101
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Yuan Z, Liu E, Liu Z, Kijas JW, Zhu C, Hu S, Ma X, Zhang L, Du L, Wang H, Wei C. Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep. Anim Genet 2016; 48:55-66. [PMID: 27807880 DOI: 10.1111/age.12477] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2016] [Indexed: 01/19/2023]
Abstract
Fat-tailed sheep have commercial value because consumers prefer high-protein and low-fat food and producers care about feed conversion rate. However, fat-tailed sheep still have some scientific significance, as the fat tail is commonly regarded as a characteristic of environmental adaptability. Finding the candidate genes associated with fat tail formation is essential for breeding and conservation. To identify these candidate genes, we applied FST and hapFLK approaches in fat- and thin-tailed sheep with available 50K SNP genotype data. These two methods found 6.24 Mb of overlapped regions and 43 genes that may associated with fat tail development. Gene annotation showed that HOXA11, BMP2, PPP1CC, SP3, SP9, WDR92, PROKR1 and ETAA1 may play important roles in fat tail formation. These findings provide insight into tail fat development and a guide for molecular breeding and conservation.
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Affiliation(s)
- Z Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - E Liu
- School of Life Sciences, Capital Normal University, Beijing, China
| | - Z Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - J W Kijas
- CSIRO Agriculture Flagship, Brisbane, Australia
| | - C Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - S Hu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Ma
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - L Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - H Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - C Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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102
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A reference gene catalogue of the pig gut microbiome. Nat Microbiol 2016; 1:16161. [PMID: 27643971 DOI: 10.1038/nmicrobiol.2016.161] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/02/2016] [Indexed: 12/29/2022]
Abstract
The pig is a major species for livestock production and is also extensively used as the preferred model species for analyses of a wide range of human physiological functions and diseases1. The importance of the gut microbiota in complementing the physiology and genome of the host is now well recognized2. Knowledge of the functional interplay between the gut microbiota and host physiology in humans has been advanced by the human gut reference catalogue3,4. Thus, establishment of a comprehensive pig gut microbiome gene reference catalogue constitutes a logical continuation of the recently published pig genome5. By deep metagenome sequencing of faecal DNA from 287 pigs, we identified 7.7 million non-redundant genes representing 719 metagenomic species. Of the functional pathways found in the human catalogue, 96% are present in the pig catalogue, supporting the potential use of pigs for biomedical research. We show that sex, age and host genetics are likely to influence the pig gut microbiome. Analysis of the prevalence of antibiotic resistance genes demonstrated the effect of eliminating antibiotics from animal diets and thereby reducing the risk of spreading antibiotic resistance associated with farming systems.
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103
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Benestan L, Quinn BK, Maaroufi H, Laporte M, Clark FK, Greenwood SJ, Rochette R, Bernatchez L. Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus). Mol Ecol 2016; 25:5073-5092. [DOI: 10.1111/mec.13811] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/09/2016] [Accepted: 08/16/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Laura Benestan
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand 1030 Avenue de la Médecine Québec Québec Canada G1V 0A6
| | - Brady K. Quinn
- Department of Biological Sciences; University of New Brunswick; P.O. Box 5050 Saint John NB Canada E2L 4L5
| | - Halim Maaroufi
- Institut de Biologie Integrative et des Systemes (IBIS); Pavillon Charles-Eugène Marchand; 1030, Avenue de la Médecine Québec Québec Canada G1V 0A6
| | - Martin Laporte
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand 1030 Avenue de la Médecine Québec Québec Canada G1V 0A6
| | - Fraser K. Clark
- Department of Biomedical Sciences; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown Prince Edward Island Canada C1A 4P3
- AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown Prince Edward Island Canada C1A 4P3
| | - Spencer J. Greenwood
- Department of Biomedical Sciences; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown Prince Edward Island Canada C1A 4P3
- AVC Lobster Science Centre; Atlantic Veterinary College; University of Prince Edward Island; Charlottetown Prince Edward Island Canada C1A 4P3
| | - Rémy Rochette
