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Agung PP, Saputra F, Putra WPB, Said S, Zein MSA, Harianja FH, Sudiro A. Evaluation of potential genetic marker for growth and carcass traits in Sumba Ongole ( Bos indicus) cattle. J Adv Vet Anim Res 2024; 11:85-92. [PMID: 38680811 PMCID: PMC11055583 DOI: 10.5455/javar.2024.k751] [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: 10/04/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 05/01/2024] Open
Abstract
Objective This study was conducted to investigate the variants of the growth hormone receptor (GHR), growth hormone-releasing hormone (GHRH), pituitary-specific transcription factor-1 (PIT1), and signal transducer and activator of transcription 5A (STAT5) genes and their effect on growth performance and dressing percentage (DP) parameters. Materials and Methods A total of 401 DNA samples from Sumba Ongole (SO) cattle were utilized for the polymerase chain reaction-restriction fragment length polymorphism method, of which 200 samples were used for the study of DP association and 74 samples were used to investigate growth performance. The SO cattle growth performance includes the following: birth weight, weaning weight at 205 days of age, weaning average daily gain (ADG), yearling weight at 365 days of age, and post-weaning ADG. Results The GHR, GHRH, PIT1, and STAT5A genes showed polymorphism. The highest polymorphism information content value was shown in the STAT5A gene. The highest DP value was found in the SO cattle population with the CC genotype (STAT5A), and the lowest DP value was found in the SO cattle population with the GG genotype (GHR). The GHR and STAT5A genotypes were highly associated (p < 0.05) with the DP parameter. Based on locus combination analysis, the highest DP value was found in the SO cattle population with AG|CC genotype (GHR|STAT5A) (57.85%), AG|BB|CC genotype (GHR|GHRH|STAT5A) (57.85%), and AA|BB|BB|CC genotype 18 (GHR|GHRH|PIT1|STAT5A) (56.02%). Conclusion All investigated genes in this study were polymorphic but were not associated with several growth parameters. The GHR and STAT5A genes can be proposed as genetic markers for the high DP trait in SO cattle in Indonesia, especially the AA genotype (GHR) and CC genotype (STAT5A).
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Affiliation(s)
| | - Ferdy Saputra
- Research Center for Animal Husbandry-BRIN, Bogor, Indonesia
| | | | | | | | - Febrina Hastuti Harianja
- Center for Quality Testing and Certification of Veterinary Medicines (BBPMSOH), Bogor, Indonesia
| | - Aditya Sudiro
- PT. Karya Anugerah Rumpin (PT. KAR), Bogor, Indonesia
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El-Mansy SA, Naiel MA, Abu El-Naser IA, De Waard M, Babalghith AO, Ogaly HA, El-Saber Batiha G, Ghazy AA. The growth hormone gene polymorphism and its relationship to performance and carcass features in Egyptian Awassi lambs. Heliyon 2023; 9:e14194. [PMID: 36938391 PMCID: PMC10015200 DOI: 10.1016/j.heliyon.2023.e14194] [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: 08/31/2022] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
The main purpose of the existing experiment was to assess the allelic and genotypic polymorphisms of the Growth hormone (GH) gene and its correlation with growth indices, efficiency of consumed feed, some body indices and carcass traits of the Egyptian Awassi sheep. Forty Egyptian Awassi male lambs were selected for their growing indices (post-weaning daily gain, marketing weight, and weaning weight), feed efficiency (consumed feed and of consumed feed), body conformational indicators (skeletal muscle index, relative body index, body mass index, and body index), and carcass features (dressing %, hot carcass weight, fore-legs %, neck %, loin %, ribs %, abdominal fat %, Tail % and hind-legs %). The polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP) tool was applied to detect the genotypic and allelic GH gene polymorphisms properties. The PCR-RFLP analysis identified three main genotypes (AA, AB and BB) and two main alleles (A and B). The GH genotype (AA or AB) exhibited moderate significant influence (P < 0.05) on marketing weight, Loin% and Tail%. Also, genotype (AB or BB) of expressed GH gene significantly (P < 0.01) influence on consumed feed, post-weaning daily gain, neck% and body mass index, whereas, it had no influence on the phenotypic values of the other characteristics investigated. The presence of the A allele in the genotype was markedly associated (P < 0.01) with consumed feed, body mass index and post-weaning daily growth; conversely, the presence of the B allele in the genotype was significantly related (P < 0.05) with marketing weight, loin %, and tail %. While, GH gene expression was revealed to be highly significant (P < 0.01) in relation to post-weaning daily growth, feed intake, and neck %. According to the findings, determining the associations between GH gene variation and growth, efficiency of consumed feed, body measurements, and carcass features of Egyptian Awassi sheep and applying marker assisted selection with the GH gene to improve these traits is warranted and will be of significant economic value to sheep production.
