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Green HE, Oliveira HRD, Alvarenga AB, Scramlin-Zuelly S, Grossi D, Schinckel AP, Brito LF. Genomic background of biotypes related to growth, carcass and meat quality traits in Duroc pigs based on principal component analysis. J Anim Breed Genet 2024; 141:163-178. [PMID: 37902119 DOI: 10.1111/jbg.12831] [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] [Received: 01/19/2023] [Revised: 08/14/2023] [Accepted: 10/14/2023] [Indexed: 10/31/2023]
Abstract
As the swine industry continues to explore pork quality traits alongside growth, feed efficiency and carcass leanness traits, it becomes imperative to understand their underlying genetic relationships. Due to this increase in the number of desirable traits, animal breeders must also consider methods to efficiently perform direct genetic changes for each trait and evaluate alternative selection indexes with different sets of phenotypic measurements. Principal component analysis (PCA) and genome-wide association studies (GWAS) can be combined to understand the genetic architecture and biological mechanisms by defining biological types (biotypes) that relate these valuable traits. Therefore, the main objectives of this study were to: (1) estimate genomic-based genetic parameters; (2) define animal biotypes utilizing PCA; and (3) utilize GWAS to link the biotypes to candidate genes and quantitative trait loci (QTL). The phenotypic dataset included 2583 phenotypic records from female Duroc pigs from a terminal sire line. The pedigree file contained 193,764 animals and the genotype file included 21,309 animals with 35,651 single nucleotide polymorphisms (SNPs). Eight principal components (PCs), accounting for a total of 99.7% of the population variation, were defined for three growth, eight conventional carcass, 10 pork quality and 18 novel carcass traits. The eight biotypes defined from the PCs were found to be related to growth rate, maturity, meat quality and body structure, which were then related to candidate genes. Of the 175 candidate genes found, six of them [LDHA (SSC1), PIK3C3 (SSC6), PRKAG3 (SSC15), VRTN (SSC7), DLST (SSC7) and PAPPA (SSC1)] related to four PCs were found to be associated with previously defined QTL, linking the biotypes with biological processes involved with muscle growth, fat deposition, glycogen levels and skeletal development. Further functional analyses helped to make connections between biotypes, relating them through common KEGG pathways and gene ontology (GO) terms. These findings contribute to a better understanding of the genetic relationships between growth, carcass and meat quality traits in Duroc pigs, enabling breeders to better understand the biological mechanisms underlying the phenotypic expression of these traits.
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Affiliation(s)
- Hannah E Green
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
- Fast Genetics, Saskatoon, Saskatchewan, Canada
| | | | | | | | | | - Allan P Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
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Khan MZ, Chen W, Huang B, Liu X, Wang X, Liu Y, Chai W, Wang C. Advancements in Genetic Marker Exploration for Livestock Vertebral Traits with a Focus on China. Animals (Basel) 2024; 14:594. [PMID: 38396562 PMCID: PMC10885964 DOI: 10.3390/ani14040594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/29/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
In livestock breeding, the number of vertebrae has gained significant attention due to its impact on carcass quality and quantity. Variations in vertebral traits have been observed across different animal species and breeds, with a strong correlation to growth and meat production. Furthermore, vertebral traits are classified as quantitative characteristics. Molecular marker techniques, such as marker-assisted selection (MAS), have emerged as efficient tools to identify genetic markers associated with vertebral traits. In the current review, we highlight some key potential genes and their polymorphisms that play pivotal roles in controlling vertebral traits (development, length, and number) in various livestock species, including pigs, donkeys, and sheep. Specific genetic variants within these genes have been linked to vertebral development, number, and length, offering valuable insights into the genetic mechanisms governing vertebral traits. This knowledge has significant implications for selective breeding strategies to enhance structural characteristics and meat quantity and quality in livestock, ultimately improving the efficiency and quality of the animal husbandry industry.
