CN107058526B - 一种基于基因对共表达模式动态关联解析玉米籽粒类胡萝卜素代谢调控机制的方法 - Google Patents
一种基于基因对共表达模式动态关联解析玉米籽粒类胡萝卜素代谢调控机制的方法 Download PDFInfo
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Abstract
本发明属于功能基因组学领域,具体涉及一种基于基因对共表达模式动态关联解析玉米籽粒类胡萝卜代谢调控机制的方法,该方法是通过以下步骤实现的:通过玉米基因组数据库maizeGDB下载类胡萝卜素代谢通路中的关键基因13个;收集玉米自交系授粉后15天的籽粒转录本测序获得基因表达量数据,提取上述13个关键基因的表达量数据;动态关联分析LA模型的建立;利用动态关联分析鉴定通路中关键基因之间的调控关系。本发明基于动态关联分析,挖掘类胡萝卜素代谢途径中的13个关键基因的调控关系,解析籽粒类胡萝卜合成和累积的调控机制,为分子标记辅助育种提供最佳的基因组合,对提高玉米中胡萝卜素以及改善玉米品质有重要的意义。
Description
技术领域
本发明属于功能基因组学领域,具体涉及一种基于基因对共表达模式动态关联解析玉米籽粒类胡萝卜代谢调控机制的方法。
背景技术
玉米是一种类胡萝卜素含量丰富的作物,在主要的粮食作物中只有玉米含有维生素A源和对人体有益的叶黄素类的类胡萝素,动物自身无法合成类胡萝卜素,须从食物中获取。玉米籽粒中主要包括五种类胡萝素:叶黄素,玉米黄素,β-隐黄质,α-胡萝卜素和β-胡萝卜素,约95%存储在胚乳中,2-4%存储在玉米麸皮中,胚中总类胡萝卜素的含量仅占1%。玉米中类胡萝卜素的累积从授粉后10-15天开始,黄色籽粒玉米类胡萝卜素含量丰富并且遗传力广泛,是开发高维生素A源的良好材料。长期以来类胡萝素含量等品质性状在育种中并未被受到重视。据west统计发现:全球110多个国家,约有1亿多儿童和700万左右的孕妇受到维生素A缺乏的影响,每年有超过25万的儿童因为维生素A缺乏失明,其中一半的失明儿童在1年内死亡。维生素A对视力和细胞的分化是必要的,严重的缺乏会导致夜盲以至于失明,发育缓慢,损害黏膜组织以及生殖紊乱。发展中国家是维生素A缺乏较为严重的地区之一。解决营养不良带来的影响,对广大发展中国家来仍是一大挑战。
因此,解析类胡萝卜代谢途径中关键基因之间的调控关系,结合关键基因对类胡萝卜素含量的表型贡献,为分子标记辅助育种提供最佳的基因组合,对提高玉米中类胡罗素的含量对解决以玉米为主食的人群维生素A缺乏的现象有着重要的意义。
玉米籽粒类胡萝卜合成是复杂的数量性状,受多基因控制,且具有较高的遗传力。连锁分析和关联分析是目前较为常见的用来解析玉米类胡萝卜素合成和累积遗传机理的方法,这两种分析方法企在通过建立表型与基因型之间的联系,挖掘控制类胡萝卜表型性状的遗传位点,而这些遗传位点之间相对独立,它们之间的调控关系未知,并且传统分析方法需要多年多点的表型鉴定,费时费力。我们将创新性的利用基因对共表达模式的动态关联分析这一在酵母和人类中发展出来的新方法,挖掘类胡萝卜代谢途径中上下游基因之间的调控关系,解析籽粒类胡萝卜合成和累积的调控机制,为分子标记辅助育种提供最佳的基因组合。该研究思路创新,在植物学领域该项研究尚无报道。
发明内容
针对现有问题中存在的类胡萝卜素累积的分子机制的研究的空白等问题,本发明提供了一种基于基因对共表达模式动态关联解析玉米籽粒类胡萝卜代谢调控机制的方法,该方法通过动态关联分析,以已知的玉米籽粒类胡萝卜代谢途径中的关键基因为目标基因,鉴定关键基因之间的相互调控关系,从而解析玉米籽粒类胡萝卜代谢的调控机制,对玉米籽粒类胡萝卜生化强化提供优质的基因组合,以及为玉米其它农艺性状的关键基因之间的调控关系研究提供思路和方法。
