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Li J, Li W, Peng X, Li X, Zhao S, Wang H, Ma Y. Genetic basis of phenotypic convergence in pig terminal sires using pathway-based selection signature detection methods. Anim Genet 2024; 55:664-669. [PMID: 38830632 DOI: 10.1111/age.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024]
Abstract
The primary purpose of genetic improvement in lean pig breeds is to enhance production performance. Owing to their similar breeding directions, Duroc and Pietrain pigs are ideal models for investigating the phenotypic convergence underlying artificial selection. However, most important economic traits are controlled by a polygenic basis, so traditional strategies for detecting selection signatures may not fully reveal the genetic basis of complex traits. The pathway-based gene network analysis method utilizes each pathway as a unit, overcoming the limitations of traditional strategies for detecting selection signatures by revealing the selection of complex biological processes. Here, we utilized 13 122 398 high-quality SNPs from whole-genome sequencing data of 48 Pietrain pigs, 156 Duroc pigs and 36 European wild boars to detect selective signatures. After calculating FST and iHS scores, we integrated the pathway information and utilized the r/bioconductor graphite and signet packages to construct gene networks, identify subnets and uncover candidate genes underlying selection. Using the traditional strategy, a total of 47 genomic regions exhibiting parallel selection were identified. The enriched genes, including INO80, FZR1, LEPR and FAF1, may be associated with reproduction, fat deposition and skeletal development. Using the pathway-based selection signatures detection method, we identified two significant biological pathways and eight potential candidate genes underlying parallel selection, such as VTN, FN1 and ITGAV. This study presents a novel strategy for investigating the genetic basis of complex traits and elucidating the phenotypic convergence underlying artificial selection, by integrating traditional selection signature methods with pathway-based gene network analysis.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Wangjiao Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xia Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou, China
| | - Haiyan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
- Lingnan Modern Agricultural Science and Technology Guangdong Laboratory, Guangzhou, China
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2
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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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3
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Zhao F, Xie R, Fang L, Xiang R, Yuan Z, Liu Y, Wang L. Analysis of 206 whole-genome resequencing reveals selection signatures associated with breed-specific traits in Hu sheep. Evol Appl 2024; 17:e13697. [PMID: 38911262 PMCID: PMC11192971 DOI: 10.1111/eva.13697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 01/02/2024] [Accepted: 04/13/2024] [Indexed: 06/25/2024] Open
Abstract
As an invaluable Chinese sheep germplasm resource, Hu sheep are renowned for their high fertility and beautiful wavy lambskins. Their distinctive characteristics have evolved over time through a combination of artificial and natural selection. Identifying selection signatures in Hu sheep can provide a straightforward insight into the mechanism of selection and further uncover the candidate genes associated with breed-specific traits subject to selection. Here, we conducted whole-genome resequencing on 206 Hu sheep individuals, each with an approximate 6-fold depth of coverage. And then we employed three complementary approaches, including composite likelihood ratio, integrated haplotype homozygosity score and the detection of runs of homozygosity, to detect selection signatures. In total, 10 candidate genomic regions displaying selection signatures were simultaneously identified by multiple methods, spanning 88.54 Mb. After annotating, these genomic regions harbored collectively 92 unique genes. Interestingly, 32 candidate genes associated with reproduction were distributed in nine genomic regions detected. Out of them, two stood out as star candidates: BMPR1B and GNRH2, both of which have documented associations with fertility, and a HOXA gene cluster (HOXA1-5, HOXA9, HOXA10, HOXA11 and HOXA13) had also been linked to fertility. Additionally, we identified other genes that are related to hair follicle development (LAMTOR3, EEF1A2), ear size (HOXA1, KCNQ2), fat tail formation (HOXA10, HOXA11), growth and development (FAF1, CCNDBP1, GJB2, GJA3), fat deposition (ACOXL, JAZF1, HOXA3, HOXA4, HOXA5, EBF4), immune (UBR1, FASTKD5) and feed intake (DAPP1, RNF17, NPBWR2). Our results offer novel insights into the genetic mechanisms underlying the selection of breed-specific traits in Hu sheep and provide a reference for sheep genetic improvement programs.
