子代测定是动植物育种中的关键环节,一般使用混合线性模型基于限制性最大似然(restricted maximum likehood,REML)法来估算子代测定数据中随机效应的方差分量,并估计固定效应(最佳线性无偏估计,BLUEs)和预测随机效应(最佳线性无偏预测,B...子代测定是动植物育种中的关键环节,一般使用混合线性模型基于限制性最大似然(restricted maximum likehood,REML)法来估算子代测定数据中随机效应的方差分量,并估计固定效应(最佳线性无偏估计,BLUEs)和预测随机效应(最佳线性无偏预测,BLUPs)。当前动植物遗传评估的先锋软件是ASReml,但其是商业软件,费用昂贵。虽然有如Echidna或R程序包sommer等免费软件,但是Echidna软件用法复杂,而R程序包功能有限。因此本研究利用R语言基于Echidna软件编写R程序包AFEchidna,方便用户通过该程序包使用混合线性模型不仅可求解方差分量、遗传参数和随机效应BLUP值,还可进行多个性状、多个方差结构和多个遗传参数的批量分析,不同模型间的比较以及基因组BLUP分析。开发AFEchidna包来壮大遗传评估免费软件,并期望其效率能接近于商业软件。展开更多
Functional analysis of control genes is playing an important role in animal development.The research is mainly focused on developing a method of estimating the gene's effect or function in the development of anima...Functional analysis of control genes is playing an important role in animal development.The research is mainly focused on developing a method of estimating the gene's effect or function in the development of animals.In this article,the gene's expression and control are described by models of quantitative genetics,which include the genetic models about the genes with no interaction and interaction effect.On this basis,a method analyzing the functions of control genes in batches is advanced,the method includes three steps as follows: Firstly,describe the gene's expression and control with multiple regression models in statistic method in different conditions.Secondly,collect the material of gene's polymorphism related to the gene's expression and control.Because,gene's polymorphism or the codominant molecular marker electropherogram in a gene locus present 3 states,and can be expressed with -1,0 and 1 respectively.The author thinks it can be regarded as levels in orthogonal layout.Discard the materials of gene's polymorphism not fitting the orthogonal layout,and use the materials of gene's polymorphism fitting the orthogonal layout as the data to estimate the gene's effects.Thirdly,analyze the gene's effect or function with equations as follows:suppose that a quantitative trait is controlled by N gene loci,in each locus there are two alleles,the alleles' effects are A GM1 ?a GM1 ;A GM2 ? a GM2 ;...;A GMi ?a GMi ;...;A GMN ;a GMN units respectively.When the genotype in a locus is heterozygous A GMi a GMi ,the interaction coefficient of alleles in a locus is K units.If there is no interaction among different gene loci,the author thinks,the gene's effects and gene's type can be estimated by using such equation: P GM =2∑Ni=1(A i-a i+K i)+∑Ni=1(A i-a i)M GMi -∑Ni=1K GMi M GMi 2 If there are interactions among different gene loci,and the effect of the x th gene's state combined with the y th gene's state in the k th gene group is defined as Y xyr ,and let gene group electropherogram states be r (where r∈ ),the author thinks,the gene group's effects can be estimated by the equation: Y xyr = K PCxy0 +K PCxy r+K PCxy' r 2+K PCxy'' 3+K PCxy(3') r 4+K PCxy(4') r 5+K PCxy(5') r 6+K PCxy(6') r 7+K PCxy(7') r 8 If there are interactions among more genes,the analogous method can also be used. In this way,be using the gene's codominent marker materials fitting the orthogonal layout,the gene's expression and control can be researched by the method of multiple regression,the gene's relative effect can be estimated,the overdominant gene's overdominant coefficient can be assessed,the gene's type can be identified,the interaction gene group's relative effect and the interaction gene's relation can be estimated as well,and furthermore,the gene's relation can be expressed in equations.For the sake of understanding the method used in this paper,the rout to prove it is given as well.Finally,the author thinks,this method is very useful to research the gene's function in molecular developmental biology.展开更多
