1
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Wang J, Yu J, Lipka AE, Zhang Z. Interpretation of Manhattan Plots and Other Outputs of Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:63-80. [PMID: 35641759 DOI: 10.1007/978-1-0716-2237-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
With increasing marker density, estimation of recombination rate between a marker and a causal mutation using linkage analysis becomes less important. Instead, linkage disequilibrium (LD) becomes the major indicator for gene mapping through genome-wide association studies (GWAS). In addition to the linkage between the marker and the causal mutation, many other factors may contribute to the LD, including population structure and cryptic relationships among individuals. As statistical methods and software evolve to improve statistical power and computing speed in GWAS, the corresponding outputs must also evolve to facilitate the interpretation of input data, the analytical process, and final association results. In this chapter, our descriptions focus on (1) considerations in creating a Manhattan plot displaying the strength of LD and locations of markers across a genome; (2) criteria for genome-wide significance threshold and the different appearance of Manhattan plots in single-locus and multiple-locus models; (3) exploration of population structure and kinship among individuals; (4) quantile-quantile (QQ) plot; (5) LD decay across the genome and LD between the associated markers and their neighbors; (6) exploration of individual and marker information on Manhattan and QQ plots via interactive visualization using HTML. The ultimate objective of this chapter is to help users to connect input data to GWAS outputs to balance power and false positives, and connect GWAS outputs to the selection of candidate genes using LD extent.
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Affiliation(s)
- Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, China.
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
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2
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Brashear WA, Bredemeyer KR, Murphy WJ. Genomic architecture constrained placental mammal X Chromosome evolution. Genome Res 2021; 31:1353-1365. [PMID: 34301625 PMCID: PMC8327908 DOI: 10.1101/gr.275274.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/22/2021] [Indexed: 01/02/2023]
Abstract
Susumu Ohno proposed that the gene content of the mammalian X Chromosome should remain highly conserved due to dosage compensation. X Chromosome linkage (gene order) conservation is widespread in placental mammals but does not fall within the scope of Ohno's prediction and may be an indirect result of selection on gene content or selection against rearrangements that might disrupt X-Chromosome inactivation (XCI). Previous comparisons between the human and mouse X Chromosome sequences have suggested that although single-copy X Chromosome genes are conserved between species, most ampliconic genes were independently acquired. To better understand the evolutionary and functional constraints on X-linked gene content and linkage conservation in placental mammals, we aligned a new, high-quality, long-read X Chromosome reference assembly from the domestic cat (incorporating 19.3 Mb of targeted BAC clone sequence) to the pig, human, and mouse assemblies. A comprehensive analysis of annotated X-linked orthologs in public databases demonstrated that the majority of ampliconic gene families were present on the ancestral placental X Chromosome. We generated a domestic cat Hi-C contact map from an F1 domestic cat/Asian leopard cat hybrid and demonstrated the formation of the bipartite structure found in primate and rodent inactivated X Chromosomes. Conservation of gene order and recombination patterns is attributable to strong selective constraints on three-dimensional genomic architecture necessary for superloop formation. Species with rearranged X Chromosomes retain the ancestral order and relative spacing of loci critical for superloop formation during XCI, with compensatory inversions evolving to maintain these long-range physical interactions.
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Affiliation(s)
- Wesley A Brashear
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Kevin R Bredemeyer
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
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3
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Johnsson M, Whalen A, Ros-Freixedes R, Gorjanc G, Chen CY, Herring WO, de Koning DJ, Hickey JM. Genetic variation in recombination rate in the pig. Genet Sel Evol 2021; 53:54. [PMID: 34171988 PMCID: PMC8235837 DOI: 10.1186/s12711-021-00643-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00643-0.
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Affiliation(s)
- Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK. .,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden.
| | - Andrew Whalen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
| | - Roger Ros-Freixedes
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.,Departament de Ciència Animal, Universitat de Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
| | - Ching-Yi Chen
- Pig Improvement Company, Genus plc, 100 Bluegrass Commons Blvd., Ste2200, Hendersonville, TN, 37075, USA
| | - William O Herring
- Pig Improvement Company, Genus plc, 100 Bluegrass Commons Blvd., Ste2200, Hendersonville, TN, 37075, USA
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
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4
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Zhou R, Li ST, Yao WY, Xie CD, Chen Z, Zeng ZJ, Wang D, Xu K, Shen ZJ, Mu Y, Bao W, Jiang W, Li R, Liang Q, Li K. The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication. Mol Ecol Resour 2021; 21:2077-2092. [PMID: 33825319 DOI: 10.1111/1755-0998.13396] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/17/2021] [Accepted: 03/29/2021] [Indexed: 01/27/2023]
Abstract
There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.
