扁穗牛鞭草标记—性状关联分析及HcDREB转录因子基因克隆
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摘要
扁穗牛鞭草(Hemarthria compressa)是禾本科牛鞭草属的多年生草,具有生长期长、生长速度快、再生力强、适应性强等特点,被广泛用于南方草地畜牧业,在水土保持、生态治理中也显示出广阔的应用前景。我国野生扁穗牛鞭草资源丰富,具有多样的生态类型。鉴于此,研究其遗传多样性、群体遗传关系及对重要农艺性状的QTL进行定位,对扁穗牛鞭草遗传改良具有重要的理论和实际意义。为此,本研究采用SRAP和EST-SSR两种分子标记,对来自我国西南区的40份野生扁穗牛鞭草及3个国审品种的遗传多样性和群体结构进行分析,利用关联分析检测与其重要农艺性状关联的分子标记。
低温、干旱和盐碱是植物生长发育的主要限制因素。与单个功能基因的抗逆性不同,DREB转录因子可以同时调控下游多个逆境诱导基因的表达,参与胁迫信号的传导过程,实现对植物的抗逆性的综合改良,在植物的抗寒、抗旱和抗盐胁迫中发挥着重要作用。作为暖季型禾草,扁穗牛鞭草比较耐寒,能耐4℃左右的低温,但冬季停止生长,不耐旱,干旱条件会导致扁穗牛鞭草生长不良。本研究从“广益”扁穗牛鞭草中分离克隆DREB转录因子基因,并进行功能分析,为通过转基因技术在分子水平改良扁穗牛鞭草提供理论依据和技术支持。目前,本论文取得的主要结果如下：
1、扁穗牛鞭草种质资源表型及相关分析结果表明：43份扁穗牛鞭草叶色、花期、花序性状、花药颜色等存在丰富变异；不同材料的茎部、叶部、分蘖、生物量、生殖性状等14个数量性状指标存在不同程度的变异,变异系数平均值为24.4%,变异程度最大的是花序数／生殖枝,变异系数达57.4%,表明扁穗牛鞭草种质具有较大的表型变异。
2、遗传多样性分析结果表明,15对SRAP引物对43份牛鞭草种质资源共扩增得到315条扩增条带,其中多态性条带294条,多态性比例(PPB)为93.2%,平均每对引物扩增的多态性条带为19.6条,多态信息含量为0.340-0.500,29条SRAP特异性条带能鉴定24份无性系。23对EST-SSR引物共扩增出323条清晰可辨的条带,其中多态性条带260条,多态性条带比率(PPB)达80.4%,每对引物平均扩增多态性条带11.3条,多态信息含量(PIC)为0.354-0.500。34条EST-SSR特异性条带能鉴定20份材料。SRAP分子标记和EST-SSR分子标记遗传相似系数Gs分别为0.640～0.949和0.690～0.913,表明西南区扁穗牛鞭草种质间存在较为丰富的遗传变异,但3个国审品种有着较近的亲缘关系,遗传基础较窄。
3、扁穗牛鞭草农艺性状与SRAP和EST-SSR分子标记关联分析结果表明,分子标记位点间存在连锁不平衡；基于SRAP标记和(?)EST-SSR标记的群体结构分析表明,43份扁穗牛鞭草无性系构成的自然群体存在群体结构；累计有43个SRAP标记位点和38个EST-SSR标记位点与扁穗牛鞭草性状关联。多个标记同时与2个及以上性状相关联,绝大部分性状与多个位点关联。
4、采用RACE技术从扁穗牛鞭草中克隆到一个DREB2类转录因子,将其命名为HcDREB2。序列分析表明,该基因序列全长为1345bp,编码一个由264个氨基酸组成的蛋白,推测氨基酸序列中有1个高度保守的AP2结构域,及在AP2结构域的V14和E19间具有DREB2转录因子特有的AEIR序列；HcDREB2与其他已知的DREB2基因在保守的AP2/EREBP结构域处具有很高的同源性外,在其它区域同源性不高。
5、实时荧光定量分析结果表明,HcDREB2基因的表达受低温、高盐、干旱的诱导,而不受ABA胁迫所诱导,其表达属非ABA依赖途径。在4℃、20%PEG和250mMNaCl处理1h,HcDREB2基因的表达量最高,处理4h,表达量最低,处理8h,HcDREB2基因的表达量再次达到峰值。
6、利用酵母单杂交系统,对扁穗牛鞭草HcDREB2与DRE顺式作用元件的特异识别和结合能力进行检测,结果显示,HcDREB2能与顺式作用元件DRE特异结合,激活下游目的基因的转录。
Hemarthria compressa is a kind of perennial grass, with long growth period, fast growth, strong regeneration ability and well adaptability. So it is already widely used in animal husbandry in the south, and shows broad prospect of application in soil and water conservation and ecological management. There are rich wild H.compressa resources, which has the variety of ecological types. For that reason, it is very important to study its genetic diversity, colony genetic relationship, positioning of main gene for genetic improvement of H.compressa in theory and practice. In order to accelerate breeding process of H.compressa and explore the genetic diversity and genetic relationship among wild H.compressa resources, SRAP and EST-SSR molecular markers were used to study the genetic diversity and group structure among43H.compressa materials, and the association analysis method was used to detect the molecular marker associated with important agronomic traits.
