二穗短柄草耐旱抗氧化机理及其相关基因的SNP研究
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摘要
二穗短柄草(Brachypodium distachyon L.)是一种冷季型温带禾本科植物,原产于地中海和中东,在中东、北非、亚洲和欧洲广泛分布。目前,二穗短柄草已成为研究谷物、牧草、草坪草和能源草的模式植物。二穗短柄草基因组研究结果为禾本科作物研究奠定了基础,并且人们对二穗短柄草的研究已经取得了很多成果。植物的抗旱性是复杂的数量性状,关联分析是研究基因与复杂的数量性状的基本工具,并且通过直接测序法获得的单核苷酸多态性准确率可以达到100%,结果具有很高的准确性。
本研究利用57份二穗短柄草二倍体资源,在温室条件下对其进行抗旱性鉴定；并以抗性材料T-9和最敏感材料B2C为材料,分析干旱胁迫下其与抗旱相关的抗氧系统中抗氧化产物及其酶活性的变化,确定了5个编码抗氧化酶的基因作为候选基因,分析其单核苷酸多态性等；根据57份材料的非变性聚丙烯酰胺胶中POD酶活性染色变化,根据蛋白质谱的结果,确定了8个POD候选基因,对候选基因的核苷酸多态性及与抗旱性状的关联等一系列分析。全文的具体研究结果如下
1二穗短柄草的抗旱性鉴定
在温室条件下对二穗短柄草抗旱性的自然变异进行鉴定。结果表明,57份二穗短柄草的抗旱性差异很大,根据主成分分析结果分成了4个组,其中抗性组有3份材料,中抗组有16份材料,敏感组有32份材料,最敏感组有6份材料。抗性组表现出很轻微的叶片萎蔫,叶绿素荧光和叶片相对含水量相对于对照降低程度都很小敏感组表现出很严重的叶片萎蔫,并且叶绿素荧光值和叶片相对含水量相对于对照降低程度很大。干旱胁迫明显增加了叶片中总糖的含量,但是各个组之间并没有明显的差异。
2二穗短柄草的抗氧化机理
在干旱胁迫下抗性材料Tek-9(T-9)和最敏感材料BdTR2C (B2C)叶片中过氧化氢和丙二醛含量增加,根中超氧阴离子含量增加；与抗性材料T-9相比,B2C中的过氧化氢和丙二醛的增加量更多。在叶片中,T-9的谷胱甘肽过氧化物酶(GPX)活性增加,B2C的过氧化氢酶(CAT)和单脱氢抗坏血酸还原酶(MDHAR)活性降低。干旱胁迫也增加了两份材料根中的CAT和MDHAR的活性,并且T-9的增加量多。在T-9根中的GPX、抗坏血酸过氧化物酶(APX)、脱氢抗坏血酸还原酶(DHAR)和谷光甘肽还原酶(GR)的活性也增强了,但是在B2C根中超氧化物歧化酶(SOD)的活性降低。
3抗氧化物酶候选基因的单核苷酸多态性分析
根据二穗短柄草叶片中抗氧化物酶活性表达稳定或者上调的基因转录水平上的表达情况确定候选基因。候选基因包括编码APX、GPX、CAT、MDHAR和DHAR的基因。其中编码GPX、MDHAR和DHAR的基因转录水平表达情况和干旱胁迫下的酶活性变化一致。编码CAT、GPX、DHAR、MDHAR和APX五个基因的平均核苷酸多态性(π)为0.0027。5个基因的平均单核苷酸多态性(SNP)为每133bp有1个SNP。所有基因的连锁不平衡(LD)衰减范围近于1.6kb。用编码DHAR、MDHAR和CAT基因构建邻近法系统树(Neighbor-joining tree),各个材料的聚类情况和其抗旱情况基本一致。因此这些基因的单核苷酸多态性(SNP)可以作为二穗短柄草的抗旱标记。
4过氧化物酶(POD)的单核苷酸多态性及其关联分析
通过对二穗短柄草57份材料的POD酶活性染色发现,抗性材料和敏感材料中蛋白条带的位置不一致,就对不同位置的条带进行蛋白的质谱分析,确定了8个POD的候选基因。
二穗短柄草的8个POD候选基因扩增测序得到9178bp基因组序列,占总基因序列的56%；序列比较分析后共获得90个SNPs(平均102bp有1个SNP)。编码区长4396bp,共检测到44个SNP(平均100bp有1个SNP)。8个POD基因都符合中性进化。8个PODs候选基因的单倍体,平均单倍型多样性为0.652。8个POD基因的连锁不平衡估算,共获得SNP位点间r2值557个,其中34%(190个)的位点存在显著的连锁不平衡。
8个基因总共含有90个SNP,与抗旱生理性状紧密相关联的SNP占总数的30%,其中抗性基因中有21个,占总显著相关联SNP数的70%,而敏感基因中仅有9个与抗旱性状显著相关联,仅占21%。在P=0.05水平上,基因Bradilg63060.1与抗旱性状相关联的SNP数最多,为10个(占这个基因总SNP数的55.6%),其次为抗性基因Bradi3g41340.1,显著关联的SNP数为6个(占这个基因总SNP数60%)；其中显著相关联SNP数最少的基因为敏感基因Bradilg26870.1和Bradilg65820.2,占基因总SNP的百分率分别为7.1%和12.5%。因此Bradilg63060.1可以作为抗旱标记及其转基因的基因资源。并且8个POD基因90个SNP结果分析,转换与颠换的比率为1.5：1,因此碱基突变的主要类型为转换。