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Affiliation(s)
- Salah A. El-Mansy
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt
| | - Mohammed A.E. Naiel
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt
- Corresponding author.
| | | | - Michel De Waard
- FranceSmartox Biotechnology, 6 Rue Des Platanes, F-38120 Saint-Egrève, France
- L’institut du Thorax, INSERM, CNRS, UNIV NANTES, F-44007 Nantes, France
- LabEx Ion Channels, Science & Therapeutics, Université de Nice Sophia-Antipolis, F-06560 Valbonne, France
| | - Ahmad O. Babalghith
- Medical Genetics Department, College of Medicine, Umm Al-Qura University, Saudi Arabia
| | - Hanan A. Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha, 61421, Saudi Arabia
- Biochemistry and Molecular Biology Department, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Abdullah A. Ghazy
- Department of Animal Production, Faculty of Agriculture, Suez Canal University, 41522, Ismailia, Egypt
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Edea Z, Jung KS, Shin SS, Yoo SW, Choi JW, Kim KS. Signatures of positive selection underlying beef production traits in Korean cattle breeds. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:293-305. [PMID: 32568261 PMCID: PMC7288235 DOI: 10.5187/jast.2020.62.3.293] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Accepted: 03/15/2020] [Indexed: 01/01/2023]
Abstract
The difference in the breeding programs and population history may have diversely
shaped the genomes of Korean native cattle breeds. In the absence of phenotypic
data, comparisons of breeds that have been subjected to different selective
pressures can aid to identify genomic regions and genes controlling qualitative
and complex traits. In this study to decipher genetic variation and identify
evidence of divergent selection, 3 Korean cattle breeds were genotyped using the
recently developed high-density GeneSeek Genomic Profiler F250 (GGP-F250) array.
The three Korean cattle breeds clustered according to their coat color
phenotypes and breeding programs. The Heugu breed reliably showed smaller
effective population size at all generations considered. Across the autosomal
chromosomes, 113 and 83 annotated genes were identified from Hanwoo-Chikso and
Hanwoo-Heugu comparisons, respectively of which 16 genes were shared between the
two pairwise comparisons. The most important signals of selection were detected
on bovine chromosomes 14 (24.39–25.13 Mb) and 18 (13.34–15.07 Mb),
containing genes related to body size, and coat color (XKR4,
LYN, PLAG1, SDR16C5,
TMEM68, CDH15, MC1R, and
GALNS). Some of the candidate genes are also associated
with meat quality traits (ACSF3, EIF2B1,
BANP, APCDD1, and GALM)
and harbor quantitative trait locus (QTL) for beef production traits. Further
functional analysis revealed that the candidate genes (DBI,
ACSF3, HINT2, GBA2,
AGPAT5, SCAP, ELP6,
APOB, and RBL1) were involved in gene
ontology (GO) terms relevant to meat quality including fatty acid oxidation,
biosynthesis, and lipid storage. Candidate genes previously known to affect beef
production and quality traits could be used in the beef cattle selection
strategies.
