isolation in the bird order Galliformes. We compiled and analyzed hybridization occurrences from literature and recorded measures of postzygotic reproductive isolation. We used a text-mining approach leveraging a historical aviculture magazine to quantify the degree of domestication across species. We obtained divergence time, morphology, habitat, and clutch size data from open sources. We found 123 species pairs (involving 77 species) with known offspring fertility (sterile, only males fertile, or both sexes fertile). We found that divergence time and clutch size were significant predictors of reproductive isolation (McFadden's Pseudo-R2 = 0.59), but not habitat or morphological mismatch. Perhaps most interesting, we found a significant relationship between domestication and reproductive compatibility after correcting for phylogeny, removing extreme values, and addressing potential biases (F1,74 = 5.43, R2 = 0.06, P-value = 0.02). We speculate that the genetic architecture and disruption in selective reproductive regimes associated with domestication may impact reproductive isolation, causing domesticated species to be more reproductively labile.
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Affiliation(s)
- James M Alfieri
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Reina Hingoranee
- Department of Epidemiology and Biostatistics, Texas A&M University, College Station, TX, USA
| | - Giridhar N Athrey
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - Heath Blackmon
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
- Department of Biology, Texas A&M University, College Station, TX, USA
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10
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Poklukar K, Mestre C, Škrlep M, Čandek-Potokar M, Ovilo C, Fontanesi L, Riquet J, Bovo S, Schiavo G, Ribani A, Muñoz M, Gallo M, Bozzi R, Charneca R, Quintanilla R, Kušec G, Mercat MJ, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Servin B. A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits. Genet Sel Evol 2023; 55:88. [PMID: 38062367 PMCID: PMC10704730 DOI: 10.1186/s12711-023-00858-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments. RESULTS Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene. CONCLUSIONS In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.
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Affiliation(s)
- Klavdija Poklukar
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000, Ljubljana, Slovenia
| | - Camille Mestre
- GenPhySE, Université de Toulouse, INRAE, INP, ENVT, 31320, Castanet-Tolosan, France
| | - Martin Škrlep
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000, Ljubljana, Slovenia
| | | | - Cristina Ovilo
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña Km. 7,5, 28040, Madrid, Spain
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRAE, INP, ENVT, 31320, Castanet-Tolosan, France
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy
| | - Maria Muñoz
- Departamento Mejora Genética Animal, INIA-CSIC, Crta. de la Coruña Km. 7,5, 28040, Madrid, Spain
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Rome, Italy
| | - Ricardo Bozzi
- DAGRI-Animal Science Section, Università Di Firenze, Via Delle Cascine 5, 50144, Florence, Italy
| | - Rui Charneca
- MED- Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, 7006-554, Évora, Portugal
| | - Raquel Quintanilla
- Programa de Genética y Mejora Animal, IRTA, Torre Marimon, Caldes de Montbui, 08140, Barcelona, Spain
| | - Goran Kušec
- Faculty of Agrobiotechnical Sciences, University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia
| | - Marie-José Mercat
- IFIP Institut du Porc, La Motte au Vicomte, BP 35104, 35651, Le Rheu Cedex, France
| | - Christoph Zimmer
- Bauerliche Erzeugergemeinschaft Schwäbisch Hall, Haller Str. 20, 74549, Wolpertshausen, Germany
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, 82317, Baisogala, Lithuania
| | - Jose P Araujo
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, 4990-706, Ponte de Lima, Portugal
| | - Čedomir Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, 11080, Belgrade-Zemun, Serbia
| | - Radomir Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080, Belgrade-Zemun, Serbia
| | - Danijel Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, 10000, Zagreb, Croatia
| | - Bertrand Servin
- GenPhySE, Université de Toulouse, INRAE, INP, ENVT, 31320, Castanet-Tolosan, France.
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11
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Benjamin NR, Crooijmans RPMA, Jordan LR, Bolt CR, Schook LB, Schachtschneider KM, Groenen MAM, Roca AL. Swine global genomic resources: insights into wild and domesticated populations. Mamm Genome 2023; 34:520-530. [PMID: 37805667 DOI: 10.1007/s00335-023-10012-5] [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: 05/02/2023] [Accepted: 07/25/2023] [Indexed: 10/09/2023]
Abstract
Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids. Collecting samples from diverse populations of suids is resource intensive and may negatively impact endangered populations. Here we catalog extensive tissue and DNA samples from suids in collections in both Europe and North America. We include samples that have previously been used for whole genome sequencing, targeted DNA sequencing, RNA sequencing, and reduced representation bisulfite sequencing (RRBS). This work provides an important centralized resource for researchers who wish to access published databases.
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Affiliation(s)
- Neal R Benjamin
- The Program in Ecology, Evolution and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Luke R Jordan
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
| | - Courtni R Bolt
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Chicago, Chicago, IL, USA
| | - Kyle M Schachtschneider
- National Center for Supercomputing Applications, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA.
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Alfred L Roca
- The Program in Ecology, Evolution and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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12
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Jamieson A, Carmagnini A, Howard-McCombe J, Doherty S, Hirons A, Dimopoulos E, Lin AT, Allen R, Anderson-Whymark H, Barnett R, Batey C, Beglane F, Bowden W, Bratten J, De Cupere B, Drew E, Foley NM, Fowler T, Fox A, Geigl EM, Gotfredsen AB, Grange T, Griffiths D, Groß D, Haruda A, Hjermind J, Knapp Z, Lebrasseur O, Librado P, Lyons LA, Mainland I, McDonnell C, Muñoz-Fuentes V, Nowak C, O'Connor T, Peters J, Russo IRM, Ryan H, Sheridan A, Sinding MHS, Skoglund P, Swali P, Symmons R, Thomas G, Trolle Jensen TZ, Kitchener AC, Senn H, Lawson D, Driscoll C, Murphy WJ, Beaumont M, Ottoni C, Sykes N, Larson G, Frantz L. Limited historical admixture between European wildcats and domestic cats. Curr Biol 2023; 33:4751-4760.e14. [PMID: 37935117 DOI: 10.1016/j.cub.2023.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/07/2023] [Accepted: 08/09/2023] [Indexed: 11/09/2023]
Abstract
Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities.
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Affiliation(s)
- Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK; Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany
| | - Alberto Carmagnini
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany; School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS London, UK
| | - Jo Howard-McCombe
- School of Biological Sciences, University of Bristol, BS8 1TQ Bristol, UK; RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, EH12 6TS Edinburgh, UK
| | - Sean Doherty
- Department of Archaeology, University of Exeter, EX4 4QE Exeter, UK
| | - Alexandra Hirons
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Evangelos Dimopoulos
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK; Department of Veterinary Medicine, University of Cambridge, CB3 0ES Cambridge, UK
| | - Audrey T Lin
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Richard Allen
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Hugo Anderson-Whymark
- Department of Scottish History and Archaeology, National Museums Scotland, EH1 1JF Edinburgh, UK
| | - Ross Barnett
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Colleen Batey
- Institute for Northern Studies, University of the Highlands and Islands, KW15 1FL Kirkwall, UK; Department of Archaeology, University of Durham, DH1 3LE Durham, UK
| | - Fiona Beglane
- CERIS, School of Science, Atlantic Technological University, F91 YW50 Sligo, Ireland
| | - Will Bowden
- Department of Classics and Archaeology, University of Nottingham, NG7 2RD Nottingham, UK
| | - John Bratten
- Department of Anthropology, University of West Florida, Pensacola, FL 32514, USA
| | - Bea De Cupere
- Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Ellie Drew
- York Archaeological Trust, YO1 7BX York, UK
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Tom Fowler
- Department of Classics and Archaeology, University of Nottingham, NG7 2RD Nottingham, UK
| | - Allison Fox
- Manx National Heritage, Manx Museum, IM1 3LY Douglas, Isle of Man
| | - Eva-Maria Geigl
- Université Paris-Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | | | - Thierry Grange
- Université Paris-Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - David Griffiths
- Department for Continuing Education, University of Oxford, OX1 2JA Oxford, UK
| | - Daniel Groß
- Museum Lolland-Falster, 4800 Nykøbing Falster, Denmark
| | - Ashleigh Haruda
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | | | - Zoe Knapp
- Department of Archaeology, University of Reading, RG6 6AB Reading, UK
| | - Ophélie Lebrasseur
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Universite de Toulouse, Universite Paul Sabatier, 31000 Toulouse, France; The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Pablo Librado
- Centre for Anthropobiology and Genomics of Toulouse, CNRS UMR 5288, Universite de Toulouse, Universite Paul Sabatier, 31000 Toulouse, France
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Ingrid Mainland
- UHI Archaeology Institute, University of the Highlands and Islands, Orkney, Scotland
| | | | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, CB10 1SD Cambridge, UK
| | - Carsten Nowak
- Centre for Wildlife Genetics & LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberg Research Institute, 60325 Frankfurt, Germany
| | - Terry O'Connor
- BioArCh, Department of Archaeology, University of York, YO10 5DD York, UK
| | - Joris Peters
- SNSB, State Collection of Palaeoanatomy Munich, 85586 Poing, Germany; Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany
| | | | - Hannah Ryan
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK
| | - Alison Sheridan
- Department of Scottish History and Archaeology, National Museums Scotland, EH1 1JF Edinburgh, UK
| | | | | | - Pooja Swali
- The Francis Crick Institute, NW1 1AT London, UK
| | | | - Gabor Thomas
- Department of Archaeology, University of Reading, RG6 6AB Reading, UK
| | - Theis Zetner Trolle Jensen
- Section for Molecular Ecology and Evolution, GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, EH1 1JF Edinburgh, UK; School of Geosciences, University of Edinburgh, EH8 9XP Edinburgh, UK
| | - Helen Senn
- RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, EH12 6TS Edinburgh, UK
| | - Daniel Lawson
- School of Mathematics, University of Bristol, BS8 1UG Bristol, UK
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ Bristol, UK
| | - Claudio Ottoni
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133 Roma, Italy
| | - Naomi Sykes
- Department of Archaeology, University of Exeter, EX4 4QE Exeter, UK
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, OX1 3TG Oxford, UK.