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Affiliation(s)
- Rong Zhou
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shang-Tong Li
- National Institute of Biological Sciences (NIBS, Beijing, China
| | - Wen-Ye Yao
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chun-Di Xie
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Zhi-Jie Zeng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Di Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Kui Xu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhao-Ji Shen
- Guangdong Provincial key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, China.,Fulcrum gene science and technology (Beijing) Ltd, Beijing, China
| | - Yulian Mu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenbin Bao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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5
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Wu Q, Zhou Y, Wang Y, Zhang Y, Shen Y, Su Q, Gao G, Xu H, Zhou X, Liu B. Whole-genome sequencing reveals breed-differential CNVs between Tongcheng and Large White pigs. Anim Genet 2020; 51:940-944. [PMID: 32808316 DOI: 10.1111/age.12993] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2020] [Indexed: 01/26/2023]
Abstract
Large phenotypic differences have been observed between Tongcheng and Large White pigs. However, little is known about their genetic basis. This study performed a genome-wide comparison of CNVs between Tongcheng and Large White pigs using genome sequencing data. By combining the advantages of three different strategies (read depth, paired-end mapping and split read), we detected in total 18 687 CNVs that covered approximately 3.5% of the pig genome length for Tongcheng and Large White pigs. We identified 1864 breed-stratified CNVs (top 10%) by performing VST statistics. Functional enrichment analyses for genes located in breed-stratified CNVs were found to be involved in pigmentation, behavior, immune system and reproductive processes, which coincide with phenotypic differences between the two breeds. Using a systematic analysis of the genome and transcriptome data, we further identified four novel breed-differential CNVs on the functional genes (disease-resistant, DCUN1D2 and SPARCL1; lipid metabolism, PLEKHA2 and SLCO1A2). Subsequent PCR validation confirmed their accurate breakpoint positions in 33 Tongcheng pigs and 33 Large White pigs. This study provides essential information on differential CNVs for further research on the genetic basis of phenotypic differences between Tongcheng and Large White pigs.
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Affiliation(s)
- Q Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Y Shen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Q Su
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - G Gao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - H Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - X Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - B Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture and College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
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6
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Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs. Sci Rep 2020; 10:9433. [PMID: 32523001 PMCID: PMC7286894 DOI: 10.1038/s41598-020-66061-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 05/14/2020] [Indexed: 12/05/2022] Open
Abstract
Chinese indigenous pigs exhibit considerable phenotypic diversity, but their population structure and the genetic basis of agriculturally important traits need further exploration. Here, we sequenced the whole genomes of 24 individual pigs representing 22 breeds distributed throughout China. For comparison with European and commercial breeds (one pig per breed), we included seven published pig genomes with our new genomes for analyses. Our results showed that breeds grouped together based on morphological classifications are not necessarily more genetically similar to each other than to breeds from other groups. We found that genetic material from European pigs likely introgressed into five Chinese breeds. We have identified two new subpopulations of domestic pigs that encompass morphology-based criteria in China. The Southern Chinese subpopulation comprises the classical South Chinese Type and part of the Central China Type. In contrast, the Northern Chinese subpopulation comprises the North China Type, the Lower Yangtze River Basin Type, the Southwest Type, the Plateau Type, and the remainder of the Central China Type. Eight haplotypes and two recombination sites were identified within a conserved 40.09 Mb linkage-disequilibrium (LD) block on the X chromosome. Potential candidate genes (LEPR, FANCC, COL1A1, and PCCA) influencing body size were identified. Our findings provide insights into the phylogeny of Chinese indigenous pig breeds and benefit gene mining efforts to improve major economic traits.
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7
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Li G, Figueiró HV, Eizirik E, Murphy WJ. Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species. Mol Biol Evol 2020; 36:2111-2126. [PMID: 31198971 PMCID: PMC6759079 DOI: 10.1093/molbev/msz139] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ∼40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.
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Affiliation(s)
- Gang Li
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Henrique V Figueiró
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - Eduardo Eizirik
- PUCRS, Escola de Ciências, Laboratory of Genomics and Molecular Biology, Porto Alegre, Brazil.,INCT-EECBio, Brazil
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
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8
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Genome-wide recombination map construction from single individuals using linked-read sequencing. Nat Commun 2019; 10:4309. [PMID: 31541091 PMCID: PMC6754380 DOI: 10.1038/s41467-019-12210-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 08/28/2019] [Indexed: 12/19/2022] Open
Abstract
Meiotic recombination rates vary across the genome, often involving localized crossover hotspots and coldspots. Studying the molecular basis and mechanisms underlying this variation has been challenging due to the high cost and effort required to construct individualized genome-wide maps of recombination crossovers. Here we introduce a new method, called ReMIX, to detect crossovers from gamete DNA of a single individual using Illumina sequencing of 10X Genomics linked-read libraries. ReMIX reconstructs haplotypes and identifies the valuable rare molecules spanning crossover breakpoints, allowing quantification of the genomic location and intensity of meiotic recombination. Using a single mouse and stickleback fish, we demonstrate how ReMIX faithfully recovers recombination hotspots and landscapes that have previously been built using hundreds of offspring. ReMIX provides a high-resolution, high-throughput, and low-cost approach to quantify recombination variation across the genome, providing an exciting opportunity to study recombination among multiple individuals in diverse organisms. Variation of recombination rates within genomes has important implications in genetics and evolution. Here, the authors develop a method for building genome-wide recombination maps from single individuals using linked-read sequencing data, and report its application in mouse and stickleback fish.