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Affiliation(s)
- Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kyoung Sub Jung
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Sung-Sub Shin
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Song-Won Yoo
- Korea Institute for Animal Products Quality Evaluation, Sejong 30100, Korea
| | - Jae Won Choi
- Institute of Livestock and Veterinary Research, Cheongju 28153, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
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MALDI-TOF-MS-based high throughput genotyping of mutations associated with body measurement traits in cattle. Mamm Genome 2020; 31:228-239. [PMID: 32385542 DOI: 10.1007/s00335-020-09840-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
Abstract
Exploration of genes in relation to body measurement traits through large-scaled mutation identification is highly conductive for the genomics-assisted breeding of superior productivity cattle. In this investigation, 31 objective mutations were genotyped synchronously in 384 yellow cattle of 8 breeds through the application of optimized MALDI-TOF-MS and multiplex PCR techniques. High genotyping rate was obtained as well as greatly decreased cost which was below one thirtieth of the routine analysis. Results from genotyping revealed 23 mutations as valid mutations in the studied cattle population with gene heterozygosity and effective allele number varying from 0.0052 to 0.4998 and 1.0052 to 1.9991, respectively. Among the 23 effective mutations, 12 was classified as moderate polymorphism (0.25 < PIC < 0.5) while the other 11 belonged to low polymorphism (PIC < 0.25), 7 mutations did not obey the HW equilibrium (p < 0.05) and linkage mainly appeared between mutations of UCP2 and PTHR1 genes. Furthermore, 8 body measurement traits in the 384 cattle were recorded to validate their association with tag mutations, and significant correlations were found in 12 mutations of 9 genes including PTHR1, CDK6, IHH, HHIP, GHRL, COL1A1, INS, GDF5 and UCP2, of which, PTHR1 was proved to be the most potential contributor to bone modeling in cattle. Results highlight the potential application value of 12 novel mutations in enhancing cattle production traits as well as the high genotyping rate achieved by MALDI-TOF-MS coupled with multiplex PCR technique.
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Jin Y, Yang Q, Gao J, Tang Q, Duan B, Yu T, Qi X, Liu J, Wang R, Dang R, Lei C, Chen H, Lan X. Detection of Insertions/Deletions Within SIRT1, SIRT2 and SIRT3 Genes and Their Associations with Body Measurement Traits in Cattle. Biochem Genet 2018; 56:663-676. [PMID: 29869077 DOI: 10.1007/s10528-018-9868-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 05/31/2018] [Indexed: 11/27/2022]
Abstract
Growth traits are complex quantitative traits controlled by numerous candidate genes, and they can be well-evaluated using body measurement traits. As the members of the nicotinamide adenine dinucleotide-dependent family of histone deacetylases, class I sirtuin genes (including SIRT1, SIRT2 and SIRT3) play crucial roles in regulating lipid metabolism, cellular growth and metabolism, suggesting that they are potential candidate genes affecting body measurement traits in animals. Hence, the objective of this work aimed to detect novel insertions/deletions (indels) of SIRT1, SIRT2 and SIRT3 genes in 955 cattle belonging to five breeds, as well as to evaluate their effects on body measurement traits. Herein, the novel 12-bp indel of SIRT1 gene, the 7-bp indel of SIRT2 gene and the 26-bp indel of SIRT3 gene were firstly reported, respectively. The association analysis indicated that the indels within SIRT1 and SIRT2 genes were significantly associated with body measurement traits such as body weight, chest circumference, height at hip cross, hip width, body height, etc. (P < 0.05 or P < 0.01). Therefore, based on these findings, the two novel indel variants within bovine SIRT1 and SIRT2 genes could be considered as potential molecular markers for growth traits in cattle selection practices and breeding.