| | - Laurent Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität, 80539 Munich, Germany; School of Biological and Chemical Sciences, Queen Mary University of London, E1 4NS London, UK.
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13
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Lobo D, López-Bao JV, Godinho R. The population bottleneck of the Iberian wolf impacted genetic diversity but not admixture with domestic dogs: A temporal genomic approach. Mol Ecol 2023; 32:5986-5999. [PMID: 37855673 DOI: 10.1111/mec.17171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023]
Abstract
After decades of intense persecution, the Iberian wolf subspecies faced a severe bottleneck in the 1970s that considerably reduced its range and population size, nearly leading to its extinction in central and southern Iberian Peninsula. Such population decline could have impacted the genetic diversity of Iberian wolves through different processes, namely genetic drift and dynamics of hybridization with domestic dogs. By contrasting the genomes of 68 contemporary with 54 historical samples spanning the periods before and immediately after the 1970s bottleneck, we found evidence of its impact on genetic diversity and dynamics of wolf-dog hybridization. Our genome-wide assessment revealed that wolves and dogs form two well-differentiated genetic groups in Iberia and that hybridization rates did not increase during the bottleneck. However, an increased number of hybrid individuals was found over time during the population re-expansion, particularly at the edge of the wolf range. We estimated a low percentage of dog ancestry (~1.4%) in historical samples, suggesting that dog introgression was not a key driver for wolf extinction in central and southern Iberia. Our findings also unveil a significant decline in genetic diversity in contemporary samples, with the highest proportion of homozygous segments in the genome being recently inherited. Overall, our study provides unprecedented insight into the impact of a sharp decline on the Iberian wolf genome and refines our understanding of the ecological and evolutionary drivers of wolf-dog hybridization in the wild.
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Affiliation(s)
- Diana Lobo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - José Vicente López-Bao
- Biodiversity Research Institute (CSIC - Oviedo University - Principality of Asturias) Oviedo University, Mieres, Spain
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS, Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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14
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Zong W, Wang J, Zhao R, Niu N, Su Y, Hu Z, Liu X, Hou X, Wang L, Wang L, Zhang L. Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs. J Anim Sci Biotechnol 2023; 14:136. [PMID: 37805653 PMCID: PMC10559557 DOI: 10.1186/s40104-023-00929-x] [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: 05/23/2023] [Accepted: 08/03/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND During approximately 10,000 years of domestication and selection, a large number of structural variations (SVs) have emerged in the genome of pig breeds, profoundly influencing their phenotypes and the ability to adapt to the local environment. SVs (≥ 50 bp) are widely distributed in the genome, mainly in the form of insertion (INS), mobile element insertion (MEI), deletion (DEL), duplication (DUP), inversion (INV), and translocation (TRA). While studies have investigated the SVs in pig genomes, genome-wide association studies (GWAS)-based on SVs have been rarely conducted. RESULTS Here, we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools, with 53.95% of the SVs being reported for the first time. These high-quality SVs were used to recover the population genetic structure, confirming the accuracy of genotyping. Potential functional SV loci were then identified based on positional effects and breed stratification. Finally, GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions. We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7, with FKBP5 containing the most significant SV locus for almost all traits. In addition, we found several significant loci in intramuscular fat, abdominal circumference, heart weight, and liver weight, etc. CONCLUSIONS: We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits, 7 skeletal traits, and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.
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Affiliation(s)
- Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jinbu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, 030801, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanfang Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ziping Hu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xin Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xinhua Hou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ligang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lixian Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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15
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Li Z, Liu X, Wang C, Li Z, Jiang B, Zhang R, Tong L, Qu Y, He S, Chen H, Mao Y, Li Q, Pook T, Wu Y, Zan Y, Zhang H, Li L, Wen K, Chen Y. The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation. Genome Res 2023; 33:1833-1847. [PMID: 37914227 PMCID: PMC10691484 DOI: 10.1101/gr.277638.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 09/12/2023] [Indexed: 11/03/2023]
Abstract
Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.
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Affiliation(s)
- Zhengcao Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China;
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Chen Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Zhenyang Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Bo Jiang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Ruifeng Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Lu Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Youping Qu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Sheng He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Haifan Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Yafei Mao
- Bio-X Institutes, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Qingnan Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Torsten Pook
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6700 AH, The Netherlands
| | - Yu Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Yanjun Zan
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266000, China
| | - Hui Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Lu Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Keying Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China;
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16
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Fabbri G, Molinaro L, Mucci N, Pagani L, Scandura M. Anthropogenic hybridization and its influence on the adaptive potential of the Sardinian wild boar (Sus scrofa meridionalis). J Appl Genet 2023; 64:521-530. [PMID: 37369962 PMCID: PMC10457222 DOI: 10.1007/s13353-023-00763-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: 11/21/2022] [Revised: 05/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023]
Abstract
The wild boar (Sus scrofa meridionalis) arrived in Sardinia with the first human settlers in the early Neolithic with the potential to hybridize with the domestic pig (S. s. domesticus) throughout its evolution on the island. In this paper, we investigated the possible microevolutionary effects of such introgressive hybridization on the present wild boar population, comparing Sardinian wild specimens with several commercial pig breeds and Sardinian local pigs, along with a putatively unadmixed wild boar population from Central Italy, all genotyped with a medium density SNP chip. We first aimed at identifying hybrids in the population using different approaches, then examined genomic regions enriched for domestic alleles in the hybrid group, and finally we applied two methods to find regions under positive selection to possibly highlight instances of domestic adaptive introgression into a wild population. We found three hybrids within the Sardinian sample (3.1% out of the whole dataset). We reported 11 significant windows under positive selection with a method that looks for overly differentiated loci in the target population, compared with other two populations. We also identified 82 genomic regions with signs of selection in the domestic pig but not in the wild boar, two of which overlapped with genomic regions enriched for domestic alleles in the hybrid pool. Genes in these regions can be linked with reproductive success. Given our results, domestic introgression does not seem to be pervasive in the Sardinian wild boar. Nevertheless, we suggest monitoring the possible spread of advantageous domestic alleles in the coming years.
