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Wang Y, Zhang D, Liu Y. Research Progress on the Regulating Factors of Muscle Fiber Heterogeneity in Livestock: A Review. Animals (Basel) 2024; 14:2225. [PMID: 39123750 PMCID: PMC11311112 DOI: 10.3390/ani14152225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
The type of muscle fiber plays a crucial role in the growth, development, and dynamic plasticity of animals' skeletal muscle. Additionally, it is a primary determinant of the quality of both fresh and processed meat. Therefore, understanding the regulatory factors that contribute to muscle fibers' heterogeneity is of paramount importance. Recent advances in sequencing and omics technologies have enabled comprehensive cross-verification of research on the factors affecting the types of muscle fiber across multiple levels, including the genome, transcriptome, proteome, and metabolome. These advancements have facilitated deeper exploration into the related biological questions. This review focused on the impact of individual characteristics, feeding patterns, and genetic regulation on the proportion and interconversion of different muscle fibers. The findings indicated that individual characteristics and feeding patterns significantly influence the type of muscle fiber, which can effectively enhance the type and distribution of muscle fibers in livestock. Furthermore, non-coding RNA, genes and signaling pathways between complicated regulatory mechanisms and interactions have a certain degree of impact on muscle fibers' heterogeneity. This, in turn, changes muscle fiber profile in living animals through genetic selection or environmental factors, and has the potential to modulate the quality of fresh meat. Collectively, we briefly reviewed the structure of skeletal muscle tissue and then attempted to review the inevitable connection between the quality of fresh meat and the type of muscle fiber, with particular attention to potential events involved in regulating muscle fibers' heterogeneity.
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Affiliation(s)
| | | | - Yiping Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (Y.W.); (D.Z.)
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Li X, Xin A, Ma L, Gou X, Fang S, Dong X, Ni B, Tang L, Zhu L, Yan D, Kong X. Molecular genetic characterization and meat-use functional gene identification in Jianshui yellow-brown ducks through combined resequencing and transcriptome analysis. Front Vet Sci 2023; 10:1269904. [PMID: 38179331 PMCID: PMC10765987 DOI: 10.3389/fvets.2023.1269904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
The Jianshui yellow-brown duck is a unique country-specific waterfowl species in Yunnan Province, well known for its tender meat. However, there is a lack of comprehensive systematic research on the molecular genetic characteristics, especially germplasm resources and economic traits, of the Jianshui yellow-brown ducks. This study investigated the molecular genetic characteristics of Jianshui yellow-brown ducks, compared their selection signals with those of ancestral mallard and meat-type Pekin ducks, and identified genes specific to their meat-use performance. Furthermore, this study also evaluated the breeding potential for its meat performance. In this study, phylogenetic trees, PCA and Admixture analysis were used to investigate the population genetic structure among local duck breeds in China; population genetic differentiation index (Fst), nucleotide diversity and Tajima's D were used to detect selected loci and genes in the population of Jianshui yellow-brown ducks; and transcriptome technology was used to screen for differentially expressed genes in the liver, sebum and breast muscle tissues, and finally, the results of the genome selection signals and transcriptome data were integrated to excavate functional genes affecting the meat performance of the Jianshui yellow-brown ducks. The results of the genetic structure of the population showed that Jianshui yellow-brown ducks were clustered into a separate group. Selection signal analysis indicated significant selection pressure on certain genes related to meat characteristics (ELOVL2, ELOVL3, GDF10, VSTM2A, PHOSPHO1, and IGF2BP1) in both Jianshui yellow-brown ducks and mallards. Transcriptomic data analysis suggested that ELOVL3, PHOSPHO1, and GDF10 are vital candidate genes influencing meat production and quality in Jianshui yellow-brown ducks. A comparison of selection signals between Jianshui yellow-brown ducks and Pekin ducks revealed only 21 selected genes in the Jianshui yellow-brown duck population, and no significant genes were related to meat traits. Moreover, whole-genome resequencing data suggested that the Jianshui yellow-brown duck represents a unique category with distinct genetic mechanisms. Through selection signaling and transcriptomic approaches, we successfully screened and identified important candidate genes affecting meat traits in Jianshui yellow-brown ducks. Furthermore, the Jianshui yellow-brown duck has good potential for improved meat performance, highlighting the need for further improvement.