The severity and frequency of drought stress is unexpected to increase because of climate change, which can significantly affect on plant growth and development. Drought stress is highly variable in nature, with frequency changes in intensity and duration. And the drought is a complicated trait, and is regulated by many genes. So it is very important sutible for analysis materials and methods. Brachypodium distachyon is a temperate wild grass species and is a powerful model system for studying grain, energy, forge and turf grasses. The gene and genomic results were bases on analysis grasses. And they have large natural various. So Brachypodium distachyon was good materials for analysis drought stress. Association analysis is a good tool for the study on the relationship between genes and quantitative traits. And the accuracy was100%according to sequence directly. This research was carried out the phenotypic diversity of drought tolerance in57natural populations of Brachypodium in greenhouse for twice. Drought tolerant (T-9) and susceptible accession (B2C) were used to determine production of reactive oxygen species and antioxidative response of the leaves and roots of Brachypodium to drought stress. And5genes related to antioxidative as the candidate genes for analysis the single nucleotide polymorphisms were selected. And8peroxides genes were candidate genes according to the results of native gel analysis and MALDT-TOF-MS. Association analysis on8PODs gene SNPs and traits related to drought was present. The main results are described as followed:
1. Natural variation of drought response in Brachypodium distachyon
Two experiments were conducted in a greenhouse to assess the drought tolerance of57natural populations of Brachypodium. Principle component analysis revealed that reductions in chlorophyll fluorescence (Fv/Fm) and leaf water content (LWC) under drought stress explained most of the phenotypic variation, which was used to classify the tolerant and susceptible accessions. Four groups of accessions differing in drought tolerance were identified, with3tolerant,16moderately tolerant,32susceptible and6most susceptible accessions. The tolerant group had little leaf wilting and fewer reduction in Fv/Fm and LWC, while the most susceptible groups showed severe leaf wilting and more reductions in Fv/Fm and LWC. Drought stress increased total water soluble sugar (WSS) concentration, but no differences in the increased WSS were found among different groups of accessions.