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9
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Buckley RM, Kortschak RD, Adelson DL. Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse. PLoS Comput Biol 2018; 14:e1006091. [PMID: 29677183 PMCID: PMC5931693 DOI: 10.1371/journal.pcbi.1006091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 05/02/2018] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
The forces driving the accumulation and removal of non-coding DNA and ultimately the evolution of genome size in complex organisms are intimately linked to genome structure and organisation. Our analysis provides a novel method for capturing the regional variation of lineage-specific DNA gain and loss events in their respective genomic contexts. To further understand this connection we used comparative genomics to identify genome-wide individual DNA gain and loss events in the human and mouse genomes. Focusing on the distribution of DNA gains and losses, relationships to important structural features and potential impact on biological processes, we found that in autosomes, DNA gains and losses both followed separate lineage-specific accumulation patterns. However, in both species chromosome X was particularly enriched for DNA gain, consistent with its high L1 retrotransposon content required for X inactivation. We found that DNA loss was associated with gene-rich open chromatin regions and DNA gain events with gene-poor closed chromatin regions. Additionally, we found that DNA loss events tended to be smaller than DNA gain events suggesting that they were able to accumulate in gene-rich open chromatin regions due to their reduced capacity to interrupt gene regulatory architecture. GO term enrichment showed that mouse loss hotspots were strongly enriched for terms related to developmental processes. However, these genes were also located in regions with a high density of conserved elements, suggesting that despite high levels of DNA loss, gene regulatory architecture remained conserved. This is consistent with a model in which DNA gain and loss results in turnover or "churning" in regulatory element dense regions of open chromatin, where interruption of regulatory elements is selected against.
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Affiliation(s)
- Reuben M. Buckley
- Department of Genetics and Evolution, The University of Adelaide, North Tce, Adelaide, Australia
| | - R. Daniel Kortschak
- Department of Genetics and Evolution, The University of Adelaide, North Tce, Adelaide, Australia
| | - David L. Adelson
- Department of Genetics and Evolution, The University of Adelaide, North Tce, Adelaide, Australia
- * E-mail:
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10
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Lago LV, Nery da Silva A, Zanella EL, Groke Marques M, Peixoto JO, da Silva MVGB, Ledur MC, Zanella R. Identification of Genetic Regions Associated with Scrotal Hernias in a Commercial Swine Herd. Vet Sci 2018; 5:vetsci5010015. [PMID: 29382056 PMCID: PMC5876567 DOI: 10.3390/vetsci5010015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 01/17/2023] Open
Abstract
In this paper, we have used two approaches to detect genetic associations with scrotal hernias in commercial pigs. Firstly, we have investigated the effects of runs of homozygosity (ROH) with the appearance of scrotal hernias, followed by a Genome Wide Association Study (GWAS). The phenotype classification was based on visual appearance of scrotal hernias. Each affected animal was matched to a healthy control from the same pen. In the total, 68 animals were genotyped using the Porcine SNP60 Beadchip, out of those, 41 animals had the presence of hernias and 27 were healthy animals. Fifteen animals were removed from the analysis due to differences in genetic background, leaving 18 healthy animals and 35 piglets with scrotal hernia. Further, the detection of extended haplotypes shared ROH were conducted for health (control) and affected (case) animals and a permutation test was used to test whether the ROH segments were more frequent in case/case pairs than non-case/case pairs. Using the ROH, we have identified an association (p = 0.019) on chromosome 2(SSC2) being segregated on animals with the presence of scrotal hernias. Using a GWAS, a region composed by 3 SNPs on the sexual chromosome X (SSCX) were associated with scrotal hernias (p < 1.6 × 10-5), this region harbors the Androgen Receptor Gene (AR).
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Affiliation(s)
- Luisa Vitória Lago
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
| | - Arthur Nery da Silva
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
| | - Eraldo L Zanella
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
- Docentes do Programa de Pós-Graduação em Bioexperimentação-UPF, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
| | | | - Jane O Peixoto
- Embrapa Suínos e Aves, Rodovia BR-153, Km110, Concórdia, SC 89715-899, Brazil.
| | - Marcos V G B da Silva
- Embrapa Gado de Leite, Rua Eugênio do Nascimento, 610, Juiz de Fora, MG 36038-330, Brazil.
| | - Mônica C Ledur
- Embrapa Suínos e Aves, Rodovia BR-153, Km110, Concórdia, SC 89715-899, Brazil.
| | - Ricardo Zanella
- College of Veterinary Medicine, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
- Docentes do Programa de Pós-Graduação em Bioexperimentação-UPF, University of Passo Fundo, BR 285, São José, Passo Fundo, RS 99052-900, Brazil.