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Affiliation(s)
- Yunyun Jin
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qing Yang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jiayang Gao
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Qi Tang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Bo Duan
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Ting Yu
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xinglei Qi
- Xianan Cattle Technology Development Company, Biyang, 463700, Henan, People's Republic of China
- Bureau of Animal Husbandry, Biyang, 463700, Henan, People's Republic of China
| | - Jiming Liu
- Animal Husbandry Technology Promotion Station of Jiangxi, Nanchang, 330000, Jiangxi, People's Republic of China
| | - Rongmin Wang
- Animal Husbandry Technology Promotion Station of Jiangxi, Nanchang, 330000, Jiangxi, People's Republic of China
| | - Ruihua Dang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Hong Chen
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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HAN YJ, CHEN Y, LIU Y, LIU XL. Sequence variants of the LCORL gene and its association with growth and carcass traits in Qinchuan cattle in China. J Genet 2017; 96:9-17. [DOI: 10.1007/s12041-016-0732-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Cheng Y, Liu S, Su D, Lu C, Zhang X, Wu Q, Li S, Fu H, Yu H, Hao L. Distribution and linkage disequilibrium analysis of polymorphisms of GH1 gene in different populations of pigs associated with body size. J Genet 2016; 95:79-87. [PMID: 27019435 DOI: 10.1007/s12041-015-0611-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Growth hormone (GH) has been considered as a candidate gene for growth and body size in pigs. In this study, polymorphisms of the GH1 gene were evaluated for associations with body size traits in 190 pig individuals. Seventeen single-nucleotide polymorphisms (SNPs) were identified in GH1 gene of the large pig breeds and miniature pig breeds using direct sequencing and genotyped by allele-specific PCR approach. Notably, six (g.237A>G, g.283T>C, g.309A>G, g.318A>G, g.540A>G and g.544A>G) of them were significantly associated with body size, of which three loci (g.283T>C, g.309A>G, g.318A>G) located in the signal-peptide coding region of GH1 gene compose a CGG haplotype for large pigs and TAA haplotype for miniature pigs (P <0.001), two loci (g.540A>G and g.544A>G) located in the second intron of GH1 gene compose a GG haplotype for large pigs and AA haplotype for miniature pigs (P < 0.001). Our results demonstrate that these SNPs in GH1 gene are associated with the body size of pigs providing genetic basis for pig breeding with the improved economic benefits.
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Affiliation(s)
- Yunyun Cheng
- College of Animal Science, Jilin University, 5333 Xi'an Road, Changchun, Jilin 130062, People's Republic of
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Lim D, Strucken EM, Choi BH, Chai HH, Cho YM, Jang GW, Kim TH, Gondro C, Lee SH. Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea. PLoS One 2016; 11:e0151324. [PMID: 27023061 PMCID: PMC4811422 DOI: 10.1371/journal.pone.0151324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 02/26/2016] [Indexed: 01/01/2023] Open
Abstract
Korean Hanwoo cattle have been subjected to intensive artificial selection over the past four decades to improve meat production traits. Another three cattle varieties very closely related to Hanwoo reside in Korea (Jeju Black and Brindle) and in China (Yanbian). These breeds have not been part of a breeding scheme to improve production traits. Here, we compare the selected Hanwoo against these similar but presumed to be unselected populations to identify genomic regions that have been under recent selection pressure due to the breeding program. Rsb statistics were used to contrast the genomes of Hanwoo versus a pooled sample of the three unselected population (UN). We identified 37 significant SNPs (FDR corrected) in the HW/UN comparison and 21 known protein coding genes were within 1 MB to the identified SNPs. These genes were previously reported to affect traits important for meat production (14 genes), reproduction including mammary gland development (3 genes), coat color (2 genes), and genes affecting behavioral traits in a broader sense (2 genes). We subsequently sequenced (Illumina HiSeq 2000 platform) 10 individuals of the brown Hanwoo and the Chinese Yanbian to identify SNPs within the candidate genomic regions. Based on allele frequency differences, haplotype structures, and literature research, we singled out one non-synonymous SNP in the APP gene (APP: c.569C>T, Ala199Val) and predicted the mutational effect on the protein structure. We found that protein-protein interactions might be impaired due to increased exposed hydrophobic surfaces of the mutated protein. The APP gene has also been reported to affect meat tenderness in pigs and obesity in humans. Meat tenderness has been linked to intramuscular fat content, which is one of the main breeding goals for brown Hanwoo, potentially supporting a causal influence of the herein described nsSNP in the APP gene.