2. Antioxidative metabolism of Brachypodium Distachyon under drought stress
Drought stress increased the accumulation of hydrogen peroxide (H2O2) and degree of lipid pexoxidation (Malondialdehyde, MDA) in the leaves and superoxide (O2) concentration in the roots, but to a greater extent in the B2C compared with T-9. An enhanced leaf activity of glutathione peroxidase (GPX) in T-9and the decreased activities of catalase (CAT) and monodehydroascorbate reductase (MDHAR) in B2C were observed, respectively. Drought stress increased root activities of CAT and MDHAR in both accessions, to a greater degree in the tolerant T-9. Drought stress also increased root activities of GPX, ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR) and glutathione reductase (GR) in the T-9but decreased activity of superoxide dismutse (SOD) in the B2C.
3. Nucleotide diversity and linkage disequilibrium in antioxidative candidate genes for drought tolerance of Brachypodium distachyon
The section of these genes was based on the significant changes in enzyme activities observed between the control and drought-stressed plants, either tolerant T-9, or susceptible B2C, or both. The average nucleotide diversity (π) for CAT, GPX, DHAR, MDHAR, and APX (encoding ascorbate peroxidase) was0.0027among accessions contrasting drought tolerance. The average single nucleotide polymorphism (SNP) frequency across these five genes was one SNP per133bβ in the total length. The linkage disequilibrium (LD) decay extended to a distance of1.6kb across all genes. The neighbor-joining tree analyses of DHAR, MDHAR, and CA T generally separated accessions differing in drought tolerance.
4. Nucleotide diversity and association analysis on POD genes and drought traits
Make sure8candidate genes through POD enzyme native gel analysis in57Brachypodium distachyon and MALDT-TOF-MS.
90SNPs were from8POD genes with the sequence length9178bp. Coding part had44SNPs with the sequence length4396bp. And8genes belonged to natural test. The average indel diversity was0.652. There was557r2according to linkage disequilibrium analysis, and significant points were190and the ratio34%.
The number of SNPs related with drought traits accounted for30%in90SNPs according to association analysis. There were21SNPs significantly related with drought traits in tolerance genes and accounted for70%, but the susceptible genes only have9SNPs and accounted for21%.
The most related SNPs was the gene Bradilg63060.1and more related was the gene Bradi3g41340.1. There were a few related SNPs in the susceptible gene Bradilg26870.1and Bradilg65820.2and accounted for7.1%and12.5%, respectively. So the drought tolerant gene Bradilg63060.1was a good gene for molecular marker and transfer genes. The ration between transition and transversion was1.5:1based on SNP analysis results. Therefor the transition was the main base mutation.
本研究利用57份二穗短柄草二倍体资源,在温室条件下对其进行抗旱性鉴定；并以抗性材料T-9和最敏感材料B2C为材料,分析干旱胁迫下其与抗旱相关的抗氧系统中抗氧化产物及其酶活性的变化,确定了5个编码抗氧化酶的基因作为候选基因,分析其单核苷酸多态性等；根据57份材料的非变性聚丙烯酰胺胶中POD酶活性染色变化,根据蛋白质谱的结果,确定了8个POD候选基因,对候选基因的核苷酸多态性及与抗旱性状的关联等一系列分析。全文的具体研究结果如下
1二穗短柄草的抗旱性鉴定
在温室条件下对二穗短柄草抗旱性的自然变异进行鉴定。结果表明,57份二穗短柄草的抗旱性差异很大,根据主成分分析结果分成了4个组,其中抗性组有3份材料,中抗组有16份材料,敏感组有32份材料,最敏感组有6份材料。抗性组表现出很轻微的叶片萎蔫,叶绿素荧光和叶片相对含水量相对于对照降低程度都很小敏感组表现出很严重的叶片萎蔫,并且叶绿素荧光值和叶片相对含水量相对于对照降低程度很大。干旱胁迫明显增加了叶片中总糖的含量,但是各个组之间并没有明显的差异。
2二穗短柄草的抗氧化机理
