青瓯柑S-SAP标记与杨梅转录组多态性cSSRs标记筛选策略研究
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摘要
瓯柑(Citrus suavissima Hort. ex Tanaka)是浙江南部最具特色的地方柑橘栽培品种,青瓯柑是于2005年所发现的普通瓯柑芽变新种类,但目前尚无可用于早期鉴别的特异分子标记。杨梅(Wyrica rubra Sieb. et Zucc., Myricaceae)是原产我国的特产果树,我国有着丰富的资源,但其可用的多态性cSSRs (cDNA-SSRs)比较缺乏。为此,本研究旨在开发青瓯柑特异S-SAP标记以及建立基于转录组的杨梅多态性cSSRs标记的筛选策略。研究取得了以下主要结果。
1、对经典S-SAP标记技术做了调整,建立了瓯柑EcoR I单酶切S-SAP标记技术体系,并且从EAT和C12选择性扩增产物中,筛选出了一条长约250bp特异于青瓯柑的S-SAP标记。对该标记条带进行了克隆测序,确定其长度为247bp该标记十分稳定,可以直接用来证明青瓯柑是普通瓯柑的真实芽变。该标记相应的EcoR I单酶切S-SAP标记技术分析体系,也能够为青瓯柑新品种审定和种苗鉴定提供技术支持；该技术体系也可以为其他果树同类研究提供技术参考。同时,本研究也克隆出了4条瓯柑的RNaseH-LTR片段序列,可用于近缘柑橘种类品种的S-SAP分析研究。
2、从杨梅‘荸荠’转录组的UniGenes序列鉴别出了6883个cSSR位点,相应的cSSR位点分布频率为1个cSSR位点/3.2Kb。在所有cSSR位点当中,重复序列长度小于或等于12bp cSSR位点约占58%,14-22bpcSSR位点约占35%,等于或长于24bp的cSSR位点约占7%；二核苷酸和三核苷酸cSSR位点是主要类型,两者所占比例超过75%,AG/CT和AAG/CTT分别在二核苷酸和三核苷酸cSSR位点中所占比例最高,同其他类型cSSR位点一样,它们的数量随着重复次数增加而减少。在所有杨梅转录组cSSRs中,有594个复合cSSRs,其约占总cSSRs的10%。杨梅转录组上有5914cSSRs被系统地分为11类。此5914cSSRs共包含6330个cSSR位点,占杨梅转录组总cSSR位点数的92.0%。
3、基于11类cSSRs的多态性比较分析,本研究设计出了杨梅转录组多态性cSSRs标记筛选的策略。该策略为：首先,优先选取2-ntL、Compound B、 Compound A cSSRs和Compound D这四类cSSRs进行筛选多态性cSSRs;其次,从3-ntL中,可以快速获取大量的多态性cSSRs;此外,2-ntM cSSRs可以用于从中筛选出多态性水平较高的cSSRS。采用此策略,可以大大地提高杨梅转录组多态性cSSRs标记筛选的效率,为大量筛选多态性cSSRs标记提供很大便利。
4、本研究也获得了109个杨梅多态性cSSRs标记,其能够产生389个等位基因(多态性比率为93.8%)。利用这些cSSRs标记,进一步确认了部分杨梅样品的遗传关系。这109个cSSRs标记,可以作为杨梅分子遗传育种的一项重要研究资源。
Ougan (Citrus suavissima Hort. ex Tanaka) is the most special cultivar of citrus in the south of Zhejiang Province. Green Ougan is a newly variety found in2005of mandarin derived from the bud mutation of Ordinary Ougan, but there still was no available molecular markers for early distinguishing of the new variety. Chinese bayberry (Myrica rubra Sieb. et Zucc., Myricaceae) is one specialty of fruit tree which is native to China, and there are plenty of the resoureces in the country, but the available polymorphic cSSRs (cDNA-cSSRs) were scarce. Therefore, this research was armed at developing the S-SAP marker specific for Green Ougan and establishing a strategy for screening polymorphic cSSRs from those derived from Chinese bayberry transcriptome. The main results are as follows:
1. Some modifications were made to S-SAP technique, and a system of S-SAP technique for Ougan was established, in which genomic DNA was digested solely with EcoR I. From the selective amplification products generated with the primers of C12and EAT, an about250bp band specific for Green Ougan was screened out, which size was confirmed to be247bp with cloning and sequencing. The results could be used to proof that Green Ougan is an authentic bud sport of Ordinary Ougan and also provide technical supports for the cultivar registration and the seedling identification of Green Ougan. The S-SAP technique based on digestion solely with EcoR I, could also provide some technical references to the similar studies of other fruit trees. Meanwhile, four RNaseH-LTR fragment sequences of mandarin were obtained by cloning, and they should be able to be applied to the S-SAP analysis of the varieties of citrus close-related to mandarin.