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Affiliation(s)
- Xinpeng Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Aiguo Xin
- Poultry Husbandry and Disease Research Institute, Yunnan Academy of Animal Husbandry and Veterinary Sciences, Kunming, China
| | - Li Ma
- Animal Husbandry and Veterinary College, Yunnan Vocational and Technical College of Agriculture, Kunming, China
| | - Xiao Gou
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Suyun Fang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xinxing Dong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Bin Ni
- School of Life Science and Engineering, Foshan University, Foshan, China
| | - Lin Tang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Li Zhu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Dawei Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiaoyan Kong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
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3
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Cao C, Cai Y, Li Y, Li T, Zhang J, Hu Z, Zhang J. Characterization and comparative transcriptomic analysis of skeletal muscle in female Pekin duck and Hanzhong Ma duck during different growth stages using RNA-seq. Poult Sci 2023; 102:103122. [PMID: 37832186 PMCID: PMC10568565 DOI: 10.1016/j.psj.2023.103122] [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: 06/27/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
Duck is an economically important poultry, and there is currently a major focus on improving its meat quality through breeding. There are wide variations in the growth regulation mechanisms of different duck breeds, that fundamental research on skeletal muscle growth is essential for understanding the regulation of unknown genes. The study aimed to broaden the understanding the duck skeletal muscle development and thereby to improve the performance of domestic ducks. In this study, RNA-seq data from skeletal muscles (breast muscle and leg muscle) of Pekin duck and Hanzhong Ma duck sampled at d 17, 21, and 27 of embryo (E17d, E21d, and E27d), as well as at 6-mo-old following birth (M6), to investigate and compare the mRNA temporal expression profiles and associated pathways that regulate skeletal myogenesis of different duck breeds. There were 331 to 1,440 annotated differentially expressed genes (DEGs) in breast muscle and 380 to 1,790 annotated DEGs in leg muscle from different databases between 2 duck breeds. Gene ontology (GO) enrichment in skeletal muscles indicated that these DEGs were mainly involved in biosynthetic process, developmental process, regulation of protein metabolic process and regulation of gene expression. KEGG analysis in skeletal muscles showed that a total of 41 DEGs were mapped to 7 KEGG pathways, including ECM-receptor interaction, focal adhesion, carbon metabolism, regulation of actin cytoskeleton, calcium signaling pathway, biosynthesis of amino acids and PPAR signaling pathway. The differential expression of 8 selected DEGs was verified by qRT-PCR, and the results were consistent with RNA-seq data. The identified DEGs, such as SDC, SPP1, PAK1, MYL9, PGK1, NOS1, PHGDH, TNNT2, FN1, and AQP4, were specially highlighted, indicating their associations with muscle development in the Pekin duck and Hanzhong Ma duck. This study provides a basis for revealing the differences in skeletal muscle development between Pekin duck and Hanzhong Ma duck.
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Affiliation(s)
- Chang Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Yingjie Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Yuxiao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Tao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Jiqiao Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Zhigang Hu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Jianqin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, PR China.
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Yuan S, Tian S, Meng C, Ji F, Zhou B, Rushdi HE, Ye M. The Identification of Functional Genes Affecting Fat-Related Meat Traits in Meat-Type Pigeons Using Double-Digest Restriction-Associated DNA Sequencing and Molecular Docking Analysis. Animals (Basel) 2023; 13:3256. [PMID: 37893980 PMCID: PMC10603692 DOI: 10.3390/ani13203256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/26/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The Chinese indigenous Shiqi (SQ) pigeon and the imported White King (WK) pigeon are two meat-type pigeon breeds of economical and nutritional importance in China. They displayed significant differences in such meat quality traits as intramuscular fat (IMF) content and fatty acid (FA) compositions in the breast muscles. In this study, we aimed to screen candidate genes that could affect fat-related meat quality traits in meat-type pigeons. We investigated the polymorphic variations at the genomic level using double-digest restriction-associated DNA (ddRAD) sequencing in 12 squabs of SQ and WK pigeons that exhibited significant inter-breed differences in IMF content as well as FA and amino acid compositions in the breast muscles, and screened candidate genes influencing fat-related traits in squabs through gene ontology analysis and pathway analysis. By focusing on 6019 SNPs, which were located in genes with correct annotations and had the potential to induce changes in the encoded proteins, we identified 19 genes (ACAA1, ACAA2, ACACB, ACADS, ACAT1, ACOX3, ACSBG1, ACSBG2, ACSL1, ACSL4, ELOVL6, FADS1, FADS2, HACD4, HADH, HADHA, HADHB, MECR, OXSM) as candidate genes that could affect fat-related traits in squabs. They were significantly enriched in the pathways of FA metabolism, degradation, and biosynthesis (p < 0.05). Results from molecular docking analysis further revealed that three non-synonymous amino acid alterations, ACAA1(S357N), ACAA2(T234I), and ACACB(H1418N), could alter the non-bonding interactions between the enzymatic proteins and their substrates. Since ACAA1, ACAA2, and ACACB encode rate-limiting enzymes in FA synthesis and degradation, alterations in the enzyme-substrate binding affinity may subsequently affect the catalytic efficiency of enzymes. We suggested that SNPs in these three genes were worthy of further investigation into their roles in explaining the disparities in fat-related traits in squabs.