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Affiliation(s)
- Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 522000, China
| | | | | | | | | | | | | | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 522000, China
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Liu K, Hou L, Yin Y, Wang B, Liu C, Zhou W, Niu P, Li Q, Huang R, Li P. Genome-wide association study reveals new QTL and functional candidate genes for the number of ribs and carcass length in pigs. Anim Genet 2023. [PMID: 36911996 DOI: 10.1111/age.13315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/11/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023]
Abstract
The number of ribs (NR) and carcass length (CL) are important economic traits in pig breeding programs. Pigs with a higher NR and longer CL produce greater pork yields. In the present study, Suhuai pigs with NR and CL phenotypes were genotyped using the Neogen® GGP Porcine 80 K SNP array to identify the QTL affecting NR and CL and dissect the candidate genes for the two traits. The SNP-chip data was imputed to the whole-genome sequence (iWGS) to increase the probability of identifying causal variants. Through genome-wide association studies (GWAS) based on both chip and iWGS data, significant SNPs were detected on Sus scrofa chromosome (SSC) 1, SSC4 and SSC7 for NR and on SSC5, SSC16 and SSC17 for CL. Moreover, two SNPs (H3GA0022644 and WU_10.2_7_103460706) on SSC7 detected in chip-based GWAS were significantly associated with both NR and CL. Through Bayes fine mapping, one reported QTL for NR on SSC7 and two reported QTL for CL on SSC17 were verified, and two new QTL (SSC1: 14.05-15.84 Mb and SSC4: 64.83-66.59 Mb) affecting NR and two new QTL (SSC5: 58.31-59.84 Mb and SSC16: 22.98-23.43 Mb) affecting CL were detected. According to the biological functions of genes, MTHFD1L on SSC1 and SULF1 on SSC4 are novel functional candidate genes for NR, and EMP1 on SSC5 and EGFLAM on SSC16 are novel functional candidate genes for CL. Overall, our findings provide a basis for identifying new causal genes and mutations affecting NR and CL.
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Affiliation(s)
- Kaiyue Liu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Liming Hou
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Yanzhen Yin
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Binbin Wang
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Chenxi Liu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Wuduo Zhou
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Peipei Niu
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Qiang Li
- Huaiyin Xinhuai Pig Breeding Farm of Huaian City, Huaian, China
| | - Ruihua Huang
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Pinghua Li
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
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Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs. Genes (Basel) 2022; 13:genes13081454. [PMID: 36011365 PMCID: PMC9407794 DOI: 10.3390/genes13081454] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 12/24/2022] Open
Abstract
Growth rate plays a critical role in the pig industry and is related to quantitative traits controlled by many genes. Here, we aimed to identify causative mutations and candidate genes responsible for pig growth traits. In this study, 2360 Duroc pigs were used to detect significant additive, dominance, and epistatic effects associated with growth traits. As a result, a total number of 32 significant SNPs for additive or dominance effects were found to be associated with various factors, including adjusted age at a specified weight (AGE), average daily gain (ADG), backfat thickness (BF), and loin muscle depth (LMD). In addition, the detected additive significant SNPs explained 2.49%, 3.02%, 3.18%, and 1.96% of the deregressed estimated breeding value (DEBV) variance for AGE, ADG, BF, and LMD, respectively, while significant dominance SNPs could explain 2.24%, 13.26%, and 4.08% of AGE, BF, and LMD, respectively. Meanwhile, a total of 805 significant epistatic effects SNPs were associated with one of ADG, AGE, and LMD, from which 11 sub-networks were constructed. In total, 46 potential genes involved in muscle development, fat deposition, and regulation of cell growth were considered as candidates for growth traits, including CD55 and NRIP1 for AGE and ADG, TRIP11 and MIS2 for BF, and VRTN and ZEB2 for LMD, respectively. Generally, in this study, we detected both new and reported variants and potential candidate genes for growth traits of Duroc pigs, which might to be taken into account in future molecular breeding programs to improve the growth performance of pigs.
