51
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Quan J, Wu Z, Ye Y, Peng L, Wu J, Ruan D, Qiu Y, Ding R, Wang X, Zheng E, Cai G, Huang W, Yang J. Metagenomic Characterization of Intestinal Regions in Pigs With Contrasting Feed Efficiency. Front Microbiol 2020; 11:32. [PMID: 32038603 PMCID: PMC6989599 DOI: 10.3389/fmicb.2020.00032] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/09/2020] [Indexed: 11/13/2022] Open
Abstract
Greater feed efficiency (FE) is critical in increasing profitability while reducing the environmental impact of pig production. Previous studies that identified swine FE-associated bacterial taxa were limited in either sampling sites or sequencing methods. This study characterized the microbiomes within the intestine of FE contrasting Duroc × (Landrace × Yorkshire) (DLY) pigs with a comprehensive representation of diverse sampling sites (ileum, cecum, and colon) and a metagenomic sequencing approach. A total of 226 pigs were ranked according to their FE between weaning to 140 day old, and six with extreme phenotypes were selected, three for each of the high and low groups. The results revealed that the cecum and colon had similar microbial taxonomic composition and function, and had higher capacity in polysaccharide metabolism than the ileum. We found in cecum that the high FE pigs had slightly higher richness and evenness in their micriobiota than the low FE pigs. We identified 12 phyla, 17 genera, and 39 species (e.g., Treponema porcinum, Treponema bryantii, and Firmicutes bacterium CAG:110) that were potentially associated with swine FE variation in cecum microbiota through LEfSe analysis. Species enriched in the cecum of the high FE pigs had a greater ability to utilize dietary polysaccharides and dietary protein according to the KEGG annotation. Analysis of antibiotic resistance based on the CARD database annotation indicated that the macB resistant gene might play an important role in shaping the microbial community in the cecum of pigs with contrasting FE. The bacteria from the genus Prevotella was highly enriched in the cecum of low FE pigs, which may impair the establishment of a more effective nutrient harvesting microbiota because of the interaction between Prevotella and other benefical microbes. These findings improved our understanding of the microbial compositions in the different gut locations of DLY pigs and identified many biomarkers associated with FE variation wich may be used to develop strategies to improve FE in pigs.
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Affiliation(s)
- Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China.,Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Yong Ye
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Longlong Peng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Xingwang Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Wen Huang
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
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52
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Keel BN, Snelling WM, Lindholm-Perry AK, Oliver WT, Kuehn LA, Rohrer GA. Using SNP Weights Derived From Gene Expression Modules to Improve GWAS Power for Feed Efficiency in Pigs. Front Genet 2020; 10:1339. [PMID: 32038708 PMCID: PMC6985563 DOI: 10.3389/fgene.2019.01339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/09/2019] [Indexed: 01/24/2023] Open
Abstract
The "large p small n" problem has posed a significant challenge in the analysis and interpretation of genome-wide association studies (GWAS). The use of prior information to rank genomic regions and perform SNP selection could increase the power of GWAS. In this study, we propose the use of gene expression data from RNA-Seq of multiple tissues as prior information to assign weights to SNP, select SNP based on a weight threshold, and utilize weighted hypothesis testing to conduct a GWAS. RNA-Seq libraries from hypothalamus, duodenum, ileum, and jejunum tissue of 30 pigs with divergent feed efficiency phenotypes were sequenced, and a three-way gene x individual x tissue clustering analysis was performed, using constrained tensor decomposition, to obtain a total of 10 gene expression modules. Loading values from each gene module were used to assign weights to 49,691 commercial SNP markers, and SNP were selected using a weight threshold, resulting in 10 SNP sets ranging in size from 101 to 955 markers. Weighted GWAS for feed intake in 4,200 pigs was performed separately for each of the 10 SNP sets. A total of 36 unique significant SNP associations were identified across the ten gene modules (SNP sets). For comparison, a standard unweighted GWAS using all 49,691 SNP was performed, and only 2 SNP were significant. None of the SNP from the unweighted analysis resided in known QTL related to swine feed efficiency (feed intake, average daily gain, and feed conversion ratio) compared to 29 (80.6%) in the weighted analyses, with 9 SNP residing in feed intake QTL. These results suggest that the heritability of feed intake is driven by many SNP that individually do not attain genome-wide significance in GWAS. Hence, the proposed procedure for prioritizing SNP based on gene expression data across multiple tissues provides a promising approach for improving the power of GWAS.