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11
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Fu Y, Li C, Tang Q, Tian S, Jin L, Chen J, Li M, Li C. Genomic analysis reveals selection in Chinese native black pig. Sci Rep 2016; 6:36354. [PMID: 27808243 PMCID: PMC5093412 DOI: 10.1038/srep36354] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/13/2016] [Indexed: 12/12/2022] Open
Abstract
Identification of genomic signatures that help reveal mechanisms underlying desirable traits in domesticated pigs is of significant biological, agricultural and medical importance. To identify the genomic footprints left by selection during domestication of the Enshi black pig, a typical native and meat-lard breed in China, we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations. Combining this data with the available whole genomes of 13 Chinese wild boars, we identified 417 protein-coding genes embedded in the selected regions of Enshi black pigs. These genes are mainly involved in developmental and metabolic processes, response to stimulus, and other biological processes. Signatures of selection were detected in genes involved in body size and immunity (RPS10 and VASN), lipid metabolism (GSK3), male fertility (INSL6) and developmental processes (TBX19). These findings provide a window into the potential genetic mechanism underlying development of desirable phenotypes in Enshi black pigs during domestication and subsequent artificial selection. Thus, our results illustrate how domestication has shaped patterns of genetic variation in Enshi black pigs and provide valuable genetic resources that enable effective use of pigs in agricultural production.
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Affiliation(s)
- Yuhua Fu
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Cencen Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Jianhai Chen
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
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12
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Li G, Hillier LW, Grahn RA, Zimin AV, David VA, Menotti-Raymond M, Middleton R, Hannah S, Hendrickson S, Makunin A, O'Brien SJ, Minx P, Wilson RK, Lyons LA, Warren WC, Murphy WJ. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (BETHESDA, MD.) 2016; 6:1607-16. [PMID: 27172201 PMCID: PMC4889657 DOI: 10.1534/g3.116.028746] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/23/2016] [Indexed: 01/03/2023]
Abstract
High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location.
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Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843
| | - LaDeana W Hillier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Robert A Grahn
- College of Veterinary Medicine, University of Missouri-Columbia, Missouri 65201 Population Health and Reproduction, University of California-Davis, California 95616
| | - Aleksey V Zimin
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742
| | - Victor A David
- National Cancer Institute-Frederick, National Institutes of Health, Maryland 21702
| | | | | | - Steven Hannah
- Nestlé Purina PetCare Company, St. Louis, Missouri 63134
| | - Sher Hendrickson
- Department of Biology, Shepherd University, Shepherdstown, West Virginia 25443 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Alex Makunin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Stephen J O'Brien
- National Cancer Institute-Frederick, National Institutes of Health, Maryland 21702 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Pat Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Leslie A Lyons
- College of Veterinary Medicine, University of Missouri-Columbia, Missouri 65201 Population Health and Reproduction, University of California-Davis, California 95616
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843
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13
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Groenen MAM. A decade of pig genome sequencing: a window on pig domestication and evolution. Genet Sel Evol 2016; 48:23. [PMID: 27025270 PMCID: PMC4812630 DOI: 10.1186/s12711-016-0204-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/16/2016] [Indexed: 12/02/2022] Open
Abstract
Insight into how genomes change and adapt due to selection addresses key questions in evolutionary biology and in domestication of animals and plants by humans. In that regard, the pig and its close relatives found in Africa and Eurasia represent an excellent group of species that enables studies of the effect of both natural and human-mediated selection on the genome. The recent completion of the draft genome sequence of a domestic pig and the development of next-generation sequencing technology during the past decade have created unprecedented possibilities to address these questions in great detail. In this paper, I review recent whole-genome sequencing studies in the pig and closely-related species that provide insight into the demography, admixture and selection of these species and, in particular, how domestication and subsequent selection of Sus scrofa have shaped the genomes of these animals.
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Affiliation(s)
- Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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14
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Li G, Davis BW, Eizirik E, Murphy WJ. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Res 2016; 26:1-11. [PMID: 26518481 PMCID: PMC4691742 DOI: 10.1101/gr.186668.114] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 10/13/2015] [Indexed: 12/27/2022]
Abstract
Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X- and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven post-divergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.
