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Choi JY, Shin D, Lee HJ, Oh JD. Comparison of long noncoding RNA between muscles and adipose tissues in Hanwoo beef cattle. Anim Cells Syst (Seoul) 2019; 23:50-58. [PMID: 30834159 PMCID: PMC6394308 DOI: 10.1080/19768354.2018.1512522] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate the expression of mRNA and can affect various biological processes and phenotypes. Currently, studies of lncRNAs in cattle are under way, but their exact function for several tissues has not yet been established. Hanwoo cattle (Bos taurus coreanae) have inhabited the Korean peninsula for about 6000 years and are one of the representative domesticated animals in Korea. As a result of intensive breeding, the meat of Hanwoo cattle is high in marbling content and is preferred by Koreans and other East Asian people. In this study, the expression of lncRNAs was identified in 36 samples from skeletal muscle and three adipose tissues (intramuscular, subcutaneous, and omental) of nine Hanwoo individuals. We identified 76 tissue-specific lncRNAs for each of the four tissues using the differences in expression levels. Through QTL information, we could identify 12 lncRNAs associated with shear force and six lncRNAs associated with body weight, which are two important traits in the Hanwoo population breeding strategy. By the physical position comparison of lncRNA and Bovine transcripts information, we could identify 11 lncRNAs that were in bovine transcripts, and four of the 11 genes related to transcripts of lncRNAs were biologically associated with muscle function. We believe this Hanwoo lncRNAs study will help reveal the lncRNA role in the physiological mechanisms of these four tissues.
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Affiliation(s)
- Jae-Young Choi
- The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju, Republic of Korea
| | - Donghyun Shin
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju, Republic of Korea
| | - Hyun-Jeong Lee
- Animal Nutritional & Physiology Team, National Institute of Animal Science, Wanju, Republic of Korea
| | - Jae-Don Oh
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju, Republic of Korea
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Gastrointestinal Spatiotemporal mRNA Expression of Ghrelin vs Growth Hormone Receptor and New Growth Yield Machine Learning Model Based on Perturbation Theory. Sci Rep 2016; 6:30174. [PMID: 27460882 PMCID: PMC4962052 DOI: 10.1038/srep30174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 06/28/2016] [Indexed: 12/16/2022] Open
Abstract
The management of ruminant growth yield has economic importance. The current work presents a study of the spatiotemporal dynamic expression of Ghrelin and GHR at mRNA levels throughout the gastrointestinal tract (GIT) of kid goats under housing and grazing systems. The experiments show that the feeding system and age affected the expression of either Ghrelin or GHR with different mechanisms. Furthermore, the experimental data are used to build new Machine Learning models based on the Perturbation Theory, which can predict the effects of perturbations of Ghrelin and GHR mRNA expression on the growth yield. The models consider eight longitudinal GIT segments (rumen, abomasum, duodenum, jejunum, ileum, cecum, colon and rectum), seven time points (0, 7, 14, 28, 42, 56 and 70 d) and two feeding systems (Supplemental and Grazing feeding) as perturbations from the expected values of the growth yield. The best regression model was obtained using Random Forest, with the coefficient of determination R2 of 0.781 for the test subset. The current results indicate that the non-linear regression model can accurately predict the growth yield and the key nodes during gastrointestinal development, which is helpful to optimize the feeding management strategies in ruminant production system.
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Sudrajad P, Sharma A, Dang CG, Kim JJ, Kim KS, Lee JH, Kim S, Lee SH. Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:1541-1546. [PMID: 26954199 PMCID: PMC5088372 DOI: 10.5713/ajas.15.0836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/12/2016] [Accepted: 02/23/2016] [Indexed: 12/25/2022]
Abstract
Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.
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Affiliation(s)
- Pita Sudrajad
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea.,Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Jakarta Selatan 12540, Indonesia
| | - Aditi Sharma
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju 565-851, Korea
| | - Chang Gwon Dang
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 232-950, Korea
| | - Jong Joo Kim
- School of Biotechnology, Yeungnam University, Daegu 717-749, Korea
| | - Kwan Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
| | - Sidong Kim
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 232-950, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
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Allais S, Levéziel H, Hocquette JF, Rousset S, Denoyelle C, Journaux L, Renand G. Fine mapping of quantitative trait loci underlying sensory meat quality traits in three French beef cattle breeds. J Anim Sci 2014; 92:4329-41. [PMID: 25149327 DOI: 10.2527/jas.2014-7868] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are significantly associated with meat tenderness in the Blonde d'Aquitaine breed. Overall, these results greatly contribute to the goal of building a panel of markers that can be used to select animals of high meat quality.
