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Lim KS, Lee KT, Park JE, Chung WH, Jang GW, Choi BH, Hong KC, Kim TH. Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using RNA sequencing. Anim Genet 2016; 48:166-174. [DOI: 10.1111/age.12518] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2016] [Indexed: 01/07/2023]
Affiliation(s)
- K. S. Lim
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
- College of Life Science and Biotechnology; Korea University; Seoul 136-713 Korea
| | - K. T. Lee
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - J. E. Park
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - W. H. Chung
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - G. W. Jang
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - B. H. Choi
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - K. C. Hong
- College of Life Science and Biotechnology; Korea University; Seoul 136-713 Korea
| | - T. H. Kim
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
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Abstract
Meat pH is an important factor influencing meat quality traits in swine. This study evaluated a large number of genetic variants that covered all of the swine chromosomal regions. Approximately 68,000 single nucleotide polymorphisms (SNPs), found on Illumina Porcine SNP chips, were tested for associations with meat pH values. A genome-wide association study (GWAS) found that 19 SNPs on Sus scrofa chromosome 4 were significantly associated with pH. Two major candidate genomic regions were defined: a 1.08-Mb region (at nucleotide 30118313 to 31207050) contained 10 significant SNPs, based on an effect value of 5.0; and a 2.7-Mb genomic region (at nucleotide 73293076 to 76023681) contained 9 significant SNPs. Three putative genes--PKHD1L1, VCPIP1, and LOC102166532--were identified by GWAS near significant SNPs. These genes may account for variations in pH levels. Three pseudogenes and two non-coding RNAs were also detected by GWAS analysis. Estimations of expected and observed P values for pH revealed significant departures from the null hypothesis. A total of 9 haplotype blocks (HB) were constructed: HBs 1, 3, and 5 showed significant effects on pH24 and pH45, whereas an association was not confirmed between pH24 and HBs 4, 6, and 8. Findings from this study indicate that the three genes identified may influence pH of pig meat.
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Affiliation(s)
- H Y Chung
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - K T Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - G W Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - J G Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - J G Hong
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - T H Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
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Kim BS, Kim SC, Park CM, Lee SH, Cho SH, Kim NK, Jang GW, Yoon DH, Yang BS, Hong SK, Seong HH, Choi BH. Genetic Polymorphisms of the Bovine NOV Gene Are Significantly Associated with Carcass Traits in Korean Cattle. Asian-Australas J Anim Sci 2014; 26:780-7. [PMID: 25049850 PMCID: PMC4093253 DOI: 10.5713/ajas.2012.12514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 01/04/2013] [Accepted: 12/30/2012] [Indexed: 11/27/2022]
Abstract
The objective of this study was to investigate single nucleotide polymorphisms (SNPs) in the bovine nephroblastoma overexpressed (NOV) gene and to evaluate whether these polymorphisms affect carcass traits in the Korean cattle population. We resequenced to detect SNPs from 24 unrelated individuals and identified 19 SNPs within the full 8.4-kb gene, including the 1.5-kb promoter region. Of these 19 SNPs, four were selected for genotyping based on linkage disequilibrium (LD). We genotyped 429 steers to assess the associations of these four SNPs with carcass traits. Statistical analysis revealed that g.7801T>C and g.8379A>C polymorphisms in the NOV gene were associated with carcass weight (p = 0.012 and 0.008, respectively), and the g.2005A>G polymorphism was associated with the back fat thickness (BF) trait (p = 0.0001). One haplotype of the four SNPs (GGTA) was significantly associated with BF (p = 0.0005). Our findings suggest that polymorphisms in the NOV gene may be among the important genetic factors affecting carcass yield in beef cattle.