- Department of Biological Sciences; University of New Brunswick; P.O. Box 5050 Saint John NB Canada E2L 4L5
| | - Louis Bernatchez
- Departement de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Pavillon Charles-Eugène-Marchand 1030 Avenue de la Médecine Québec Québec Canada G1V 0A6
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104
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Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas. Sci Rep 2016; 6:29963. [PMID: 27444145 PMCID: PMC4995607 DOI: 10.1038/srep29963] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/28/2016] [Indexed: 12/27/2022] Open
Abstract
Sheep has successfully adapted to the extreme high-altitude Himalayan region. To identify genes underlying such adaptation, we genotyped genome-wide single nucleotide polymorphisms (SNPs) of four major sheep breeds living at different altitudes in Nepal and downloaded SNP array data from additional Asian and Middle East breeds. Using a di value-based genomic comparison between four high-altitude and eight lowland Asian breeds, we discovered the most differentiated variants at the locus of FGF-7 (Keratinocyte growth factor-7), which was previously reported as a good protective candidate for pulmonary injuries. We further found a SNP upstream of FGF-7 that appears to contribute to the divergence signature. First, the SNP occurred at an extremely conserved site. Second, the SNP showed an increasing allele frequency with the elevated altitude in Nepalese sheep. Third, the electrophoretic mobility shift assays (EMSA) analysis using human lung cancer cells revealed the allele-specific DNA-protein interactions. We thus hypothesized that FGF-7 gene potentially enhances lung function by regulating its expression level in high-altitude sheep through altering its binding of specific transcription factors. Especially, FGF-7 gene was not implicated in previous studies of other high-altitude species, suggesting a potential novel adaptive mechanism to high altitude in sheep at the Himalayas.
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105
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Song S, Yao N, Yang M, Liu X, Dong K, Zhao Q, Pu Y, He X, Guan W, Yang N, Ma Y, Jiang L. Exome sequencing reveals genetic differentiation due to high-altitude adaptation in the Tibetan cashmere goat (Capra hircus). BMC Genomics 2016; 17:122. [PMID: 26892324 PMCID: PMC4758086 DOI: 10.1186/s12864-016-2449-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 02/09/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The Tibetan cashmere goat (Capra hircus), one of the most ancient breeds in China, has historically been a critical source of meat and cashmere production for local farmers. To adapt to the high-altitude area, extremely harsh climate, and hypoxic environment that the Tibetan cashmere goat lives in, this goat has developed distinct phenotypic traits compared to lowland breeds. However, the genetic components underlying this phenotypic adaptation remain largely unknown. RESULTS We obtained 118,700 autosomal SNPs through exome sequencing of 330 cashmere goats located at a wide geographic range, including the Tibetan Plateau and low-altitude regions in China. The great majority of SNPs showed low genetic differentiation among populations; however, approximately 2-3% of the loci showed more genetic differentiation than expected under a selectively neutral model. Together with a combined analysis of high- and low-altitude breeds, we revealed 339 genes potentially under high-altitude selection. Genes associated with cardiovascular system development were significantly enriched in our study. Among these genes, the most evident one was endothelial PAS domain protein 1 (EPAS1), which has been previously reported to be involved in complex oxygen sensing and significantly associated with high-altitude adaptation of human, dog, and grey wolf. The missense mutation Q579L that we identified in EPAS1, which occurs next to the Hypoxia-Inducible Factor-1 (HIF-1) domain, was exclusively enriched in the high-altitude populations. CONCLUSIONS Our study provides insights concerning the population variation in six different cashmere goat populations in China. The variants in cardiovascular system-related genes may explain the observed phenotypic adaptation of the Tibetan cashmere goat.
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Affiliation(s)
- Shen Song
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China.
| | - Na Yao
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Min Yang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Xuexue Liu
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Kunzhe Dong
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Qianjun Zhao
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Yabin Pu
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Xiaohong He
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Weijun Guan
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Ning Yang
- Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100094, China.