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Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Eduardo Eizirik
- Faculdade de Biociências, PUCRS, Porto Alegre, RS 90619-900, Brazil
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
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15
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Guo Y, Hou L, Zhang X, Huang M, Mao H, Chen H, Ma J, Chen C, Ai H, Ren J, Huang L. A meta analysis of genome-wide association studies for limb bone lengths in four pig populations. BMC Genet 2015. [PMID: 26219668 PMCID: PMC4518597 DOI: 10.1186/s12863-015-0257-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Limb bone length is an economically important trait in pigs, because it is negatively correlated with backfat thickness, and is also a determinant to the yield of hip and loin. Moreover, abnormal growth of the limb bone leads to leg structural weakness. Until now, the genetic architecture of the pig lime bone length remains poorly understood. The object of this study was to map genomic loci for limb bone length by genome-wide association study (GWAS) on 4 pig populations. Results We measured the lengths of five limb bones including scapula, humerus, ulna, femur and tibia that were dissected from the right-side carcass of 925, 331, 314 and 434 animals from White Duroc × Erhualian F2 intercross, Erhualian, Laiwu and Sutai populations, respectively. We genotyped the 2004 pigs for 62,163 single nucleotide polymorphisms (SNPs) on the Porcine SNP60 BeadChip, and performed GWAS and a GWAS meta analysis in the 4 populations. In total, we identified 12 and 4 loci associated with the limb bone lengths at suggestive and genome-wide significant levels respectively, of which 4 loci were reported for the first time. The most prominent locus was identified in a 924-kb (kilo base pairs) linkage disequilibrium block on Sus Scrofa chromosome (SSC) 7, and High Mobility Group AT-hook 1 (HMGA1) appears to be a strong candidate gene in this region. Another promising locus is located in the middle of SSC4, and Pleiomorphic Adenoma Gene 1 (PLAG1) is a functionally plausible candidate gene underlying the locus. Because the lengths of the 5 limb bones are highly correlated to each other, most of significant loci were associated with all of the 5 traits; however, several loci showed specific effect on the length of one limb bone, such as the locus at the proximal end of SSC2 associated with only the scapula length. Conclusion To our knowledge, this study was the first GWAS meta analysis for limb bone lengths in pigs. As expected, the meta analysis is more powerful to identify genomic loci. A total of 16 loci were identified in this study, including four novel loci. HMGA1 and PLAG1 are two appearing candidate genes for pig limb bone lengths, which warrant further investigations. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0257-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuanmei Guo
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lijuan Hou
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Xufei Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China. .,Current address: Wenzhou Medical University, WenZhou, 325000, China.
| | - Min Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huirong Mao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Hao Chen
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Junwu Ma
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Congying Chen
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Huashui Ai
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Jun Ren
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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16
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Qiao R, Gao J, Zhang Z, Li L, Xie X, Fan Y, Cui L, Ma J, Ai H, Ren J, Huang L. Genome-wide association analyses reveal significant loci and strong candidate genes for growth and fatness traits in two pig populations. Genet Sel Evol 2015; 47:17. [PMID: 25885760 PMCID: PMC4358731 DOI: 10.1186/s12711-015-0089-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 01/08/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Recently, genome-wide association studies (GWAS) have been reported on various pig traits. We performed a GWAS to analyze 22 traits related to growth and fatness on two pig populations: a White Duroc × Erhualian F2 intercross population and a Chinese Sutai half-sib population. RESULTS We identified 14 and 39 loci that displayed significant associations with growth and fatness traits at the genome-wide level and chromosome-wide level, respectively. The strongest association was between a 750 kb region on SSC7 (SSC for Sus scrofa) and backfat thickness at the first rib. This region had pleiotropic effects on both fatness and growth traits in F2 animals and contained a promising candidate gene HMGA1 (high mobility group AT-hook 1). Unexpectedly, population genetic analysis revealed that the allele at this locus that reduces fatness and increases growth is derived from Chinese indigenous pigs and segregates in multiple Chinese breeds. The second strongest association was between the region around 82.85 Mb on SSC4 and average backfat thickness. PLAG1 (pleiomorphic adenoma gene 1), a gene under strong selection in European domestic pigs, is proximal to the top SNP and stands out as a strong candidate gene. On SSC2, a locus that significantly affects fatness traits mapped to the region around the IGF2 (insulin-like growth factor 2) gene but its non-imprinting inheritance excluded IGF2 as a candidate gene. A significant locus was also detected within a recombination cold spot that spans more than 30 Mb on SSCX, which hampered the identification of plausible candidate genes. Notably, no genome-wide significant locus was shared by the two experimental populations; different loci were observed that had both constant and time-specific effects on growth traits at different stages, which illustrates the complex genetic architecture of these traits. CONCLUSIONS We confirm several previously reported QTL and provide a list of novel loci for porcine growth and fatness traits in two experimental populations with Chinese Taihu and Western pigs as common founders. We showed that distinct loci exist for these traits in the two populations and identified HMGA1 and PLAG1 as strong candidate genes on SSC7 and SSC4, respectively.
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Affiliation(s)
- Ruimin Qiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Jun Gao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Zhiyan Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Lin Li
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Xianhua Xie
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Yin Fan
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Leilei Cui
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Huashui Ai
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China.