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Affiliation(s)
- Fuping Zhao
- State Key Laboratory of Animal Biotech BreedingInstitute of Animal Science, Chinese Academy of Agricultural SciencesBeijingChina
| | - Rui Xie
- State Key Laboratory of Animal Biotech BreedingInstitute of Animal Science, Chinese Academy of Agricultural SciencesBeijingChina
- Department of Animal Genetics, Breeding and Reproduction, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Lingzhao Fang
- Center for Quantitative Genetics and GenomicsAarhus UniversityAarhusDenmark
| | - Ruidong Xiang
- Faculty of Veterinary and Agricultural ScienceThe University of MelbourneParkvilleVictoriaAustralia
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of EducationYangzhou UniversityYangzhouChina
| | - Yang Liu
- Department of Animal Genetics, Breeding and Reproduction, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Lixian Wang
- State Key Laboratory of Animal Biotech BreedingInstitute of Animal Science, Chinese Academy of Agricultural SciencesBeijingChina
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Haque MA, Alam MZ, Iqbal A, Lee YM, Dang CG, Kim JJ. Genome-Wide Association Studies for Body Conformation Traits in Korean Holstein Population. Animals (Basel) 2023; 13:2964. [PMID: 37760364 PMCID: PMC10526087 DOI: 10.3390/ani13182964] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
The objective of this study was to identify quantitative trait loci (QTL) and nearby candidate genes that influence body conformation traits. Phenotypic data for 24 body conformation traits were collected from a population of 2329 Korean Holstein cattle, and all animals were genotyped using the 50 K Illumina bovine SNP chip. A total of 24 genome-wide significant SNPs associated with 24 body conformation traits were identified by genome-wide association analysis. The selection of the most promising candidate genes was based on gene ontology (GO) terms and the previously identified functions that influence various body conformation traits as determined in our study. These genes include KCNA1, RYBP, PTH1R, TMIE, and GNAI3 for body traits; ANGPT1 for rump traits; MALRD1, INHBA, and HOXA13 for feet and leg traits; and CDK1, RHOBTB1, and SLC17A1 for udder traits, respectively. These findings contribute to our understanding of the genetic basis of body conformation traits in this population and pave the way for future breeding strategies aimed at enhancing desirable traits in dairy cattle.
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Affiliation(s)
- Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea; (M.A.H.); (M.Z.A.); (A.I.); (Y.-M.L.)
| | - Mohammad Zahangir Alam
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea; (M.A.H.); (M.Z.A.); (A.I.); (Y.-M.L.)
| | - Asif Iqbal
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea; (M.A.H.); (M.Z.A.); (A.I.); (Y.-M.L.)
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea; (M.A.H.); (M.Z.A.); (A.I.); (Y.-M.L.)
| | - Chang-Gwon Dang
- Animal Breeding and Genetics Division, National Institute of Animal Science, Cheonan 31000, Chungcheongnam-do, Republic of Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea; (M.A.H.); (M.Z.A.); (A.I.); (Y.-M.L.)