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Affiliation(s)
- Siyu Yuan
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
| | - Shaoqi Tian
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
| | - Chuang Meng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Feng Ji
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100089, China;
| | - Bin Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
| | - Hossam E. Rushdi
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Manhong Ye
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
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Effects of Fatty-Type and Lean-Type on Growth Performance and Lipid Droplet Metabolism in Pekin Ducks. Animals (Basel) 2022; 12:ani12172268. [PMID: 36077988 PMCID: PMC9455037 DOI: 10.3390/ani12172268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Lipid deposition in animals is closely related to lipid anabolism. In order to further explore how differences in different metabolic types regulate lipid deposition, we compared the growth performance and lipid droplet metabolism of fatty-type ducks and lean-type ducks. The results showed that fatty-type ducks showed a faster growth rate and more fat deposition in the early growth stage after feeding the same diet, and produced more lipoproteins in serum and deposited in adipose tissue. However, fewer triglycerides accumulated in the liver. We believe that this performance of fatty-type ducks is caused by the increased expression level of lipid droplet-related genes. Abstract The reasons for differences in lipid depositions between fatty-type (F-T) and lean-type (L-T) ducks remain unknown. The present study aimed to compare the growth performance, lipid deposition, and gene expression related to lipid droplet formation in F-T and L-T Pekin ducks. One-day-old, 140 each L-T and F-T male ducks were selected and distributed separately into 20 replicate cages. All ducks were fed commercial diets up to 35 d of age. F-T ducks had a higher average daily gain from 21 to 28 d of age. On 35-day-old, F-T ducks had higher serum levels of high- and low-density lipoprotein cholesterol, cholesterol, albumin, and hydroxybutyrate dehydrogenase activity than L-T ducks. F-T ducks had higher abdominal fat and subcutaneous fat percentages than those in L-T ducks. Liver histological examination showed that L-T ducks contained more lipid droplets in the liver, which gradually decreased with increasing age. The average adipocyte area and diameter of abdominal fat and subcutaneous fat in the F-T and L-T ducks increased with age and were higher in F-T ducks than those in L-T ducks. Furthermore, the gene expression of perilipin 1, perilipin 2, angiopoietin-like protein 4, adipose triglyceride lipase, alpha/beta-hydrolase domain-containing protein 5 (ABHD5), and serine/threonine kinase 17a in the liver, abdominal fat, and subcutaneous fat of F-T ducks was higher than that in L-T ducks, and it increased with age. Compared to L-T ducks, F-T ducks had higher expression of ABHD5 in the abdominal fat and subcutaneous fat and lower expression in the liver. Thus, F-T ducks displayed lower hepatic lipid deposition and a higher percentage of abdominal fat and subcutaneous fat, suggesting that F-T ducks had higher lipid storage capacity due to increased gene expression related to lipid droplets.