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Affiliation(s)
- Giulia Fabbri
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2A, 07100, Sassari, Italy.
| | - Ludovica Molinaro
- Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell'Emilia, Bologna, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Biology, University of Padua, Viale G. Colombo 3, 35131, Padua, Italy
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2A, 07100, Sassari, Italy
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17
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Emken S, Witzel C, Kierdorf U, Frölich K, Kierdorf H. Wild boar versus domestic pig-Deciphering of crown growth in porcine second molars. J Anat 2023; 242:1078-1095. [PMID: 36774334 PMCID: PMC10184542 DOI: 10.1111/joa.13838] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 02/13/2023] Open
Abstract
Based on the previously established periodicity of enamel growth marks, we reconstructed crown growth parameters of mandibular second molars from two wild boar and two domestic pigs of the Linderöd breed. Body weight gain and progression of dental development were markedly faster in the domestic pigs than the wild boar. While the final crown dimensions of the M2 did not differ between domestic pigs and wild boar, mean crown formation time (CFT) of this tooth was considerably shorter in the domestic pigs (162 days) than in the wild boar (205 days). The difference in CFT was mainly attributable to a higher enamel extension rate (EER) in the domestic pig. Generally, EER was highest in the cuspalmost deciles of the length of the enamel-dentine-junction and markedly dropped in cervical direction, with lowest values occurring in the cervicalmost decile. In consequence, the cuspal half of the M2 crown was formed about three times faster than the cervical half. In contrast to the EER, no marked difference in daily enamel secretion rate (DSR) was recorded between domestic pigs and wild boar. The duration of enamel matrix apposition as well as linear enamel thickness in corresponding crown portions was only slightly lower in the domestic pigs than the wild boar. Thus, the earlier completion of M2 crown growth in the domestic pig was mainly achieved by a higher EER and not by an increased DSR. The more rapid recruitment of secretory ameloblasts in the course of molar crown formation of domestic pigs compared to wild boar is considered a side-effect of the selection for rapid body growth during pig domestication.
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Affiliation(s)
- Simon Emken
- Department of BiologyUniversity of HildesheimHildesheimGermany
| | - Carsten Witzel
- Department of BiologyUniversity of HildesheimHildesheimGermany
| | - Uwe Kierdorf
- Department of BiologyUniversity of HildesheimHildesheimGermany
| | - Kai Frölich
- Department of BiologyUniversity of HildesheimHildesheimGermany
- Tierpark Arche Warder e.VWarderGermany
| | - Horst Kierdorf
- Department of BiologyUniversity of HildesheimHildesheimGermany
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18
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Razmaitė V, Šiukščius A, Marašinskienė Š. Cranial Morphology of Lithuanian Indigenous Wattle Pigs and Their Hybrids with Wild Boar. Animals (Basel) 2023; 13:ani13091453. [PMID: 37174490 PMCID: PMC10177289 DOI: 10.3390/ani13091453] [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: 03/15/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
The diversity of domestic pig breeds and their hybridization increases the variety of phenotypes expressed in hybrids. The aim of this study was to quantify the differences of cranial morphologies between local Lithuanian Indigenous Wattle pigs and theirhybrids with wild boar. A total of sixteen craniometric measurements were performed on the lateral, ventral and dorsal sides of 71 skulls of Lithuanian Indigenous Wattle pigs and their hybrids, including 1/4 wild boar (WB), 1/2 wild boar and 3/4 wild boar genotypes. The weight of the skull was affected by the genotype, live weight and sex of the animal. The size of the skull, particularly related to skull length parameters, increased consistently with the increase of the wild boar proportion in the hybrids. However, the Sus scrofa genotype did not affect the skull height. Clear discrimination was possible between the local Lithuanian breed pigs and their hybrids with different proportions of wild boar and between individual groups of hybrids. The most correct classification was determined on the basis of the overall and length parameters of the crania. This could contribute to better management and utilization of hybrids.
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Affiliation(s)
- Violeta Razmaitė
- Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, 82317 Baisogala, Lithuania
| | - Artūras Šiukščius
- Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, 82317 Baisogala, Lithuania
| | - Šarūnė Marašinskienė
- Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, 82317 Baisogala, Lithuania
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19
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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.
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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
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20
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Robinson J, Kyriazis CC, Yuan SC, Lohmueller KE. Deleterious Variation in Natural Populations and Implications for Conservation Genetics. Annu Rev Anim Biosci 2023; 11:93-114. [PMID: 36332644 PMCID: PMC9933137 DOI: 10.1146/annurev-animal-080522-093311] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.
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Affiliation(s)
- Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, California, USA;
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Stella C Yuan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , ,
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA; , , .,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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21
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Capomaccio S, Ablondi M, Colombi D, Sartori C, Giontella A, Cappelli K, Mancin E, Asti V, Mantovani R, Sabbioni A, Silvestrelli M. Exploring the Italian equine gene pool via high-throughput genotyping. Front Genet 2023; 14:1099896. [PMID: 36755577 PMCID: PMC9900106 DOI: 10.3389/fgene.2023.1099896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Introduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent "colonization". In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool. Materials and Methods: The Italian dataset comprised 1,308 individuals and 22 breeds genotyped at a 70 k density that was merged with publicly available data to facilitate comparison with the global equine diversity. After quality control and supervised subsampling to ensure consistency among breeds, the merged dataset with the global equine diversity contained data for 1,333 individuals from 54 populations. Multidimensional scaling, admixture, gene flow, and effective population size were analyzed. Results and Discussion: The results show that some of the native Italian breeds preserve distinct gene pools, potentially because of adaptation to the different geographical contexts of the peninsula. Nevertheless, the comparison with international breeds highlights the presence of strong gene flow from renowned breeds into several Italian breeds, probably due to historical introgression. Coldblood breeds with stronger genetic identity were indeed well differentiated from warmblood breeds, which are highly admixed. Other breeds showed further peculiarities due to their breeding history. Finally, we observed some breeds that exist more on cultural, traditional, and geographical point of view than due to actual genetic distinctiveness.
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Affiliation(s)
- Stefano Capomaccio
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy,*Correspondence: Stefano Capomaccio, ; Michela Ablondi,
| | - Michela Ablondi
- Department of Veterinary Science, University of Parma, Parma, Italy,*Correspondence: Stefano Capomaccio, ; Michela Ablondi,
| | - Daniele Colombi
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Department of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Cristina Sartori
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy
| | - Katia Cappelli
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy
| | - Enrico Mancin
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Vittoria Asti
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Maurizio Silvestrelli
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy,Sport Horse Research Centre (CRCS), University of Perugia, Perugia, Italy
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22
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Peng Y, Derks MFL, Groenen MAM, Zhao Y, Bosse M. Distinct traces of mixed ancestry in western commercial pig genomes following gene flow from Chinese indigenous breeds. Front Genet 2023; 13:1070783. [PMID: 36712875 PMCID: PMC9880450 DOI: 10.3389/fgene.2022.1070783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023] Open
Abstract
Studying gene flow between different livestock breeds will benefit the discovery of genes related to production traits and provide insight into human historical breeding. Chinese pigs have played an indispensable role in the breeding of Western commercial pigs. However, the differences in the timing and volume of the contribution of pigs from different Chinese regions to Western pigs are not yet apparent. In this paper, we combine the whole-genome sequencing data of 592 pigs from different studies and illustrate patterns of gene flow from Chinese pigs into Western commercial pigs. We describe introgression patterns from four distinct Chinese indigenous groups into five Western commercial groups. There were considerable differences in the number and length of the putative introgressed segments from Chinese pig groups that contributed to Western commercial pig breeds. The contribution of pigs from different Chinese geographical locations to a given western commercial breed varied more than that from a specific Chinese pig group to different Western commercial breeds, implying admixture within Europe after introgression. Within different Western commercial lines from the same breed, the introgression patterns from a given Chinese pig group seemed highly conserved, suggesting that introgression of Chinese pigs into Western commercial pig breeds mainly occurred at an early stage of breed formation. Finally, based on analyses of introgression signals, allele frequencies, and selection footprints, we identified a ∼2.65 Mb Chinese-derived haplotype under selection in Duroc pigs (CHR14: 95.68-98.33 Mb). Functional and phenotypic studies demonstrate that this PRKG1 haplotype is related to backfat and loin depth in Duroc pigs. Overall, we demonstrate that the introgression history of domestic pigs is complex and that Western commercial pigs contain distinct traces of mixed ancestry, likely derived from various Chinese pig breeds.
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Affiliation(s)
- Yebo Peng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Martijn FL Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
- Topigs Norsvin Research Center, Beuningen, Netherlands
| | - Martien AM Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands
- Amsterdam Insitute of Life and Environment (A-Life), VU University Amsterdam, Amsterdam, Netherlands
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23
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He J, Zhang Y, Li H, Xie Y, Huang G, Peng C, Zhao P, Wang Z. Hybridization alters the gut microbial and metabolic profile concurrent with modifying intestinal functions in Tunchang pigs. Front Microbiol 2023; 14:1159653. [PMID: 37152756 PMCID: PMC10157192 DOI: 10.3389/fmicb.2023.1159653] [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: 02/06/2023] [Accepted: 03/15/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction Hybridization has been widely used among Chinese wild boars to improve their growth performance and maintain meat quality. Most studies have focused on the genetic basis for such variation. However, the differences in the gut environment between hybrid and purebred boars, which can have significant impacts on their health and productivity, have been poorly understood. Methods In the current study, metagenomics was used to detect the gut microbial diversity and composition in hybrid Batun (BT, Berkshire × Tunchang) pigs and purebred Tunchang (TC) pigs. Additionally, untargeted metabolomic analysis was used to detect differences in gut metabolic pathways. Furthermore, multiple molecular experiments were conducted to demonstrate differences in intestinal functions. Results As a result of hybridization in TC pigs, a microbial change was observed, especially in Prevotella and Lactobacillus. Significant differences were found in gut metabolites, including fatty acyls, steroids, and steroid derivatives. Furthermore, the function of the intestinal barrier was decreased by hybridization, while the function of nutrient metabolism was increased. Discussion Evidences were shown that hybridization changed the gut microbiome, gut metabolome, and intestinal functions of TC pigs. These findings supported our hypothesis that hybridization altered the gut microbial composition, thereby modifying the intestinal functions, even the host phenotypes. Overall, our study highlights the importance of considering the gut microbiome as a key factor in the evaluation of animal health and productivity, particularly in the context of genetic selection and breeding programs.