文摘子代测定是动植物育种中的关键环节,一般使用混合线性模型基于限制性最大似然(restricted maximum likehood,REML)法来估算子代测定数据中随机效应的方差分量,并估计固定效应(最佳线性无偏估计,BLUEs)和预测随机效应(最佳线性无偏预测,BLUPs)。当前动植物遗传评估的先锋软件是ASReml,但其是商业软件,费用昂贵。虽然有如Echidna或R程序包sommer等免费软件,但是Echidna软件用法复杂,而R程序包功能有限。因此本研究利用R语言基于Echidna软件编写R程序包AFEchidna,方便用户通过该程序包使用混合线性模型不仅可求解方差分量、遗传参数和随机效应BLUP值,还可进行多个性状、多个方差结构和多个遗传参数的批量分析,不同模型间的比较以及基因组BLUP分析。开发AFEchidna包来壮大遗传评估免费软件,并期望其效率能接近于商业软件。
基金supported by financial support from the National Key Research and Development Program of China(2021YFF1200200)the National Natural Science Foundation of China(22161132008)+2 种基金the Natural Science Foundation of Shanghai,China(19520714100 and 19ZR1475800)the Starry Night Science Fund of Zhejiang University Shanghai Institute for Advanced Study(SNZJU-SIAS-006)the Natural Science Foundation of Zhejiang Province(LQ21C050001)。
文摘Functional analysis of control genes is playing an important role in animal development.The research is mainly focused on developing a method of estimating the gene's effect or function in the development of animals.In this article,the gene's expression and control are described by models of quantitative genetics,which include the genetic models about the genes with no interaction and interaction effect.On this basis,a method analyzing the functions of control genes in batches is advanced,the method includes three steps as follows: Firstly,describe the gene's expression and control with multiple regression models in statistic method in different conditions.Secondly,collect the material of gene's polymorphism related to the gene's expression and control.Because,gene's polymorphism or the codominant molecular marker electropherogram in a gene locus present 3 states,and can be expressed with -1,0 and 1 respectively.The author thinks it can be regarded as levels in orthogonal layout.Discard the materials of gene's polymorphism not fitting the orthogonal layout,and use the materials of gene's polymorphism fitting the orthogonal layout as the data to estimate the gene's effects.Thirdly,analyze the gene's effect or function with equations as follows:suppose that a quantitative trait is controlled by N gene loci,in each locus there are two alleles,the alleles' effects are A GM1 ?a GM1 ;A GM2 ? a GM2 ;...;A GMi ?a GMi ;...;A GMN ;a GMN units respectively.When the genotype in a locus is heterozygous A GMi a GMi ,the interaction coefficient of alleles in a locus is K units.If there is no interaction among different gene loci,the author thinks,the gene's effects and gene's type can be estimated by using such equation: P GM =2∑Ni=1(A i-a i+K i)+∑Ni=1(A i-a i)M GMi -∑Ni=1K GMi M GMi 2 If there are interactions among different gene loci,and the effect of the x th gene's state combined with the y th gene's state in the k th gene group is defined as Y xyr ,and let gene group electropherogram states be r (where r∈ ),the author thinks,the gene group's effects can be estimated by the equation: Y xyr = K PCxy0 +K PCxy r+K PCxy' r 2+K PCxy'' 3+K PCxy(3') r 4+K PCxy(4') r 5+K PCxy(5') r 6+K PCxy(6') r 7+K PCxy(7') r 8 If there are interactions among more genes,the analogous method can also be used. In this way,be using the gene's codominent marker materials fitting the orthogonal layout,the gene's expression and control can be researched by the method of multiple regression,the gene's relative effect can be estimated,the overdominant gene's overdominant coefficient can be assessed,the gene's type can be identified,the interaction gene group's relative effect and the interaction gene's relation can be estimated as well,and furthermore,the gene's relation can be expressed in equations.For the sake of understanding the method used in this paper,the rout to prove it is given as well.Finally,the author thinks,this method is very useful to research the gene's function in molecular developmental biology.