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Integrating genome-wide association study and pathway analysis reveals physiological aspects affecting heifer early calving defined at different ages in Nelore cattle. Genomics 2022; 114:110395. [DOI: 10.1016/j.ygeno.2022.110395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022]
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7
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Hou H, Wang X, Yang C, Cai X, Lv W, Tu Y, Bao A, Wu Q, Zhao W, Yao J, Ding W. Comparative Genome and Transcriptome Integration Studies Reveal the Mechanism of Pectoral Muscle Development and Function in Pigeons. Front Genet 2022; 12:735795. [PMID: 34987544 PMCID: PMC8721168 DOI: 10.3389/fgene.2021.735795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/26/2021] [Indexed: 11/13/2022] Open
Abstract
Pigeon breed resources provide a genetic model for the study of phenomics. The pectoral muscles play a key role for the meat production performance of the meat pigeon and the athletic ability of the High flyers. Euro-pigeons and Silver King pigeons are commercial varieties that exhibit good meat production performance. In contrast to the domestication direction of meat pigeons, the traditional Chinese ornamental pigeon breed, High flyers, has a small and light body. Here, we investigate the molecular mechanism of the pectoral muscle development and function of pigeons using whole-genome and RNA sequencing data. The selective sweep analysis (FST and log2 (θπ ratio)) revealed 293 and 403 positive selection genes in Euro-pigeons and Silver King, respectively, of which 65 genes were shared. With the Silver King and Euro-pigeon as the control group, the High flyers were selected for 427 and 566 genes respectively. There were 673 differentially expressed genes in the breast muscle transcriptome between the commercial meat pigeons and ornamental pigeons. Pigeon genome selection signal combined with the breast muscle transcriptome revealed that six genes (SLC16A10, S100B, SYNE1, HECW2, CASQ2 and LOC110363470) from commercial varieties of pigeons and five genes (INSC, CALCB, ZBTB21, B2M and LOC110356506) from Chinese traditional ornamental pigeons were positively selected which were involved in pathways related to muscle development and function. This study provides new insights into the selection of different directions and the genetic mechanism related to muscle development in pigeons.
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Affiliation(s)
- Haobin Hou
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Xiaoliang Wang
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Changsuo Yang
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Xia Cai
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Wenwei Lv
- National Poultry Engineer Research Center, Shanghai, China
| | - Yingying Tu
- National Poultry Engineer Research Center, Shanghai, China
| | | | - Quanli Wu
- Shanghai Jinhuang Pigeon Company, Shanghai, China
| | - Weimin Zhao
- Shanghai Jinhuang Pigeon Company, Shanghai, China
| | - Junfeng Yao
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
| | - Weixing Ding
- Shanghai Academy of Agricultural Sciences, Shanghai, China.,National Poultry Engineer Research Center, Shanghai, China
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8
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Song Q, Wang Z, Zhang H, Li X, Zhang Y, Xu Q, Chang G, Zhang H, Chen G. Single nucleotide polymorphism scanning and expression analysis of ACSL1 from different duck breeds. CANADIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1139/cjas-2020-0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Accumulating studies have indicated that the long-chain fatty acyl-CoA1 (ACSL1) gene is related to fat deposition and meat quality in mammals. However, few studies have investigated the relationship between ACSL1 and lipid deposition in ducks. To examine this, we assessed the physicochemical property, homologous alignment, and phylogenetic analyses of the ACSL1 amino acid sequence using bioinformatics tools. The analysis indicated that the ACSL1 amino acid sequence varies in animals, and the duck ACSL1 protein is most closely related to that of chicken. Two single nucleotide polymorphism (SNP) sites were identified at 1749 and 1905 bp of the coding region of ACSL1 by sequencing. Quantitative real-time PCR and western blotting were used to measure mRNA and protein levels in abdominal fat, breast muscle, and liver tissue of Pekin duck (BD) and Cherry Valley duck (CD). mRNA and protein expression were significantly higher in BD than in CD in abdominal fat and liver tissue (P < 0.05). In breast muscle, the mRNA level of ACSL1 was also significantly higher in BD than in CD (P < 0.05), and protein expression in BD tended to be higher than that of CD. These results suggest that ACSL1 may contribute to lipid deposition and meat quality in ducks.
