小麦光周期基因Photoperiod-B1的DNA甲基化分析
摘要
光周期现象在植物中普遍存在，植物体内部的周期节律与外部环境的协调一致对植物的生存非常重要。小麦（Triticum aestivum L.）是全球重要粮食作物，光周期不敏感特性能够提高小麦的适应能力，扩大引种范围。Ppd-B1基因是小麦重要光周期基因。前人研究表明，拷贝数变异是造成Ppd-B1不敏感位点形成的原因。但是对于该基因，表观遗传修饰方面还未见报道。本文从DNA甲基化方面对小麦Ppd-B1基因进行了深入研究，进一步探索影响其光周期不敏感位点形成的因素。主要研究进展如下：（1）小麦Ppd-B1基因启动子区域甲基化水平在多样性小麦品种中存在多态性。
利用亚硫酸氢盐测序技术对105份多样性小麦品种Ppd-B1基因启动子区域进行甲基化水平的检测。结果显示，不同小麦品种在测序区域的甲基化水平呈现丰富的多态性。根据测序区段每个胞嘧啶位点甲基化水平，通过聚类分析，将多样性材料划分为两种甲基化单倍型：甲基化单倍型a和甲基化单倍型b。（2）小麦Ppd-B1基因不同甲基化单倍型在总体甲基化水平和单个胞嘧啶位点甲基化水平呈现差异。
从总体甲基化水平分析，单倍型b的甲基化程度在CG和CHG序列形式上较单倍型a高。从单个胞嘧啶位点甲基化水平分析，在CG序列形式上，单倍型b在绝大多数位点（12/13）的甲基化程度较高；在CHG序列形式上，单倍性b在多数位点（4/10）甲基化程度较高，少数位点（2/10）甲基化程度较低；在CHH序列形式上，两者在多数位点中甲基化差异不显著（29/40）。说明单倍型b为甲基化程度较高的类型，单倍型a为甲基化程度较低的类型。（3）小麦Ppd-B1基因不同甲基化单倍型与重要农艺性状相关联。
将不同甲基化单倍型与一年三地多样性小麦材料农艺性状进行关联分析。结果显示，不同的甲基化单倍型在抽穗期、株高、千粒重等重要农艺性状差异显著。甲基化程度较高的单倍型b相对甲基化程度较低的单倍型a，具有较早的抽穗期、较矮的株高和较高的千粒重。将“复壮30×偃展1号”重组自交系F7代甲基化类型与两年两地抽穗期进行关联分析，发现低甲基化类型较高甲基化类型抽穗晚，说明高甲基化使Ppd-B1基因表现出光不敏感的特性。（4）小麦Ppd-B1基因高甲基化单倍型在小麦驯化过程中受到选择。
不同的甲基化单倍型在野生种、地方品种和现代育成品种中的分布存在差异。低甲基化类型在野生小麦材料中占据主导地位。而在地方品种和现代育成品种中，高甲基化类型所占比重明显提高。说明Ppd-B1高甲基化类型在小麦驯化过程中受到选择。（5）小麦Ppd-B1基因甲基化与拷贝数变异之间不存在相关性。
相关性分析结果显示，CG、CHG、CHH三种胞嘧啶序列形式的甲基化水平之间存在显著的正相关。但是拷贝数变异与任何一种序列形式的甲基化水平之间皆不存在相关性。说明Ppd-B1基因的DNA甲基化水平和拷贝数变异是两种独立作用的因素。（6）小麦Ppd-B1基因甲基化水平与表达量呈正相关。
荧光实时定量结果显示，在多样性小麦品种和重组自交系材料中，不同甲基化单倍型的Ppd-B1基因表达水平存在差异。高甲基化单倍型的表达量显著高于低甲基化类型。多样性品种的总体甲基化水平和CG甲基化水平均与表达量呈正相关。（7）小麦Ppd-A1、Ppd-D1基因甲基化水平在代表材料中不存在差异。
我们同时检测了A、D基因组对应Ppd-B1基因甲基化水平存在差异的区域。结果显示，Ppd-A1和Ppd-D1在代表材料测序区域的DNA甲基化程度无差异。所以推测DNA甲基化是B基因组独有的特征。
Photoperiod is a common phenomenon in plants and coordinated the internal circadianrhythms with external environment is very important for plant survival. Wheat (Triticumaestivum L.) is one of the world's most important food crops which also affected byPhotoperiod. Photoperiod insensitivity (day neutral phenotype) enabled wheat adapt to abroad range of environments. Photoperiod-B1a is an important photoperiod insensitive allelewhich conferred day neutral phenotype in wheat. Previous studies suggested that copynumber variation (CNV) played a significant role in Ppd-B1allele’s formation. But theepigenetic modifications for this gene have not been reported. In this study, we furtherinvestigate the mechanism underlying photoperiod insensitivity allele Ppd-B1a from theepigenetic perspective—DNA methylation. The main progresses were as follows:(1) DNA methylation patterns in Ppd-B1promotor region showed rich polymorphisms.