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Affiliation(s)
- Dajeong Lim
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Eva M. Strucken
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Bong Hwan Choi
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Han Ha Chai
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Yong Min Cho
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Gul Won Jang
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Tae-Hun Kim
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chung Nam National University, Daejeon 305–764, Republic of Korea
- * E-mail:
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Ma D, Ma A, Huang Z, Wang G, Wang T, Xia D, Ma B. Transcriptome Analysis for Identification of Genes Related to Gonad Differentiation, Growth, Immune Response and Marker Discovery in The Turbot (Scophthalmus maximus). PLoS One 2016; 11:e0149414. [PMID: 26925843 PMCID: PMC4771204 DOI: 10.1371/journal.pone.0149414] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/01/2016] [Indexed: 11/18/2022] Open
Abstract
Background Turbot Scophthalmus maximus is an economically important species extensively aquacultured in China. The genetic selection program is necessary and urgent for the sustainable development of this industry, requiring more and more genome background knowledge. Transcriptome sequencing is an excellent alternative way to identify transcripts involved in specific biological processes and exploit a considerable quantity of molecular makers when no genome sequences are available. In this study, a comprehensive transcript dataset for major tissues of S. maximus was produced on basis of an Illumina platform. Results Total RNA was isolated from liver, spleen, kidney, cerebrum, gonad (testis and ovary) and muscle. Equal quantities of RNA from each type of tissues were pooled to construct two cDNA libraries (male and female). Using the Illumina paired-end sequencing technology, nearly 44.22 million clean reads in length of 100 bp were generated and then assembled into 106,643 contigs, of which 71,107 were named unigenes with an average length of 892 bp after the elimination of redundancies. Of these, 24,052 unigenes (33.83% of the total) were successfully annotated. GO, KEGG pathway mapping and COG analysis were performed to predict potential genes and their functions. Based on our sequence analysis and published documents, many candidate genes with fundamental roles in sex determination and gonad differentiation (dmrt1), growth (ghrh, myf5, prl/prlr) and immune response (TLR1/TLR21/TLR22, IL-15/IL-34), were identified for the first time in this species. In addition, a large number of credible genetic markers, including 21,192 SSRs and 8,642 SNPs, were identified in the present dataset. Conclusion This informative transcriptome provides valuable new data to increase genomic resources of Scophthalmus maximus. The future studies of corresponding gene functions will be very useful for the management of reproduction, growth and disease control in turbot aquaculture breeding programs. The molecular markers identified in this database will aid in genetic linkage analyses, mapping of quantitative trait loci, and acceleration of marker assisted selection programs.
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Affiliation(s)
- Deyou Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Dalian Ocean University, Dalian, 116023, China
| | - Aijun Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- * E-mail:
| | - Zhihui Huang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Guangning Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Ting Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Dandan Xia
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Benhe Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao Key Laboratory for Marine Fish Breeding and Biotechnology, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
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Sugita H, Ardiyanti A, Yokota S, Yonekura S, Hirayama T, Shoji N, Yamauchi E, Suzuki K, Katoh K, Roh SG. Effect of single nucleotide polymorphisms in GH gene promoter region on carcass traits and intramuscular fatty acid compositions in Japanese Black cattle. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.04.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang ZN, Li MJ, Lan XY, Li MX, Lei CZ, Chen H. Tetra-primer ARMS-PCR identifies the novel genetic variations of bovine HNF-4α gene associating with growth traits. Gene 2014; 546:206-13. [PMID: 24914496 DOI: 10.1016/j.gene.2014.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/20/2014] [Accepted: 06/06/2014] [Indexed: 12/29/2022]