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Affiliation(s)
- Qianqian Song
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, People’s Republic of China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, People’s Republic of China
| | - Hongliang Zhang
- Bureau of Agriculture and Rural of the Lhasa, Lhasa 850000, People’s Republic of China
| | - Xiangxiang Li
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People’s Republic of China
| | - Yang Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, People’s Republic of China
| | - Qi Xu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, People’s Republic of China
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, People’s Republic of China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People’s Republic of China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, People’s Republic of China
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9
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Hepatic Proteomic Analysis Reveals That Enhanced Carboxylic Acid Metabolism and Oxidoreduction Promote Muscle and Fat Deposition in Muscovy Duck. Animals (Basel) 2021; 11:ani11082180. [PMID: 34438637 PMCID: PMC8388526 DOI: 10.3390/ani11082180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 12/02/2022] Open
Abstract
Simple Summary Liver plays an important role in lipid synthesis and muscle growth in poultry. The current study measured the growth traits and the proteome of Muscovy duck liver at 14, 28, 42, and 56 days, aiming at exploring the key regulatory proteins for intramuscular fat deposition and muscle growth. The results showed that Muscovy duck grew most rapidly at 28 vs. 42 days of age, subcutaneous and abdominal fat were deposited rapidly, but intramuscular fat content decreased. At the same time, the abundance of liver proteins regarding the tricarboxylic acid cycle and oxidoreduction increased significantly. This study provides a profile of the fat deposition and liver proteome for Muscovy duck. Abstract Liver is responsible for 90% of lipid synthesis in poultry; thus, it plays an important role in the growth of Muscovy ducks, which have a high fat deposition ability in a time-dependent manner. Therefore, male Muscovy ducks at 14, 28, 42, and 56 days were selected for body weight (BW), carcass weight (CW), subcutaneous fat thickness (SFT), abdominal fat weight (AFW), intramuscular fat content (IMF), and breast muscle fiber (BMF) diameter and density determination. Two-dimensional electrophoresis (2-DE) combining liquid chromatography linked to tandem mass spectrometry (LC-MS/MS) was used to analyze proteomic changes in liver at each stage. The BW, CW, AFW, SFT, and BMF diameter and density were significantly increased, while IMF content was significantly decreased at 28 to 42 days of age (p < 0.05). There were 57 differentially abundant protein (DEP) spots representing 40 proteins identified among the ages, in which 17, 41 and 4 spots were differentially abundant at 14 vs. 28, 28 vs. 42, and 42 vs. 56, respectively. Gene Ontology enrichment analysis found that DEPs were mostly enriched in the oxidation-reduction process, carboxylic acid metabolism, etc. Protein–protein interaction showed that catalase (CAT), triosephosphate isomerase (TPI), and protein disulfide-isomerase (PDI) were the key proteins responsible for the growth of Muscovy duck. In conclusion, 28 to 42 days of age is the crucial period for Muscovy ducks, and the ability of metabolism and antioxidants were significantly enhanced in liver.
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Wang L, Zhang Y, Zhang B, Zhong H, Lu Y, Zhang H. Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs. BMC Genomics 2021; 22:441. [PMID: 34118873 PMCID: PMC8201413 DOI: 10.1186/s12864-021-07764-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/02/2021] [Indexed: 11/21/2022] Open
Abstract
Background Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. One such breed, the Nanyang black pig, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model in which to investigate lipid position trait mechanisms in pigs. An understanding of lipid deposition in pigs might improve pig meat traits in future breeding and promote the selection progress of pigs through modern molecular breeding techniques. Here, transcriptome and tandem mass tag-based quantitative proteome (TMT)-based proteome analyses were carried out using longissimus dorsi (LD) tissues from individual Nanyang black pigs that showed high levels of genetic variation. Results A large population of Nanyang black pigs was phenotyped using multi-production trait indexes, and six pigs were selected and divided into relatively high and low lipid deposition groups. The combined transcriptomic and proteomic data identified 15 candidate genes that determine lipid deposition genetic divergence. Among them, FASN, CAT, and SLC25A20 were the main causal candidate genes. The other genes could be divided into lipid deposition-related genes (BDH2, FASN, CAT, DHCR24, ACACA, GK, SQLE, ACSL4, and SCD), PPARA-centered fat metabolism regulatory factors (PPARA, UCP3), transcription or translation regulators (SLC25A20, PDK4, CEBPA), as well as integrin, structural proteins, and signal transduction-related genes (EGFR). Conclusions This multi-omics data set has provided a valuable resource for future analysis of lipid deposition traits, which might improve pig meat traits in future breeding and promote the selection progress in pigs, especially in Nanyang black pigs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07764-2.
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Affiliation(s)
- Liyuan Wang
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China.,National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Haian Zhong
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Yunfeng Lu
- College of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding/Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, Beijing, China.