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Affiliation(s)
- B S Kim
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - S C Kim
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - C M Park
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - S H Lee
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - S H Cho
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - N K Kim
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - G W Jang
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - D H Yoon
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - B S Yang
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - S K Hong
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - H H Seong
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
| | - B H Choi
- Animal Genome and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Chuksan gil 77, Kwonsun-gu, Suwon, Korea
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Choi BH, Lee KT, Lee HJ, Jang GW, Lee HY, Cho BW, Han JY, Kim TH. Detection of quantitative trait Loci affecting fat deposition traits in pigs. Asian-Australas J Anim Sci 2014; 25:1507-10. [PMID: 25049509 PMCID: PMC4093036 DOI: 10.5713/ajas.2012.12116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 05/11/2012] [Accepted: 04/20/2012] [Indexed: 11/27/2022]
Abstract
Quantitative trait loci (QTL) associated with fat deposition traits in pigs are important gene positions in a chromosome that influence meat quality of pork. For QTL study, a three generation resource population was constructed from a cross between Korean native boars and Landrace sows. A total of 240 F2 animals from intercross of F1 were produced. 80 microsatellite markers covering chromosomes 1 to 10 were selected to genotype the resource population. Intervals between adjacent markers were approximately 19 cM. Linkage analysis was performed using CRIMAP software version 2.4 with a FIXED option to obtain the map distances. For QTL analysis, the public web-based software, QTL express (http://www.qtl.cap.ed.ac.uk) was used. Two significant and two suggestive QTL were identified on SSC 6, 7, and 8 as affecting body fat and IMF traits. For QTL affecting IMF, the most significant association was detected between marker sw71 and sw1881 on SSC 6, and a suggestive QTL was identified between sw268 and sw205 on SSC8. These QTL accounted for 26.58% and 12.31% of the phenotypic variance, respectively. A significant QTL affecting IMF was detected at position 105 cM between markers sw71 and sw1881 on SSC 6.
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Affiliation(s)
- B H Choi
- Pusan National University, Miryang 627-706, Gyeongnam, Korea
| | - K T Lee
- Pusan National University, Miryang 627-706, Gyeongnam, Korea
| | - H J Lee
- Pusan National University, Miryang 627-706, Gyeongnam, Korea
| | - G W Jang
- Pusan National University, Miryang 627-706, Gyeongnam, Korea
| | - H Y Lee
- Pusan National University, Miryang 627-706, Gyeongnam, Korea
| | - B W Cho
- Pusan National University, Miryang 627-706, Gyeongnam, Korea
| | - J Y Han
- Seoul National University, Seoul 151-742, Korea
| | - T H Kim
- Pusan National University, Miryang 627-706, Gyeongnam, Korea
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Yeon SH, Lee SH, Choi BH, Lee HJ, Jang GW, Lee KT, Kim KH, Lee JH, Chung HY. Genetic variation of FASN is associated with fatty acid composition of Hanwoo. Meat Sci 2013; 94:133-8. [PMID: 23403305 DOI: 10.1016/j.meatsci.2013.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
Abstract
The objective of this study was to identify genetic variants in the bovine fatty acid synthase (FASN) gene and to evaluate associations with fatty acid composition from longissimus lumborum muscle using 90 purebred Hanwoo steers. Sequence alignments observed 6 genetic variants located in exons 20, 24, 32, 34, and 39, and PCR-RFLP analysis confirmed these variations. Genotypes of the g.15532A>C locus were significantly associated with Linolenic acid (C18:3), and genotypes of the g.17924G>A locus were significantly associated with Palmitic (C16:0), Palmitoleic (C16:1), Oleic (C18:1), saturated fatty acids, and unsaturated fatty acids. The analysis revealed that SFA and UFA showed significant correlations with fatty acid composition (Myristic (C14:0), Palmitic (C16:0), Stearic (C18:0), Oleic (C18:1), and Eicosenoic (C20:1) acids). Oleic acid (C18:1) was negatively correlated with Myristic (C14:0), Palmitic (C16:0), and Palmitoleic (C16:1) acids (P<0.001).