Low temperature, drought and saline-alkali are main limiting factors. Unlike single functional genes, the DREB transcription factors can regulate multiple stress-inducible genes expression simultaneously, and participate in physiological and biochemical process involved stress tolerance, result in increasing in stress resistance. The DREB transcription factor is very important to resistet to low temperature, drought and saline-alkali. As the warm-season grass, H.compressa is cold-tolerant, it can keep green in such4℃, and stop growing in winter. H.compressa can not withstand drought, and it will fail to grow well on drought soils. In the study, DREB-like gene was isolated and cloned from H.compressa and its function was analysed.The main results were as followed:
1Trait differences and correlation analysis showed that:there were rich variation among43H.compressa clones in qualitative traits, such leaf colour, flowering phase, inflorescence shape and anther color. Similarityly, there were abundant variation among43H.compressa clones showed in stem, leaf, tiller, biomass and panicle characteristic. The degree of variation of every trait was different. The mean coefficient of variation was24.4%. Coefficient of variation of number of inflorescence per fertile stem is the largest at57.4%. It indicated that there were abundant variation within the species.
2The result of genetic diversity showed that315PCR bands were detected in total of15pairs of SRAP primers, among which,294bands were polymorphic, accounting for93.2%of the total. The amplified bands and polymorphic bands per pair primer were averagely20.9and19.6, respectively. The polymorphic information content was from0.340to0.500.24H.compressa clones were identified through29special bands. A total of323fragments were amplificated with23pairs of EST-SSR primers of poaceae, among which,260fragments were polymorphic, accounting for80.4%of the total. The polymorphic information content was from0.354to0.500.20clones could be identified through34special bands. The Genetic similarity coefficient of SRAP and EST-SSR was0.640-0.949and0.690-0.913. The result showed that there were rich genetic variance, but there was genetic relationship among three varieties.
3The different degrees of LD were detected among molecular marker. Genetic structure analysis showed that the H.compressa population was composed of four subpopulations based on SRAP molecular marker and five subpopulations based on EST-SSR molecular marker. The association analysis between two molecular markers and14agronomic traits was performed by using TASSEL GLM (general linear model) program.43SRAP locis and38EST-SSR locis associated with traits were screened respectively. Some locis were found to associate with a same trait. There were a few locis associated with two or more traits simultaneously, which might be the genetic reason of correlation among traits or pleiotropic phenomena.
4A DREB2like genes from H.compressa under the low temperature stress were cloned by RT-PCR and RACE methods, named HcDREB2. Nucleotide sequence analysis indicated that the HcDREB had an ORF encoding264amino acids with predicted molecular weight of28.8kD and a isoelectric point of5.13. The putative protein contains a highly conserved AP2domain, a nuclear localization signal and an acidic activation domain. There were a specific motif AEIR between V14and E19in AP2/ERBP domain, which confirmed the HcDREB gene belong to DREB2subfimily. No significant sequence similarity with those of other known DREBs except for the conserved AP2DNA-binding domain.