Abstract
Hepatocyte nuclear factor-4α (HNF-4α), a member of the hepatocyte nuclear factor family, plays an important role in regulating the expression of genes involved in the development, differentiation and normal function of liver and pancreatic β cells, as well as the maintenance of glucose homeostasis. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is a new method offering fast detection and extreme simplicity at a negligible cost for SNP genotyping. In this paper, we characterize the polymorphisms of the bovine HNF-4α gene in three Chinese indigenous cattle breeds (n=660). Six novel SNPs were identified including 1 mutation in the coding region and others in introns. The statistical analyses indicated that 4 SNPs (g.T53729C, g.A53861G, g.A65188C and g.T65444C) affected growth traits markedly (P<0.05) in Qinchuan cattle (2 years after birth). Besides, haplotypes involving these 4 SNP sites in the bovine HNF-4α gene were identified and their effects on growth traits were also analyzed. The results showed that haplotypes 2, 7, 9 and 11 were predominant and accounted for 73.2%, 59.6%, and 67.1% in Qinchuan, Nanyang and Jiaxian cattle breeds, respectively. Hap9 (TAAT) was extremely predominant in all test populations, which suggested that individuals with Hap9 were more adapted to the environment. Furthermore, 4 combined haplotypes were constructed to guarantee the reliability of analysis results in Qinchuan cattle. There were also significant differences in body length (P<0.05). These findings will benefit for the application of DNA marker related to the growth traits on marker-assisted selection (MAS), and improve the performance of beef cattle.
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Affiliation(s)
- Zi-nian Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Mi-jie Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Xian-yong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Ming-xun Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Chu-zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
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12
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Ma DM, Han LQ, Bai JJ, Li SJ, Fan JJ, Yu LY, Quan YC. A 66-bp deletion ingrowth hormone releasing hormonegene 5′-flanking region with largemouth bass recessive embryonic lethal. Anim Genet 2014; 45:421-6. [DOI: 10.1111/age.12143] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2014] [Indexed: 11/30/2022]
Affiliation(s)
- D M Ma
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture of the People's Republic of China, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China
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13
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Li ZJ, Guo WJ, Tian YD, Han RL, Sun YJ, Xue J, Lan XY, Chen H. Characterisation of the genetic effects of the ADFP gene and its association with production traits in dairy goats. Gene 2014; 538:244-50. [PMID: 24487056 DOI: 10.1016/j.gene.2014.01.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 01/17/2014] [Accepted: 01/21/2014] [Indexed: 11/18/2022]
Abstract
Adipose differentiation-related protein (ADFP) is important for regulation of lipid metabolism and insulin secretion in beta-cells. In this study, we investigated polymorphisms within the caprine ADFP gene and determined its relationship with production traits. As there was no sequence information available for the caprine ADFP gene, we generated DNA sequence data and examined the genomic organisation. The caprine ADFP gene is organised into 7 exons and 6 introns that span approximately 8.7 kbp and is transcribed into mRNA containing 1,353 bp of sequence coding for a protein of 450 amino acids. The protein sequences showed substantial similarity (71-99%) to orthologues from cattle, human and mouse. We identified polymorphisms in the sequences using DNA sequencing, PCR-RFLP and forced PCR-RFLP methods. Seven single nucleotide polymorphisms (SNPs) were identified using samples from 4 different goat populations consisting of 1408 healthy and unrelated individuals. Six haplotypes involving the 7 SNPs from the caprine ADFP gene were identified and their effects on production traits were analysed. Haplotype 6 had the highest haplotype frequency and was highly significantly associated with chest circumference and milk yield in the analysed populations. The results of this study suggest that the ADFP gene is a strong candidate gene affecting production traits and may be used for marker-assisted selection and management in Chinese dairy goat breeding programmes.