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17
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Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L, Zhang F, Zhang L, Cui L, He W, Yang J, Yao X, Zhou L, Han L, Li J, Sun S, Xie X, Lai B, Su Y, Lu Y, Yang H, Huang T, Deng W, Nielsen R, Ren J, Huang L. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 2015; 47:217-25. [DOI: 10.1038/ng.3199] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 12/29/2014] [Indexed: 12/30/2022]
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18
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Fernández AI, Muñoz M, Alves E, Folch JM, Noguera JL, Enciso MP, Rodríguez MDC, Silió L. Recombination of the porcine X chromosome: a high density linkage map. BMC Genet 2014; 15:148. [PMID: 25526890 PMCID: PMC4293812 DOI: 10.1186/s12863-014-0148-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/08/2014] [Indexed: 01/22/2023] Open
Abstract
Background Linkage maps are essential tools for the study of several topics in genome biology. High density linkage maps for the porcine autosomes have been constructed exploiting the high density data provided by the PorcineSNP60 BeadChip. However, a high density SSCX linkage map has not been reported up to date. The aim of the current study was to build an accurate linkage map of SSCX to provide precise estimates of recombination rates along this chromosome and creating a new tool for QTL fine mapping. Results A female-specific high density linkage map was built for SSCX using Sscrofa10.2 annotation. The total length of this chromosome was 84.61 cM; although the average recombination rate was 0.60 cM/Mb, both cold and hot recombination regions were identified. A Bayesian probabilistic to genetic groups and revealed that the animals used in the current study for linkage map construction were likely to be carriers of X chromosomes of European origin. Finally, the newly generated linkage map was used to fine-map a QTL at 16 cM for intramuscular fat content (IMF) measured on longissimus dorsi. The sulfatase isozyme S gene constitutes a functional and positional candidate gene underlying the QTL effect. Conclusions The current study presents for the first time a high density linkage map for SSCX and supports the presence of cold and hot recombination intervals along this chromosome. The large cold recombination region in the central segment of the chromosome is not likely to be due to structural differences between X chromosomes of European and Asian origin. In addition, the newly generated linkage map has allowed us to fine-map a QTL on SSCX for fat deposition. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0148-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana I Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain.
| | - María Muñoz
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain. .,The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, EH25 9RG, UK.
| | - Estefânia Alves
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain.
| | - Josep María Folch
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, 08193, Spain. .,Present Address: Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autonoma Barcelona, Bellaterra, 08193, Spain.
| | - Jose Luis Noguera
- Genètica i Millora Animal, IRTA, Av. Alcalde Rovira Roure, 191, Lleida, 25198, Spain.
| | - Miguel Pérez Enciso
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, 08193, Spain. .,Present Address: Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Edifici CRAG, Campus Universitat Autonoma Barcelona, Bellaterra, 08193, Spain. .,Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain.
| | | | - Luis Silió
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain.
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19
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Ma J, Gilbert H, Iannuccelli N, Duan Y, Guo B, Huang W, Ma H, Riquet J, Bidanel JP, Huang L, Milan D. Fine mapping of fatness QTL on porcine chromosome X and analyses of three positional candidate genes. BMC Genet 2013; 14:46. [PMID: 23725562 PMCID: PMC3691627 DOI: 10.1186/1471-2156-14-46] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 05/06/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Porcine chromosome X harbors four QTL strongly affecting backfat thickness (BFT), ham weight (HW), intramuscular fat content (IMF) and loin eye area (LEA). The confidence intervals (CI) of these QTL overlap and span more than 30 cM, or approximately 80 Mb. This study therefore attempts to fine map these QTL by joint analysis of two large-scale F₂ populations (Large White × Meishan and White Duroc × Erhualian constructed by INRA and JXAU respectively) and furthermore, to determine whether these QTL are caused by mutations in three positional candidate genes (ACSL4, SERPINA7 and IRS4) involved in lipid biosynthesis. RESULTS A female-specific linkage map with an average distance of 2 cM between markers in the initial QTL interval (SW2456-SW1943) was created and used here. The CI of QTL for BFT, HW and LEA were narrowed down to 6-7 cM, resulting from the joint analysis. For IMF, two linked QTL were revealed in the INRA population but not in the JXAU population, causing a wider CI (13 cM) for IMF QTL. Linkage analyses using two subsets of INRA F₁ dam families demonstrate that the BFT and HW QTL were segregating in the Meishan pigs. Moreover, haplotype comparisons between these dams suggest that within the refined QTL region, the recombination coldspot (~34 Mb) flanked by markers MCSE3F14 and UMNP1218 is unlikely to contain QTL genes. Two SNPs in the ACSL4 gene were identified and showed significant association with BFT and HW, but they and the known polymorphisms in the other two genes are unlikely to be causal mutations. CONCLUSION The candidate QTL regions have been greatly reduced and the QTL are most likely located downstream of the recombination coldspot. The segregation of SSCX QTL for BFT and HW within Meishan breed provides an opportunity for us to make effective use of Meishan chromosome X in crossbreeding. Further studies should attempt to identify the impact of additional DNA sequence (e.g. CNV) and expression variation in the three genes or their surrounding genes on these traits.