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5
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Binversie EE, Momen M, Rosa GJM, Davis BW, Muir P. Across-breed genetic investigation of canine hip dysplasia, elbow dysplasia, and anterior cruciate ligament rupture using whole-genome sequencing. Front Genet 2022; 13:913354. [PMID: 36531249 PMCID: PMC9755188 DOI: 10.3389/fgene.2022.913354] [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: 04/05/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Here, we report the use of genome-wide association study (GWAS) for the analysis of canine whole-genome sequencing (WGS) repository data using breed phenotypes. Single-nucleotide polymorphisms (SNPs) were called from WGS data from 648 dogs that included 119 breeds from the Dog10K Genomes Project. Next, we assigned breed phenotypes for hip dysplasia (Orthopedic Foundation for Animals (OFA) HD, n = 230 dogs from 27 breeds; hospital HD, n = 279 dogs from 38 breeds), elbow dysplasia (ED, n = 230 dogs from 27 breeds), and anterior cruciate ligament rupture (ACL rupture, n = 279 dogs from 38 breeds), the three most important canine spontaneous complex orthopedic diseases. Substantial morbidity is common with these diseases. Previous within- and between-breed GWAS for HD, ED, and ACL rupture using array SNPs have identified disease-associated loci. Individual disease phenotypes are lacking in repository data. There is a critical knowledge gap regarding the optimal approach to undertake categorical GWAS without individual phenotypes. We considered four GWAS approaches: a classical linear mixed model, a haplotype-based model, a binary case-control model, and a weighted least squares model using SNP average allelic frequency. We found that categorical GWAS was able to validate HD candidate loci. Additionally, we discovered novel candidate loci and genes for all three diseases, including FBX025, IL1A, IL1B, COL27A1, SPRED2 (HD), UGDH, FAF1 (ED), TGIF2 (ED & ACL rupture), and IL22, IL26, CSMD1, LDHA, and TNS1 (ACL rupture). Therefore, categorical GWAS of ancestral dog populations may contribute to the understanding of any disease for which breed epidemiological risk data are available, including diseases for which GWAS has not been performed and candidate loci remain elusive.
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Affiliation(s)
- Emily E. Binversie
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Mehdi Momen
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Guilherme J. M. Rosa
- Department of Animal and Dairy Sciences, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Peter Muir
- Comparative Orthopaedic and Genetics Research Laboratory, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States,*Correspondence: Peter Muir,
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6
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Li G, Tang J, Huang J, Jiang Y, Fan Y, Wang X, Ren J. Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds. Front Genet 2022; 13:774196. [PMID: 35559012 PMCID: PMC9086400 DOI: 10.3389/fgene.2022.774196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.
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Affiliation(s)
- Guixin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jianhong Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.,Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Jinyan Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yongchuang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yin Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, Nanchang, China
| | - Xiaopeng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jun Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
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7
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Tang Z, Fu Y, Xu J, Zhu M, Li X, Yu M, Zhao S, Liu X. Discovery of selection-driven genetic differences of Duroc, Landrace, and Yorkshire pig breeds by EigenGWAS and F st analyses. Anim Genet 2020; 51:531-540. [PMID: 32400898 DOI: 10.1111/age.12946] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 01/08/2023]
Abstract
Pigs are one of the earliest domesticated animals and multiple breeds have been developed to meet the various demands of consumers. EigenGWAS is a novel strategy to identify candidate genes that underlying population genetic differences and to infer candidate regions under selection as well. In this study, EigenGWAS and Fst analyses were performed using the public re-sequencing data of three typical commercial pig breeds, Duroc, Landrace and Yorkshire. The intersection of genome-wide significant SNPs detected by EigenGWAS and top-ranked 1% SNPs of Fst results were treated as signals under selection. Using the data of all three breeds, 3062 signals under selection were detected and the nearby genomic regions within 300 kb upstream and downstream covered 6.54% of whole genome. Pairs of breeds were analysed along with the pathway analysis. The gene function enrichment results indicated that many candidate genes located in the genomic regions of the signals under selection were associated with biological processes related to growth, metabolism, reproduction, sensory perception, etc. Among the candidate genes, the FSHB, AHR, PTHLH, KDR and FST genes were reported to be associated with reproductive performance; the KIT, KITLG, MITF, MC1R and EDNRB genes were previously identified to affect coat colour; the RETREG1, TXNIP, BMP5, PPARD and RBP4 genes were reported to be associated with lipid metabolism and growth traits. The identified genetic differences across the three commercial breeds will advance understanding of the artificial selection history of pigs and the signals under selection will suggest potential uses in pig genomic breeding programmes.