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11
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Guo L, Sun H, Zhao Q, Xu Z, Zhang Z, Liu D, Qadri QR, Ma P, Wang Q, Pan Y. Positive selection signatures in Anqing six-end-white pig population based on reduced-representation genome sequencing data. Anim Genet 2021; 52:143-154. [PMID: 33458851 DOI: 10.1111/age.13034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2020] [Indexed: 12/26/2022]
Abstract
Anqing six-end-white (AQ) pig performs well on resistance to coarse fodder and disease, reproduction and meat quality, offering high potential for exploitation. Environmental conditions and strict selections from local farmers have cultivated the AQ pig to be an outstanding and unique local pig breed. Thus we aim to detect genetic positive selection signatures within the AQ pig population to explore underlying genetic mechanisms. A relative extended haplotype homozygosity (REHH) test was performed in the population of 79 AQ pigs to seek evidence demonstrating that selective actions have left an imprint on the whole genome. In total, 430 500 REHH tests were performed on 53 067 core regions with average REHH tests of 8.11, average lengths of 11.50 kb and an overall length of 610.38 Mb which accounted for 26.94% of the whole genome. Finally, a total of 1819 core haplotypes (P < 0.01) and 586 candidate genes were obtained. These genes were mainly related to meat quality (MYOG, SNX19), resistance to disease (CRISPLD2, CD14) and reproduction traits (ERBB2, NRP2). A panel of genes within the 30 top significant REHH tests was mainly categorized to traits of meat quality and disease resistance. Among 13 KEGG pathways, MAPK, GnRH and Oxytocin signaling pathways, associated with the biological processes of crucial economic traits, were noteworthy. The excellent characteristics of the AQ pig benefited from the combination of natural and human factors. We provide a sketch map that shows the distribution of selection footprints on the whole genome of AQ pig and found potential genes for future studies.
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Affiliation(s)
- L Guo
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - H Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Z Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Z Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - D Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q R Qadri
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - P Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road, Shanghai, East, 200240, China
| | - Q Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Yuhangtang Road, Hangzhou, East, 310058, China
| | - Y Pan
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Yuhangtang Road, Hangzhou, East, 310058, China
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Wang Z, Liang W, Li X, Zhang Y, Xu Q, Chen G, Zhang H, Chang G. Characterization and expression of MUSTN1 gene from different duck breeds. Anim Biotechnol 2020; 33:723-730. [DOI: 10.1080/10495398.2020.1828905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Wenshuang Liang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Xiangxiang Li
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Yang Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Qi Xu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou, People's Republic of China
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13
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Lee D, Lee J, Heo KN, Kwon K, Moon Y, Lim D, Lee KT, Kim J. Population analysis of the Korean native duck using whole-genome sequencing data. BMC Genomics 2020; 21:554. [PMID: 32787779 PMCID: PMC7430827 DOI: 10.1186/s12864-020-06933-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Advances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis to discover unique genomic characteristics of domesticated animals. Duck is one of the most popular domesticated waterfowls, which is economically important as a source of meat, eggs, and feathers. The objective of this study is to perform population and functional analyses of Korean native duck, which has a distinct meat flavor and texture phenotype, using whole-genome sequencing data. To study the distinct genomic features of Korean native duck, we conducted population-level genomic analysis of 20 Korean native ducks together with 15 other duck breeds. RESULTS A total of 15.56 million single nucleotide polymorphisms were detected in Korean native duck. Based on the unique existence of non-synonymous single nucleotide polymorphisms in Korean native duck, a total of 103 genes related to the unique genomic characteristics of Korean native duck were identified in comparison with 15 other duck breeds, and their functions were investigated. The nucleotide diversity and population structures among the used duck breeds were then compared, and their phylogenetic relationship was analyzed. Finally, highly differentiated genomic regions among Korean native duck and other duck breeds were identified, and functions of genes in those regions were examined. CONCLUSIONS This is the first study to compare the population of Korean native duck with those of other duck breeds by using whole-genome sequencing data. Our findings can be used to expand our knowledge of genomic characteristics of Korean native duck, and broaden our understanding of duck breeds.
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Affiliation(s)
- Daehwan Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jongin Lee
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kang-Neung Heo
- National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngbeen Moon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dajeong Lim
- National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Kyung-Tai Lee
- National Institute of Animal Science, Wanju, 55365, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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14
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Jia C, Li C, Fu D, Chu M, Zan L, Wang H, Liang C, Yan P. Identification of genetic loci associated with growth traits at weaning in yak through a genome-wide association study. Anim Genet 2019; 51:300-305. [PMID: 31877578 DOI: 10.1111/age.12897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2019] [Indexed: 12/18/2022]
Abstract
A multilocus GWAS was performed to explore the genetic architecture of four growth traits in yak. In total, 354 female yaks for which measurements of body weight (BW), withers height (WH), body length (BL) and chest girth (CG) at weaning were available underwent genotyping with the Illumina BovineHD BeadChip (770K). After quality control, we retained 98 688 SNPs and 354 animals for GWAS analysis. We identified seven, 18, seven and nine SNPs (corresponding to seven, 17, seven and eight candidate genes) associated with BW, WH, BL and CG at weaning respectively. Interestingly, most of these candidate genes were reported to be involved in growth-related processes such as muscle formation, lipid deposition, feed efficiency, carcass composition and development of the central and peripheral nervous system. Our results offer novel insight into the molecular architecture underpinning yak growth traits. Further functional analyses are thus warranted to explore the molecular mechanisms whereby these genes affect these traits of interest.