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Niu N, Liu Q, Hou X, Liu X, Wang L, Zhao F, Gao H, Shi L, Wang L, Zhang L. Genome-wide association study revealed ABCD4 on SSC7 and GREB1L and MIB1 on SSC6 as crucial candidate genes for rib number in Beijing Black pigs. Anim Genet 2022; 53:690-695. [PMID: 35776924 DOI: 10.1111/age.13237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/09/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022]
Abstract
As one of the few animals with variation in the number of rib pairs (RIB), the pig is a good model to study the mechanism of RIB regulation. Quantitative trait loci (QTL) for porcine RIB are present on Sus scrofa chromosome 7 (SSC7). Although several candidate genes exist in this QTL region on SSC7, the causal gene has yet to be verified. Beijing Black pig with 14-17 RIB is a good population for candidate gene mining and 1104 individuals were genotyped using the Illumina Porcine 50K BeadChip. A total of 14 SNPs from 95.49 to 97.78 Mb on SSC7 showed genome-wide significant association with RIB. On SSC7, a locuszoom plot using pairwise linkage disequilibrium displayed the narrowest linkage region encompassing only two genes, ABCD4 and VRTN. In mice, a transcriptome expression profile was obtained using three embryos at E9.5 (the critical period for rib formation). ABCD4 was highly expressed, but no expression of VRTN was detected. On SSC6, there were four genome-wide significant SNPs from 106.42 to 106.92 Mb associated with RIB. GREB1L and MIB1, in this region, were regarded as novel candidate genes. These results revealed a crucial candidate causal gene on SSC7 and novel genes on SSC6 for rib number and provided interesting new insights into its genetic basis.
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Affiliation(s)
- Naiqi Niu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qian Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhua Hou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ligang Wang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fuping Zhao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongmei Gao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijun Shi
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Department of Animal Genetics and Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhong YJ, Yang Y, Wang XY, Di R, Chu MX, Liu QY. Expression analysis and single-nucleotide polymorphisms of SYNDIG1L and UNC13C genes associated with thoracic vertebral numbers in sheep ( Ovis aries). Arch Anim Breed 2021; 64:131-138. [PMID: 34084911 PMCID: PMC8131962 DOI: 10.5194/aab-64-131-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/10/2021] [Indexed: 11/20/2022] Open
Abstract
The objective of the current study was to analyze expression levels of synapse differentiation inducing 1-like
(SYNDIG1L) and unc-13 homolog C (UNC13C) genes in different tissues, while single-nucleotide polymorphisms
(SNPs) of two genes were associated with multiple thoracic vertebrae traits
in both Small-tailed Han sheep (STH) and Sunite sheep (SNT). The expression
levels of SYNDIG1L and UNC13C were analyzed in the brain, cerebellum, heart, liver, spleen,
lung, kidney, adrenal gland, uterine horn, longissimus muscle, and abdominal
adipose tissues of two sheep breeds with different thoracic vertebral
number (TVN) sheep (T13 groups and T14 groups) by real-time quantitative
polymerase chain reaction (RT-qPCR). Meanwhile, the polymorphisms of UNC13C gene g.52919279C>T
and SYNDIG1L gene g.82573325C>A in T14 and T13 were
genotyped by the Sequenom MassARRAY® SNP assay, and
association analysis was performed with the TVN. The results demonstrated
that UNC13C gene was extensively expressed in 11 tissues. The expression of
UNC13C gene in longissimus muscle of T14 groups of STH was significantly higher
than that of T13 groups (P<0.05). SYNDIG1L gene was overexpressed in brain
and cerebellum tissues, and the expression level of UNC13C gene in the brain and
cerebellum of T13 groups in SNT was significantly higher than that of T14
groups (P<0.01). Association analysis showed that SNPs found in the
UNC13C gene had no significant effects on TVN for both two genes. The polymorphism
of SYNDIG1L g.82573325C>A was significantly correlated with the TVN in
both STH (P<0.05) and SNT (P<0.01). Taken together, the
SYNDIG1L gene was related to thoracic vertebral development, and this variation may
be potentially used as a molecular marker to select the multiple thoracic
vertebrae in sheep.