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Affiliation(s)
- Junwu Ma
- INRA, UMR444 Laboratoire de Génétique Cellulaire, Castanet-Tolosan F-31326, France
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20
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Bischoff SR, Tsai SQ, Hardison NE, Motsinger-Reif AA, Freking BA, Nonneman DJ, Rohrer GA, Piedrahita JA. Differences in X-chromosome transcriptional activity and cholesterol metabolism between placentae from swine breeds from Asian and Western origins. PLoS One 2013; 8:e55345. [PMID: 23383161 PMCID: PMC3561265 DOI: 10.1371/journal.pone.0055345] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/21/2012] [Indexed: 12/19/2022] Open
Abstract
To gain insight into differences in placental physiology between two swine breeds noted for their dissimilar reproductive performance, that is, the Chinese Meishan and white composite (WC), we examined gene expression profiles of placental tissues collected at 25, 45, 65, 85, and 105 days of gestation by microarrays. Using a linear mixed model, a total of 1,595 differentially expressed genes were identified between the two pig breeds using a false-discovery rate q-value ≤0.05. Among these genes, we identified breed-specific isoforms of XIST, a long non-coding RNA responsible X-chromosome dosage compensation in females. Additionally, we explored the interaction of placental gene expression and chromosomal location by DIGMAP and identified three Sus scrofa X chromosomal bands (Xq13, Xq21, Xp11) that represent transcriptionally active clusters that differ between Meishan and WC during placental development. Also, pathway analysis identified fundamental breed differences in placental cholesterol trafficking and its synthesis. Direct measurement of cholesterol confirmed that the cholesterol content was significantly higher in the Meishan versus WC placentae. Taken together, this work identifies key metabolic pathways that differ in the placentae of two swine breeds noted for differences in reproductive prolificacy.
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Affiliation(s)
- Steve R. Bischoff
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Shengdar Q. Tsai
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Nicholas E. Hardison
- Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Alison A. Motsinger-Reif
- Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Bradley A. Freking
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Dan J. Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Gary A. Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Jorge A. Piedrahita
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
- Center for Comparative Medicine and Translational Research, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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21
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Abstract
Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig--the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1, and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs, most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs, carrying the Dominant white, Patch, or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.
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Bouza C, Hermida M, Pardo BG, Vera M, Fernández C, de la Herrán R, Navajas-Pérez R, Álvarez-Dios JA, Gómez-Tato A, Martínez P. An Expressed Sequence Tag (EST)-enriched genetic map of turbot (Scophthalmus maximus): a useful framework for comparative genomics across model and farmed teleosts. BMC Genet 2012; 13:54. [PMID: 22747677 PMCID: PMC3464660 DOI: 10.1186/1471-2156-13-54] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 07/02/2012] [Indexed: 12/18/2022] Open
Abstract
Background The turbot (Scophthalmus maximus) is a relevant species in European aquaculture. The small turbot genome provides a source for genomics strategies to use in order to understand the genetic basis of productive traits, particularly those related to sex, growth and pathogen resistance. Genetic maps represent essential genomic screening tools allowing to localize quantitative trait loci (QTL) and to identify candidate genes through comparative mapping. This information is the backbone to develop marker-assisted selection (MAS) programs in aquaculture. Expressed sequenced tag (EST) resources have largely increased in turbot, thus supplying numerous type I markers suitable for extending the previous linkage map, which was mostly based on anonymous loci. The aim of this study was to construct a higher-resolution turbot genetic map using EST-linked markers, which will turn out to be useful for comparative mapping studies. Results A consensus gene-enriched genetic map of the turbot was constructed using 463 SNP and microsatellite markers in nine reference families. This map contains 438 markers, 180 EST-linked, clustered at 24 linkage groups. Linkage and comparative genomics evidences suggested additional linkage group fusions toward the consolidation of turbot map according to karyotype information. The linkage map showed a total length of 1402.7 cM with low average intermarker distance (3.7 cM; ~2 Mb). A global 1.6:1 female-to-male recombination frequency (RF) ratio was observed, although largely variable among linkage groups and chromosome regions. Comparative sequence analysis revealed large macrosyntenic patterns against model teleost genomes, significant hits decreasing from stickleback (54%) to zebrafish (20%). Comparative mapping supported particular chromosome rearrangements within Acanthopterygii and aided to assign unallocated markers to specific turbot linkage groups. Conclusions The new gene-enriched high-resolution turbot map represents a useful genomic tool for QTL identification, positional cloning strategies, and future genome assembling. This map showed large synteny conservation against model teleost genomes. Comparative genomics and data mining from landmarks will provide straightforward access to candidate genes, which will be the basis for genetic breeding programs and evolutionary studies in this species.
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Affiliation(s)
- Carmen Bouza
- Departamento de Genética, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Campus de Lugo, 27002, Lugo, Spain
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Burgos-Paz W, Souza CA, Castelló A, Mercadé A, Okumura N, Sheremet'eva IN, Huang LS, Cho IC, Paiva SR, Ramos-Onsins S, Pérez-Enciso M. Worldwide genetic relationships of pigs as inferred from X chromosome SNPs. Anim Genet 2012; 44:130-8. [PMID: 22590984 DOI: 10.1111/j.1365-2052.2012.02374.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2012] [Indexed: 02/04/2023]
Abstract
The phylogeography of the porcine X chromosome has not been studied despite the unique characteristics of this chromosome. Here, we genotyped 59 single nucleotide polymorphisms (SNPs) in 312 pigs from around the world, representing 39 domestic breeds and wild boars in 30 countries. Overall, widespread commercial breeds showed the highest heterozygosity values, followed by African and American populations. Structuring, as inferred from FST and analysis of molecular variance, was consistently larger in the non-pseudoautosomal (NPAR) than in the pseudoautosomal regions (PAR). Our results show that genetic relationships between populations can vary widely between the NPAR and the PAR, underscoring the fact that their genetic trajectories can be quite different. NPAR showed an increased commercial-like genetic component relative to the PAR, probably because human selection processes to obtain individuals with high productive parameters were mediated by introgressing boars rather than sows.