在干旱胁迫下抗性材料Tek-9(T-9)和最敏感材料BdTR2C (B2C)叶片中过氧化氢和丙二醛含量增加,根中超氧阴离子含量增加；与抗性材料T-9相比,B2C中的过氧化氢和丙二醛的增加量更多。在叶片中,T-9的谷胱甘肽过氧化物酶(GPX)活性增加,B2C的过氧化氢酶(CAT)和单脱氢抗坏血酸还原酶(MDHAR)活性降低。干旱胁迫也增加了两份材料根中的CAT和MDHAR的活性,并且T-9的增加量多。在T-9根中的GPX、抗坏血酸过氧化物酶(APX)、脱氢抗坏血酸还原酶(DHAR)和谷光甘肽还原酶(GR)的活性也增强了,但是在B2C根中超氧化物歧化酶(SOD)的活性降低。
3抗氧化物酶候选基因的单核苷酸多态性分析
根据二穗短柄草叶片中抗氧化物酶活性表达稳定或者上调的基因转录水平上的表达情况确定候选基因。候选基因包括编码APX、GPX、CAT、MDHAR和DHAR的基因。其中编码GPX、MDHAR和DHAR的基因转录水平表达情况和干旱胁迫下的酶活性变化一致。编码CAT、GPX、DHAR、MDHAR和APX五个基因的平均核苷酸多态性(π)为0.0027。5个基因的平均单核苷酸多态性(SNP)为每133bp有1个SNP。所有基因的连锁不平衡(LD)衰减范围近于1.6kb。用编码DHAR、MDHAR和CAT基因构建邻近法系统树(Neighbor-joining tree),各个材料的聚类情况和其抗旱情况基本一致。因此这些基因的单核苷酸多态性(SNP)可以作为二穗短柄草的抗旱标记。
4过氧化物酶(POD)的单核苷酸多态性及其关联分析
通过对二穗短柄草57份材料的POD酶活性染色发现,抗性材料和敏感材料中蛋白条带的位置不一致,就对不同位置的条带进行蛋白的质谱分析,确定了8个POD的候选基因。
二穗短柄草的8个POD候选基因扩增测序得到9178bp基因组序列,占总基因序列的56%；序列比较分析后共获得90个SNPs(平均102bp有1个SNP)。编码区长4396bp,共检测到44个SNP(平均100bp有1个SNP)。8个POD基因都符合中性进化。8个PODs候选基因的单倍体,平均单倍型多样性为0.652。8个POD基因的连锁不平衡估算,共获得SNP位点间r2值557个,其中34%(190个)的位点存在显著的连锁不平衡。
8个基因总共含有90个SNP,与抗旱生理性状紧密相关联的SNP占总数的30%,其中抗性基因中有21个,占总显著相关联SNP数的70%,而敏感基因中仅有9个与抗旱性状显著相关联,仅占21%。在P=0.05水平上,基因Bradilg63060.1与抗旱性状相关联的SNP数最多,为10个(占这个基因总SNP数的55.6%),其次为抗性基因Bradi3g41340.1,显著关联的SNP数为6个(占这个基因总SNP数60%)；其中显著相关联SNP数最少的基因为敏感基因Bradilg26870.1和Bradilg65820.2,占基因总SNP的百分率分别为7.1%和12.5%。因此Bradilg63060.1可以作为抗旱标记及其转基因的基因资源。并且8个POD基因90个SNP结果分析,转换与颠换的比率为1.5：1,因此碱基突变的主要类型为转换。
The severity and frequency of drought stress is unexpected to increase because of climate change, which can significantly affect on plant growth and development. Drought stress is highly variable in nature, with frequency changes in intensity and duration. And the drought is a complicated trait, and is regulated by many genes. So it is very important sutible for analysis materials and methods. Brachypodium distachyon is a temperate wild grass species and is a powerful model system for studying grain, energy, forge and turf grasses. The gene and genomic results were bases on analysis grasses. And they have large natural various. So Brachypodium distachyon was good materials for analysis drought stress. Association analysis is a good tool for the study on the relationship between genes and quantitative traits. And the accuracy was100%according to sequence directly. This research was carried out the phenotypic diversity of drought tolerance in57natural populations of Brachypodium in greenhouse for twice. Drought tolerant (T-9) and susceptible accession (B2C) were used to determine production of reactive oxygen species and antioxidative response of the leaves and roots of Brachypodium to drought stress. And5genes related to antioxidative as the candidate genes for analysis the single nucleotide polymorphisms were selected. And8peroxides genes were candidate genes according to the results of native gel analysis and MALDT-TOF-MS. Association analysis on8PODs gene SNPs and traits related to drought was present. The main results are described as followed:
1. Natural variation of drought response in Brachypodium distachyon