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Affiliation(s)
- Z Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Y Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - J Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - M Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - M Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - S Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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8
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Identification of mRNAs Related to Tibial Cartilage Development of Yorkshire Piglets. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2365416. [PMID: 31781601 PMCID: PMC6875239 DOI: 10.1155/2019/2365416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/22/2019] [Accepted: 09/16/2019] [Indexed: 11/17/2022]
Abstract
Cartilage dysplasia is one of the important reasons for the weakness of pig limbs and hooves. Porcine rickets with weak limbs and hooves bring huge economic losses to the pig industry. However, research on the development of pig cartilage is lacking. This study investigated the key genes and molecular mechanisms involved in cartilage development via an RNA-seq technique. Samples of proximal tibia cartilage were collected from three normal piglets with 1 day, 14 days, and 28 days of age, respectively, and then these samples were divided into two comparison groups (1-day vs. 14-day group, 14-day vs. 28-day group). Through the transcriptome analysis, 108 differentially expressed genes (DEGs), such as FORL2, were obtained from 1-day vs. 14-day comparison group, and 3602 DEGs were obtained from 14-day vs. 28-day comparison group, including SOX9, BMP6, and MMP13. The gene ontology (GO) functional and KEGG pathway enrichment revealed that many functions of DEGs were related to bone development. The pathways of DEGs from Day 1 vs. Day 14 were mainly enriched in mineral absorption, but the DEGs of Day 14 vs. Day 28 were enriched in osteoclast differentiation. Then, the expression patterns of six candidate genes were verified via qPCR. In conclusion, candidate genes affecting cartilage development in Yorkshire pigs were obtained by transcriptome analysis, and the clues showed that Day 14 to Day 28 is a more active and extensive period in cartilage developments, which played a key role in revealing the molecular mechanism of pig cartilage development basis, also compensating for vacancies in cartilage research.
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Just F, Reyer H, Muráni E, Ponsuksili S, Oster M, Wimmers K. Genetic variants of major genes contributing to phosphate and calcium homeostasis and their association with serum parameters in pigs. J Appl Genet 2018; 59:325-333. [PMID: 29931419 PMCID: PMC6061000 DOI: 10.1007/s13353-018-0449-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 04/12/2018] [Accepted: 06/08/2018] [Indexed: 12/29/2022]
Abstract
Calcium and phosphorus are irreplaceable components of life. Tracking the fate of calcium and phosphorus in organisms deserves high attention due to their relevance in bone metabolism and subsequently animal health. Indeed, bone serves as reservoir for calcium and phosphorus, whose formation and resorption follow specific molecular routes including hormones, receptors, and transcription factors. The objective of the study was to analyze the genetic variation of major components driving mineral utilization such as calcitonin receptor, calcium sensing receptor, fibroblast growth factor 23 (FGF23), parathyroid hormone receptor, osteopontin, stanniocalcin 1, RAF-type zinc finger domain containing 1 (TRAFD1), and vitamin D receptor. A German Landrace pig population (n = 360) was used to perform an association analysis between selected single nucleotide polymorphisms (SNP) and relevant serum parameters (calcium, phosphorus, calcium/phosphorus ratio, alkaline phosphatase). Analyzed SNPs in FGF23 (rs710498025) and TRAFD1 (rs345195312) were significantly (p ≤ 0.05) associated with the serum calcium/phosphorus ratio and serum phosphorus levels, respectively. This might represent a modulation of the homeostatic balance between calcium and phosphorus. Furthermore, TRAFD1 is known to be involved in skeletal disorders which emphasize its link to phosphorus utilization and immune system. However, none of the analyzed genetic variants of these major regulators of phosphate and calcium homeostasis showed significant associations after correction for multiple testing (q value > 0.05). Thus, minor contributors as well as unknown and yet to be elucidated regulators of mineral homeostasis need to be characterized towards the implementation of improved phosphorus efficiency in pig breeding programs.