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Affiliation(s)
- Ying-Jie Zhong
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Yang Yang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Xiang-Yu Wang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Ran Di
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Ming-Xing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Qiu-Yue Liu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
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Willson HE, Rojas de Oliveira H, Schinckel AP, Grossi D, Brito LF. Estimation of Genetic Parameters for Pork Quality, Novel Carcass, Primal-Cut and Growth Traits in Duroc Pigs. Animals (Basel) 2020; 10:ani10050779. [PMID: 32365996 PMCID: PMC7278482 DOI: 10.3390/ani10050779] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 01/21/2023] Open
Abstract
Simple Summary There is a growing interest in worldwide swine breeding programs to genetically select for pork quality and primal cuts in addition to the traditional growth and carcass leanness traits. Accurate population genetic parameters are needed to estimate correlated responses to selection and incorporate novel traits in the selection objective. Therefore, we estimated heritabilities and genetic correlations for 39 pork quality, growth and carcass traits in Duroc pigs. In general, moderate and favorable genetic correlations were observed between pork quality (e.g., loin color and marbling scores) and carcass traits. Additionally, moderate to low correlations were found among pork quality, growth and carcass traits. Our findings suggest that pig breeders can successfully incorporate pork quality and novel carcass traits in the selection objectives without undesirable impacts upon growth rate and carcass leanness. Abstract More recently, swine breeding programs have aimed to include pork quality and novel carcass (e.g., specific primal cuts such as the Boston butt or belly that are not commonly used in selection indexes) and belly traits together with growth, feed efficiency and carcass leanness in the selection indexes of terminal-sire lines, in order to efficiently produce pork with improved quality at a low cost to consumers. In this context, the success of genetic selection for such traits relies on accurate estimates of heritabilities and genetic correlations between traits. The objective of this study was to estimate genetic parameters for 39 traits in Duroc pigs (three growth, eight conventional carcass (commonly measured production traits; e.g., backfat depth), 10 pork quality and 18 novel carcass traits). Phenotypic measurements were collected on 2583 purebred Duroc gilts, and the variance components were estimated using both univariate and bivariate models and REML procedures. Moderate to high heritability estimates were found for most traits, while genetic correlations tended to be low to moderate overall. Moderate to high genetic correlations were found between growth, primal-cuts and novel carcass traits, while low to moderate correlations were found between pork quality and growth and carcass traits. Some genetic antagonisms were observed, but they are of low to moderate magnitude. This indicates that genetic progress can be achieved for all traits when using an adequate selection index.
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Affiliation(s)
- Hannah E. Willson
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (H.E.W.); (H.R.d.O.); (A.P.S.)
| | - Hinayah Rojas de Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (H.E.W.); (H.R.d.O.); (A.P.S.)
| | - Allan P. Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (H.E.W.); (H.R.d.O.); (A.P.S.)
| | | | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (H.E.W.); (H.R.d.O.); (A.P.S.)