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Affiliation(s)
- Zhuan-Jian Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China; College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 45002, China
| | - Wen-Jiao Guo
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Ya-Dong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 45002, China
| | - Rui-Li Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan 45002, China
| | - Yu-Jia Sun
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Jing Xue
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
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14
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Parra-Bracamonte GM, Lopez-Villalobos N, Sifuentes-Rincon AM, Morris S, Lopez-Bustamante LA, Meza-Garcia LA. Single and composite influence of growth-related candidate gene polymorphisms on additive genetic variation of birth weight in charolais beef cattle. Trop Anim Health Prod 2013; 46:509-12. [DOI: 10.1007/s11250-013-0520-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2013] [Indexed: 10/25/2022]
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15
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Cai H, Lan X, Li A, Zhou Y, Sun J, Lei C, Zhang C, Chen H. SNPs of bovine HGF gene and their association with growth traits in Nanyang cattle. Res Vet Sci 2013; 95:483-8. [PMID: 23632198 DOI: 10.1016/j.rvsc.2013.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 03/07/2013] [Accepted: 04/02/2013] [Indexed: 12/17/2022]
Abstract
Hepatocyte growth factor (HGF) is one of the multifunctional cell factors that regulates cellular proliferation, motility and morphogenesis in mammalians. And its medical research has deep significance. In this paper, polymorphisms of HGF gene were investigated in 1433 health and irrelated Chinese cattle by PCR-RFLP and DNA sequencing approach. Ten novel Single nucleotide polymorphisms (SNPs) were identified, which included one missense mutation, g.72801G>A in the coding region, and the others in the intron. Association analysis between four of them, g.288T>C, g.72801G>A, g.77172G>T, and g.77408T>G, and growth traits in Nanyang, were performed. The results indicated that SNPs within bovine HGF gene were significantly associated with growth traits. Phylogenetic analysis showed that the genetic background of Caoyuan Red cattle was different from the others in the tested breeds. The findings will provide a background for application of bovine HGF gene in the selection program in Chinese cattle.
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Affiliation(s)
- Hanfang Cai
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
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16
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Zhou Y, Lan X, Xu Y, Zhang B, Li M, Huang Y, Sun J, Cai H, Lei C, Chen H. Exploring polymorphisms and potential application roles of the bovine Nfix gene in breeding. Genome 2012; 55:845-51. [DOI: 10.1139/gen-2012-0114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to detect mutations of the nuclear factor I/X (Nfix) gene and examine the association of its polymorphisms with growth traits in cattle. Six sequence variants (SVs) including five single-nucleotide mutations and an indel with multiple alleles were detected, among which four polymorphisms within the Nfix gene were identified in 1159 individuals of five cattle breeds by sequencing and forced PCR–RFLP methods. The results of haplotype analysis showed 14 haplotypes within the breeds. Three haplotypes were shared by the five cattle breeds. Hap1 (ACAI) was extremely predominant in all test populations, which suggested that individuals with Hap1 (ACAI) were more adapted to the steppe environment. Association analysis in Nanyang cattle showed that two SVs of the Nfix gene were significantly associated with growth traits at different ages. In addition, the locations of the SVs showed that the 3′ terminal of the bovine Nfix gene was unstable. Combining this instability with its characteristic of multiple alternative splicing, we conjectured that some SVs might have a relationship with the formation of the splices through which growth traits are modulated. This study will provide useful information for the selection and detection of multiple forms of alternative splicing of the bovine Nfix gene.
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Affiliation(s)
- Yang Zhou
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Yao Xu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Bao Zhang
- College of Medicine, Xi’an Jiaotong University, Key Laboratory of National Ministry of Health for Forensic Sciences, Xi’an, Shaanxi 710061, China
| | - Mijie Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Jiajie Sun
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Hanfang Cai
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
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17
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Genetic variations of ANGPTL6 gene and their associations with growth traits and slaughter traits in Qinchuan cattle. Mol Biol Rep 2012; 39:9223-32. [DOI: 10.1007/s11033-012-1795-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 06/09/2012] [Indexed: 12/20/2022]
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18
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Abstract
Studies in humans have independently identified single nucleotide polymorphisms (SNPs) in the fat mass and obesity associated (FTO) gene associated with obesity in multiple populations. It was shown that FTO participated in the regulation of energy homeostasis and associated with increased lipolytic activity in adipocytes. To ascertain whether there were mutations in the bovine FTO gene, this study investigated the variation of the FTO gene through PCR-SSCP and sequencing. Five synonymous mutations, two missense mutations, and three intronic SNPs were identified in 614 cattle from five independent populations. Haplotype frequencies and linkage disequilibrium (LD) coefficients of these SNPs in three Chinese indigenous cattle breeds were analyzed. Two LD blocks were found in the Qinchuan and Nanyang cattle breeds and three LD blocks were found in the Jiaxian cattle breed, suggesting the possibility of a recombination hotspot between exon 5 and intron 5 of the bovine FTO gene. The variations detected here might have an impact on the FTO gene activity and function.
