The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage di...
The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a $BayesC{\pi}$ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.
The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a $BayesC{\pi}$ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.
* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.
가설 설정
Several explanations have been proposed for our scant outcomes from genetic markers. First, the currently identified SNPs might not fully describe genetic diversity. For instance, these SNPs may not capture some forms of genetic variability that are due to copy number variation.
제안 방법
Our study successfully uncovered many variants related to QTLs. However, the traits YWT, CWT, and BFT measured in Hanwoo have QTL with larger additive effects than WWT, LMA, and Marb.
The 17 QTL detected by LDRM or LDVCM were integrated using the BayesCπ analysis to remove possible redundancies among those QTL.
The aim of this study was to detect additive QTL for growth and carcass quality traits in Korean cattle, Hanwoo, by applying three different genome wide association analyses, a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium method (LDLA), and the Bayes Cπ method.
These result SNP is small, this is due to the so called Beavis effect (Xu, 2003). Therefore, the work in this study is more related to QTL position rather than the precise estimation of their effects.
, Cary, NC, USA). Two fixed effects were fitted in the models: year and season of birth (5 levels) for all the traits and region where the steers were born (41 levels) for WWT, YWT, and Marb, and three covariates, weaning age for WWT, yearling age for YWT, slaughter age for CWT, BFT, and LMA, was also fitted. Pedigrees of the base population animals were traced back for 2 generations to create the numerator relationship matrix, and 1,033 animals were included in the pedigree analysis.
대상 데이터
4 Mb) of BTA14, which encompasses family with sequence similarity 110, member B (FAM110B), ubx domain protein 2B (UBXN2B), and thymocyte selection-associated high mobility group box (TOX) as positional and functional candidate genes for the CWT QTL in cattle. A QTL for BFT was detected in the proximal region (0.5 to 1.5 Mb) of the BTA 6, in which Locus (LOC) 100139637 gene was located. Another QTL was detected for Marb in the proximal region of the BTA29 (26.
Information about particular genes, located near SNP significantly associated with each trait, was extracted from online sources (http://www.ensembl.org/index.html, http://www.genecards.org/cgi-bin/cardsearch.pl#top, and http://www.uniprot.org).
The steers (N = 486) for phenotype and molecular data were chosen among the progeny of candidate bulls for progeny testing in the Hanwoo Improvement Center of National Agriculture Cooperative Federation in Seosan, Chungnam province, Korea. The data set comprised 61 sires and their 486 steers that were born between spring of 2005 and fall of 2007. The number of steers for each of the 61 paternal sire families ranged from 2 to 13 with the average of eight steers.
The steers (N = 486) for phenotype and molecular data were chosen among the progeny of candidate bulls for progeny testing in the Hanwoo Improvement Center of National Agriculture Cooperative Federation in Seosan, Chungnam province, Korea. The data set comprised 61 sires and their 486 steers that were born between spring of 2005 and fall of 2007.
데이터처리
All analysis used appropriate fixed factors or covariates that were fitted in the models (p<0.05) using a general linear model procedure in SAS (SAS 9.1, SAS Institute Inc., Cary, NC, USA).
이론/모형
A dendrogram was generated by using the unweighted pair group method with arithmetic mean (UPGMA) hierarchical clustering algorithm with 1-φp as the distance measure at QTL location (p).
성능/효과
The GWAS profiles of all additive SNP effects for each trait are divided into the different statistical models (Figure 1). All SNP effects in this report were additive as was expected because predicted transmitting ability predict only additive genetic merit.
For the SNPs analyzed in this study, the average observed heterozygosity was estimated at 0.37±0.12.
Some well-known candidate genes for the traits of interest were located close to these QTL. Four major additive QTL in each analysis had high concordance including 64.1 to 64.9 Mb for BTA7 for WWT, 24.3 to 25.4 Mb for BTA14 for CWT, 0.5 to 1.5 Mb for BTA6 for BFT and 26.3 to 33.4 Mb for BTA29 for BFT. We suggest the use of combined different LD mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.
Six traits for growth and meat quality were chosen: weaning weight (WWT), 365-d yearling weight (YWT), CWT after slaughter, backfat thickness (BFT), LMA, and marbling score (Marb). Details about summary statistics for the observed carcass quality traits were described in Li (2012).