- Correspondence:
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Polymorphism of VRTN Gene g.20311_20312ins291 Was Associated with the Number of Ribs, Carcass Diagonal Length and Cannon Bone Circumference in Suhuai Pigs. Animals (Basel) 2020; 10:ani10030484. [PMID: 32183166 PMCID: PMC7142862 DOI: 10.3390/ani10030484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022] Open
Abstract
Simple Summary An increase in the number of ribs (RIB) could improve carcass length (CL) and body size. Cannon bone circumference (CBC) is a pivotal body size trait, and a large CBC could enhance the capacity to bear excessive body weight, vigorous exercise, and resistance to injuries. Several researchers showed that the vertnin (VRTN) gene g.20311_20312ins291 (NC_010449.5 7: g.20311_20312ins291) is an important variant that is related to RIB and CL of Western pigs. However, it is unknown whether this variant could affect the CBC of pigs. Our study showed that this variant was significantly associated with RIB, carcass diagonal length (CDL), and CBC in Suhuai pigs; therefore, it could be used as a potential molecular marker for improving RIB, CDL, and CBC in this breed. Abstract The vertnin (VRTN) gene g.20311_20312ins291 was reported as an important variant related to the number of ribs (RIB), and the ins/ins genotype was advantageous for improving RIB of Western pigs. The purpose of this study was to determine whether the VRTN gene g.20311_20312ins291 influences RIB, carcass traits, and body size traits, including cannon bone circumference (CBC) in Chinese Suhuai pigs. We found that the VRTN gene g.20311_20312ins291 was polymorphic in Suhuai fattening pigs and gilts. The polymorphism of g.20311_20312ins291 was significantly associated with RIB and CDL in Suhuai fattening pigs (p < 0.01), whereas this variant had no influence on carcass weight (CWT). There was a tendency of association between this variant and carcass straight length (CSL) in Suhuai fattening pigs (p = 0.06). The polymorphism of g.20311_20312ins291 was also significantly associated with CBC in Suhuai gilts (p = 0.04). Furthermore, CBC was positively genetically correlated with body length (0.22, p < 0.01) and body weight (0.15, p < 0.01). Our results indicated that the VRTN gene g.20311_20312ins291 could be used as a potential marker for improving RIB, CDL, and CBC in Suhuai pigs.
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Deng MT, Zhu F, Yang YZ, Yang FX, Hao JP, Chen SR, Hou ZC. Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks. BMC Genomics 2019; 20:1. [PMID: 30606130 PMCID: PMC6318962 DOI: 10.1186/s12864-018-5379-1] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/16/2018] [Indexed: 12/26/2022] Open
Abstract
Background Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This study aimed to identify quantitative trait loci affecting body size and carcass yields in Pekin ducks. Results We measured 18 carcass traits in 639 Pekin ducks and performed genotyping using genotyping-by-sequencing (GBS). Loci-based association analysis detected 37 significant loci for the 17 traits. Thirty-seven identified candidate genes were involved in many biological processes. One single nucleotide polymorphism (SNP) (Chr1_140105435 A > T) located in the intron of the ATPase phospholipid transporting 11A gene (ATP11A) attained genome-wide significance associated with five weight traits. Eight SNPs were significantly associated with three body size traits, including the candidate gene plexin domain containing 2 (PLXDC2) associated with breast width and tensin 3 (TNS3) associated with fossil bone length. Only two SNPs were significantly associated with foot weight and four SNPs were significantly associated with heart weight. In the gene-based analysis, three genes (LOC101791418, TUBGCP3 (encoding tubulin gamma complex-associated protein 3), and ATP11A) were associated with four traits (42-day body weight, eviscerated weight, half-eviscerated weight, and leg muscle weight percentage). However, no loci were significantly associated with leg muscle weight in this study. Conclusions The novel results of this study improve our understanding of the genetic mechanisms regulating body growth in ducks and thus provide a genetic basis for breeding programs aimed at maximizing the economic potential of Pekin ducks. Electronic supplementary material The online version of this article (10.1186/s12864-018-5379-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meng-Ting Deng
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Zhu
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yu-Ze Yang
- Beijing General Station of Animal Husbandry, Beijing, 100107, China
| | - Fang-Xi Yang
- Beijing Golden Star Duck Co., LTD, Beijing, 100076, China
| | - Jin-Ping Hao
- Beijing Golden Star Duck Co., LTD, Beijing, 100076, China
| | - Si-Rui Chen
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
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Valluzzi C, Rando A, Di Gregorio P. Genetic variability of Nero Lucano pig breed at IGF2, LEP, MC4R, PIK3C3, RYR1 and VRTN loci. ITALIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1080/1828051x.2019.1649606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Carmelisa Valluzzi
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Potenza, Italy
| | - Andrea Rando
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Potenza, Italy
| | - Paola Di Gregorio
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, University of Basilicata, Potenza, Italy
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Huang J, Zhang M, Ye R, Ma Y, Lei C. Effects of increased vertebral number on carcass weight in PIC pigs. Anim Sci J 2017; 88:2057-2062. [PMID: 28776879 DOI: 10.1111/asj.12881] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 06/15/2017] [Indexed: 12/12/2022]
Abstract
Variation of the vertebral number is associated with carcass traits in pigs. However, results from different populations do not match well with others, especially for carcass weight. Therefore, effects of increased vertebral number on carcass weight were investigated by analyzing the relationship between two loci multi-vertebra causal loci (NR6A1 g.748 C > T and VRTN g.20311_20312ins291) and carcass weight in PIC pigs. Results from the association study between vertebral number and carcass weight showed that increased thoracic number had negative effects on carcass weight, but the results were not statistically significant. Further, VRTN Ins/Ins genotype increased more than one thoracic than that of Wt/Wt genotype on average in this PIC population. Meanwhile, there was a significant negative effect of VRTN Ins on carcass weight (P < 0.05). Thus, our results suggested negative effect of increased thoracic number on carcass weight in PIC pigs.