Using bisulfite genomic sequencing, we found DNA methylation patterns in Ppd-B1promotor region showed rich polymorphisms among a large germplasms. Two methylationhaplotypes (haplotype a&b) were classified according to the methylation polymorphisms ineach cytosine sites (single methylation polymorphisms, SMPs).(2) Methylation patterns varied between Ppd-B1methylation haplotypes.
For the overall methylation patterns, haplotype b showed significantly highermethylation levels than haplotype a in both CG and CHG contexts. For each cytosine site, inCG and CHG motifs, haplotype b showed higher methylation levels in most positions (12/13and4/10). But for CHH, most cytosine site (29/40) showed no difference. In brief, themethylation levels were relative higher in haplotype b at both overall methylation level andeach cytosine site methylation level.(3) Ppd-B1methylation haplotypes associated with important agronomic traits
Association analysis was conducted between different methylation haplotypes andagronomic traits among105diverse wheat cultivars under three different environments in2011, China. And the results suggested that there were significant associations betweendifferent methylation haplotypes and agricultural traits. Compared with haplotype a,haplotype b associated with more favorable traits such as earlier heading time, reduced plantheight and higher1000-kernel weight. A linkage analysis was conducted between‘Fuzhuang30×Yanzhan1’ F7population methylation types and heading dates and the result showed that the heading dates of haplotype b was earlier than haplotype a. Both associationanalysis and linkage analysis suggested that the high methylation haplotype associated withearlier heading dates and conferred this gene photoperiod insensitive characteristics.(4) Ppd-B1methylation haplotypes underwent selection during wheat domestication.
Different methylation haplotypes were differently distributed among wild species,landraces and modern cultivars. Low methylation haplotype predominate in ancient species.But in landraces and modern cultivars, high methylation haplotype became the leadinghaplotype which indicated that during wheat domestication high methylation patterns ofPpd-B1gene was selected.(5) There was no correlation between Ppd-B1methylation and copy number variation
Correlation analysis results showed that there were significant positive correlationsbetween different cytosine contexts methylation levels except CG and CHH. But there was nocorrelation between the relative copy number and methylation patterns in either cytosinemethylation context. So DNA methylation patterns and copy number variation were twoindependent factors affecting heading dates in wheat.(6) Positive correlation between Ppd-B1methylation and expression
Quantitative Real-time PCR results suggested that the expression level of Ppd-B1wasaffected by DNA methylation—high methylation pattern associated with high expression.Correlation analysis results showed that there were significant positive correlations betweenthe CG as well as the total methylation levels and the relative expression amounts.(7) Methylation difference is a unique characteristic for B genome
Using bisulfite genomic sequencing, we detected the corresponding regions whichshowed different methylation status of Ppd-B1in A and D genomes. But the methylationpatterns showed no differences in Ppd-A1and Ppd-D1alleles which indicated that differentmethylation patterns might be a unique feature for Ppd-B1.
利用亚硫酸氢盐测序技术对105份多样性小麦品种Ppd-B1基因启动子区域进行甲基化水平的检测。结果显示，不同小麦品种在测序区域的甲基化水平呈现丰富的多态性。根据测序区段每个胞嘧啶位点甲基化水平，通过聚类分析，将多样性材料划分为两种甲基化单倍型：甲基化单倍型a和甲基化单倍型b。（2）小麦Ppd-B1基因不同甲基化单倍型在总体甲基化水平和单个胞嘧啶位点甲基化水平呈现差异。
从总体甲基化水平分析，单倍型b的甲基化程度在CG和CHG序列形式上较单倍型a高。从单个胞嘧啶位点甲基化水平分析，在CG序列形式上，单倍型b在绝大多数位点（12/13）的甲基化程度较高；在CHG序列形式上，单倍性b在多数位点（4/10）甲基化程度较高，少数位点（2/10）甲基化程度较低；在CHH序列形式上，两者在多数位点中甲基化差异不显著（29/40）。说明单倍型b为甲基化程度较高的类型，单倍型a为甲基化程度较低的类型。（3）小麦Ppd-B1基因不同甲基化单倍型与重要农艺性状相关联。
将不同甲基化单倍型与一年三地多样性小麦材料农艺性状进行关联分析。结果显示，不同的甲基化单倍型在抽穗期、株高、千粒重等重要农艺性状差异显著。甲基化程度较高的单倍型b相对甲基化程度较低的单倍型a，具有较早的抽穗期、较矮的株高和较高的千粒重。将“复壮30×偃展1号”重组自交系F7代甲基化类型与两年两地抽穗期进行关联分析，发现低甲基化类型较高甲基化类型抽穗晚，说明高甲基化使Ppd-B1基因表现出光不敏感的特性。（4）小麦Ppd-B1基因高甲基化单倍型在小麦驯化过程中受到选择。
不同的甲基化单倍型在野生种、地方品种和现代育成品种中的分布存在差异。低甲基化类型在野生小麦材料中占据主导地位。而在地方品种和现代育成品种中，高甲基化类型所占比重明显提高。说明Ppd-B1高甲基化类型在小麦驯化过程中受到选择。（5）小麦Ppd-B1基因甲基化与拷贝数变异之间不存在相关性。
相关性分析结果显示，CG、CHG、CHH三种胞嘧啶序列形式的甲基化水平之间存在显著的正相关。但是拷贝数变异与任何一种序列形式的甲基化水平之间皆不存在相关性。说明Ppd-B1基因的DNA甲基化水平和拷贝数变异是两种独立作用的因素。（6）小麦Ppd-B1基因甲基化水平与表达量呈正相关。
荧光实时定量结果显示，在多样性小麦品种和重组自交系材料中，不同甲基化单倍型的Ppd-B1基因表达水平存在差异。高甲基化单倍型的表达量显著高于低甲基化类型。多样性品种的总体甲基化水平和CG甲基化水平均与表达量呈正相关。（7）小麦Ppd-A1、Ppd-D1基因甲基化水平在代表材料中不存在差异。