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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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Bae JS, Cheong HS, Kim LH, NamGung S, Park TJ, Chun JY, Kim JY, Pasaje CFA, Lee JS, Shin HD. Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genomics 2010; 11:232. [PMID: 20377913 PMCID: PMC2859865 DOI: 10.1186/1471-2164-11-232] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 04/09/2010] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recently, the discovery of copy number variation (CNV) led researchers to think that there are more variations of genomic DNA than initially believed. Moreover, a certain CNV region has been found to be associated with the onset of diseases. Therefore, CNV is now known as an important genomic variation in biological mechanisms. However, most CNV studies have only involved the human genome. The study of CNV involving other animals, including cattle, is severely lacking. RESULTS In our study of cattle, we used Illumina BovineSNP50 BeadChip (54,001 markers) to obtain each marker's signal intensity (Log R ratio) and allelic intensity (B allele frequency), which led to our discovery of 855 bovine CNVs from 265 cows. For these animals, the average number of CNVs was 3.2, average size was 149.8 kb, and median size was 171.5 kb. Taking into consideration some overlapping regions among the identified bovine CNVs, 368 unique CNV regions were detected. Among them, there were 76 common CNVRs with > 1% CNV frequency. Together, these CNVRs contained 538 genes. Heritability errors of 156 bovine pedigrees and comparative pairwise analyses were analyzed to detect 448 common deletion polymorphisms. Identified variations in this study were successfully validated using visual examination of the genoplot image, Mendelian inconsistency, another CNV identification program, and quantitative PCR. CONCLUSIONS In this study, we describe a map of bovine CNVs and provide important resources for future bovine genome research. This result will contribute to animal breeding and protection from diseases with the aid of genomic information.
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Affiliation(s)
- Joon Seol Bae
- Laboratory of Genomic Diversity, Department of Life Science, Sogang University, Shinsu-dong, Mapo-gu, Seoul, Republic of Korea
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Han SH, Cho IC, Kim JH, Ko MS, Jeong HY, Oh HS, Lee SS. AGHR polymorphism and its associations with carcass traits in Harrwoo cattle. Genes Genomics 2009. [DOI: 10.1007/bf03191136] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Discovery of Candidate SNP Related to Meat Quality Using the BcSNPdb and Cattle QTLdb in Hanwoo. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2008. [DOI: 10.5187/jast.2008.50.6.775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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A critical analysis of production-associated DNA polymorphisms in the genes of cattle, goat, sheep, and pig. Mamm Genome 2008; 19:591-617. [PMID: 18836775 DOI: 10.1007/s00335-008-9141-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 08/12/2008] [Indexed: 10/21/2022]
Abstract
Increasing productivity is one of the main objectives in animal production. Traditional breeding methods have led to increased gains in some traits but gains are not easily attainable in traits with low heritabilities. Exploiting the genetic variations underlying desired phenotypes is the goal of today's animal producers. Such positive genetic variants must, however, be known before possible application. Consequently, candidate genes of traits of interest have been searched for possible relationships with such traits or to explain reported quantitative trait loci (QTL) for such traits. DNA variants or polymorphisms have been identified in many such genes and their relationships with production traits determined. However, only a few genes have been evaluated, given the wealth of information on reported QTL for production traits, and in most cases genes are only partially investigated. This review presents available information on DNA variants for production traits and discusses steps that are required for effective utilization of this information for successful marker-assisted selection programs.
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