2. In the UniGenes derived from RNA-seq of the transcriptome of Chinese bayberry cv. Biqi,6883cSSR loci were identified with1/3.2Kb in frequency.≤12bp,14-22bp and≥24bp cSSR loci respectively accounted for58%,35%and7%or so; di-and tri-nucleotide cSSR loci took up over75%; AG/CT and AAG/CTT were the most in corresponding cSSR loci and their number decreased with the repeat number increasing. In all the cSSRs derived from the transcriptome of Chinese bayberry, there were594compound cSSRs about accounting for10%, and5914 cSSRs were divided comprehensively into eleven types. The5914cSSRs contained6330cSSR loci occupying92.0%of all loci.
3. A strategy was devised to screen for polymorphic cSSRs based on the analysis of polymorphisms in each type of cSSR. And it was that the2-ntL, Compound B, Compound A, and Compound D cSSRs should be preferentially selected for screening polymorphic cSSRs. In addition,3-ntL cSSRs could be suitable for obtaining abundant polymorphic cSSRs efficiently, and2-ntM cSSRs suitable for screening highly polymorphic cSSRs. Using the strategy, the efficiency of screening polymorphic cSSRs could be greatly raised and that could greatly facilitate consequently screening polymorphic cSSRs in large scale.
4.109polymorphic cSSRs were also obtained and they can generate389alleles with polymorphism ratio being93.8%. Using these cSSR markers, the relationships among some Chinese bayberry samples were furtherly confirmed. And the109cSSR markers should be a promising genomic resource for molecular breeding of Chinese bayberry.
1、对经典S-SAP标记技术做了调整,建立了瓯柑EcoR I单酶切S-SAP标记技术体系,并且从EAT和C12选择性扩增产物中,筛选出了一条长约250bp特异于青瓯柑的S-SAP标记。对该标记条带进行了克隆测序,确定其长度为247bp该标记十分稳定,可以直接用来证明青瓯柑是普通瓯柑的真实芽变。该标记相应的EcoR I单酶切S-SAP标记技术分析体系,也能够为青瓯柑新品种审定和种苗鉴定提供技术支持；该技术体系也可以为其他果树同类研究提供技术参考。同时,本研究也克隆出了4条瓯柑的RNaseH-LTR片段序列,可用于近缘柑橘种类品种的S-SAP分析研究。
2、从杨梅‘荸荠’转录组的UniGenes序列鉴别出了6883个cSSR位点,相应的cSSR位点分布频率为1个cSSR位点/3.2Kb。在所有cSSR位点当中,重复序列长度小于或等于12bp cSSR位点约占58%,14-22bpcSSR位点约占35%,等于或长于24bp的cSSR位点约占7%；二核苷酸和三核苷酸cSSR位点是主要类型,两者所占比例超过75%,AG/CT和AAG/CTT分别在二核苷酸和三核苷酸cSSR位点中所占比例最高,同其他类型cSSR位点一样,它们的数量随着重复次数增加而减少。在所有杨梅转录组cSSRs中,有594个复合cSSRs,其约占总cSSRs的10%。杨梅转录组上有5914cSSRs被系统地分为11类。此5914cSSRs共包含6330个cSSR位点,占杨梅转录组总cSSR位点数的92.0%。
3、基于11类cSSRs的多态性比较分析,本研究设计出了杨梅转录组多态性cSSRs标记筛选的策略。该策略为：首先,优先选取2-ntL、Compound B、 Compound A cSSRs和Compound D这四类cSSRs进行筛选多态性cSSRs;其次,从3-ntL中,可以快速获取大量的多态性cSSRs;此外,2-ntM cSSRs可以用于从中筛选出多态性水平较高的cSSRS。采用此策略,可以大大地提高杨梅转录组多态性cSSRs标记筛选的效率,为大量筛选多态性cSSRs标记提供很大便利。
4、本研究也获得了109个杨梅多态性cSSRs标记,其能够产生389个等位基因(多态性比率为93.8%)。利用这些cSSRs标记,进一步确认了部分杨梅样品的遗传关系。这109个cSSRs标记,可以作为杨梅分子遗传育种的一项重要研究资源。