我们同时检测了A、D基因组对应Ppd-B1基因甲基化水平存在差异的区域。结果显示，Ppd-A1和Ppd-D1在代表材料测序区域的DNA甲基化程度无差异。所以推测DNA甲基化是B基因组独有的特征。
Photoperiod is a common phenomenon in plants and coordinated the internal circadianrhythms with external environment is very important for plant survival. Wheat (Triticumaestivum L.) is one of the world's most important food crops which also affected byPhotoperiod. Photoperiod insensitivity (day neutral phenotype) enabled wheat adapt to abroad range of environments. Photoperiod-B1a is an important photoperiod insensitive allelewhich conferred day neutral phenotype in wheat. Previous studies suggested that copynumber variation (CNV) played a significant role in Ppd-B1allele’s formation. But theepigenetic modifications for this gene have not been reported. In this study, we furtherinvestigate the mechanism underlying photoperiod insensitivity allele Ppd-B1a from theepigenetic perspective—DNA methylation. The main progresses were as follows:(1) DNA methylation patterns in Ppd-B1promotor region showed rich polymorphisms.
Using bisulfite genomic sequencing, we found DNA methylation patterns in Ppd-B1promotor region showed rich polymorphisms among a large germplasms. Two methylationhaplotypes (haplotype a&b) were classified according to the methylation polymorphisms ineach cytosine sites (single methylation polymorphisms, SMPs).(2) Methylation patterns varied between Ppd-B1methylation haplotypes.
For the overall methylation patterns, haplotype b showed significantly highermethylation levels than haplotype a in both CG and CHG contexts. For each cytosine site, inCG and CHG motifs, haplotype b showed higher methylation levels in most positions (12/13and4/10). But for CHH, most cytosine site (29/40) showed no difference. In brief, themethylation levels were relative higher in haplotype b at both overall methylation level andeach cytosine site methylation level.(3) Ppd-B1methylation haplotypes associated with important agronomic traits
Association analysis was conducted between different methylation haplotypes andagronomic traits among105diverse wheat cultivars under three different environments in2011, China. And the results suggested that there were significant associations betweendifferent methylation haplotypes and agricultural traits. Compared with haplotype a,haplotype b associated with more favorable traits such as earlier heading time, reduced plantheight and higher1000-kernel weight. A linkage analysis was conducted between‘Fuzhuang30×Yanzhan1’ F7population methylation types and heading dates and the result showed that the heading dates of haplotype b was earlier than haplotype a. Both associationanalysis and linkage analysis suggested that the high methylation haplotype associated withearlier heading dates and conferred this gene photoperiod insensitive characteristics.(4) Ppd-B1methylation haplotypes underwent selection during wheat domestication.
Different methylation haplotypes were differently distributed among wild species,landraces and modern cultivars. Low methylation haplotype predominate in ancient species.But in landraces and modern cultivars, high methylation haplotype became the leadinghaplotype which indicated that during wheat domestication high methylation patterns ofPpd-B1gene was selected.(5) There was no correlation between Ppd-B1methylation and copy number variation
Correlation analysis results showed that there were significant positive correlationsbetween different cytosine contexts methylation levels except CG and CHH. But there was nocorrelation between the relative copy number and methylation patterns in either cytosinemethylation context. So DNA methylation patterns and copy number variation were twoindependent factors affecting heading dates in wheat.(6) Positive correlation between Ppd-B1methylation and expression
Quantitative Real-time PCR results suggested that the expression level of Ppd-B1wasaffected by DNA methylation—high methylation pattern associated with high expression.Correlation analysis results showed that there were significant positive correlations betweenthe CG as well as the total methylation levels and the relative expression amounts.(7) Methylation difference is a unique characteristic for B genome
Using bisulfite genomic sequencing, we detected the corresponding regions whichshowed different methylation status of Ppd-B1in A and D genomes. But the methylationpatterns showed no differences in Ppd-A1and Ppd-D1alleles which indicated that differentmethylation patterns might be a unique feature for Ppd-B1.
引文
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