本发明所采用的具体技术方案为:
本发明提供了一种基于基因对共表达模式动态关联解析玉米籽粒类胡萝卜代谢调控机制的方法,包括以下步骤:
(1)通过玉米基因组数据库maizeGDB下载类胡萝卜素代谢通路中的关键基因13个;
(2)收集玉米自交系授粉后15天的籽粒转录本测序获得基因表达量数据,提取上述13个关键基因的表达量数据;
(3)动态关联分析LA模型的建立;
(4)利用动态关联分析鉴定通路中关键基因之间的调控关系。
进一步的,所述玉米籽粒类胡萝卜素代谢通路中的关键基因为ZDS1,PDS1,PSY1, lcyB,lcyE,HYD1,HYD4,CYP97A,crtRB1,CYP97C,ZEP2,ZEP1,VDE。
进一步的,所述玉米自交系分成了2 组:热带和亚热带、温带,小组内采用完全随机区组法,设2 个重复,每个自交系每个重复播种1 行。所有材料均进行自交,收获未成熟的授粉后15天的籽粒,每个自交系的两个重复各取3-4 穗,每穗取1-2 粒籽粒,混合提取籽粒总RNA,随机选择368 个样品用于RNA-seq。
上述RNA-seq具体包括以下步骤:首先,用Pol y(T)寡聚核苷酸从总RNA中抽取全部带Pol y(A)尾的RNA,主要为mRNA,然后将截获的mRNA随机打断成片段,用六碱基随机引物合成cDNA第一链,并加入逆转录酶合成cDNA第二链,经过试剂盒纯化并对cDNA片段进行末端修饰,连接测序接头,再经琼脂糖凝胶电泳回收目的大小片段,进行PCR扩增,从而完成整个文库构建工作,构建好的文库用Illumina GAⅡ基因分析系统进行序列测定及分析,获得基因表达量数据集。
本发明所得到的基因表达量数据集需要进行缺失值预处理:对于数据集中的每个基因,如果其表达值在高于30%的样本中缺失,则在后续的分析中舍弃该基因。
进一步的,所述动态关联分析方法为建立动态关联分析模型,所述动态关联分析模型LA的数学定义如下:
LA(X, Y|Z)=Eg'(z) 公式1
所述X,Y和Z表示玉米籽粒基因的表达量;
其中,所述X,Y和Z均为类胡萝卜代谢通路里13个关键基因的表达量。假设X,Y,Z是均值为0,方差为1的连续随机变量,则X,Y的相关性表示为E(XY);LA描述条件期望时,即当Z=z,g(z)=E(XY|Z=z),g(z)检测的是当Z=z时,XY基因对的共表达模式;g(z)的导数表示为g'(z),用于共表达模式变化的期望测定;LA的数学定义如下:
当Z符合标准正态分布时,LA值可简单的表示为LA(X,Y|Z)=E(XYZ);
则LA(X, Y|Z)表示为:E(XYZ)=(x 1 y 1 z 1+x 2 y 2 z 2 +...+x m y m z m )/m 公式2。
LA用来反应基因对共表达模式的动态变化,即当Z基因表达量较高时,XY基因对的表达量呈正相关(co-regulated),E(XY|Z=1)为正数;当Z基因表达量较低时,XY基因对的表达量呈负相关(contra-regulated,),E(XY|Z=0)为负数,因此基因对的表达调控模式由正相关(co-regulated)转变为负相关(contra-regulated),LA值记为正;相反,基因对的表达调控模式由负相关(contra-regulated)转变为正相关(co-regulated),LA值记为负。
进一步的,所述动态关联分析模型通过随机模拟的方法生成LA值的参考分布,具体评估方法如下:混合所有基因的表达量值;在每次模拟中,用放回随机抽样法随机抽取一对基因(X,Y)的表达量值,Z基因取全基因组所有基因,计算XY基因对在全基因组的LA值,可分别得到LA的正极大值和负极小值;重复模拟一百万次,分别得到LA的正值参考分布和负值参考分布。用LA正负参考分布的99%分位数作为LA正负显著性阈值。