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Affiliation(s)
- Jiayi He
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yunchao Zhang
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Hui Li
- Long Jian Animal Husbandry Company, Haikou, China
| | - Yanshe Xie
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Guiqing Huang
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Pengju Zhao
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
- *Correspondence: Pengju Zhao,
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Sanya, China
- College of Animal Science, Zhejiang University, Hangzhou, China
- Zhengguang Wang,
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24
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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.
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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
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25
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Neaux D, Harbers H, Blanc B, Ortiz K, Locatelli Y, Herrel A, Debat V, Cucchi T. The effect of captivity on craniomandibular and calcaneal ontogenetic trajectories in wild boar. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:575-585. [PMID: 35286754 DOI: 10.1002/jez.b.23130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Deciphering the plastic (i.e., nonheritable) changes induced by human control over wild animals in the archeological record is challenging. Previous studies detected morphological markers associated with captivity in the cranium, mandible, and calcaneus of adult wild boar (Sus scrofa) but the developmental trajectories leading up to these changes during ontogeny remain unknown. To assess the impact of growth in a captive environment on morphological structures during postnatal ontogeny, we used an experimental approach focusing on the same three structures and taxon. We investigated the form and size differences of captive-reared and wild-caught wild boar during growth using three-dimensional landmark-based geometric morphometrics. Our results provide evidence of an influence of captivity on the morphology of craniomandibular structures, as wild specimens are smaller than captive individuals at similar ages. The food resources inherent to anthropogenic environments may explain some of the observed differences between captive-reared and wild specimens. The calcaneus presents a different contrasted pattern of plasticity as captive and wild individuals differ in terms of form but not in terms of size. The physically more constrained nature of the calcaneus and the direct influence of mobility reduction on this bone may explain these discrepancies. These results provide new methodological perspectives for bioarchaeological approaches as they imply that the plastic mark of captivity can be observed in juvenile specimens in the same way it has been previously described in adults.
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Affiliation(s)
- Dimitri Neaux
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, UMR 7209, Muséum National d'Histoire Naturelle CNRS, Paris, France
- Laboratoire Paléontologie Evolution Paléoécosystèmes Paléoprimatologie, UMR 7262, Université de Poitiers CNRS, Poitiers, France
| | - Hugo Harbers
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, UMR 7209, Muséum National d'Histoire Naturelle CNRS, Paris, France
| | - Barbara Blanc
- Réserve Zoologique de la Haute-Touche, Muséum National d'Histoire Naturelle, Obterre, France
| | - Katia Ortiz
- Réserve Zoologique de la Haute-Touche, Muséum National d'Histoire Naturelle, Obterre, France
- Institut de Systématique, Evolution, Biodiversité, UMR 7205, Muséum National d'Histoire Naturelle CNRS UPMC EPHE, UA, Paris, France
| | - Yann Locatelli
- Réserve Zoologique de la Haute-Touche, Muséum National d'Histoire Naturelle, Obterre, France
- Physiologie de la Reproduction et des Comportements, UMR 7247, INRAE CNRS Université de Tours IFCE, Nouzilly, France
| | - Anthony Herrel
- Mécanismes Adaptatifs et Evolution, UMR 7179, Muséum National d'Histoire Naturelle CNRS, Paris, France
| | - Vincent Debat
- Institut de Systématique, Evolution, Biodiversité, UMR 7205, Muséum National d'Histoire Naturelle CNRS UPMC EPHE, UA, Paris, France
| | - Thomas Cucchi
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements, UMR 7209, Muséum National d'Histoire Naturelle CNRS, Paris, France
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26
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Ropars J, Giraud T. Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration. Curr Opin Microbiol 2022; 70:102236. [PMID: 36368125 DOI: 10.1016/j.mib.2022.102236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/29/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022]
Abstract
Humans have domesticated genetically distant fungi for similar uses, the fermentation of lipid-rich and sugar-rich food to generate attractive aspects, odor and aroma, and to improve shelf life and product safety. Multiple independent domestication events also occurred within species. We review recent evidence of phenotypic convergence during the domestication of fungi for making cheese (Saccharomyces cerevisiae, Penicillium roqueforti, P. camemberti, and Geotrichum candidum) and for dry-cured meat making (P. nalgiovense and P. salamii). Convergence following adaptation to similar ecological niches involved colony aspect (fluffiness and color), lipolysis, proteolysis, volatile compound production, and competitive ability against food spoilers. We review evidence for convergence in genetic diversity loss in domesticated populations and in the degeneration of unused traits, such as toxin production and sexual reproduction. Phenotypic convergence sometimes occurred by similar mechanisms of genomic adaptation, in particular horizontal gene transfers and loss of genes.
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Affiliation(s)
- Jeanne Ropars
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, Bâtiment 680, 12 route RD128, 91190 Gif-sur-Yvette, France.
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27
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Li Q, Wang L, Xing K, Yang Y, Abiola Adetula A, Liu Y, Yi G, Zhang H, Sweeney T, Tang Z. Identification of circRNAs Associated with Adipogenesis Based on RNA-seq Data in Pigs. Genes (Basel) 2022; 13:2062. [PMID: 36360299 PMCID: PMC9689998 DOI: 10.3390/genes13112062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 04/10/2024] Open
Abstract
Adipocytes or fat cells play a vital role in the storage and release of energy in pigs, and many circular RNAs (circRNAs) have emerged as important regulators in various tissues and cell types in pigs. However, the spatio-temporal expression pattern of circRNAs between different adipose deposition breeds remains elusive. In this study, RNA sequencing (RNA-seq) produced transcriptome profiles of Western Landrace (lean-type) and Chinese Songliao black pigs (obese-type) with different thicknesses of subcutaneous fat tissues and were used to identify circRNAs involved in the regulation of adipogenesis. Gene expression analysis revealed 883 circRNAs, among which 26 and 11 circRNAs were differentially expressed between Landrace vs. Songliao pigs and high- vs. low-thickness groups, respectively. We also analyzed the interaction between circRNAs and microRNAs (miRNAs) and constructed their interaction network in adipogenesis; gene ontology classification and pathway analysis revealed two vital circRNAs, with the majority of their target genes enriched in biological functions such as fatty acids biosynthesis, fatty acid metabolism, and Wnt/TGF-β signaling pathways. These candidate circRNAs can be taken as potential targets for further experimental studies. Our results show that circRNAs are dynamically expressed and provide a valuable basis for understanding the molecular mechanism of circRNAs in pig adipose biology.
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Affiliation(s)
- Qiaowei Li
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528200, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- 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 Center for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Liyuan Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- 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 Center for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yalan Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528200, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- 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 Center for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Adeyinka Abiola Adetula
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- 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 Center for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- 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 Center for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- 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 Center for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Hongfu Zhang
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Torres Sweeney
- School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528200, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- 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 Center for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Research Centre of Animal Nutritional Genomics, State Key Laboratory of Animal Nutrition, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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28
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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.
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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.
