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Naserkheil M, Manzari Z, Dang CG, Lee SS, Park MN. Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle. Curr Issues Mol Biol 2022; 44:6075-92. [PMID: 36547075 DOI: 10.3390/cimb44120414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.
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Kumar A, Kaur M, Ahlawat S, Sharma U, Singh MK, Singh KV, Chhabra P, Vijh RK, Yadav A, Arora R. Transcriptomic diversity in longissimus thoracis muscles of Barbari and Changthangi goat breeds of India. Genomics 2021; 113:1639-1646. [PMID: 33862183 DOI: 10.1016/j.ygeno.2021.04.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 02/24/2021] [Accepted: 04/07/2021] [Indexed: 01/13/2023]
Abstract
The present study is an attempt to examine the differential expression of genes in longissimus thoracis muscles between meat and wool type Indian goat breeds. Barbari goat is considered the best meat breed while Changthangi is famous for its fine fibre quality. RNA sequencing data was generated from four biological replicates of longissimus thoracis muscles of Barbari and Changthangi goats. A clear demarcation could be observed between the breeds in terms of expression of genes associated with lipid metabolism (FASN, SCD, THRSP, DGAT2 and FABP3). Most significant genes with high connectivity identified by gene co-expression network analysis were associated with triacylglycerol biosynthesis pathway in Barbari goat. Highly interactive genes identified in Changthangi goat were mainly associated with muscle fibre type. This study provides an insight into the differential expression of genes in longissimus thoracis muscles between Barbari and Changthangi goats that are adapted to and reared in different agro-climatic regions.
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Affiliation(s)
- Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; Kurukshetra University, Kurukshetra 136119, Haryana, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India; Kurukshetra University, Kurukshetra 136119, Haryana, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Manoj Kumar Singh
- Incharge Barbari Goat Unit, Genetics and Breeding Division, Central Institute for Research on Goats, Makhdoom, Farah, 281122 Mathura, Uttar Pradesh, India.
| | - Karan Veer Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - Ramesh Kumar Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Anita Yadav
- Kurukshetra University, Kurukshetra 136119, Haryana, India.
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
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Dixit SP, Sivalingam J, Tyagi AK, Saroha V, Sharma A, Nagda RK. Association of novel SNPs in the candidate genes affecting caprine milk fatty acids related to human health. Meta Gene 2015; 4:45-56. [PMID: 25853060 PMCID: PMC4372655 DOI: 10.1016/j.mgene.2015.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 01/06/2015] [Accepted: 01/06/2015] [Indexed: 01/13/2023] Open
Abstract
In the present investigation, 618 milk samples of Sirohi breed of goat were collected, and analyzed for conjugated linoleic acid (CLA, C18:2) and other fatty acids. The CLA in studied goat milk samples was 4.87 mg/g of milk fat and C18:2 cis-9, trans-11 contributes 2.9 mg/g of milk fat and trans10 cis12 contributes 0.82 mg/g of milk fat. The saturated fatty acids in the milk accounted for 69.55% and unsaturated fatty acid accounted for 28.50%. The unsaturated fatty acid was constituted by monounsaturated fatty acid (24.57%) and polyunsaturated fatty acids (3.96%.). The major contribution (45.56%) in total fatty acid was of C12:0, C14:0 and C16:0. C18:0 and short chain ones (C4:0, C6:0, C8:0, and C10:0) have a neutral or cholesterol-decreasing effect. The DNA sequence analysis of the genes (DGAT1, SCAP, PPARG, OLR, FABP3 and PRL) in a random panel of 8 Sirohi goats revealed 38 SNPs across the targeted regions. Out of the studied SNPs (38) across these genes, 22 SNPs had significant effect on one or a group of fatty acids including CLA. The genotypes at these loci showed significant differences in the least square means of a particular fatty acid or a group of fatty acids including CLA and its isomers.
