基于E-bayes的F_2群体胚乳性状QTL上位性的分析
|
摘要
在F2群体中,采用经验贝叶斯统计方法(E-bayes)对谷类作物的胚乳性状QTL进行上位性分析,并通过计算机模拟加以验证.研究表明,基于E-bayes的胚乳性状QTL上位性分析,能准确地定位各QTL,同时有效地估计出QTL的各种遗传效应.
In F2 populations,Empirical bayes( E-bayes) method was used to analyze the epistasis of quantitative trait loci( QTL)underlying endosperm traits. The feasibility and efficiency of the method were verified by Monte Carlo simulations. The result showed that the method could efficiently detect endosperm QTLs and precisely estimate their epistatic effects.
In F2 populations,Empirical bayes( E-bayes) method was used to analyze the epistasis of quantitative trait loci( QTL)underlying endosperm traits. The feasibility and efficiency of the method were verified by Monte Carlo simulations. The result showed that the method could efficiently detect endosperm QTLs and precisely estimate their epistatic effects.
引文
[1]WANG X L,LARKINS B A.Genetic analysis of amino acid accumulation in opaque-2 maize endosperm[J].Plant Physiol,2001,125:1766-1777.
[2]WANG X L,WOO Y M,KIM C S,et al.Quantitative trait locus mapping of loci influencing elongation factor lacontent in maize endosperm[J].Plant Physiol,2001,125:1271-1282.
[3]WU R L,LOU X Y,MA C X,et al.An improved genetic model generates high resolution mapping of QTL for protein quality in maize endosperm[J].PNAS,2002,99(17):11281-11286.
[4]XU C,HE X,XU S Z.Mapping quantitative trait loci underlying triploid endosperm traits[J].Heredity,2003,90(3):228-235.
[5]WU R L,MA C X,MARIA G M,et al.Statistical methods for dissecting triploid endospermtraits using molecular markers:an autogamous model[J].Genetics,2002,162:875-892.
[6]WEN Y X,WU W R.Methods for mapping QTLs underlying endosperm traits based on random hybridization design[J].Chinese Science Bulletin,2006,51(16):1976-1981.
[7]KAO C H.Multiple-interval mapping for quantitative trait loci controlling endospermtrait[J].Genetics,2004,167(4):1987-2002.
[8]CUI Y,WU R L.Statistical model for characterizing epistatic control of triploid endosperm triggered by maternal and offspring QTLs[J].Genetical Research,2005,86:65-75.
[9]HU Z Q,XU C W.A new statistical method for mapping QTLs underlying endospermtraits[J].Chinese Science Bulletin,2005,50(14):1470-1476.
[10]WEN Y X,WU W R.Interval mapping of quantitative trait loci underlying triploid endospermtraits using F3 seeds[J].Journal of Genetics and Genomics,2007,34(5):429-436.
[11]WEN Y X,WU W R.Experimental designs and statistical methods for mapping quantitative trait loci underlying triploid endosperm traits without maternal genetic variation[J].Journal of Heredity,2008,99(5):546-551.
[12]何小红.应用遗传交配设计检测数量性状上位性QTL方法的研究[D].南京:南京农业大学,2010.
[13]温永仙.基于BC1F1:2种子的胚乳QTL区间定位[J].生物数学学报,2011,3:540-546.
[14]王亚民,孙长森,汤在祥,等.谷物胚乳性状QTL区间作图的贝叶斯方法[J].扬州大学学报:农业与生命科学版,2008,29(3):12-17.
[15]王亚民,汤在祥,陆鑫,等.基于贝叶斯统计的谷物胚乳性状QTL多区间作图方法[J].作物学报,2009,35(9):1569-1575.
[16]XU S Z,HU Z.Mapping quantitative trait loci using the MCMC procedure in SAS[J].Heredity,2010,106(2):357-369.
[17]XU S Z.An empirical Bayes method for estimating epistatic effects of quantitative trait loci[J].Biometrics,2007,6(63):513-521.
[18]CAI X D,HUANG A H,XU S Z.Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping[J].BMC Bioinformatics,2011,12:211-224.
[19]CHEN J Q,WU J G,SHI C H,et al.Analysis of epistasis:a genetic model for triploid endosperm traits[J].Journal of Zhejiang University,2007,33(1):1-7.
[20]ZHOU X,MATTHEW S.Genome-wide efficient mixed-model analysis for association studies[J].Nature Genetics,2012,7(44):821-824.
[21]梁文科,张世煌,戚廷香,等.应用混合线性模型(AD)分析热带温带玉米群体间的遗传关系[J].作物学报,2006,32(7):1018-1023.