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29
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Fontanesi L. Genetics and genomics of pigmentation variability in pigs: A review. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Sá P, Santos D, Chiaia H, Leitão A, Cordeiro JM, Gama LT, Amaral AJ. Lost pigs of Angola: Whole genome sequencing reveals unique regions of selection with emphasis on metabolism and feed efficiency. Front Genet 2022; 13:1003069. [PMID: 36353101 PMCID: PMC9639768 DOI: 10.3389/fgene.2022.1003069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
Angola, in the western coast of Africa, has been through dramatic social events that have led to the near-disappearance of native swine populations, and the recent introduction of European exotic breeds has also contributed to the erosion of this native swine repertoire. In an effort to investigate the genetic basis of native pigs in Angola (ANG) we have generated whole genomes from animals of a remote local pig population in Huambo province, which we have compared with 78 genomes of European and Asian pig breeds as well as European and Asian wild boars that are currently in public domain. Analyses of population structure showed that ANG pigs grouped within the European cluster and were clearly separated from Asian pig breeds. Pairwise FST ranged from 0.14 to 0.26, ANG pigs display lower levels of genetic differentiation towards European breeds. Finally, we have identified candidate regions for selection using a complementary approach based on various methods. All results suggest that selection towards feed efficiency and metabolism has occurred. Moreover, all analysis identified CDKAL1 gene, which is related with insulin and cholesterol metabolism, as a candidate gene overlapping signatures of selection unique to ANG pigs. This study presents the first assessment of the genetic relationship between ANG pigs and other world breeds and uncovers selection signatures that may indicate adaptation features unique to this important genetic resource.
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Affiliation(s)
- Pedro Sá
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
| | - Dulce Santos
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
| | - Hermenegildo Chiaia
- Faculdade de Medicina Veterinária, Universidade José Eduardo dos Santos, Huambo, Angola
| | - Alexandre Leitão
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
| | - José Moras Cordeiro
- Faculdade de Medicina Veterinária, Universidade José Eduardo dos Santos, Huambo, Angola
| | - Luís T. Gama
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
| | - Andreia J. Amaral
- CIISA—Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
- Laboratório Associado para a Ciência Animal e Veterinária (AL4AnimalS), Avenida da Universidade Técnica, Lisboa, Portugal
- *Correspondence: Andreia J. Amaral,
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31
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Zhang W, Li X, Jiang Y, Zhou M, Liu L, Su S, Xu C, Li X, Wang C. Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing. Front Genet 2022; 13:1022261. [PMID: 36324508 PMCID: PMC9618877 DOI: 10.3389/fgene.2022.1022261] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
The genetic resources among pigs in Anhui Province are diverse, but their value and potential have yet to be discovered. To illustrate the genetic diversity and population structure of the Anhui pigs population, we resequenced the genome of 150 pigs from six representative Anhui pigs populations and analyzed this data together with the sequencing data from 40 Asian wild boars and commercial pigs. Our results showed that Anhui pigs were divided into two distinct types based on ancestral descent: Wannan Spotted pig (WSP) and Wannan Black pig (WBP) origins from the same ancestor and the other four populations origins from another ancestor. We also identified several potential selective sweep regions associated with domestication characteristics among Anhui pigs, including reproduction-associated genes (CABS1, INSL6, MAP3K12, IGF1R, INSR, LIMK2, PATZ1, MAPK1), lipid- and meat-related genes (SNX19, MSTN, MC5R, PRKG1, CREBBP, ADCY9), and ear size genes (MSRB3 and SOX5). Therefore, these findings expand the catalogue and how these genetic differences among pigs and this newly generated data will be a valuable resource for future genetic studies and for improving genome-assisted breeding of pigs and other domesticated animals.
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32
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Liu M, Yu C, Zhang Z, Song M, Sun X, Piálek J, Jacob J, Lu J, Cong L, Zhang H, Wang Y, Li G, Feng Z, Du Z, Wang M, Wan X, Wang D, Wang YL, Li H, Wang Z, Zhang B, Zhang Z. Whole-genome sequencing reveals the genetic mechanisms of domestication in classical inbred mice. Genome Biol 2022; 23:203. [PMID: 36163035 PMCID: PMC9511766 DOI: 10.1186/s13059-022-02772-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studies using mouse models. However, the genetic mechanism of laboratory mouse domestication remains unknown due to lack of adequate genomic sequences of wild mice. Results We analyze the genetic relationships by whole-genome resequencing of 36 wild mice and 36 inbred strains. All classical inbred mice cluster together distinctly from wild and wild-derived inbred mice. Using nucleotide diversity analysis, Fst, and XP-CLR, we identify 339 positively selected genes that are closely associated with nervous system function. Approximately one third of these positively selected genes are highly expressed in brain tissues, and genetic mouse models of 125 genes in the positively selected genes exhibit abnormal behavioral or nervous system phenotypes. These positively selected genes show a higher ratio of differential expression between wild and classical inbred mice compared with all genes, especially in the hippocampus and frontal lobe. Using a mutant mouse model, we find that the SNP rs27900929 (T>C) in gene Astn2 significantly reduces the tameness of mice and modifies the ratio of the two Astn2 (a/b) isoforms. Conclusion Our study indicates that classical inbred mice experienced high selection pressure during domestication under laboratory conditions. The analysis shows the positively selected genes are closely associated with behavior and the nervous system in mice. Tameness may be related to the Astn2 mutation and regulated by the ratio of the two Astn2 (a/b) isoforms. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02772-1.
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Affiliation(s)
- Ming Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,International Society of Zoological Sciences, Beijing, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhichao Zhang
- Novogene Bioinformatics Institute, Beijing, China.,Glbizzia Biosciences, Beijing, China
| | - Mingjing Song
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiuping Sun
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
| | - Jaroslav Piálek
- House Mouse Group, Research Facility Studenec, Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jens Jacob
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests / Institute for Epidemiology and Pathogen Diagnostics, Münster, Germany
| | - Jiqi Lu
- School of Life Science, Zhengzhou University, Zhengzhou, Henan, China
| | - Lin Cong
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Hongmao Zhang
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Yong Wang
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Guoliang Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Feng
- Plant Protection Research Institute Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Zhenglin Du
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Meng Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Xinru Wan
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Dawei Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan-Ling Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongjun Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zuoxin Wang
- Department of Psychology and Program in Neuroscience, Florida State University, Tallahassee, FL, 32306, USA
| | - Bing Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,International Society of Zoological Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
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33
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Nishide Y, Oguchi K, Murakami M, Moriyama M, Koga R, Fukatsu T. Endosymbiotic bacteria of the boar louse Haematopinus apri (Insecta: Phthiraptera: Anoplura). Front Microbiol 2022; 13:962252. [PMID: 36003934 PMCID: PMC9393614 DOI: 10.3389/fmicb.2022.962252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Insects exclusively feeding on vertebrate blood are usually dependent on symbiotic bacteria for provisioning of B vitamins. Among them, sucking lice are prominent in that their symbiotic bacteria as well as their symbiotic organs exhibit striking diversity. Here we investigated the bacterial diversity associated with the boar louse Haematopinus apri in comparison with the hog louse Haematopinus suis. Amplicon sequencing analysis identified the primary endosymbiont predominantly detected from all populations of H. apri with some minor secondary bacterial associates. Sequencing and phylogenetic analysis of bacterial 16S rRNA gene confirmed that the endosymbionts of the boar louse H. apri, the hog louse H. suis and the cattle louse Haematopinus eurysternus form a distinct clade in the Gammaproteobacteria. The endosymbiont clade of Haematopinus spp. was phylogenetically distinct from the primary endosymbionts of other louse lineages. Fluorescence in situ hybridization visualized the endosymbiont localization within midgut epithelium, ovarial ampulla and posterior oocyte of H. apri, which were substantially the same as the endosymbiont localization previously described in H. suis and H. eurysternus. Mitochondrial haplotype analysis revealed that, although the domestic pig was derived from the wild boar over the past 8,000 years of human history, the populations of H. apri constituted a distinct sister clade to the populations of H. suis. Based on these results, we discussed possible evolutionary trajectories of the boar louse, the hog louse and their endosymbionts in the context of swine domestication. We proposed ‘Candidatus Haematopinicola symbiotica’ for the distinct clade of the endosymbionts of Haematopinus spp.
