A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo
2
조회
0
다운로드
4
인용
0
참고문헌
키워드
초록
Objective: A whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs) with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo. Methods: The data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant. Results: A total of 18 (0), 15 (3), 12 (8), 15 (18) , 11 (7), and 21 (1) SNPs were detected at the 5% chromosome (genome) - wise level for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA) and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL) regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29) were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA). Conclusion: The application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.
Abstract
Objective: A whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs) with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo. Methods: The data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant. Results: A total of 18 (0), 15 (3), 12 (8), 15 (18) , 11 (7), and 21 (1) SNPs were detected at the 5% chromosome (genome) - wise level for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA) and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL) regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29) were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA). Conclusion: The application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.
참고문헌 (30)
- MacLeod IM, "Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms", J Anim Breed Genet, 127, pp.133~142 (2010)
- 이윤미, "A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Carcass Traits in Hanwoo Populations", ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 23(4), pp.417~424 (2010), 아세아·태평양축산학회
- Pausch H, "Genome-wide association study identifies two major loci affecting calving ease and growth-related traits in cattle", Genetics, 187, pp.289~297 (2011)
- Nishimura S, "Genome-wide association study identified three major QTL for carcass weight including the PLAG1-CHCHD7 QTN for stature in Japanese Black cattle", BMC Genet, 13 (2012)
- Kim JB, "Historical look at the genetic improvement in Korean cattle - Review", Asian-Australas J Anim Sci, 13, pp.1467~1481 (2000)
- Venkata Reddy B, "Beef quality traits of heifer in comparison with steer, bull and cow at various feeding environments", Anim Sci J, 86, pp.1~16 (2015)
- Rowe SJ, "Detecting dominant QTL with variance component analysis in simulated pedigrees", Genet Res, 90, pp.363~374 (2008)
- Kim JJ, "Detection of quantitative trait loci for growth and beef carcass fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) cattle", J Anim Sci, 81, pp.1933~1942 (2003)
- Lee SH, "Predicting unobserved phenotypes for complex traits from whole-genome SNP data", Plos Genet, 4 (2008)
- Su GS, "Estimating additive and non-additive genetic variances and predicting genetic merits using genome-wide dense single nucleotide polymorphism markers", Plos One, 7, pp.e45293~ (2012)
- Druet T, "Imputation of genotypes from different single nucleotide polymorphism panels in dairy cattle", J Dairy Sci, 93, pp.5443~5454 (2010)
- Sun YV, "ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies", Bioinformatics, 22, pp.2945~2947 (2006)
- McClure MC, "A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle", Anim Genet, 41, pp.597~607 (2010)
- Casas E, "Detection of quantitative trait loci for growth and carcass composition in cattle", J Anim Sci, 81, pp.2976~2983 (2003)
- Mizoshita K, "Identification of a 1.1-Mb region for a carcass weight QTL onbovine Chromosome 14", Mamm Genome, 16, pp.532~537 (2005)
- I. S. Choi, "Analysis of Microsatellite Markers on Bovine Chromosomes 1 and 14 for Potential Allelic Association with Carcass Traits in Hanwoo (Korean Cattle)", ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 19(7), pp.927~930 (2006), 아세아·태평양축산학회
- Takasuga A, "Identification of bovine QTL for growth and carcass traits in Japanese Black cattle by replication and identical-by-descent mapping", Mamm Genome, 18, pp.125~136 (2007)
- Casas E, "Identification of quantitative trait loci for growth and carcass composition in cattle", Anim Genet, 35, pp.2~6 (2004)
- 이윤미, "Detection of Quantitative Trait Loci for Growth and Carcass Traits on BTA6 in a Hanwoo Population", ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 23(3), pp.287~291 (2010), 아세아·태평양축산학회
- Sukegawa S, "Replicated association of the single nucleotide polymorphism in EDG1 with marbling in three general populations of Japanese Black beef cattle", BMC Res Notes, 3, pp.66~ (2010)
- Boysen TJ, "Novel use of derived genotype probabilities to discover significant dominance effects for milk production traits in dairy cattle", Genetics, 193, pp.431~442 (2013)
- Lippman ZB, "Heterosis: revisiting the magic", Trends Genet, 23, pp.60~66 (2007)
- Hayes BJ, "Mate selection strategies to exploit across- and within-breed dominance variation", J Anim Breed Genet-Zeitschrift Fur Tierzuchtung Und Zuchtungsbiologie, 117, pp.347~359 (2000)
- Dekkers JCM, "Optimizing purebred selection for crossbred performance using QTL with different degrees of dominance", Genet Sel Evol, 36, pp.297~324 (2004)
- Beavis WD, "Molecular dissection of complex traits", pp.145~162 (1998), CRC Press
- Ashwell MS, "Detection of quantitative trait loci affecting milk production, health, and reproductive traits in Holstein cattle", J Dairy Sci, 87, pp.468~475 (2004)
- Wibowo TA, "Genome assembly anchored QTL map of bovine chromosome 14", Int J Biol Sci, 4, pp.406~414 (2008)
- Karim L, "Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature", Nat Genet, 43, pp.405~413 (2011)
- Blott S, "Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition", Genetics, 163, pp.253~266 (2003)
- Garcia MD, "Markers on bovine chromosome 20 associated with carcass quality and composition traits and incidence of contracting infectious bovine keratoconjunctivitis", Anim Biotechnol, 21, pp.188~202 (2010)