本发明的有益效果为:
(1)本发明基于动态关联分析,挖掘类胡萝卜素代谢途径中的13个关键基因的调控关系,解析籽粒类胡萝卜合成和累积的调控机制,为分子标记辅助育种提供最佳的基因组合,对提高玉米中胡萝卜素以及改善玉米品质有重要的意义。
(2)本发明基于同一个代谢途径中的基因,表达模式相近这一科学假设,以类胡萝卜代谢途径中关键基因的共表达模式动态关联为突破口,可快速有效的解析类胡萝卜代谢途径的调控机制;
(3)通过基因对共表达网络的构建,可鉴定上下游基因的调控关系;根据关键基因的调控关系,比如高表达的PSY1以及低表达的lcyE和crtRB1组合,为用于类胡萝卜的分子标记辅助育种中,可相较于传统的单基因分子标记辅助育种,多基因组合可显著提高育种效率。
附图说明
图1为本发明实施例1类胡萝卜素代谢通路图。
图2为本发明实施例1 lcyE调控基因对ZEP1和VDE共表达模式
图3为本发明实施例1 VDE调控基因对lcyB和CYP97A共表达模式。
图4为本发明实施例1 VDE调控基因对lcyB和ZEP1共表达模式。
具体实施方式:
下面结合附图和具体实施例对本发明作进一步说明,下述说明仅是实例性的,不限定本发明的保护范围。
实施例1
一种本发明所述基于动态关联分析挖掘玉米籽粒油脂代谢调控机制的方法,主要包括三步,类胡萝卜代谢通路中关键基因的收集、基因表达量数据的收集、关键基因之间调控关系的鉴定。
(1)类胡萝卜代谢通路中关键基因的收集:
通过maizeGDB查找类胡萝卜素代谢通路中基因,分别为ZDS1,PDS1,PSY1,lcyB, lcyE,HYD1,HYD4,CYP97A,crtRB1,CYP97C,ZEP2,ZEP1,VDE。类胡萝素代谢过程图(1)。
(2)基因表达量数据的收集:
368份自交系(本发明所使用的玉米可为任意品种,本发明所使用的为中国农业大学宋同明教授培育的35份高油玉米自交系(Yang 等,2010b))于2010 年在湖北荆州种植,根据系谱信息分成了2 组(热带和亚热带、温带),小组内采用完全随机区组法,设2 个重复,每个自交系每个重复播种1 行。所有材料均进行自交,收获未成熟的授粉后15天(15DAP)的籽粒,每个自交系的两个重复各取3-4 穗,每穗取1-2 粒籽粒,混合提取籽粒总RNA,随机选择368 个样品用于RNA-seq。样品的RNA-Seq工作是由深圳华大基因研究院(BeijingGenomics Institute,BGI)完成,测序方法简要描述如下:首先,用Pol y(T)寡聚核苷酸从总RNA中抽取全部带Pol y(A)尾的RNA,主要为mRNA,然后将截获的mRNA随机打断成片段,用六碱基随机引物(random hexamers)合成cDNA第一链,并加入逆转录酶等合成cDNA第二链,经过试剂盒(Ampure XP beads)纯化并对cDNA片段进行末端修饰,连接测序接头,再经琼脂糖凝胶电泳回收目的大小片段,进行PCR扩增,从而完成整个文库构建工作,构建好的文库用Illumina GAⅡ基因分析系统进行序列测定及分析。转录本测序获得的368个玉米自交系中28769个基因的表达量数据,对基因表达量数据集进行的缺失值预处理如下:基因表达数据因为实验中的噪声、检测技术等原因而存在缺失。对于数据集中的每个基因,如果其表达值在高于30%的样本中缺失,则在后续的分析中舍弃该基因,获取的13个基因的基因表达量见表1。
表1
(3)动态关联分析模型的建立:
所述动态关联分析方法为建立动态关联分析模型,所述动态关联分析模型LA的数学定义如下:
LA(X, Y|Z)=Eg'(z) 公式1
所述X,Y和Z表示玉米籽粒基因的表达量;