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Affiliation(s)
- Yudai Nishide
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- *Correspondence: Yudai Nishide,
| | - Kohei Oguchi
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Japan
| | - Maria Murakami
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Minoru Moriyama
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ryuichi Koga
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takema Fukatsu
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Takema Fukatsu,
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34
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Gong H, Liu W, Wu Z, Zhang M, Sun Y, Ling Z, Xiao S, Ai H, Xin Y, Yang B, Huang L. Evolutionary insights into porcine genomic structural variations based on a novel constructed dataset from 24 worldwide diverse populations. Evol Appl 2022. [DOI: 10.1111/eva.13455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Huanfa Gong
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, College of Animal Sciences Zhejiang University Hangzhou P.R. China
- Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, College of Animal Sciences Zhejiang University Hangzhou P.R. China
| | - Weiwei Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Zhongzi Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Mingpeng Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Yingchun Sun
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Yuyun Xin
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology Jiangxi Agricultural University Nanchang P.R. China
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35
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Garcia-Erill G, Jørgensen CHF, Muwanika VB, Wang X, Rasmussen MS, de Jong YA, Gaubert P, Olayemi A, Salmona J, Butynski TM, Bertola LD, Siegismund HR, Albrechtsen A, Heller R. Warthog Genomes Resolve an Evolutionary Conundrum and Reveal Introgression of Disease Resistance Genes. Mol Biol Evol 2022; 39:6627297. [PMID: 35779009 PMCID: PMC9250280 DOI: 10.1093/molbev/msac134] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
African wild pigs have a contentious evolutionary and biogeographic history. Until recently, desert warthog (Phacochoerus aethiopicus) and common warthog (P. africanus) were considered a single species. Molecular evidence surprisingly suggested they diverged at least 4.4 million years ago, and possibly outside of Africa. We sequenced the first whole-genomes of four desert warthogs and 35 common warthogs from throughout their range. We show that these two species diverged much later than previously estimated, 400,000–1,700,000 years ago depending on assumptions of gene flow. This brings it into agreement with the paleontological record. We found that the common warthog originated in western Africa and subsequently colonized eastern and southern Africa. During this range expansion, the common warthog interbred with the desert warthog, presumably in eastern Africa, underlining this region’s importance in African biogeography. We found that immune system–related genes may have adaptively introgressed into common warthogs, indicating that resistance to novel diseases was one of the most potent drivers of evolution as common warthogs expanded their range. Hence, we solve some of the key controversies surrounding warthog evolution and reveal a complex evolutionary history involving range expansion, introgression, and adaptation to new diseases.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Christian H F Jørgensen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Vincent B Muwanika
- Department of Environmental Management, Makerere University, PO Box 7062, Kampala, Uganda
| | - Xi Wang
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Malthe S Rasmussen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Yvonne A de Jong
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Philippe Gaubert
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria
| | - Jordi Salmona
- Laboratoire Évolution & Diversité Biologique, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Thomas M Butynski
- Eastern Africa Primate Diversity and Conservation Program & Lolldaiga Hills Research Programme, PO Box 149, Nanyuki 10400, Kenya
| | - Laura D Bertola
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Anders Albrechtsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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36
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Mary N, Iannuccelli N, Petit G, Bonnet N, Pinton A, Barasc H, Faure A, Calgaro A, Grosbois V, Servin B, Ducos A, Riquet J. Genome-wide analysis of hybridization in wild boar populations reveals adaptive introgression from domestic pig. Evol Appl 2022; 15:1115-1128. [PMID: 35899256 PMCID: PMC9309462 DOI: 10.1111/eva.13432] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 04/19/2022] [Accepted: 05/31/2022] [Indexed: 11/15/2022] Open
Abstract
The admixture of domestic pig into French wild boar populations has been monitored since the 1980s thanks to the existence of a cytogenetic difference between the two sub-species. The number of chromosomes is 2n = 36 in wild boar and 2n = 38 in pig, respectively. This difference makes it possible to assign the "hybrid" status to wild boar individuals controlled with 37 or 38 chromosomes. However, it does not make it possible to determine the timing of the hybridization(s), nor to guarantee the absence of domestic admixture in an animal with 2n = 36 chromosomes. In order to analyze hybridization in greater detail and to avoid the inherent limitations of the cytogenetic approach, 362 wild boars (WB) recently collected in different French geographical areas and in different environments (farms, free ranging in protected or unprotected areas, animals with 2n = 36, 37 or 38 chromosomes) were genotyped on a 70K SNP chip. Principal component analyses allowed the identification of 13 "outliers" (3.6%), for which the proportion of the genome of "domestic" origin was greater than 40% (Admixture analyses). These animals were probably recent hybrids, having Asian domestic pig ancestry for most of them. For the remaining 349 animals studied, the proportion of the genome of "wild" origin varied between 83% and 100% (median: 94%). This proportion varied significantly depending on how the wild boar populations were managed. Local ancestry analyses revealed adaptive introgression from domestic pig, suggesting a critical role of genetic admixture in improving the fitness and population growth of WB. Overall, our results show that the methods used to monitor the domestic genetic contributions to wild boar populations should evolve in order to limit the level of admixture between the two gene pools.
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Affiliation(s)
- Nicolas Mary
- GenPhySE, INRAE, ENVTUniversité de ToulouseCastanet TolosanFrance
| | | | | | - Nathalie Bonnet
- GenPhySE, INRAE, ENVTUniversité de ToulouseCastanet TolosanFrance
| | - Alain Pinton
- GenPhySE, INRAE, ENVTUniversité de ToulouseCastanet TolosanFrance
| | - Harmonie Barasc
- GenPhySE, INRAE, ENVTUniversité de ToulouseCastanet TolosanFrance
| | - Amélie Faure
- GenPhySE, INRAE, ENVTUniversité de ToulouseCastanet TolosanFrance
| | - Anne Calgaro
- GenPhySE, INRAE, ENVTUniversité de ToulouseCastanet TolosanFrance
| | | | - Bertrand Servin
- GenPhySE, INRAE, ENVTUniversité de ToulouseCastanet TolosanFrance
| | - Alain Ducos
- GenPhySE, INRAE, ENVTUniversité de ToulouseCastanet TolosanFrance
| | - Juliette Riquet
- GenPhySE, INRAE, ENVTUniversité de ToulouseCastanet TolosanFrance
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37
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Beckman AK, Richey BMS, Rosenthal GG. Behavioral responses of wild animals to anthropogenic change: insights from domestication. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03205-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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38
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Zhang C, Zhao J, Guo Y, Xu Q, Liu M, Cheng M, Chao X, Schinckel AP, Zhou B. Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs. Front Vet Sci 2022; 9:909039. [PMID: 35847642 PMCID: PMC9280686 DOI: 10.3389/fvets.2022.909039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022] Open
Abstract
Copy number variation (CNV) has been considered to be an important source of genetic variation for important phenotypic traits of livestock. In this study, we performed whole-genome CNV detection on Suhuai (SH) (n = 23), Chinese Min Zhu (MZ) (n = 11), and Large White (LW) (n = 12) pigs based on next-generation sequencing data. The copy number variation regions (CNVRs) were annotated and analyzed, and 10,885, 10,836, and 10,917 CNVRs were detected in LW, MZ, and SH pigs, respectively. Some CNVRs have been randomly selected for verification of the variation type by real-time PCR. We found that SH and LW pigs are closely related, while MZ pigs are distantly related to the SH and LW pigs by CNVR-based genetic structure, PCA, VST, and QTL analyses. A total of 14 known genes annotated in CNVRs were unique for LW pigs. Among them, the cyclin T2 (CCNT2) is involved in cell proliferation and the cell cycle. The FA Complementation Group M (FANCM) is involved in defective DNA repair and reproductive cell development. Ten known genes annotated in 47 CNVRs were unique for MZ pigs. The genes included glycerol-3-phosphate acyltransferase 3 (GPAT3) is involved in fat synthesis and is essential to forming the glycerol triphosphate. Glutathione S-transferase mu 4 (GSTM4) gene plays an important role in detoxification. Eleven known genes annotated in 23 CNVRs were unique for SH pigs. Neuroligin 4 X-linked (NLGN4X) and Neuroligin 4 Y-linked (NLGN4Y) are involved with nerve disorders and nerve signal transmission. IgLON family member 5 (IGLON5) is related to autoimmunity and neural activities. The unique characteristics of LW, MZ, and SH pigs are related to these genes with CNV polymorphisms. These findings provide important information for the identification of candidate genes in the molecular breeding of pigs.
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Affiliation(s)
- Chunlei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yanli Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Qinglei Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Mingzheng Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Meng Cheng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaohuan Chao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Allan P. Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Bo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Bo Zhou
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39
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Tang H, Ouyang J, Liu S, Xiong Y, Wu Y, Wang L, Wang C, Yan X, Shen Y, Chen H. Population structure of 3907 worldwide pigs and the introgression of Chinese indigenous pigs by European pigs. Anim Genet 2022; 53:599-612. [PMID: 35735069 DOI: 10.1111/age.13234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 05/25/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
With the improvement in sequencing technology and the decrease in sequencing cost, increasing amounts of genomic data for pigs have been uploaded to public databases. However, no researchers have to date integrated all currently available data to uncover the global genetic status of pigs. Meanwhile, little is known about the introgression from European to Chinese pigs and its underlying influences. Therefore, we integrated the effective genotype data of 3907 pigs from 193 populations worldwide using population genetic analysis, gene flow analysis and a sharing-IBD study. These findings illustrate not only the population structure of 59 Chinese native breeds and others but also the amounts of gene flow and introgression that have occurred between Western and Chinese pigs. In addition, we demonstrate the presence of introgressed European haplotypes in Chinese indigenous breeds and identify relevant introgressed regions that contain genes associated with growth and feed efficiency. Moreover, we compare the introgression patterns of Western and Chinese pigs and further discuss possible explanations for why the level of introgression differs between Chinese pig breeds and Western modern breeds. Collectively, this study provides a fine global population structure analysis of pigs and presents evidence of European pigs being interbred with local breeds in China.