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Affiliation(s)
- Franziska Just
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Eduard Muráni
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Michael Oster
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany. .,Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany.
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10
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Rothammer S, Bernau M, Kremer-Rücker PV, Medugorac I, Scholz AM. Genome-wide QTL mapping results for regional DXA body composition and bone mineral density traits in pigs. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-51-2017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. In a previous study, genome-wide mapping of quantitative trait loci (QTL) for five body composition traits, three bone mineral traits and live weight was performed using whole-body dual-energy X-ray absorptiometry (DXA) data. Since QTL for bone mineral traits were rare, the current study aimed to clarify whether the mapping results were influenced by the analysed body regions. Thus, the same material (551 pigs) and methods as in the whole-body QTL mapping study were used. However, for evaluation of the DXA scans, we manually defined two body regions: (i) from the last ribs to the pelvis (A) and (ii) including the pelvis and the hind limbs (P). Since live weight was not affected by the regional analysis, it was omitted from the QTL mapping design. Our results show an overall high consistency of mapping results especially for body composition traits. Two thirds of the initial whole-body QTL are significant for both A and P. Possible causes for the still low number of bone mineral QTL and the lower consistency found for these traits are discussed. For body composition traits, the data presented here show high genome-wide Pearson correlations between mapping results that are based on DXA scans with the time-saving whole-body standard setting and mapping results for DXA data that were obtained by time-consuming manual definition of the regions of interest. However, our results also suggest that whole-body or regional DXA scans might generally be less suitable for mapping of bone mineral traits in pigs. An analysis of single reference bones could be more useful.
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11
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Sevane N, Dunner S, Boado A, Cañon J. Polymorphisms in ten candidate genes are associated with conformational and locomotive traits in Spanish Purebred horses. J Appl Genet 2016; 58:355-361. [PMID: 27917442 DOI: 10.1007/s13353-016-0385-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/11/2016] [Accepted: 11/24/2016] [Indexed: 01/08/2023]
Abstract
The Spanish Purebred horses, also known as Andalusian horses, compete to the highest standards in international dressage events. Gait and conformation could be used as early selection criteria to detect young horses with promising dressage ability. Although the genetic background of equine size variation has been recently uncovered, the genetic basis of horse conformational and locomotive traits is not known, hampered by the complex genetic architecture underlying quantitative traits and the lack of phenotypic data. The aim of this study was to validate the loci associated with size in 144 Spanish Purebred horses, and to seek novel associations between loci previously associated with the development of osteochondrosis (OC) lesions and 20 conformational and locomotive traits. Ten loci were associated with different conformational and locomotive traits (LCORL/NCAPG, HMGA2, USP31, MECR, COL24A1, MGP, FAM184B, PTH1R, KLF3 and SGK1), and the LCORL/NCAPG association with size in the Spanish Purebred horse was validated. Except for HMGA2, all polymorphisms seem to influence both the prevalence of OC lesions and morphological characters, supporting the link between conformation and OC. Also, the implication of most genes in either immune and inflammatory responses and cellular growth, or ossification processes, reinforces the role that these mechanisms have in the aetiology of OC, as well as their reflection on the general conformation of the individual. These polymorphisms could be used in marker-assisted selection (MAS) programmes to improve desirable conformational traits, but taking into account their possible detrimental effect on OC prevalence.