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Affiliation(s)
- C Jia
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - C Li
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - D Fu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - M Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - L Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - H Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - C Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - P Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
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15
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Guo X, Wang J, Ma C, Wang Z, Chen H, Su H, Wan Y, Jiang R. Genome-wide re-sequencing and transcriptome analysis reveal candidate genes associated with the pendulous comb phenotype in domestic chickens. Anim Sci J 2019; 91:e13308. [PMID: 31808219 DOI: 10.1111/asj.13308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 09/21/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022]
Abstract
To determine the causative variations associated with two chicken comb phenotypes, pendulous comb (PC) or upright comb (UC), two pooled genomic DNA samples from PC and UC chickens were re-sequenced by Next-Generation Sequencer, and genome-wide Single nucleotide polymorphisms (SNPs) were detected. Using three selective sweep approaches, FST , θπ, and Tajima's D, with top 5% window values serving as the threshold, a total of 84 positively selective genes (PSGs) were identified. There were no SNPs in exons of the PSGs with significant differences in allele frequencies between the two comb phenotype groups. Then, 515 differentially expressed genes (DEGs) between the PC and UC were identified by RNA-seq. Three genes including CD36 (CD36 molecule), ADAMTSL3 (ADAMTS-like 3), and AOX1 (aldehyde oxidases 1) are overlapped between PSGs and DEGs. After genotyping seven candidate SNPs in the regulatory regions of the three overlapping genes in 120 chickens from two other breeds, two variants (rs14607046 and rs731818051) in the regulatory regions of AOX1 and ADAMTSL3 were found to have significant differences in allele frequency between the PC and UC, suggesting that the two variants may be causative mutations for PC. Overall, our study shed light on the genetic basis underlying the PC phenotype in chickens.
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Affiliation(s)
- Xing Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jiangxian Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Chendong Ma
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhicheng Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Hong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Hu Su
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yi Wan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Runshen Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
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17
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Analysis of Anasplatyrhynchos genome resequencing data reveals genetic signatures of artificial selection. PLoS One 2019; 14:e0211908. [PMID: 30735526 PMCID: PMC6368380 DOI: 10.1371/journal.pone.0211908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 01/22/2019] [Indexed: 02/05/2023] Open
Abstract
Three artificially selected duck populations (AS), higher lean meat ratios (LTPD), higher fat ratios (FTPD) and higher quality meat (CMD), have been developed in China, providing excellent populations for investigation of artificial selection effects. However, the genetic signatures of artificial selection are unclear. In this study, we sequenced the genome sequences of these three artificially selected populations and their ancestral population (mallard, M). We then compared the genome sequences between AS and M and between LTPD and FTPD using integrated strategies such as anchoring scaffolds to pseudo-chromosomes, mutation detection, selective screening, GO analysis, qRT-PCR, and protein multiple sequences alignment to uncover genetic signatures of selection. We anchored duck scaffolds to pseudo-chromosomes and obtained 28 pseudo-chromosomes, accounting for 84% of duck genome in length. Totally 78 and 99 genes were found to be under selection between AS and M and between LTPD and FTPD. Genes under selection between AS and M mainly involved in pigmentation and heart rates, while genes under selection between LTPD and FTPD involved in muscle development and fat deposition. A heart rate regulator (HCN1), the strongest selected gene between AS and M, harbored a GC deletion in AS and displayed higher mRNA expression level in M than in AS. IGF2R, a regulator of skeletal muscle mass, was found to be under selection between FTPD and LTPD. We also found two nonsynonymous substitutions in IGF2R, which might lead to higher IGF2R mRNA expression level in FTPD than LTPD, indicating the two nonsynonymous substitutions might play a key role for the regulation of duck skeletal muscle mass. Taken together, these results of this study provide valuable insight for the genetic basis of duck artificial selection.
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