[22]HE X H,ZHANG Y M.Mapping epistatic quantitative trait loci underlying endosperm traits using all markers on the entiregenome in a random hybridization design[J].Heredity,2008,101:39-47.
[23]Mo H D,Genetic Expression for Endosperm Traits[R].Raleigh:North Carolina State University,1987.
[24]SYLVAIN A.A survey of cross-validation procedures for model selection[J].Statistics Surveys,2010,4:40-79.
[25]XU S Z.Principles of Statistical Genomics[M].New York:Springer,2012:259-266.
[2]WANG X L,WOO Y M,KIM C S,et al.Quantitative trait locus mapping of loci influencing elongation factor lacontent in maize endosperm[J].Plant Physiol,2001,125:1271-1282.
[3]WU R L,LOU X Y,MA C X,et al.An improved genetic model generates high resolution mapping of QTL for protein quality in maize endosperm[J].PNAS,2002,99(17):11281-11286.
[4]XU C,HE X,XU S Z.Mapping quantitative trait loci underlying triploid endosperm traits[J].Heredity,2003,90(3):228-235.
[5]WU R L,MA C X,MARIA G M,et al.Statistical methods for dissecting triploid endospermtraits using molecular markers:an autogamous model[J].Genetics,2002,162:875-892.
[6]WEN Y X,WU W R.Methods for mapping QTLs underlying endosperm traits based on random hybridization design[J].Chinese Science Bulletin,2006,51(16):1976-1981.
[7]KAO C H.Multiple-interval mapping for quantitative trait loci controlling endospermtrait[J].Genetics,2004,167(4):1987-2002.
[8]CUI Y,WU R L.Statistical model for characterizing epistatic control of triploid endosperm triggered by maternal and offspring QTLs[J].Genetical Research,2005,86:65-75.
[9]HU Z Q,XU C W.A new statistical method for mapping QTLs underlying endospermtraits[J].Chinese Science Bulletin,2005,50(14):1470-1476.
[10]WEN Y X,WU W R.Interval mapping of quantitative trait loci underlying triploid endospermtraits using F3 seeds[J].Journal of Genetics and Genomics,2007,34(5):429-436.
[11]WEN Y X,WU W R.Experimental designs and statistical methods for mapping quantitative trait loci underlying triploid endosperm traits without maternal genetic variation[J].Journal of Heredity,2008,99(5):546-551.
[12]何小红.应用遗传交配设计检测数量性状上位性QTL方法的研究[D].南京:南京农业大学,2010.
[13]温永仙.基于BC1F1:2种子的胚乳QTL区间定位[J].生物数学学报,2011,3:540-546.
[14]王亚民,孙长森,汤在祥,等.谷物胚乳性状QTL区间作图的贝叶斯方法[J].扬州大学学报:农业与生命科学版,2008,29(3):12-17.
[15]王亚民,汤在祥,陆鑫,等.基于贝叶斯统计的谷物胚乳性状QTL多区间作图方法[J].作物学报,2009,35(9):1569-1575.
[16]XU S Z,HU Z.Mapping quantitative trait loci using the MCMC procedure in SAS[J].Heredity,2010,106(2):357-369.
[17]XU S Z.An empirical Bayes method for estimating epistatic effects of quantitative trait loci[J].Biometrics,2007,6(63):513-521.
[18]CAI X D,HUANG A H,XU S Z.Fast empirical Bayesian LASSO for multiple quantitative trait locus mapping[J].BMC Bioinformatics,2011,12:211-224.
[19]CHEN J Q,WU J G,SHI C H,et al.Analysis of epistasis:a genetic model for triploid endosperm traits[J].Journal of Zhejiang University,2007,33(1):1-7.
[20]ZHOU X,MATTHEW S.Genome-wide efficient mixed-model analysis for association studies[J].Nature Genetics,2012,7(44):821-824.
[21]梁文科,张世煌,戚廷香,等.应用混合线性模型(AD)分析热带温带玉米群体间的遗传关系[J].作物学报,2006,32(7):1018-1023.
[22]HE X H,ZHANG Y M.Mapping epistatic quantitative trait loci underlying endosperm traits using all markers on the entiregenome in a random hybridization design[J].Heredity,2008,101:39-47.
[23]Mo H D,Genetic Expression for Endosperm Traits[R].Raleigh:North Carolina State University,1987.
[24]SYLVAIN A.A survey of cross-validation procedures for model selection[J].Statistics Surveys,2010,4:40-79.
[25]XU S Z.Principles of Statistical Genomics[M].New York:Springer,2012:259-266.