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Affiliation(s)
- Jieping Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,College of Life Science, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Mingming Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.,College of Life Science, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Runqing Ye
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Yun Ma
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.,Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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12
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Casiró S, Velez-Irizarry D, Ernst CW, Raney NE, Bates RO, Charles MG, Steibel JP. Genome-wide association study in an F2 Duroc x Pietrain resource population for economically important meat quality and carcass traits. J Anim Sci 2017; 95:545-558. [PMID: 28380601 DOI: 10.2527/jas.2016.1003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Meat quality is essential for consumer acceptance, it ultimately impacts pork production profitability and it is subject to genetic control. The objective of this study was to map genomic regions associated with economically important meat quality and carcass traits. We performed a genome-wide association (GWA) analysis to map regions associated with 38 meat quality and carcass traits recorded for 948 F2 pigs from the Michigan State University Duroc × Pietrain resource population. The F0, F1, and 336 F2 pigs were genotyped with the Illumina Porcine SNP60 BeadChip, while the remaining F2 pigs were genotyped with the GeneSeek Genomic Profiler for Porcine Low Desnisty (LD) chip, and imputed with high accuracy ( = 0.97). Altogether the genomic dataset comprised 1,019 animals and 44,911 SNP. A Gaussian linear mixed model was fitted to estimate the breeding values and the variance components. A linear transformation was performed to estimate the marker effects and variances. Type I error rate was controlled at a False Discovery Rate of 5%. Seven putative QTL found in this study were previously reported in other studies. Two novel QTL associated with tenderness (TEN) were located on SSC3 [135.6:137.5Mb; False Discovery rate (FDR) < 0.03] and SSC5 (67.3:69.1Mb; FDR < 0.02). The QTL region identified on SSC15 includes Protein Kinase AMP-activated ɣ 3-subunit gene (), which has been associated with 24-h pH (pH24), drip loss (DL) and cook yield (CY). Also, novel candidate genes were identified for TEN in the region on SSC5 [A Kinase (PRKA) Anchor Protein 3 (], and for tenth rib backfat thickness (BF10) [Carnitine O-Acetyltransferase ()] on SSC1. The association of gene polymorphisms with pork quality traits has been reported for several pig populations. However, there are no SNP for this gene on the chip used, thus we genotyped the animals for 2 non-synonymous variants ( and ). We then performed a GWA conditioning on the genotype of both SNP and was associated with pH24, DL, protein content (PRO) and CY ( < 0.004) and T30N with Juiciness, TEN, shear force, pH24, PRO, and CY < 0.04). Finally, we performed a GWA conditioning on the genotype of the SNP peak detected in this study, and T30N remained associated only with PRO ( < 0.02). Therefore, in this study we identified 2 novel QTL regions, suggest 2 novel candidate genes, and conclude that other SNP in PRKAG3 or nearby gene(s) explain the observed associations on SSC15 in this population.