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Affiliation(s)
- Natalia Sevane
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, 28040, Spain.
| | - Susana Dunner
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, 28040, Spain
| | - Ana Boado
- Traumatología Equina, El Boalo, Madrid, 28413, Spain
| | - Javier Cañon
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, 28040, Spain
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12
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Sevane N, Dunner S, Boado A, Cañon J. Candidate gene analysis of osteochondrosis in Spanish Purebred horses. Anim Genet 2016; 47:570-8. [DOI: 10.1111/age.12453] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2016] [Indexed: 01/05/2023]
Affiliation(s)
- N. Sevane
- Departamento de Producción Animal; Facultad de Veterinaria; Universidad Complutense; Madrid 28040 Spain
| | - S. Dunner
- Departamento de Producción Animal; Facultad de Veterinaria; Universidad Complutense; Madrid 28040 Spain
| | - A. Boado
- Traumatología Equina; El Boalo Madrid 28413 Spain
| | - J. Cañon
- Departamento de Producción Animal; Facultad de Veterinaria; Universidad Complutense; Madrid 28040 Spain
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13
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Scholz AM, Bünger L, Kongsro J, Baulain U, Mitchell AD. Non-invasive methods for the determination of body and carcass composition in livestock: dual-energy X-ray absorptiometry, computed tomography, magnetic resonance imaging and ultrasound: invited review. Animal 2015; 9:1250-64. [PMID: 25743562 PMCID: PMC4492221 DOI: 10.1017/s1751731115000336] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 02/08/2015] [Indexed: 12/24/2022] Open
Abstract
The ability to accurately measure body or carcass composition is important for performance testing, grading and finally selection or payment of meat-producing animals. Advances especially in non-invasive techniques are mainly based on the development of electronic and computer-driven methods in order to provide objective phenotypic data. The preference for a specific technique depends on the target animal species or carcass, combined with technical and practical aspects such as accuracy, reliability, cost, portability, speed, ease of use, safety and for in vivo measurements the need for fixation or sedation. The techniques rely on specific device-driven signals, which interact with tissues in the body or carcass at the atomic or molecular level, resulting in secondary or attenuated signals detected by the instruments and analyzed quantitatively. The electromagnetic signal produced by the instrument may originate from mechanical energy such as sound waves (ultrasound - US), 'photon' radiation (X-ray-computed tomography - CT, dual-energy X-ray absorptiometry - DXA) or radio frequency waves (magnetic resonance imaging - MRI). The signals detected by the corresponding instruments are processed to measure, for example, tissue depths, areas, volumes or distributions of fat, muscle (water, protein) and partly bone or bone mineral. Among the above techniques, CT is the most accurate one followed by MRI and DXA, whereas US can be used for all sizes of farm animal species even under field conditions. CT, MRI and US can provide volume data, whereas only DXA delivers immediate whole-body composition results without (2D) image manipulation. A combination of simple US and more expensive CT, MRI or DXA might be applied for farm animal selection programs in a stepwise approach.
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Affiliation(s)
- A. M. Scholz
- Livestock Center Oberschleißheim,
Ludwig-Maximilians-University Munich,
Sankt-Hubertusstrasse 12, 85764
Oberschleißheim, Germany
| | - L. Bünger
- SRUC, Animal and Veterinary Sciences,
Roslin Institute Building, Easter Bush,
Midlothian, Scotland EH25 9RG,
UK
| | - J. Kongsro
- Norsvin, Department of Animal and Aquacultural
Sciences, c/o Norwegian University of Life Sciences,
PO Box 5003, N-1432 Ås,
Norway
| | - U. Baulain
- Institute of Farm Animal Genetics,
Friedrich-Loeffler-Institut, Hoeltystr.10,
31535 Neustadt, Germany
| | - A. D. Mitchell
- Agricultural Research Service (Retired), US Department of
Agriculture, 10300 Baltimore Avenue, BARC-West,
Beltsville, MD 20705, USA
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14
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Rothammer S, Kremer PV, Bernau M, Fernandez-Figares I, Pfister-Schär J, Medugorac I, Scholz AM. Genome-wide QTL mapping of nine body composition and bone mineral density traits in pigs. Genet Sel Evol 2014; 46:68. [PMID: 25359100 PMCID: PMC4210560 DOI: 10.1186/s12711-014-0068-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 09/19/2014] [Indexed: 12/20/2022] Open