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Affiliation(s)
- Brittney N. Keel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, United States
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53
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A Transcriptome Analysis Identifies Biological Pathways and Candidate Genes for Feed Efficiency in DLY Pigs. Genes (Basel) 2019; 10:genes10090725. [PMID: 31540540 PMCID: PMC6771153 DOI: 10.3390/genes10090725] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/08/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022] Open
Abstract
Feed cost accounts for approximately 65–75% of overall commercial pork production costs. Therefore, improving the feed efficiency of pig production is important. In this study, 12 individuals with either extremely high (HE) or low (LE) feed efficiency were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs. After the pigs were slaughtered, we collected small intestine mucosal tissue. Next, RNA sequencing (RNA-seq) analysis was used to reveal the presence and quantity of genes expressed between these extremely HE- and LE-groups. We found 433 significantly differentially expressed genes (DEGs) between the HE- and LE-groups. Of these, 389 and 44 DEGs were upregulated and downregulated in the HE-group, respectively. An enrichment analysis showed that the DEGs were mainly enriched in functions related to apical plasma membrane composition, transporter activity, transport process and hormone regulation of digestion and absorption. Protein network interaction and gene function analyses revealed that SLC2A2 was an important candidate gene for FE in pigs, which may give us a deeper understanding of the mechanism of feed efficiency. Furthermore, some significant DEGs identified in the current study could be incorporated into artificial selection programs for increased feeding efficiency in pigs.
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54
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Ding R, Yang M, Quan J, Li S, Zhuang Z, Zhou S, Zheng E, Hong L, Li Z, Cai G, Huang W, Wu Z, Yang J. Single-Locus and Multi-Locus Genome-Wide Association Studies for Intramuscular Fat in Duroc Pigs. Front Genet 2019; 10:619. [PMID: 31316554 PMCID: PMC6609572 DOI: 10.3389/fgene.2019.00619] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 06/13/2019] [Indexed: 12/26/2022] Open
Abstract
Intramuscular fat (IMF) is an important quantitative trait of meat, which affects the associated sensory properties and nutritional value of pork. To gain a better understanding of the genetic determinants of IMF, we used a composite strategy, including single-locus and multi-locus association analyses to perform genome-wide association studies (GWAS) for IMF in 1,490 Duroc boars. We estimated the genomic heritability of IMF to be 0.23 ± 0.04. A total of 30 single nucleotide polymorphisms (SNPs) were found to be significantly associated with IMF. The single-locus mixed linear model (MLM) and multiple-locus methods multi-locus random-SNP-effect mixed linear model (mrMLM), fast multi-locus random-SNP-effect efficient mixed model association (FASTmrEMMA), and integrative sure independence screening expectation maximization Bayesian least absolute shrinkage and selection operator model (ISIS EM-BLASSO) analyses identified 5, 9, 8, and 21 significant SNPs, respectively. Interestingly, a novel quantitative trait locus (QTL) on SSC 7 was found to affect IMF. In addition, 10 candidate genes (BDKRB2, GTF2IRD1, UTRN, TMEM138, DPYD, CASQ2, ZNF518B, S1PR1, GPC6, and GLI1) were found to be associated with IMF based on their potential functional roles in IMF. GO analysis showed that most of the genes were involved in muscle and organ development. A significantly enriched KEGG pathway, the sphingolipid signaling pathway, was reported to be associated with fat deposition and obesity. Identification of novel variants and functional genes will advance our understanding of the genetic mechanisms of IMF and provide specific opportunities for marker-assisted or genomic selection in pigs. In general, such a composite single-locus and multi-locus strategy for GWAS may be useful for understanding the genetic architecture of economic traits in livestock.
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Affiliation(s)
- Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Ming Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group, Co., Ltd., Guangdong, China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Shaoyun Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Zicong Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China.,National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group, Co., Ltd., Guangdong, China
| | - Wen Huang
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China.,National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group, Co., Ltd., Guangdong, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, China
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55
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Zhou B. Classical Swine Fever in China-An Update Minireview. Front Vet Sci 2019; 6:187. [PMID: 31249837 PMCID: PMC6584753 DOI: 10.3389/fvets.2019.00187] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/28/2019] [Indexed: 11/17/2022] Open
Abstract
Classical swine fever (CSF) remains one of the most economically important viral diseases of domestic pigs and wild boar worldwide. The causative agent is CSF virus, it is highly contagious, with high morbidity and mortality rates; as such, it is an OIE-listed disease. Owing to a nationwide policy of vaccinations of pigs, CSF is well-controlled in China, with large-scale outbreaks rarely seen. Sporadic outbreaks are however still reported every year. In order to cope with future crises and to eradicate CSF, China should strengthen and support biosecurity measures such as the timely reporting of suspected disease, technologies for reliable diagnoses, culling infected herds, and tracing possible contacts, as well as continued vaccination and support of research into drug and genetic therapies. This mini-review summarizes the epidemiology of and control strategies for CSF in China.