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Affiliation(s)
- S H Yeon
- National Institute of Animal Science, Pyeongchang, Republic of Korea
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Kim TH, Kim KS, Choi BH, Yoon DH, Jang GW, Lee KT, Chung HY, Lee HY, Park HS, Lee JW. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci 2008; 83:2255-63. [PMID: 16160034 DOI: 10.2527/2005.83102255x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To understand molecular genetic characteristics of Korean pigs, the genetic relationships of nine pig breeds including two Korean pigs (Korean native pig and Korean wild pig), three Chinese pigs (Min pig, Xiang pig, and Wuzhishan pig), and four European breeds (Berkshire, Duroc, Landrace, and Yorkshire) were characterized from a 16-microsatellite loci analysis. The mean heterozygosity within breeds ranged from 0.494 to 0.703. Across multiple loci, significant deviation from Hardy-Weinberg equilibrium was observed in most pig breeds, except for two Chinese pigs (Min pig and Wuzhishan pig). This deviation was in the direction of heterozygote deficit. Across population loci, 36 of 144 significantly deviated (P < 0.05) from Hardy-Weinberg equilibrium. The mean FST, a measure of genetic divergence among subpopulations, of all loci indicated that 26.1% of total variation could be attributed to the breed difference. Relationship trees based on the Nei's DA genetic distance and scatter diagram from principal component analysis consistently displayed pronounced genetic differentiation among the Korean wild pig, Xiang pig, and Wuzhishan pig. Individual assignment test using a Bayesian method showed 100% success in assigning Korean and Chinese individual pigs into their correct breeds of origin and 100% exclusion success from all alternative reference populations at P < 0.001. These findings indicate that the Korean native pig has been experiencing progressive interbreeding with Western pig breeds after originating from a North China pig breed with a black coat color. Considering the close genetic relationship of Korean pigs to the Western breeds such as Berkshire and Landrace, our findings can be used as valuable genetic information for the preservation and further genetic improvement of the Korean native pig.
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Affiliation(s)
- T H Kim
- Animal Genomics and Bioinformatics Division, National Livestock Research Institute, RDA, Suwon, Gyeonggi 441-706, Republic of Korea.
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Chung HY, Kim TH, Choi BH, Jang GW, Lee JW, Lee KT, Ha JM. Isolation and characterization of the bovine microsatellite loci. Biochem Genet 2007; 44:527-41. [PMID: 17139452 DOI: 10.1007/s10528-006-9055-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Microsatellite loci were isolated using five repetitive probes for Korean native cattle. Eleven microsatellite loci were developed based on a biotin hybrid capture method, and enrichment of the genomic libraries (AAAT, TG, AG, T, and TGC repeats) was performed using Sau3AI adapters. The isolated markers were tested in two half-sib Korean cattle families and four imported breeds (Angus, Limousine, Holstein, and Shorthorn). Nine informative microsatellite loci were observed, and two microsatellite loci were revealed as monomorphic in Korean cattle. In the imported breeds, however, all of the markers were informative. In total, 213 alleles were obtained at the 11 loci across five breeds, and the average number of alleles found per locus, considering all populations, was 4.26. Heterozygosity was 0.71 (expected) and 0.57 (observed). The range of the polymorphic information content for the markers in all cattle populations was 0.43-0.69. Eleven percent of genetic variation was attributed to differentiation between populations as determined by the mean F (ST) values. The remaining 89% corresponded to differences among individuals. The isolated markers may be used to identify and classify the local breeds on a molecular basis.
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Affiliation(s)
- H Y Chung
- Animal Genomics and Bioinformatics Division, National Livestock Research Institute, Suwon, Korea.
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Affiliation(s)
- H Y Chung
- Animal Genomics and Bioinformatics Division, National Livestock Research Institute, Suwon 441-701 Korea
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Choi BH, Lee JS, Jang GW, Lee HY, Lee JW, Lee KT, Chung HY, Park HS, Oh SJ, Sun SS, Myung KH, Cheong IC, Kim TH. Mapping of the Porcine Calpastatin Gene and Association Study of Its Variance with Economic Traits in Pigs. Asian Australas J Anim Sci 2006. [DOI: 10.5713/ajas.2006.1085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Jang GW, Cho KH, Kim TH, Oh SJ, Cheong IC, Lee KJ. Association of Candidate Genes with Production Traits in Korean Dairy Proven and Young Bulls. Asian Australas J Anim Sci 2005. [DOI: 10.5713/ajas.2005.165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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