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Affiliation(s)
- Hongbo Tang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Jing Ouyang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Siyu Liu
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yanpeng Xiong
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yongfei Wu
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Luping Wang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Cong Wang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Xueming Yan
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yangyang Shen
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Hao Chen
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
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40
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Abstract
The recent and ever-growing problem of boar (Sus scrofa forms including wild boar, hybrid and feral pig) expansion is a very complex issue in wildlife management. The damages caused to biodiversity and the economies are addressed in different ways by the various countries, but research is needed to shed light on the causal factors of this emergency before defining a useful collaborative management policy. In this review, we screened more than 280 references published between 1975–2022, identifying and dealing with five hot factors (climate change, human induced habitat modifications, predator regulation on the prey, hybridization with domestic forms, and transfaunation) that could account for the boar expansion and its niche invasion. We also discuss some issues arising from this boar emergency, such as epizootic and zoonotic diseases or the depression of biodiversity. Finally, we provide new insights for the research and the development of management policies.
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41
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Liu L, Megens HJ, Crooijmans RP, Bosse M, Huang Q, Sonsbeek GBV, Groenen MA, Madsen O. The Visayan warty pig (Sus cebifrons) genome provides insight into chromosome evolution and sensory adaptation in pigs. Mol Biol Evol 2022; 39:6596366. [PMID: 35642310 PMCID: PMC9178973 DOI: 10.1093/molbev/msac110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks post-zygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent post-divergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.
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Affiliation(s)
- Langqing Liu
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | | | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Qitong Huang
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands.,Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | | | - Martien Am Groenen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
| | - Ole Madsen
- Animal Breeding and Genomics, Wageningen University & Research, The Netherlands
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42
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ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs. Nature 2022; 606:358-367. [PMID: 35477154 PMCID: PMC9157047 DOI: 10.1038/s41586-022-04769-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 04/19/2022] [Indexed: 12/12/2022]
Abstract
The composition of the intestinal microbiome varies considerably between individuals and is correlated with health1. Understanding the extent to which, and how, host genetics contributes to this variation is essential yet has proved to be difficult, as few associations have been replicated, particularly in humans2. Here we study the effect of host genotype on the composition of the intestinal microbiota in a large mosaic pig population. We show that, under conditions of exacerbated genetic diversity and environmental uniformity, microbiota composition and the abundance of specific taxa are heritable. We map a quantitative trait locus affecting the abundance of Erysipelotrichaceae species and show that it is caused by a 2.3 kb deletion in the gene encoding N-acetyl-galactosaminyl-transferase that underpins the ABO blood group in humans. We show that this deletion is a ≥3.5-million-year-old trans-species polymorphism under balancing selection. We demonstrate that it decreases the concentrations of N-acetyl-galactosamine in the gut, and thereby reduces the abundance of Erysipelotrichaceae that can import and catabolize N-acetyl-galactosamine. Our results provide very strong evidence for an effect of the host genotype on the abundance of specific bacteria in the intestine combined with insights into the molecular mechanisms that underpin this association. Our data pave the way towards identifying the same effect in rural human populations. The host blood-type-associated ABO genotype affects the abundance of specific bacteria in the pig intestine.
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43
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Kumar H, Panigrahi M, Panwar A, Rajawat D, Nayak SS, Saravanan KA, Kaisa K, Parida S, Bhushan B, Dutt T. Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data. J Comput Biol 2022; 29:943-960. [PMID: 35639362 DOI: 10.1089/cmb.2021.0447] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.
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Affiliation(s)
- Harshit Kumar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Manjit Panigrahi
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Anuradha Panwar
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Divya Rajawat
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Sonali Sonejita Nayak
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - K A Saravanan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Kaiho Kaisa
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Subhashree Parida
- Divisions of Pharmacology and Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Bharat Bhushan
- Divisions of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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Changes in Neuropeptide Prohormone Genes among Cetartiodactyla Livestock and Wild Species Associated with Evolution and Domestication. Vet Sci 2022; 9:vetsci9050247. [PMID: 35622775 PMCID: PMC9144646 DOI: 10.3390/vetsci9050247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
The impact of evolution and domestication processes on the sequences of neuropeptide prohormone genes that participate in cell–cell signaling influences multiple biological process that involve neuropeptide signaling. This information is important to understand the physiological differences between Cetartiodactyla domesticated species such as cow, pig, and llama and wild species such as hippopotamus, giraffes, and whales. Systematic analysis of changes associated with evolutionary and domestication forces in neuropeptide prohormone protein sequences that are processed into neuropeptides was undertaken. The genomes from 118 Cetartiodactyla genomes representing 22 families were mined for 98 neuropeptide prohormone genes. Compared to other Cetartiodactyla suborders, Ruminantia preserved PYY2 and lost RLN1. Changes in GNRH2, IAPP, INSL6, POMC, PRLH, and TAC4 protein sequences could result in the loss of some bioactive neuropeptides in some families. An evolutionary model suggested that most neuropeptide prohormone genes disfavor sequence changes that incorporate large and hydrophobic amino acids. A compelling finding was that differences between domestic and wild species are associated with the molecular system underlying ‘fight or flight’ responses. Overall, the results demonstrate the importance of simultaneously comparing the neuropeptide prohormone gene complement from close and distant-related species. These findings broaden the foundation for empirical studies about the function of the neuropeptidome associated with health, behavior, and food production.
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Chen JQ, Zhang MP, Tong XK, Li JQ, Zhang Z, Huang F, Du HP, Zhou M, Ai HS, Huang LS. Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds. Zool Res 2022; 43:423-441. [PMID: 35437972 PMCID: PMC9113972 DOI: 10.24272/j.issn.2095-8137.2021.379] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/12/2022] [Indexed: 11/21/2022] Open
Abstract
In pig-to-human xenotransplantation, the transmission risk of porcine endogenous retroviruses (PERVs) is of great concern. However, the distribution of PERVs in pig genomes, their genetic variation among Eurasian pigs, and their evolutionary history remain unclear. We scanned PERVs in the current pig reference genome (assembly Build 11.1), and identified 36 long complete or near-complete PERVs (lcPERVs) and 23 short incomplete PERVs (siPERVs). Besides three known PERVs (PERV-A, -B, and -C), four novel types (PERV-JX1, -JX2, -JX3, and -JX4) were detected in this study. According to evolutionary analyses, the newly discovered PERVs were more ancient, and PERV-Bs probably experienced a bottleneck ~0.5 million years ago (Ma). By analyzing 63 high-quality porcine whole-genome resequencing data, we found that the PERV copy numbers in Chinese pigs were lower (32.0±4.0) than in Western pigs (49.1±6.5). Additionally, the PERV sequence diversity was lower in Chinese pigs than in Western pigs. Regarding the lcPERV copy numbers, PERV-A and -JX2 in Western pigs were higher than in Chinese pigs. Notably, Bama Xiang (BMX) pigs had the lowest PERV copy number (27.8±5.1), and a BMX individual had no PERV-C and the lowest PERV copy number (23), suggesting that BMX pigs were more suitable for screening and/or modification as xenograft donors. Furthermore, we identified 451 PERV transposon insertion polymorphisms (TIPs), of which 86 were shared by all 10 Chinese and Western pig breeds. Our findings provide systematic insights into the genomic distribution, variation, evolution, and possible biological function of PERVs.