Abstract
Background Since the pig is one of the most important livestock animals worldwide, mapping loci that are associated with economically important traits and/or traits that influence animal welfare is extremely relevant for efficient future pig breeding. Therefore, the purpose of this study was a genome-wide mapping of quantitative trait loci (QTL) associated with nine body composition and bone mineral traits: absolute (Fat, Lean) and percentage (FatPC, LeanPC) fat and lean mass, live weight (Weight), soft tissue X-ray attenuation coefficient (R), absolute (BMC) and percentage (BMCPC) bone mineral content and bone mineral density (BMD). Methods Data on the nine traits investigated were obtained by Dual-energy X-ray absorptiometry for 551 pigs that were between 160 and 200 days old. In addition, all pigs were genotyped using Illumina’s PorcineSNP60 Genotyping BeadChip. Based on these data, a genome-wide combined linkage and linkage disequilibrium analysis was conducted. Thus, we used 44 611 sliding windows that each consisted of 20 adjacent single nucleotide polymorphisms (SNPs). For the middle of each sliding window a variance component analysis was carried out using ASReml. The underlying mixed linear model included random QTL and polygenic effects, with fixed effects of sex, housing, season and age. Results Using a Bonferroni-corrected genome-wide significance threshold of P < 0.001, significant peaks were identified for all traits except BMCPC. Overall, we identified 72 QTL on 16 chromosomes, of which 24 were significantly associated with one trait only and the remaining with more than one trait. For example, a QTL on chromosome 2 included the highest peak across the genome for four traits (Fat, FatPC, LeanPC and R). The nearby gene, ZNF608, is known to be associated with body mass index in humans and involved in starvation in Drosophila, which makes it an extremely good candidate gene for this QTL. Conclusions Our QTL mapping approach identified 72 QTL, some of which confirmed results of previous studies in pigs. However, we also detected significant associations that have not been published before and were able to identify a number of new and promising candidate genes, such as ZNF608. Electronic supplementary material The online version of this article (doi:10.1186/s12711-014-0068-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Ivica Medugorac
- Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-University Munich, Veterinärstrasse 13, Munich, 80539, Germany.
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Rangkasenee N, Murani E, Schellander K, Cinar MU, Ponsuksili S, Wimmers K. Gene expression profiling of articular cartilage reveals functional pathways and networks of candidate genes for osteochondrosis in pigs. Physiol Genomics 2013; 45:856-65. [PMID: 23922127 DOI: 10.1152/physiolgenomics.00055.2013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Osteochondrosis (OC) is a joint disorder that frequently causes leg weakness in growing pigs, resulting in welfare problems and economic losses. We aimed to detect molecular pathways relevant to the emergence of the disease and to identify candidate genes for the liability to the disorder. Therefore, we compared microarray-based expression patterns of articular cartilage with (n=11) and without (n=11) histologically diagnosed OC lesions obtained from discordant sib-pairs. A total of 1,564 genes were found with different transcript abundance [differentially expressed (DE) genes] at q≤0.05. To further identify candidate genes, we integrated data from quantitative trait loci (QTL) and genome-wide association (GWA) studies with the expression analysis. We detected 317 DE genes within the QTL confidence intervals, of which 26 DE genes also overlapped GWA regions. Ingenuity Pathway Analysis suggests a pathogenic role of immune response, angiogenesis, and synthesis of extracellular matrix pathways for OC. These processes could facilitate the emergence of defects. But they may also promote the degradation of articular cartilage and the worsening of the disease. A functional network was derived that comprised genes with functional and positional clues of their role in bone and cartilage metabolisms and development, including extracellular matrix genes (e.g., LOX, OGN, and ASPN), angiogenesis genes (e.g., ANGPTL4 and PDGFA), and immune response genes (e.g., ICAM1, AZGP1, C1QB, C1QC, PDE4B, and CDA). The study identified molecular processes linked to OC and several genes with positional, genetic-statistical, and functional evidence for their role in the emergence of articular cartilage lesions and the liability to OC.
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