利用cDNA/EST序列大规模开发内含子多态性标记的研究
摘要
随着大规模植物功能基因组测序项目的进展,产生了大量的表达序列标签(EST)序列。内含子广泛分布于真核生物基因组中,其变异程度通常比编码序列高得多。利用内含子上的多态性,包括内含子长度多态性(ILP)和内含子单核苷酸多态性(ISNP),可开发成分子标记,称为内含子多态性(IP)标记。内含子在基因中的位置在物种间相对保守,因此通过将某个植物的EST序列与模式植物水稻或拟南芥的同源基因进行比较,可以推断该植物EST上的内含子位置(即相邻外显子之间的连接点)。在所推测的内含子位置两侧的EST序列上设计一对引物,就能够在该植物的基因组中扩增出包含所预测的内含子的片段并检测到该内含子中存在的多态性,从而开发出IP标记。也就是说,这样的引物具有开发出IP标记的潜力,因此我们称之为潜在的内含子多态性(PIP)标记。基于上述原理,本研究进行了大规模的PIP标记开发,构建了PIP数据库,并在棉花中进行了ILP标记的开发和应用,同时对ISNP的检测方法进行了探讨。主要结果如下:
1、在59个物种中开发了57,658个PIP标记。
2、建立了一个基于互联网的PIP标记数据库(http://ibi.Zju.edu.cn/pgl/pip)。该数据库提供以下功能:1)介绍PIP标记开发的流程和方法;2)查询或下载PIP标记;3)对用户提交的cDNA/EST序列进行PIP引物的在线设计;4)比较不同物种间的PIP标记的同源性。
3、对PIP标记的电子PCR分析表明,根据模式植物拟南芥对苜蓿及白杨内含子的预测的准确率分别达到99.40%和98.71%,说明内含子位置确实非常保守。
4、对模式植物基于自身开发的PIP标记的比较分析显示,水稻两个亚种(粳稻品种日本晴和籼稻品种93-11)之间及拟南芥两个生态型(Columbia和Landsberg)之间ILP频率分别为17.98%和18.61%,ISNP频率分别为51-22%和53.18%,说明植物中内含子多态性水平是非常高的,能够满足实际应用的需要。
5、合成了220对棉花PIP标记引物,对19个栽培棉和25个野生棉材料进行PCR分析,发现92.27%的引物能得到预期的扩增产物,65.02%获得单一条带,94.09%的扩增产物包含内含子。在栽培棉(包括陆地棉和海岛棉)中ILP频率仅为3.18%,但野生棉中达到47.78%,ILP标记的PIC值变化在0.061-0.721之间,平均为0.34。
6、用开发的棉花ILP标记对25个野生棉种进行聚类分析,发现ILP标记能严格区分出A、B、C、D、E、F和G七种染色体组以及二倍体和四倍体,说明ILP标记可以有效地应用于棉花分类和进化的研究。
7、对利用TILLING原理检测ISNP进行了探索,并在技术上进行了简化(称为simTILLING),提出了在分离群体中应用simTILLING技术检测ISNP标记的原理。
8、对利用引物长度差异的PCR检测SNP的方法进行了尝试。利用该方法在棉花中开发了6个EST-SNP标记。
With the progress made in large-scale plant functional genome sequencing projects, a great amount of EST (expressed sequence tag) data is becoming available. Introns are widely distributed in eukaryotic genomes and are much more variable than coding sequences. Polymorphisms in introns, including intron length polymorphism (ILP) and intron single nucleotide polymorphism (ISNP), can be developed as molecular markers named intron polymorphism (IP). The positions of introns in genes are relatively conservative among species. Therefore, by comparing the EST sequences of a plant with the homologous genes of model plant rice or Arabidopsis, the intron positions (i.e. the joints between adjacent exons) in the ESTs of this plant could be predicted. Thus, by designing a pair of primers on the EST sequence flanking the predicted intron position, a fragment containing the predicted intron could be amplified from that plant and polymorphism in the intron could be detected. In other words, the primers have the potential to develop IP markers. Hence, we call them potential intron polymorphism (PIP) markers. In this study, large-scale development of PIP markers was performed according to the above principle; a PIP database was constructed; ILP markers were developed and applied in cotton; and methods for detecting ISNPs were trialed. Main results are as follows:
1. A total of 57,658 PIP markers were developed in 59 plant species.
2. A web-based PIP database (http://ibi.zju.edu.cn/pgl/pip) was constructe, providing the following functions: 1) introduction of the procedure and method for developing PIP markers; 2) inquiry and download of PIP markers; 3) online designing of PIP primers on cDNA/EST sequences submitted by users; and 4) comparison of homology between PIP markers from different species.
3. Electronic PCR analysis on PIP markers indicated that up to 99.40% and 89.71% introns predicted by Arabidopsis were correct in Medicago truncatula and Populus trichocarpa, suggesting that intron positions are very conservative indeed.
4. Comparison analysis on the PIP markers of model plants developed based on themselves showed that the frequencies of ILPs/ISNPs between two subspecies of rice (japonica cultivar Nipponbare and indica cultivar 93-11) and between two ecotypes of Arabidopsis (Columbia and Landsberg) were 17.98%/51.22% and 18.61%/53.18%, respectively, suggesting that the intron polymorphism level is very high in plant and can meet the requirement of practical application.
5. Two hundred and twenty pairs of cotton PIP primers were synthesized. PCR analysis with these primers on 19 accessions of cultivated cotton and 25 accessions of wild cotton showed that 92.27% of the primers amplified products as expected; 65.02% amplified single bands; and 94.09% contained introns in their PCR products. The ILP frequency was only 3.18% in cultivated cotton (including G. hirsutum L. and G. barbadense L.), but was up to 47.78% in wild cotton. The PIC values of ILP loci in wild cotton varied 0.061-0.721 with an average of 0.34.
6. The ILP markers developed were used for cluster analysis of 25 wild cotton accessions. It was found that ILP markers could strictly distinguish between A, B, C, D, E, F and G genomes and between diploid and allopolyploids, suggesting that ILP markers can be effectively applied to the studies of cotton classification and evolution.
7. The feasibility of using TILLING principle to detect ISNP was investigate and technical simplification was made (named simTILLING). The principle of using simTILLING to analyze ISNP markers in segregating populations was proposed.
8. The method of detecting SNP by PCR using primers with different lengths was trialed and 6 EST-SNP markers were developed in cotton using this method.
1、在59个物种中开发了57,658个PIP标记。
2、建立了一个基于互联网的PIP标记数据库(http://ibi.Zju.edu.cn/pgl/pip)。该数据库提供以下功能:1)介绍PIP标记开发的流程和方法;2)查询或下载PIP标记;3)对用户提交的cDNA/EST序列进行PIP引物的在线设计;4)比较不同物种间的PIP标记的同源性。
3、对PIP标记的电子PCR分析表明,根据模式植物拟南芥对苜蓿及白杨内含子的预测的准确率分别达到99.40%和98.71%,说明内含子位置确实非常保守。
4、对模式植物基于自身开发的PIP标记的比较分析显示,水稻两个亚种(粳稻品种日本晴和籼稻品种93-11)之间及拟南芥两个生态型(Columbia和Landsberg)之间ILP频率分别为17.98%和18.61%,ISNP频率分别为51-22%和53.18%,说明植物中内含子多态性水平是非常高的,能够满足实际应用的需要。
5、合成了220对棉花PIP标记引物,对19个栽培棉和25个野生棉材料进行PCR分析,发现92.27%的引物能得到预期的扩增产物,65.02%获得单一条带,94.09%的扩增产物包含内含子。在栽培棉(包括陆地棉和海岛棉)中ILP频率仅为3.18%,但野生棉中达到47.78%,ILP标记的PIC值变化在0.061-0.721之间,平均为0.34。
6、用开发的棉花ILP标记对25个野生棉种进行聚类分析,发现ILP标记能严格区分出A、B、C、D、E、F和G七种染色体组以及二倍体和四倍体,说明ILP标记可以有效地应用于棉花分类和进化的研究。
7、对利用TILLING原理检测ISNP进行了探索,并在技术上进行了简化(称为simTILLING),提出了在分离群体中应用simTILLING技术检测ISNP标记的原理。
8、对利用引物长度差异的PCR检测SNP的方法进行了尝试。利用该方法在棉花中开发了6个EST-SNP标记。