5The expression of the HcDREB2gene was induced by low temperature, dehydration and high-salt conditions. No significant changes in the HcDREB expression were observed under ABA stress, which showed that the expression of HcDREB was unindependent on ABA. Its expression was changed following the inducible time. The expression of HcDREB was highest after1h under4℃,20%PEG and250mM NaCl treatment, then the expression amount was lowest after4h.
6To investigate the DNA-binding specificity in vivo activity, the yeast hybrid system was carried out, and the results confirmed that the AP2domain of HcDREB2could specifically interact with DRE cis-acting element and activate down-stream responsive genes.
低温、干旱和盐碱是植物生长发育的主要限制因素。与单个功能基因的抗逆性不同,DREB转录因子可以同时调控下游多个逆境诱导基因的表达,参与胁迫信号的传导过程,实现对植物的抗逆性的综合改良,在植物的抗寒、抗旱和抗盐胁迫中发挥着重要作用。作为暖季型禾草,扁穗牛鞭草比较耐寒,能耐4℃左右的低温,但冬季停止生长,不耐旱,干旱条件会导致扁穗牛鞭草生长不良。本研究从“广益”扁穗牛鞭草中分离克隆DREB转录因子基因,并进行功能分析,为通过转基因技术在分子水平改良扁穗牛鞭草提供理论依据和技术支持。目前,本论文取得的主要结果如下：
1、扁穗牛鞭草种质资源表型及相关分析结果表明：43份扁穗牛鞭草叶色、花期、花序性状、花药颜色等存在丰富变异；不同材料的茎部、叶部、分蘖、生物量、生殖性状等14个数量性状指标存在不同程度的变异,变异系数平均值为24.4%,变异程度最大的是花序数／生殖枝,变异系数达57.4%,表明扁穗牛鞭草种质具有较大的表型变异。
2、遗传多样性分析结果表明,15对SRAP引物对43份牛鞭草种质资源共扩增得到315条扩增条带,其中多态性条带294条,多态性比例(PPB)为93.2%,平均每对引物扩增的多态性条带为19.6条,多态信息含量为0.340-0.500,29条SRAP特异性条带能鉴定24份无性系。23对EST-SSR引物共扩增出323条清晰可辨的条带,其中多态性条带260条,多态性条带比率(PPB)达80.4%,每对引物平均扩增多态性条带11.3条,多态信息含量(PIC)为0.354-0.500。34条EST-SSR特异性条带能鉴定20份材料。SRAP分子标记和EST-SSR分子标记遗传相似系数Gs分别为0.640～0.949和0.690～0.913,表明西南区扁穗牛鞭草种质间存在较为丰富的遗传变异,但3个国审品种有着较近的亲缘关系,遗传基础较窄。
3、扁穗牛鞭草农艺性状与SRAP和EST-SSR分子标记关联分析结果表明,分子标记位点间存在连锁不平衡；基于SRAP标记和(?)EST-SSR标记的群体结构分析表明,43份扁穗牛鞭草无性系构成的自然群体存在群体结构；累计有43个SRAP标记位点和38个EST-SSR标记位点与扁穗牛鞭草性状关联。多个标记同时与2个及以上性状相关联,绝大部分性状与多个位点关联。
4、采用RACE技术从扁穗牛鞭草中克隆到一个DREB2类转录因子,将其命名为HcDREB2。序列分析表明,该基因序列全长为1345bp,编码一个由264个氨基酸组成的蛋白,推测氨基酸序列中有1个高度保守的AP2结构域,及在AP2结构域的V14和E19间具有DREB2转录因子特有的AEIR序列；HcDREB2与其他已知的DREB2基因在保守的AP2/EREBP结构域处具有很高的同源性外,在其它区域同源性不高。
5、实时荧光定量分析结果表明,HcDREB2基因的表达受低温、高盐、干旱的诱导,而不受ABA胁迫所诱导,其表达属非ABA依赖途径。在4℃、20%PEG和250mMNaCl处理1h,HcDREB2基因的表达量最高,处理4h,表达量最低,处理8h,HcDREB2基因的表达量再次达到峰值。
6、利用酵母单杂交系统,对扁穗牛鞭草HcDREB2与DRE顺式作用元件的特异识别和结合能力进行检测,结果显示,HcDREB2能与顺式作用元件DRE特异结合,激活下游目的基因的转录。
Hemarthria compressa is a kind of perennial grass, with long growth period, fast growth, strong regeneration ability and well adaptability. So it is already widely used in animal husbandry in the south, and shows broad prospect of application in soil and water conservation and ecological management. There are rich wild H.compressa resources, which has the variety of ecological types. For that reason, it is very important to study its genetic diversity, colony genetic relationship, positioning of main gene for genetic improvement of H.compressa in theory and practice. In order to accelerate breeding process of H.compressa and explore the genetic diversity and genetic relationship among wild H.compressa resources, SRAP and EST-SSR molecular markers were used to study the genetic diversity and group structure among43H.compressa materials, and the association analysis method was used to detect the molecular marker associated with important agronomic traits.