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Affiliation(s)
- S P Dixit
- National Bureau of Animal Genetic Resources, Karnal, Haryana, 131002, India
| | | | - A K Tyagi
- National Dairy Research Institute, Karnal, Haryana, 131002, India
| | - V Saroha
- National Bureau of Animal Genetic Resources, Karnal, Haryana, 131002, India
| | - A Sharma
- National Bureau of Animal Genetic Resources, Karnal, Haryana, 131002, India
| | - R K Nagda
- Rajasthan University of Veterinary and Animal Science, Vallabhnagar, Udaipur, Rajasthan, India
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Kulig H, Kowalewska-Łuczak I, Żukowski K, Kruszyński W. FABP3, FABP4 and ANXA9 SNP genotypes in relation to breeding values for milk production traits in Polish Holstein-Friesian cows. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413080085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cho SA, Park TS, Yoon DH, Cheong HS, Namgoong S, Park BL, Lee HW, Han CS, Kim EM, Cheong IC, Kim HB, Shin HD. Identification of genetic polymorphisms in FABP3 and FABP4 and putative association with back fat thickness in Korean native cattle. BMB Rep 2008; 41:29-34. [DOI: 10.5483/bmbrep.2008.41.1.029] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Abstract
Fatty acid-binding proteins (FABPs) are members of the superfamily of lipid-binding proteins (LBP). So far 9 different FABPs, with tissue-specific distribution, have been identified: L (liver), I (intestinal), H (muscle and heart), A (adipocyte), E (epidermal), Il (ileal), B (brain), M (myelin) and T (testis). The primary role of all the FABP family members is regulation of fatty acid uptake and intracellular transport. The structure of all FABPs is similar - the basic motif characterizing these proteins is beta-barrel, and a single ligand (e.g. a fatty acid, cholesterol, or retinoid) is bound in its internal water-filled cavity. Despite the wide variance in the protein sequence, the gene structure is identical. The FABP genes consist of 4 exons and 3 introns and a few of them are located in the same chromosomal region. For example, A-FABP, E-FABP and M-FABP create a gene cluster. Because of their physiological properties some FABP genes were tested in order to identify mutations altering lipid metabolism. Furthermore, the porcine A-FABP and H-FABP were studied as candidate genes with major effect on fatness traits.
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Affiliation(s)
- Agata Chmurzyńska
- Department of Animal Genetics and Breeding, August Cieszkowski Agricultural University of Poznan, Wolynska 33, Poznan 60-637, Poland
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Wu XL, Macneil MD, De S, Xiao QJ, Michal JJ, Gaskins CT, Reeves JJ, Busboom JR, Wright RW, Jiang Z. Evaluation of candidate gene effects for beef backfat via Bayesian model selection. Genetica 2005; 125:103-13. [PMID: 16175458 DOI: 10.1007/s10709-005-5255-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2005] [Accepted: 04/10/2005] [Indexed: 10/25/2022]
Abstract
Candidate gene approaches provide tools for exploring and localizing causative genes affecting quantitative traits and the underlying variation may be better understood by determining the relative magnitudes of effects of their polymorphisms. Diacyglycerol O-acyltransferase 1 (DGAT1), fatty acid binding protein (heart) 3 (FABP3), growth hormone 1 (GH1), leptin (LEP) and thyroglobulin (TG) have been previously identified as genes contributing to genetic control of subcutaneous fat thickness (SFT) in beef cattle. In the present research, Bayesian model selection was used to evaluate effects of these five candidate genes by comparing competing non-nested models and treating candidate gene effects as either random or fixed. The analyses were implemented in SAS to simplify the programming and computation. Phenotypic data were gathered from a F(2) population of Wagyu x Limousin cattle. The five candidate genes had significant but varied effects on SFT in this population. Bayesian model selection identified the DGAT1 model as the one with the greatest model probability, whether candidate gene effects were considered random or fixed, and DGAT1 had the greatest additive effect on SFT. The SAS codes developed in the study are freely available and can be downloaded at: http://www.ansci.wsu.edu/programs/.
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Affiliation(s)
- Xiao-Lin Wu
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
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