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Zhang Z, Sun Y, Du W, He S, Liu M, Tian C. Effects of vertebral number variations on carcass traits and genotyping of Vertnin candidate gene in Kazakh sheep. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:1234-1238. [PMID: 28423880 PMCID: PMC5582278 DOI: 10.5713/ajas.16.0959] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/20/2017] [Accepted: 03/21/2017] [Indexed: 11/27/2022]
Abstract
Objective The vertebral number is associated with body length and carcass traits, which represents an economically important trait in farm animals. The variation of vertebral number has been observed in a few mammalian species. However, the variation of vertebral number and quantitative trait loci in sheep breeds have not been well addressed. Methods In our investigation, the information including gender, age, carcass weight, carcass length and the number of thoracic and lumbar vertebrae from 624 China Kazakh sheep was collected. The effect of vertebral number variation on carcass weight and carcass length was estimated by general linear model. Further, the polymorphic sites of Vertnin (VRTN) gene were identified by sequencing, and the association of the genotype and vertebral number variation was analyzed by the one-way analysis of variance model. Results The variation of thoracolumbar vertebrae number in Kazakh sheep (18 to 20) was smaller than that in Texel sheep (17 to 21). The individuals with 19 thoracolumbar vertebrae (T13L6) were dominant in Kazakh sheep (79.2%). The association study showed that the numbers of thoracolumbar vertebrae were positively correlated with the carcass length and carcass weight, statistically significant with carcass length. To investigate the association of thoracolumbar vertebrae number with VRTN gene, we genotyped the VRTN gene. A total of 9 polymorphic sites were detected and only a single nucleotide polymorphism (SNP) (rs426367238) was suggested to associate with thoracic vertebral number statistically. Conclusion The variation of thoracolumbar vertebrae number positively associated with the carcass length and carcass weight, especially with the carcass length. VRTN gene polymorphism of the SNP (rs426367238) with significant effect on thoracic vertebral number could be as a candidate marker to further evaluate its role in influence of thoracolumbar vertebral number.
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Affiliation(s)
- Zhifeng Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang 830026, China
| | - Yawei Sun
- Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang 830026, China.,Key Laboratory of Genetics, Breeding and Reproduction of Grass-Feeding Animal, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Urumqi, Xinjiang 830026, China
| | - Wei Du
- Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang 830026, China.,Key Laboratory of Genetics, Breeding and Reproduction of Grass-Feeding Animal, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Urumqi, Xinjiang 830026, China
| | - Sangang He
- Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang 830026, China.,Key Laboratory of Genetics, Breeding and Reproduction of Grass-Feeding Animal, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Urumqi, Xinjiang 830026, China
| | - Mingjun Liu
- Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang 830026, China.,Key Laboratory of Genetics, Breeding and Reproduction of Grass-Feeding Animal, Ministry of Agriculture, Key Laboratory of Animal Biotechnology of Xinjiang, Urumqi, Xinjiang 830026, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China
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Sato S, Uemoto Y, Kikuchi T, Egawa S, Kohira K, Saito T, Sakuma H, Miyashita S, Arata S, Kojima T, Suzuki K. SNP- and haplotype-based genome-wide association studies for growth, carcass, and meat quality traits in a Duroc multigenerational population. BMC Genet 2016; 17:60. [PMID: 27094516 PMCID: PMC4837538 DOI: 10.1186/s12863-016-0368-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/15/2016] [Indexed: 12/21/2022] Open
Abstract
Background The aim of the present study was to compare the power of single nucleotide polymorphism (SNP)-based genome-wide association study (GWAS) and haplotype-based GWAS for quantitative trait loci (QTL) detection, and to detect novel candidate genes affecting economically important traits in a purebred Duroc population comprising seven-generation pedigree. First, we performed a simulation analysis using real genotype data of this population to compare the power (based on the null hypothesis) of the two methods. We then performed GWAS using both methods and real phenotype data comprising 52 traits, which included growth, carcass, and meat quality traits. Results In total, 836 animals were genotyped using the Illumina PorcineSNP60 BeadChip and 14 customized SNPs from regions of known candidate genes related to the traits of interest. The power of SNP-based GWAS was greater than that of haplotype-based GWAS in a simulation analysis. In real data analysis, a larger number of significant regions was