Low temperature, drought and saline-alkali are main limiting factors. Unlike single functional genes, the DREB transcription factors can regulate multiple stress-inducible genes expression simultaneously, and participate in physiological and biochemical process involved stress tolerance, result in increasing in stress resistance. The DREB transcription factor is very important to resistet to low temperature, drought and saline-alkali. As the warm-season grass, H.compressa is cold-tolerant, it can keep green in such4℃, and stop growing in winter. H.compressa can not withstand drought, and it will fail to grow well on drought soils. In the study, DREB-like gene was isolated and cloned from H.compressa and its function was analysed.The main results were as followed:
1Trait differences and correlation analysis showed that:there were rich variation among43H.compressa clones in qualitative traits, such leaf colour, flowering phase, inflorescence shape and anther color. Similarityly, there were abundant variation among43H.compressa clones showed in stem, leaf, tiller, biomass and panicle characteristic. The degree of variation of every trait was different. The mean coefficient of variation was24.4%. Coefficient of variation of number of inflorescence per fertile stem is the largest at57.4%. It indicated that there were abundant variation within the species.
2The result of genetic diversity showed that315PCR bands were detected in total of15pairs of SRAP primers, among which,294bands were polymorphic, accounting for93.2%of the total. The amplified bands and polymorphic bands per pair primer were averagely20.9and19.6, respectively. The polymorphic information content was from0.340to0.500.24H.compressa clones were identified through29special bands. A total of323fragments were amplificated with23pairs of EST-SSR primers of poaceae, among which,260fragments were polymorphic, accounting for80.4%of the total. The polymorphic information content was from0.354to0.500.20clones could be identified through34special bands. The Genetic similarity coefficient of SRAP and EST-SSR was0.640-0.949and0.690-0.913. The result showed that there were rich genetic variance, but there was genetic relationship among three varieties.
3The different degrees of LD were detected among molecular marker. Genetic structure analysis showed that the H.compressa population was composed of four subpopulations based on SRAP molecular marker and five subpopulations based on EST-SSR molecular marker. The association analysis between two molecular markers and14agronomic traits was performed by using TASSEL GLM (general linear model) program.43SRAP locis and38EST-SSR locis associated with traits were screened respectively. Some locis were found to associate with a same trait. There were a few locis associated with two or more traits simultaneously, which might be the genetic reason of correlation among traits or pleiotropic phenomena.
4A DREB2like genes from H.compressa under the low temperature stress were cloned by RT-PCR and RACE methods, named HcDREB2. Nucleotide sequence analysis indicated that the HcDREB had an ORF encoding264amino acids with predicted molecular weight of28.8kD and a isoelectric point of5.13. The putative protein contains a highly conserved AP2domain, a nuclear localization signal and an acidic activation domain. There were a specific motif AEIR between V14and E19in AP2/ERBP domain, which confirmed the HcDREB gene belong to DREB2subfimily. No significant sequence similarity with those of other known DREBs except for the conserved AP2DNA-binding domain.
5The expression of the HcDREB2gene was induced by low temperature, dehydration and high-salt conditions. No significant changes in the HcDREB expression were observed under ABA stress, which showed that the expression of HcDREB was unindependent on ABA. Its expression was changed following the inducible time. The expression of HcDREB was highest after1h under4℃,20%PEG and250mM NaCl treatment, then the expression amount was lowest after4h.
6To investigate the DNA-binding specificity in vivo activity, the yeast hybrid system was carried out, and the results confirmed that the AP2domain of HcDREB2could specifically interact with DRE cis-acting element and activate down-stream responsive genes.
引文
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