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Affiliation(s)
- W Burgos-Paz
- Center for Research in Agricultural Genomics, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Ai H, Ren J, Zhang Z, Ma J, Guo Y, Yang B, Huang L. Detection of quantitative trait loci for growth- and fatness-related traits in a large-scale White Duroc × Erhualian intercross pig population. Anim Genet 2011; 43:383-91. [PMID: 22497573 DOI: 10.1111/j.1365-2052.2011.02282.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Growth and fatness are economically important traits in pigs. In this study, a genome scan was performed to detect quantitative trait loci (QTL) for 14 growth and fatness traits related to body weight, backfat thickness and fat weight in a large-scale White Duroc × Erhualian F(2) intercross. A total of 76 genome-wide significant QTL were mapped to 16 chromosomes. The most significant QTL was found on pig chromosome (SSC) 7 for fatness with unexpectedly small confidence intervals of ∼2 cM, providing an excellent starting point to identify causal variants. Common QTL for both fatness and growth traits were found on SSC4, 5, 7 and 8, and shared QTL for fat deposition were detected on SSC1, 2 and X. Time-series analysis of QTL for body weight at six growth stages revealed the continuously significant effects of the QTL on SSC4 at the fattening period and the temporal-specific expression of the QTL on SSC7 at the foetus and fattening stages. For fatness traits, Chinese Erhualian alleles were associated with increased fat deposition except that at the major QTL on SSC7. For growth traits, most of White Duroc alleles enhanced growth rates except for those at three significant QTL on SSC6, 7 and 9. The results confirmed many previously reported QTL and also detected novel QTL, revealing the complexity of the genetic basis of growth and fatness in pigs.
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Affiliation(s)
- H Ai
- Key Laboratory for Animal Biotechnology of Jiangxi Province, Jiangxi Agricultural University, Nanchang, China
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Pinton A, Barasc H, Raymond Letron I, Bordedebat M, Mary N, Massip K, Bonnet N, Calgaro A, Dudez AM, Feve K, Riquet J, Yerle M, Ducos A. Meiotic studies of a 38,XY/39,XXY mosaic boar. Cytogenet Genome Res 2010; 133:202-8. [PMID: 21150170 DOI: 10.1159/000321794] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Klinefelter's syndrome (KS) is the most common sex chromosome abnormality identified in human males. This syndrome is generally associated with infertility. Men with KS may have a 47,XXY or a 46,XY/47,XXY karyotype. Studies carried out in humans and mice suggest that only XY cells are able to enter and complete meiosis. These cells could originate from the XY cells present in mosaic patients or from XXY cells that have lost one X chromosome. In pig, only 3 cases of pure 39,XXY have been reported until now, and no meiotic analysis was carried out. For the first time in pig species we report the analysis of a 38,XY/39,XXY boar and describe the origin of the supplementary X chromosome and the chromosomal constitutions of the germ and Sertoli cells.
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Affiliation(s)
- A Pinton
- UMR 444 INRA-ENVT Génétique Cellulaire, Toulouse, France.
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Masopust M, Vykoukalová Z, Knoll A, Bartenschlager H, Mileham A, Deeb N, Rohrer GA, Cepica S. Porcine insulin receptor substrate 4 (IRS4) gene: cloning, polymorphism and association study. Mol Biol Rep 2010; 38:2611-7. [PMID: 21104145 DOI: 10.1007/s11033-010-0402-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 11/08/2010] [Indexed: 01/28/2023]
Abstract
Using PCR and inverse PCR techniques we obtained a 4,498 bp nucleotide sequence FN424076 encompassing the complete coding sequence of the porcine insulin receptor substrate 4 (IRS4) gene and its proximal promoter. The 1,269 amino acid porcine protein deduced from the nucleotide sequence shares 92% identity with the human IRS4 and possesses the same domains and the same number of tyrosine phosphorylation motifs as the human protein. We detected substitution FN424076:g.96C<G in the promoter region that segregates in Meishan and a synonymous substitution FN424076:g.1829T<C in the coding sequence with allele C present only in Meishan. Linkage mapping placed the IRS4 gene at position 82 cM on the current USDA-USMARC linkage map of porcine chromosome X. Association analyses were performed on 555 animals of 12th-15th generation of the Meishan × Large White cross and showed that both SNPs were highly significantly associated with backfat depth (P=0.0005) and that the SNP FN424076:g1829T<C was also associated with loin depth (P=0.017). The Meishan alleles increased back fat depth and decreased loin depth. IRS4 can be considered a positional candidate gene for at least some of the QTL located at the centromeric region of porcine chromosome X.
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Affiliation(s)
- Martin Masopust
- Institute of Animal Physiology and Genetics AS CR, v.v.i., Liběchov, Czech Republic
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