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Affiliation(s)
- Jia-Qi Chen
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Ming-Peng Zhang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Xin-Kai Tong
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Jing-Quan Li
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Zhou Zhang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Fei Huang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Hui-Peng Du
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Meng Zhou
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Hua-Shui Ai
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China. E-mail:
| | - Lu-Sheng Huang
- State Key Laboratory for Swine Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China. E-mail:
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Liu Z, Yang J, Li H, Zhong Z, Huang J, Fu J, Zhao H, Liu X, Jiang S. Identifying Candidate Genes for Short Gestation Length Trait in Chinese Qingping Pigs by Whole-Genome Resequencing and RNA Sequencing. Front Genet 2022; 13:857705. [PMID: 35664295 PMCID: PMC9159352 DOI: 10.3389/fgene.2022.857705] [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: 01/19/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Gestation length is a complex polygenic trait that affects pig fetal development. The Qingping (QP) pig, a Chinese native black pig breed, is characterized by short gestation length. However, the genetic architecture of short gestation length is still not clear. The present study aimed to explore the genetic architecture of short gestation length in QP pigs. In this study, selective sweep analyses were performed to detect selective sweep signatures for short gestation length traits between 100 QP pigs and 219 pigs from 15 other breeds. In addition, differentially expressed genes for the short gestation length between QP pigs and Large White pigs were detected by RNA sequencing. Comparing candidate genes from these methods with known genes for preterm birth in the database, we obtained 111 candidate genes that were known preterm birth genes. Prioritizing other candidate genes, 839 novel prioritized candidate genes were found to have significant functional similarity to preterm birth genes. In particular, we highlighted EGFR, which was the most prioritized novel candidate relative to preterm birth genes. Experimental validations in placental and porcine trophectoderm cells suggest that EGFR is highly expressed in the QP pigs with short gestation length and could regulate the NF-κΒ pathway and downstream expression of PTGS2. These findings comprehensively identified candidate genes for short gestation length trait at the genomic and transcriptomic levels. These candidate genes provide an important new resource for further investigation and genetic improvement of gestation length.
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Affiliation(s)
- Zezhang Liu
- Key Laboratory of Swine Genetics and Breeding of the Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jun Yang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhuxia Zhong
- Key Laboratory of Swine Genetics and Breeding of the Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jian Huang
- Key Laboratory of Swine Genetics and Breeding of the Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jie Fu
- Key Laboratory of Swine Genetics and Breeding of the Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hucheng Zhao
- Key Laboratory of Swine Genetics and Breeding of the Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaolei Liu
- Key Laboratory of Swine Genetics and Breeding of the Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University Hubei Hongshan Laboratory, Wuhan, China
- 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, China
- *Correspondence: Xiaolei Liu, ; Siwen Jiang,
| | - Siwen Jiang
- Key Laboratory of Swine Genetics and Breeding of the Agricultural Ministry and Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- *Correspondence: Xiaolei Liu, ; Siwen Jiang,
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Gong Y, Zhang HY, Yuan Y, He Y, Zhang W, Han Y, Na R, Zeng Y, Luo J, Yang H, Huang Y, Zhao Y, Zhao Z, E GX. Genome-Wide Selection Sweep between Wild and Local Pigs from Europe for the Investigation of the Hereditary Characteristics of Domestication in Sus Scrofa. Animals (Basel) 2022; 12:ani12081037. [PMID: 35454283 PMCID: PMC9030587 DOI: 10.3390/ani12081037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/23/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
The phenotypic characteristics of existing domestic pigs (DPs) greatly differ from those of wild boar (WB) populations thousands of years ago. After thousands of years of human domestication, WB and DP have diverged greatly in terms of genetics. Theoretically, worldwide local pigs have independent contributions from their local WBs at the beginning of Sus scrofa domestication. The investigation of the vicissitude of the heredity material between domestic populations and their wild ancestors will help in further understanding the domestication history of domestic animals. In the present study, we performed a genome-wide association scan (GWSA) and phylogeny estimation with a total of 1098 public European Illumina 60K single nucleotide polymorphism data, which included 650 local DPs and 448 WBs. The results revealed that the phylogenetic relationship of WBs corresponds to their geographical distribution and carries large divergence with DPs, and all WB breeds (e.g., HRWB, SBWB, and TIWB) presents a closely linkage with the middle WB (e.g., HRWB, and PLWB). In addition, 64 selected candidate genes (e.g., IDH2, PIP5K1B, SMARCA2, KIF5C, and TJP2) were identified from GWSA. A total of 63 known multiple biological functional pathways were annotated by 22 genes, and ubiquinone and other terpenoid-quinone biosynthesis pathways that belong to the metabolism of cofactors and vitamins were significantly enriched (p < 0.05). The most frequent (28.57%) pathways were classified under metabolism. We confirmed that the middle European WB has made an important genetic contribution to the entire European WB populations. A series of selected genes discovered from this study provides the scientific community with a deeper understanding of the heredity performance of metabolism and emotion and the real purpose behind domestication.
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Peng Y, Cai X, Wang Y, Liu Z, Zhao Y. Genome‐wide analysis suggests multiple domestication events of Chinese local pigs. Anim Genet 2022; 53:293-306. [DOI: 10.1111/age.13183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 02/12/2022] [Accepted: 02/12/2022] [Indexed: 01/02/2023]
Affiliation(s)
- Yebo Peng
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
| | - Xinyu Cai
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
| | - Yuzhan Wang
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
| | - Zexuan Liu
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing China
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49
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Islam SS, Xue X, Caballero-Solares A, Bradbury IR, Rise ML, Fleming IA. Distinct early life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations. Mol Ecol 2022; 31:2712-2729. [PMID: 35243721 DOI: 10.1111/mec.16418] [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: 09/20/2021] [Revised: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 11/27/2022]
Abstract
Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disruption of local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic consequences posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene transcript expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of fry at the end of yolk sac absorption of a European (EO) farmed ("StofnFiskur", Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected the fewest differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the wild populations.
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Affiliation(s)
- Shahinur S Islam
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Xi Xue
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Albert Caballero-Solares
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian R Bradbury
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada.,Salmonids Section, Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Road, St. John's, NL, A1C 5X, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
| | - Ian A Fleming
- Department of Ocean Sciences, Ocean Sciences Centre, Memorial University of Newfoundland, St John's, NL, A1C 5S7, Canada
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50
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Chen J, Zhong J, He X, Li X, Ni P, Safner T, Šprem N, Han J. The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications. Anim Genet 2022; 53:281-292. [PMID: 35238061 PMCID: PMC9314987 DOI: 10.1111/age.13181] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/12/2022] [Accepted: 02/12/2022] [Indexed: 02/05/2023]
Abstract
The rapid progress of sequencing technology has greatly facilitated the de novo genome assembly of pig breeds. However, the assembly of the wild boar genome is still lacking, hampering our understanding of chromosomal and genomic evolution during domestication from wild boars into domestic pigs. Here, we sequenced and de novo assembled a European wild boar genome (ASM2165605v1) using the long‐range information provided by 10× Linked‐Reads sequencing. We achieved a high‐quality assembly with contig N50 of 26.09 Mb. Additionally, 1.64% of the contigs (222) with lengths from 107.65 kb to 75.36 Mb covered 90.3% of the total genome size of ASM2165605v1 (~2.5 Gb). Mapping analysis revealed that the contigs can fill 24.73% (93/376) of the gaps present in the orthologous regions of the updated pig reference genome (Sscrofa11.1). We further improved the contigs into chromosome level with a reference‐assistant scaffolding method. Using the ‘assembly‐to‐assembly’ approach, we identified intra‐chromosomal large structural variations (SVs, length >1 kb) between ASM2165605v1 and Sscrofa11.1 assemblies. Interestingly, we found that the number of SV events on the X chromosome deviated significantly from the linear models fitting autosomes (R2 > 0.64, p < 0.001). Specifically, deletions and insertions were deficient on the X chromosome by 66.14 and 58.41% respectively, whereas duplications and inversions were excessive on the X chromosome by 71.96 and 107.61% respectively. We further used the large segmental duplications (SDs, >1 kb) events as a proxy to understand the large‐scale inter‐chromosomal evolution, by resolving parental‐derived relationships for SD pairs. We revealed a significant excess of SD movements from the X chromosome to autosomes (p < 0.001), consistent with the expectation of meiotic sex chromosome inactivation. Enrichment analyses indicated that the genes within derived SD copies on autosomes were significantly related to biological processes involving nervous system, lipid biosynthesis and sperm motility (p < 0.01). Together, our analyses of the de novo assembly of ASM2165605v1 provides insight into the SVs between European wild boar and domestic pig, in addition to the ongoing process of meiotic sex chromosome inactivation in driving inter‐chromosomal interaction between the sex chromosome and autosomes.
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Affiliation(s)
- Jianhai Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Zhong
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xuefei He
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoyu Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Pan Ni
- Animal Husbandry and Veterinary Institute of Keqiao District, Shaoxing, Zhejiang, China
| | - Toni Safner
- Faculty of Agriculture, University of Zagreb, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, (CoE CroP-BioDiv), Zagreb, Croatia
| | - Nikica Šprem
- Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Jianlin Han
- International Livestock Research Institute, Nairobi, Kenya.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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