obtained by SNP-based GWAS than by haplotype-based GWAS. For SNP-based GWAS, 23 genome-wide significant SNP regions were detected for 17 traits, and 120 genome-wide suggestive SNP regions were detected for 27 traits. For haplotype-based GWAS, 6 genome-wide significant SNP regions were detected for four traits, and 11 genome-wide suggestive SNP regions were detected for eight traits. All genome-wide significant SNP regions detected by haplotype-based GWAS were located in regions also detected by SNP-based GWAS. Four regions detected by SNP-based GWAS were significantly associated with multiple traits: on Sus scrofa chromosome (SSC) 1 at 304 Mb; and on SSC7 at 35–39 Mb, 41–42 Mb, and 103 Mb. The vertnin gene (VRTN) in particular, was located on SSC7 at 103 Mb and was significantly associated with vertebrae number and carcass lengths. Mapped QTL regions contain some candidate genes involved in skeletal formation (FUBP3; far upstream element binding protein 3) and fat deposition (METTL3; methyltransferase like 3). Conclusion Our results show that a multigenerational pig population is useful for detecting QTL, which are typically segregated in a purebred population. In addition, a novel significant region could be detected by SNP-based GWAS as opposed to haplotype-based GWAS. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0368-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuji Sato
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
| | - Yoshinobu Uemoto
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Takashi Kikuchi
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Sachiko Egawa
- Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, 886-0004, Japan
| | - Kimiko Kohira
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Tomomi Saito
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Hironori Sakuma
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Satoshi Miyashita
- Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, 886-0004, Japan
| | - Shinji Arata
- Miyazaki Branch of National Livestock Breeding Center, Kobayashi, Miyazaki, 886-0004, Japan
| | - Takatoshi Kojima
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Keiichi Suzuki
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 981-8555, Japan
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15
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Yang J, Huang L, Yang M, Fan Y, Li L, Fang S, Deng W, Cui L, Zhang Z, Ai H, Wu Z, Gao J, Ren J. Possible introgression of the VRTN mutation increasing vertebral number, carcass length and teat number from Chinese pigs into European pigs. Sci Rep 2016; 6:19240. [PMID: 26781738 PMCID: PMC4726066 DOI: 10.1038/srep19240] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 10/12/2015] [Indexed: 11/25/2022] Open
Abstract
Vertnin (VRTN) variants have been associated with the number of thoracic vertebrae in European pigs, but the association has not been evidenced in Chinese indigenous pigs. In this study, we first performed a genome-wide association study in Chinese Erhualian pigs using one VRTN candidate causative mutation and the Illumina Porcine 60K SNP Beadchips. The VRTN mutation is significantly associated with thoracic vertebral number in this population. We further show that the VRTN mutation has pleiotropic and desirable effects on teat number and carcass (body) length across four diverse populations, including Erhualian, White Duroc × Erhualian F2 population, Duroc and Landrace pigs. No association was observed between VRTN genotype and growth and fatness traits in these populations. Therefore, testing for the VRTN mutation in pig breeding schemes would not only increase the number of vertebrae and nipples, but also enlarge body size without undesirable effects on growth and fatness traits, consequently improving pork production. Further, by using whole-genome sequence data, we show that the VRTN mutation was possibly introgressed from Chinese pigs into European pigs. Our results provide another example showing that introgressed Chinese genes greatly contributed to the development and production of modern European pig breeds.
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Affiliation(s)
- Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China.,State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Ming Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Wens Foodstuffs Group Co., Ltd, Guangdong, P.R. China
| | - Yin Fan
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Lin Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Shaoming Fang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Wenjiang Deng
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Leilei Cui
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Zhen Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Huashui Ai
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 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
| | - Jun Gao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Jun Ren
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, P.R. China
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