Two experiments were conducted in a greenhouse to assess the drought tolerance of57natural populations of Brachypodium. Principle component analysis revealed that reductions in chlorophyll fluorescence (Fv/Fm) and leaf water content (LWC) under drought stress explained most of the phenotypic variation, which was used to classify the tolerant and susceptible accessions. Four groups of accessions differing in drought tolerance were identified, with3tolerant,16moderately tolerant,32susceptible and6most susceptible accessions. The tolerant group had little leaf wilting and fewer reduction in Fv/Fm and LWC, while the most susceptible groups showed severe leaf wilting and more reductions in Fv/Fm and LWC. Drought stress increased total water soluble sugar (WSS) concentration, but no differences in the increased WSS were found among different groups of accessions.
2. Antioxidative metabolism of Brachypodium Distachyon under drought stress
Drought stress increased the accumulation of hydrogen peroxide (H2O2) and degree of lipid pexoxidation (Malondialdehyde, MDA) in the leaves and superoxide (O2) concentration in the roots, but to a greater extent in the B2C compared with T-9. An enhanced leaf activity of glutathione peroxidase (GPX) in T-9and the decreased activities of catalase (CAT) and monodehydroascorbate reductase (MDHAR) in B2C were observed, respectively. Drought stress increased root activities of CAT and MDHAR in both accessions, to a greater degree in the tolerant T-9. Drought stress also increased root activities of GPX, ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR) and glutathione reductase (GR) in the T-9but decreased activity of superoxide dismutse (SOD) in the B2C.
3. Nucleotide diversity and linkage disequilibrium in antioxidative candidate genes for drought tolerance of Brachypodium distachyon
The section of these genes was based on the significant changes in enzyme activities observed between the control and drought-stressed plants, either tolerant T-9, or susceptible B2C, or both. The average nucleotide diversity (π) for CAT, GPX, DHAR, MDHAR, and APX (encoding ascorbate peroxidase) was0.0027among accessions contrasting drought tolerance. The average single nucleotide polymorphism (SNP) frequency across these five genes was one SNP per133bβ in the total length. The linkage disequilibrium (LD) decay extended to a distance of1.6kb across all genes. The neighbor-joining tree analyses of DHAR, MDHAR, and CA T generally separated accessions differing in drought tolerance.
4. Nucleotide diversity and association analysis on POD genes and drought traits
Make sure8candidate genes through POD enzyme native gel analysis in57Brachypodium distachyon and MALDT-TOF-MS.
90SNPs were from8POD genes with the sequence length9178bp. Coding part had44SNPs with the sequence length4396bp. And8genes belonged to natural test. The average indel diversity was0.652. There was557r2according to linkage disequilibrium analysis, and significant points were190and the ratio34%.
The number of SNPs related with drought traits accounted for30%in90SNPs according to association analysis. There were21SNPs significantly related with drought traits in tolerance genes and accounted for70%, but the susceptible genes only have9SNPs and accounted for21%.
The most related SNPs was the gene Bradilg63060.1and more related was the gene Bradi3g41340.1. There were a few related SNPs in the susceptible gene Bradilg26870.1and Bradilg65820.2and accounted for7.1%and12.5%, respectively. So the drought tolerant gene Bradilg63060.1was a good gene for molecular marker and transfer genes. The ration between transition and transversion was1.5:1based on SNP analysis results. Therefor the transition was the main base mutation.
引文
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