Ougan (Citrus suavissima Hort. ex Tanaka) is the most special cultivar of citrus in the south of Zhejiang Province. Green Ougan is a newly variety found in2005of mandarin derived from the bud mutation of Ordinary Ougan, but there still was no available molecular markers for early distinguishing of the new variety. Chinese bayberry (Myrica rubra Sieb. et Zucc., Myricaceae) is one specialty of fruit tree which is native to China, and there are plenty of the resoureces in the country, but the available polymorphic cSSRs (cDNA-cSSRs) were scarce. Therefore, this research was armed at developing the S-SAP marker specific for Green Ougan and establishing a strategy for screening polymorphic cSSRs from those derived from Chinese bayberry transcriptome. The main results are as follows:
1. Some modifications were made to S-SAP technique, and a system of S-SAP technique for Ougan was established, in which genomic DNA was digested solely with EcoR I. From the selective amplification products generated with the primers of C12and EAT, an about250bp band specific for Green Ougan was screened out, which size was confirmed to be247bp with cloning and sequencing. The results could be used to proof that Green Ougan is an authentic bud sport of Ordinary Ougan and also provide technical supports for the cultivar registration and the seedling identification of Green Ougan. The S-SAP technique based on digestion solely with EcoR I, could also provide some technical references to the similar studies of other fruit trees. Meanwhile, four RNaseH-LTR fragment sequences of mandarin were obtained by cloning, and they should be able to be applied to the S-SAP analysis of the varieties of citrus close-related to mandarin.
2. In the UniGenes derived from RNA-seq of the transcriptome of Chinese bayberry cv. Biqi,6883cSSR loci were identified with1/3.2Kb in frequency.≤12bp,14-22bp and≥24bp cSSR loci respectively accounted for58%,35%and7%or so; di-and tri-nucleotide cSSR loci took up over75%; AG/CT and AAG/CTT were the most in corresponding cSSR loci and their number decreased with the repeat number increasing. In all the cSSRs derived from the transcriptome of Chinese bayberry, there were594compound cSSRs about accounting for10%, and5914 cSSRs were divided comprehensively into eleven types. The5914cSSRs contained6330cSSR loci occupying92.0%of all loci.
3. A strategy was devised to screen for polymorphic cSSRs based on the analysis of polymorphisms in each type of cSSR. And it was that the2-ntL, Compound B, Compound A, and Compound D cSSRs should be preferentially selected for screening polymorphic cSSRs. In addition,3-ntL cSSRs could be suitable for obtaining abundant polymorphic cSSRs efficiently, and2-ntM cSSRs suitable for screening highly polymorphic cSSRs. Using the strategy, the efficiency of screening polymorphic cSSRs could be greatly raised and that could greatly facilitate consequently screening polymorphic cSSRs in large scale.
4.109polymorphic cSSRs were also obtained and they can generate389alleles with polymorphism ratio being93.8%. Using these cSSR markers, the relationships among some Chinese bayberry samples were furtherly confirmed. And the109cSSR markers should be a promising genomic resource for molecular breeding of Chinese bayberry.
引文
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