其中,所述X,Y和Z均为类胡萝卜代谢通路里13个关键基因的表达量(表1, 单位:RPKM),假设X,Y,Z是均值为0,方差为1的连续随机变量,则X,Y的相关性表示为E(XY);LA描述条件期望时,即当Z=z,g(z)=E(XY|Z=z),g(z)检测的是当Z=z时,XY基因对的共表达模式;g(z)的导数表示为g'(z),用于共表达模式变化的期望测定;LA的数学定义如下:
当Z符合标准正态分布时,LA值可简单的表示为LA(X,Y|Z)=E(XYZ);
则LA(X, Y|Z)表示为:E(XYZ)=(x 1 y 1 z 1+x 2 y 2 z 2 +...+x m y m z m )/m 公式2。
LA用来反应基因对共表达模式的动态变化,即当Z基因表达量较高时,XY基因对的表达量呈正相关(co-regulated),E(XY|Z=1)为正数;当Z基因表达量较低时,XY基因对的表达量呈负相关(contra-regulated,),E(XY|Z=0)为负数,因此基因对的表达调控模式由正相关(co-regulated)转变为负相关(contra-regulated),LA值记为正;相反,基因对的表达调控模式由负相关(contra-regulated)转变为正相关(co-regulated),LA值记为负。
所述动态关联分析模型通过随机模拟的方法生成LA值的参考分布,具体评估方法如下:混合所有基因的表达量值;在每次模拟中,用放回随机抽样法随机抽取一对基因(X,Y)的表达量值,Z基因取全基因组所有基因,计算XY基因对在全基因组的LA值,可分别得到LA的正极大值和负极小值;重复模拟一百万次,分别得到LA的正值参考分布和负值参考分布。用LA正负参考分布的99%分位数作为LA正负显著性阈值。
(3)关键基因之间调控关系的鉴定
以X&Y&Z=13个类胡萝卜素代谢途径中的13个关键基因,结果按照p<0.01过滤后,具体调控关系如下:当lcyE的表达量较高的时候,ZEP1和VDE共表达模式呈正相关,当lcyE表达量较低的时候ZEP1和VDE表达模式不相关(图2)。lcyE编码番茄红素环化酶,ZEP1和VDE都属于β-胡萝卜素合成分支的基因。另外,紫黄质合成途径主要有5个基因参与,分别是lcyB、CYP97A、ZEP1、crtRB1和VDE。传统的两两基因之间的共表达分析未发现任意两个基因之间的表达相关性,但是动态共表达分析发现,lcyB和CYP97A以及lcyB和ZEP1两个基因对的共表达模式受到第三个基因VDE的调控(图3,4)。当VDE表达量较高时,lcyB和CYP97A以及lcyB和ZEP1表达模式正相关,进一步验证了该途径中,VDE基因的反馈抑制作用。类似地,我们还分析了PSY1、lcyE和crtRB1三个基因之间的动态共表达模式,LA结果显示,当PSY1表达量较高时,lcyE和crtRB1共表达模式正相关,当lcyE表达量较低时,PSY1和crtRB1共表达模式负相关,当crtRB1表达量较低时,PSY1和lcyE共表达模式负相关,具体见表2。这些结果与先前的报道一致,即上调PSY1基因表达量以及下调lcyE和crtRB1基因表达量可提高维生素A的含量。
表2 PSY1、lcyE和crtRB1基因之间的动态共表达模式
以上的这些结果证明了本发明的有效性,通过鉴定13个类胡萝素代谢通路中关键基因的调控关系,从而解析玉米籽粒类胡萝卜素代谢的调控机制,为类胡萝卜的分子标记辅助育种提供了最优基因组合,显著提高了育种效率,同时也为玉米其它数量性状的调控机制研究提供了新的思路和方法。
Claims (4)
1.一种基于基因对共表达模式动态关联解析玉米籽粒类胡萝卜素代谢调控机制的方法,其特征在于,包括以下步骤:
(1)通过玉米基因组数据库maizeGDB下载类胡萝卜素代谢通路中的关键基因13个;