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Affiliation(s)
- S Allais
- INRA, AgroParisTech, UMR1313 Unité de Génétique Animale et Biologie Intégrative, F-78350 Jouy-en-Josas, France Union Nationale des Coopératives agricoles d'Elevage et d'Insémination Animale, F-75595 Paris Cedex 12, France
| | - H Levéziel
- INRA, Université de Limoges, UMR1061 Unité de Génétique Moléculaire Animale, F-87060 Limoges, France
| | - J F Hocquette
- INRA, VetAgro Sup, UMR1213, Recherches sur les Herbivores, F-63122 Saint Genès Champanelle, France
| | - S Rousset
- INRA, Clermont Université, UMR1019 Unité de Nutrition Humaine, Centre de Recherches en Nutrition Humaine d'Auvergne, F-63001 Clermont-Ferrand, France
| | - C Denoyelle
- Institut de l'Elevage, F-75595 Paris Cedex 12, France
| | - L Journaux
- Institut de l'Elevage, F-75595 Paris Cedex 12, France
| | - G Renand
- INRA, Clermont Université, UMR1019 Unité de Nutrition Humaine, Centre de Recherches en Nutrition Humaine d'Auvergne, F-63001 Clermont-Ferrand, France
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Wang X, Zhang YQ, He DC, Yang XM, Li B, Wang DC, Guang J, Xu F, Li JY, Gao X, Gao HJ, Zhang LP, Zhang XZ. The complete mitochondrial genome of Bos taurus coreanae (Korean native cattle). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:120-1. [PMID: 24438282 DOI: 10.3109/19401736.2013.873933] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Korean native cattle is one of the famous native breeds in Korean. In the present work, we report the complete mitochondrial genome sequence of Korean native cattle for the first time. The total length of the mitogenome was 16,339 bp with the base composition of 33.4% for A, 27.2% for T, 26.0% for C, and 13.4% for G, and an A-T (60.6%)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of cattle. The complete mitochondrial genome sequence of Korean native cattle would serve as an important data set of the germplasm resources for further study.
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Affiliation(s)
- Xi Wang
- a Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science , Taiyuan , China and
| | - Yuan Qing Zhang
- a Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science , Taiyuan , China and
| | - Dong Chang He
- a Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science , Taiyuan , China and
| | - Xiao Ming Yang
- a Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science , Taiyuan , China and
| | - Bo Li
- a Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science , Taiyuan , China and
| | - Dong Cai Wang
- a Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science , Taiyuan , China and
| | - Jin Guang
- a Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science , Taiyuan , China and
| | - Fang Xu
- a Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science , Taiyuan , China and
| | - Jun Ya Li
- b Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing , China
| | - Xue Gao
- b Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing , China
| | - Hui Jiang Gao
- b Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing , China
| | - Lu Pei Zhang
- b Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing , China
| | - Xi Zhong Zhang
- a Institute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science , Taiyuan , China and
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Karisa BK, Thomson J, Wang Z, Bruce HL, Plastow GS, Moore SS. Candidate genes and biological pathways associated with carcass quality traits in beef cattle. CANADIAN JOURNAL OF ANIMAL SCIENCE 2013. [DOI: 10.4141/cjas2012-136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Karisa, B. K., Thomson, J., Wang, Z., Bruce, H. L., Plastow, G. S. and Moore, S. S. 2013. Candidate genes and biological pathways associated with carcass quality traits in beef cattle. Can. J. Anim. Sci. 93: 295–306. The objective of this study was to use the candidate gene approach to identify the genes associated with carcass quality traits in beef cattle steers at the University of Alberta Ranch at Kinsella, Canada. This approach involved identifying positional candidate genes and prioritizing them according to their functions into functional candidate genes before performing statistical association analysis. The positional candidate genes and single nucleotide polymorphisms (SNP) were identified from previously reported quantitative trait loci for component traits including body weight, average daily gain, metabolic weight, feed efficiency and energy balance. Positional candidate genes were then prioritized into functional candidate genes according to the associated gene ontology terms and their functions. A total of 116 genes were considered functional candidate genes and 117 functional SNPs were genotyped and used for multiple marker association analysis using ASReml®. Seven SNPs were significantly associated with various carcass quality traits (P≤0.005). The significant genes were associated with biological processes such as fat, glucose, protein and steroid metabolism, growth, energy utilization and DNA transcription and translation as inferred from the protein knowledgebase (UniprotKB). Gene network analysis indicated significant involvement of biological processes related to fat and steroid metabolism and regulation of transcription and translation of DNA.