| | - Yuehui Ma
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Lin Jiang
- The Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
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106
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Liu R, Jin L, Long K, Chai J, Ma J, Tang Q, Tian S, Hu Y, Lin L, Wang X, Jiang A, Li X, Li M. Detection of genetic diversity and selection at the coding region of the melanocortin receptor 1 ( MC1R ) gene in Tibetan pigs and Landrace pigs. Gene 2016; 575:537-542. [DOI: 10.1016/j.gene.2015.09.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/13/2015] [Accepted: 09/15/2015] [Indexed: 11/30/2022]
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107
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Leroy G, Besbes B, Boettcher P, Hoffmann I, Capitan A, Baumung R. Rare phenotypes in domestic animals: unique resources for multiple applications. Anim Genet 2015; 47:141-53. [PMID: 26662214 DOI: 10.1111/age.12393] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2015] [Indexed: 12/26/2022]
Abstract
Preservation of specific and inheritable phenotypes of current or potential future importance is one of the main purposes of conservation of animal genetic resources. In this review, we investigate the issues behind the characterisation, utilisation and conservation of rare phenotypes, considering their multiple paths of relevance, variable levels of complexity and mode of inheritance. Accurately assessing the rarity of a given phenotype, especially a complex one, is not a simple task, because it requires the phenotypic and genetic characterisation of a large number of animals and populations and remains dependent of the scale of the study. Once characterised, specific phenotypes may contribute to various purposes (adaptedness, production, biological model, aesthetics, etc.) with adequate introgression programmes, which justifies the consideration of (real or potential) existence of such characteristics in in situ or ex situ conservation strategies. Recent biotechnological developments (genomic and genetic engineering) will undoubtedly bring important changes to the way phenotypes are characterised, introgressed and managed.
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Affiliation(s)
- G Leroy
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - B Besbes
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - P Boettcher
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - I Hoffmann
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - A Capitan
- INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.,ALLICE, 149 rue de Bercy, F-75012, Paris, France
| | - R Baumung
- Animal Production and Health Division, Food and Agriculture Organization of the United Nations, Viale delle Terme di Caracalla, 00153, Rome, Italy
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108
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Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas. Sci Rep 2015; 5:14256. [PMID: 26404527 PMCID: PMC4585896 DOI: 10.1038/srep14256] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/21/2015] [Indexed: 01/29/2023] Open
Abstract
Species that undertake altitudinal migrations are exposed to a considerable seasonal variation in oxygen levels and temperature. How they cope with this was studied in a population of great tit (Parus major) that breeds at high elevations and winters at lower elevations in the eastern Himalayas. Comparison of population genomics of high altitudinal great tits and those living in lowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (amino sugar, nucleotide sugar metabolism and insulin signaling pathways) and hypoxia response (PI3K-akt, mTOR and MAPK signaling pathways) in the high altitudinal population. The PI3K-akt, mTOR and MAPK pathways modulate the hypoxia-inducible factors, HIF-1α and VEGF protein expression thus indirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategies observed in high altitudinal great tits differ from those described in a closely related species on the Tibetan Plateau, the sedentary ground tit (Parus humilis). This species has enhanced selection in lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparative population genomics also revealed selection for larger body size in high altitudinal great tits.
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109
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Wang Z, Chen Q, Yang Y, Liao R, Zhao J, Zhang Z, Chen Z, Zhang X, Xue M, Yang H, Zheng Y, Wang Q, Pan Y. Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data. Anim Genet 2015; 46:697-701. [PMID: 26373882 PMCID: PMC5049631 DOI: 10.1111/age.12349] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2015] [Indexed: 01/31/2023]
Abstract
The Chinese indigenous pig breeds in the Taihu Lake region are the most prolific pig breeds in the world. In this study, we investigated the genetic diversity and population structure of six breeds, including Meishan, Erhualian, Mi, Fengjing, Shawutou and Jiaxing Black, in this region using whole‐genome SNP data. A high SNP with proportions of polymorphic markers ranging from 0.925 to 0.995 was exhibited by the Chinese indigenous pigs in the Taihu Lake region. The allelic richness and expected heterozygosity also were calculated and indicated that the genetic diversity of the Meishan breed was the greatest, whereas that of the Fengjing breed was the lowest. The genetic differentiation, as indicated by the fixation index, exhibited an overall mean of 0.149. Both neighbor‐joining tree and principal components analysis were able to distinguish the breeds from each other, but structure analysis indicated that the Mi and Erhualian breeds exhibited similar major signals of admixture. With this genome‐wide comprehensive survey of the genetic diversity and population structure of the indigenous Chinese pigs in the Taihu Lake region, we confirmed the rationality of the current breed classification of the pigs in this region.
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Affiliation(s)
- Z Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - Q Chen
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - Y Yang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - R Liao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - J Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - Z Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - Z Chen
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - X Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - M Xue
- National Station of Animal Husbandry, Beijing, 100125, China
| | - H Yang
- National Station of Animal Husbandry, Beijing, 100125, China
| | - Y Zheng
- National Station of Animal Husbandry, Beijing, 100125, China
| | - Q Wang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
| | - Y Pan
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China
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110
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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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