With the progress made in large-scale plant functional genome sequencing projects, a great amount of EST (expressed sequence tag) data is becoming available. Introns are widely distributed in eukaryotic genomes and are much more variable than coding sequences. Polymorphisms in introns, including intron length polymorphism (ILP) and intron single nucleotide polymorphism (ISNP), can be developed as molecular markers named intron polymorphism (IP). The positions of introns in genes are relatively conservative among species. Therefore, by comparing the EST sequences of a plant with the homologous genes of model plant rice or Arabidopsis, the intron positions (i.e. the joints between adjacent exons) in the ESTs of this plant could be predicted. Thus, by designing a pair of primers on the EST sequence flanking the predicted intron position, a fragment containing the predicted intron could be amplified from that plant and polymorphism in the intron could be detected. In other words, the primers have the potential to develop IP markers. Hence, we call them potential intron polymorphism (PIP) markers. In this study, large-scale development of PIP markers was performed according to the above principle; a PIP database was constructed; ILP markers were developed and applied in cotton; and methods for detecting ISNPs were trialed. Main results are as follows:
1. A total of 57,658 PIP markers were developed in 59 plant species.
2. A web-based PIP database (http://ibi.zju.edu.cn/pgl/pip) was constructe, providing the following functions: 1) introduction of the procedure and method for developing PIP markers; 2) inquiry and download of PIP markers; 3) online designing of PIP primers on cDNA/EST sequences submitted by users; and 4) comparison of homology between PIP markers from different species.
3. Electronic PCR analysis on PIP markers indicated that up to 99.40% and 89.71% introns predicted by Arabidopsis were correct in Medicago truncatula and Populus trichocarpa, suggesting that intron positions are very conservative indeed.
4. Comparison analysis on the PIP markers of model plants developed based on themselves showed that the frequencies of ILPs/ISNPs between two subspecies of rice (japonica cultivar Nipponbare and indica cultivar 93-11) and between two ecotypes of Arabidopsis (Columbia and Landsberg) were 17.98%/51.22% and 18.61%/53.18%, respectively, suggesting that the intron polymorphism level is very high in plant and can meet the requirement of practical application.
5. Two hundred and twenty pairs of cotton PIP primers were synthesized. PCR analysis with these primers on 19 accessions of cultivated cotton and 25 accessions of wild cotton showed that 92.27% of the primers amplified products as expected; 65.02% amplified single bands; and 94.09% contained introns in their PCR products. The ILP frequency was only 3.18% in cultivated cotton (including G. hirsutum L. and G. barbadense L.), but was up to 47.78% in wild cotton. The PIC values of ILP loci in wild cotton varied 0.061-0.721 with an average of 0.34.
6. The ILP markers developed were used for cluster analysis of 25 wild cotton accessions. It was found that ILP markers could strictly distinguish between A, B, C, D, E, F and G genomes and between diploid and allopolyploids, suggesting that ILP markers can be effectively applied to the studies of cotton classification and evolution.
7. The feasibility of using TILLING principle to detect ISNP was investigate and technical simplification was made (named simTILLING). The principle of using simTILLING to analyze ISNP markers in segregating populations was proposed.
8. The method of detecting SNP by PCR using primers with different lengths was trialed and 6 EST-SNP markers were developed in cotton using this method.
引文
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