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Affiliation(s)
- B. K. Karisa
- Livestock Gentec and the Department of Agricultural, Food and Nutritional Science, 4.10 Agriculture Forestry Center, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - J. Thomson
- Livestock Gentec and the Department of Agricultural, Food and Nutritional Science, 4.10 Agriculture Forestry Center, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
- Montana State University, Department of Animal and Range Sciences, Bozeman MT 59717, USA
| | - Z. Wang
- Livestock Gentec and the Department of Agricultural, Food and Nutritional Science, 4.10 Agriculture Forestry Center, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - H. L. Bruce
- Livestock Gentec and the Department of Agricultural, Food and Nutritional Science, 4.10 Agriculture Forestry Center, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - G. S. Plastow
- Livestock Gentec and the Department of Agricultural, Food and Nutritional Science, 4.10 Agriculture Forestry Center, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
| | - S. S. Moore
- Livestock Gentec and the Department of Agricultural, Food and Nutritional Science, 4.10 Agriculture Forestry Center, University of Alberta, Edmonton, Alberta, Canada T6G 2P5
- The University of Queensland, Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, 4072, Queensland, Australia
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Seong J, Oh JD, Cheong IC, Lee KW, Lee HK, Suh DS, Jeon GJ, Park KD, Kong HS. Association between polymorphisms of Myf5 and POU1F1 genes with growth and carcass traits in Hanwoo (Korean cattle). Genes Genomics 2011. [DOI: 10.1007/s13258-011-0006-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Seong J, Suh DS, Park KD, Lee HK, Kong HS. Identification and analysis of MC4R polymorphisms and their association with economic traits of Korean cattle (Hanwoo). Mol Biol Rep 2011; 39:3597-601. [DOI: 10.1007/s11033-011-1133-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
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Reardon W, Mullen AM, Sweeney T, Hamill RM. Association of polymorphisms in candidate genes with colour, water-holding capacity, and composition traits in bovine M. longissimus and M. semimembranosus. Meat Sci 2010; 86:270-5. [PMID: 20510534 DOI: 10.1016/j.meatsci.2010.04.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 03/11/2010] [Accepted: 04/11/2010] [Indexed: 01/08/2023]
Abstract
The objective of this study was to determine the association of single nucleotide polymorphisms (SNP) in selected candidate genes with sensory and technological meat quality traits in commercial cattle. SNP in seven candidate genes were genotyped in 130 crossbred Bos taurus cattle using PCR-RFLP. Reported associations between calpastatin (CAST) and Warner-Bratzler shear force and carboxypeptidase E (CPE) and intra-muscular fat were not confirmed. However, SNP in CAST, amp-activated protein kinase, gamma-3 subunit (PRKAG3), growth hormone receptor (GHR) and stearoyl coA desaturase (SCD) genes were significantly associated with colour traits (p<0.05). The PRKAG3 SNP was additionally associated with cook loss in M. longissimus thoracis et lumborum (p<0.05) and tended towards association in M. semimembranosus (p<0.1). An association with pH was identified for the SCD SNP (p<0.001). The GHR polymorphism was influential on moisture and intra-muscular fat in M. semimembranosus and protein content in both muscles (p<0.05). Only CPE was associated with sensory traits (flavour in M. longissimus, p<0.01).
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Affiliation(s)
- W Reardon
- Teagasc, Ashtown Food Research Centre, Ashtown, Dublin 15, Ireland
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