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Affiliation(s)
- Bin Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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56
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Zhuang Z, Li S, Ding R, Yang M, Zheng E, Yang H, Gu T, Xu Z, Cai G, Wu Z, Yang J. Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations. PLoS One 2019; 14:e0218263. [PMID: 31188900 PMCID: PMC6561594 DOI: 10.1371/journal.pone.0218263] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/29/2019] [Indexed: 01/07/2023] Open
Abstract
Loin muscle area (LMA) and loin muscle depth (LMD) are important traits influencing the production performance of breeding pigs. However, the genetic architecture of these two traits is still poorly understood. To discern the genetic architecture of LMA and LMD, a material consisting of 6043 Duroc pigs belonging to two populations with different genetic backgrounds was collected and applied in genome-wide association studies (GWAS) with a genome-wide distributed panel of 50K single nucleotide polymorphisms (SNPs). To improve the power of detection for common SNPs, we conducted a meta-analysis in these two pig populations and uncovered additional significant SNPs. As a result, we identified 75 significant SNPs for LMA and LMD on SSC6, 7, 12, 16, and 18. Among them, 25 common SNPs were associated with LMA and LMD. One pleiotropic quantitative trait locus (QTL), which was located on SSC7 with a 283 kb interval, was identified to affect LMA and LMD. Marker ALGA0040260 is a key SNP for this QTL, explained 1.77% and 2.48% of the phenotypic variance for LMA and LMD, respectively. Another genetic region on SSC16 (709 kb) was detected and displayed prominent association with LMA and the peak SNP, WU_10.2_16_35829257, contributed 1.83% of the phenotypic variance for LMA. Further bioinformatics analysis determined eight promising candidate genes (GCLC, GPX8, DAXX, FGF21, TAF11, SPDEF, NUDT3, and PACSIN1) with functions in glutathione metabolism, adipose and muscle tissues development and lipid metabolism. This study provides the first GWAS for the LMA and LMD of Duroc breed to analyze the underlying genetic variants through a large sample size. The findings further advance our understanding and help elucidate the genetic architecture of LMA, LMD and growth-related traits in pigs.
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Affiliation(s)
- Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Shaoyun Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Ming Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Huaqiang Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zheng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China
- * E-mail: (JY); (ZW)
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
- * E-mail: (JY); (ZW)
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57
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Tang Z, Xu J, Yin L, Yin D, Zhu M, Yu M, Li X, Zhao S, Liu X. Genome-Wide Association Study Reveals Candidate Genes for Growth Relevant Traits in Pigs. Front Genet 2019; 10:302. [PMID: 31024621 PMCID: PMC6459934 DOI: 10.3389/fgene.2019.00302] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 03/19/2019] [Indexed: 12/02/2022] Open
Abstract
Improvement of the growth rate is a challenge in the pig industry, the Average Daily Gain (ADG) and Days (AGE) to 100 kg are directly related to growth performance. We performed genome-wide association study (GWAS) and genetic parameters estimation for ADG and AGE using the genomic and phonemic from four breed (Duroc, Yorkshire, Landrace, and Pietrain) populations. All analyses were performed by a multi-loci GWAS model, FarmCPU. The GWAS results of all four breeds indicate that five genome-wide significant SNPs were associated with ADG, and the nearby genomic regions explained 4.08% of the genetic variance and 1.90% of the phenotypic variance, respectively. For AGE, six genome-wide significant SNPs were detected, and the nearby genomic regions explained 8.09% of the genetic variance and 3.52% of phenotypic variance, respectively. In total, nine candidate genes were identified to be associated with growth and metabolism. Among them, TRIB3 was reported to associate with pig growth, GRP, TTR, CNR1, GLP1R, BRD2, HCRTR2, SEC11C, and ssc-mir-122 were reported to associate with growth traits in human and mouse. The newly detected candidate genes will advance the understanding of growth related traits and the identification of the novel variants will suggest a potential use in pig genomic breeding programs.
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Affiliation(s)
- Zhenshuang Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Jingya Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Lilin Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Dong Yin
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengjin Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mei Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Xiaolei Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
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