참고문헌 (33)
Blott S Kim JJ Moisio S Schmidt-Kuntzel A Cornet A Berzi P Cambisano N Ford C Grisart B Johnson D Karim L Simon P Snell R Spelman R Wong J Vilkki J Georges M Farnir F Coppieters W 2003 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 163 253 266 12586713
Cierco-Ayrolles C Dejean S Legarra A Gilbert H Druet T Ytournel F Estivals D Oumouhou N Mangin B 2010 Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of QTL location in animal pedigree? Genet Sel Evol 42 38 20969751
Daetwyler HD Pong-Wong R Villanueva B Woolliams JA 2010 The impact of genetic architecture on genome-wide evaluation methods Genetics 185 1021 1031 20407128
Druet T Georges M 2010 A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping Genetics 184 789 798 20008575
Erbe M Ytournel F Pimentel ECG Sharifi AR Simianer H 2011 Power and robustness of three whole genome association mapping approaches in selected populations J Anim Breed Genet 128 3 14 21214639
Fernando RL Nettleton D Southey BR Dekkers JCM Rothschild MF Soller M 2004 Controlling the proportion of false positives in multiple dependent tests Genetics 166 611 619 15020448
Grapes L Dekkers JCM Rothschild MF Fernando RL 2004 Comparing linkage disequilibrium-based methods for fine mapping quantitative trait loci Genetics 166 1561 1570 15082569
Hoggart CJ Whittaker JC De Iorio M Balding DJ 2008 Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies PLoS Genet 4 7 e1000130 18654633
Kim JJ Georges M 2002 Evaluation of a new fine-mapping method exploiting linkage disequilibrium: A case study analysing a QTL with major effect on milk composition on bovine chromosome 14 Asian Australas J Anim Sci 15 1250 1256
Lee YS Lee JH Lee JY Kim JJ Park HS Yeo JS 2008 Identification of candidate SNP (single nucleotide polymorphism) for growth and carcass traits related to QTL on chromosome 6 in Hanwoo (Korean Cattle) Asian Australas J Anim Sci 21 1703 1709
Li C Basarab J Snelling WM Benkel B Kneeland J Murdoch B Hansen C Moore SS 2004 Identification and fine mapping of quantitative trait loci for backfat on bovine chromosomes 2, 5, 6, 19, 21, and 23 in a commercial line of Bos taurus J Anim Sci 82 967 972 15080315
Li Y 2012 Genome-wide association study to identify QTL for growth and carcass quality traits in Korean native cattle, Hanwoo PhD Thesis Yeungnam University Gyeongsan, Gyeongbuk, Korea
Li Y Lee JH Lee YM Kim JJ 2011 Application of linkage disequilibrium mapping methods to detect QTL for carcass quality on chromosome 6 using a high density SNP map in Hanwoo Asian Australas J Anim Sci 24 457 462
MacLeod IM Hayes BJ Savin KW Chamberlain AJ McPartlan HC Goddard ME 2010 Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms J Anim Breed Genet 127 133 142 20433522
Matukumalli LK Lawley CT Schnabel RD Taylor JF Allan MF Heaton MP O’Connell J Moore SS Smith TPL Sonstegard TS Van Tassell CP 2009 Development and characterization of a high density SNP genotyping assay for cattle PloS One 4 4 e5350 19390634
McClure MC Morsci NS Schnabel RD Kim JW Yao P Rolf MM McKay SD Gregg SJ Chapple RH Northcutt SL Taylor JF 2010 A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle Anim Genet 41 597 607 20477797
Mizoshita K Takano A Watanabe T Takasuga A Sugimoto Y 2005 Identification of a 1.1-Mb region for a carcass weight QTL onbovine Chromosome 14 Mamm Genome 16 532 537 16151698
Mizoshita K Watanabe T Hayashi H Kubota C Yamakuchi H Todoroki J Sugimoto Y 2004 Quantitative trait loci analysis for growth and carcass traits in a half-sib family of purebred Japanese Black (Wagyu) cattle J Anim Sci 82 3415 3420 15537759
Morris CA Pitchford WS Cullen NG Esmailizadeh AK Hickey SM Hyndman D Dodds KG Afolayan RA Crawford AM Bottema CDK 2009 Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot Anim Genet 40 648 654 19422365
Sun X Habier D Fernando RL Garrick DJ Dekkers JCM 2011 Genomic breeding value prediction and QTL mapping of QTLMAS2010 data using Bayesian Methods BMC Proceedings 5 Suppl 3 S13 21624169
Stone RT Keele JW Shackelford SD Kappes SM Koohmaraie M 1999 A primary screen of the bovine genome for quantitative trait loci affecting carcass and growth traits J Anim Sci 77 1379 1384 10375215
Uleberg E Meuwissen THE 2010 Fine mapping and detection of the causative mutation underlying quantitative trait loci J Anim Breed Genet 127 404 410 20831565
Zhao HH Fernando RL Dekkers JCM 2007 Power and precision of alternate methods for linkage disequilibrium mapping of quantitative trait loci Genetics 175 1975 1986 17277369
※ AI-Helper는 부적절한 답변을 할 수 있습니다.