(2)收集玉米自交系授粉后15天的籽粒转录本测序获得基因表达量数据,提取上述13个关键基因的表达量数据;
(3)动态关联分析LA模型的建立;
所述动态关联分析为建立动态关联分析模型,所述动态关联分析LA的数学定义如下:
LA(X, Y|Z)=Eg'(z) 公式1
所述X, Y和Z表示玉米籽粒基因的表达量;
其中,所述X,Y和Z均为类胡萝卜代谢通路里13个关键基因的表达量,假设X,Y,Z是均值为0,方差为1的连续随机变量,则X,Y的相关性表示为E(XY);LA描述条件期望时,即当Z=z,g(z)=E(XY|Z=z),g(z)检测的是当Z=z时,XY基因对的共表达模式;g(z)的导数表示为g'(z),用于共表达模式变化的期望测定;LA的数学定义如下:
当Z符合标准正态分布时,LA值可简单的表示为LA(X, Y|Z)=E(XYZ);
则LA(X, Y|Z)表示为:E(XYZ)=(x 1 y 1 z 1+x 2 y 2 z 2 +...+x m y m z m )/m 公式2;
LA用来反应基因对共表达模式的动态变化,即当Z基因表达量较高时,XY基因对的表达量呈正相关(co-regulated),E(XY|Z=1)为正数;当Z基因表达量较低时,XY基因对的表达量呈负相关(contra-regulated),E(XY|Z=0)为负数,因此基因对的表达调控模式由正相关(co-regulated)转变为负相关(contra-regulated),LA值记为正;相反,基因对的表达调控模式由负相关(contra-regulated)转变为正相关(co-regulated),LA值记为负;
(4)利用动态关联分析鉴定通路中关键基因之间的调控关系;
所述玉米籽粒类胡萝卜素代谢通路中的关键基因为ZDS1,PDS1,PSY1,lcyB,lcyE,HYD1,HYD4,CYP97A,crtRB1,CYP97C,ZEP2,ZEP1,VDE;
所述玉米自交系分成了两组:一组为热带,一组为亚热带、温带,小组内采用完全随机区组法,设2 个重复,每个自交系每个重复播种1 行;所有材料均进行自交,收获未成熟的授粉后15天的籽粒,每个自交系的两个重复各取3-4 穗,每穗取1-2 粒籽粒,混合提取籽粒总RNA,随机选择368 个样品用于RNA-seq。
2.根据权利要求1所述的方法,其特征在于,所述RNA-seq具体包括以下步骤:首先,用Poly(T)寡聚核苷酸从总RNA中抽取全部带Poly(A)尾的RNA,主要为mRNA,然后将截获的mRNA随机打断成片段,用六碱基随机引物合成cDNA第一链,并加入逆转录酶合成cDNA第二链,经过试剂盒纯化并对cDNA片段进行末端修饰,连接测序接头,再经琼脂糖凝胶电泳回收目的大小片段,进行PCR扩增,从而完成整个文库构建工作,构建好的文库用Illumina GAⅡ基因分析系统进行序列测定及分析,获得基因表达量数据集。
3.根据权利要求2所述的方法,其特征在于,所述基因表达量数据集需要进行缺失值预处理:对于数据集中的每个基因,如果其表达值在高于30%的样本中缺失,则在后续的分析中舍弃该基因。
4.根据权利要求1所述的方法,其特征在于,所述动态关联分析LA模型通过随机模拟的方法生成LA值的参考分布,具体评估方法如下:混合13个关键基因的表达量值;在每次模拟中,用放回随机抽样法随机抽取一对基因(X,Y)的表达量值, Z基因取全基因组所有基因,计算XY基因对在全基因组的LA值,可分别得到LA的正极大值和负极小值;重复模拟一百万次,分别得到LA的正值参考分布和负值参考分布,用LA正负参考分布的99%分位数作为LA正负显著性阈值。
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