SSR分子标记开发和在香蕉种质资源遗传分析中的应用
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摘要
本研究利用SAM技术和香蕉EST数据开发SSR标记,并选取芭蕉科3属11个种／变种,82个品种(系)及7个海南岛阿宽蕉(M. itinerans)居群为研究对象,对香蕉种质资源亲缘关系及阿宽蕉居群遗传多样性进行了SSR分析。研究结果如下：
(1)从NCBI搜索的2282条香蕉EST中,发掘出含有SSR的EST序列110条,共有122个SSR位点,检出率为5.3%。SSR位点可分为37种重复单元,平均长度为20bp,其中二、三核苷酸重复单元的SSR占主导地位,其它重复类型所占比例均不足10%,而四核苷酸重复类型最少。GA和GAA是二、三核苷酸中的优势重复类型。设计引物63对,用巴西蕉DNA初筛得到41对EST-SSR功能引物,占总引物数的65.1%。应用19对高重复性和多态性好的引物对49个香蕉品种(系)进行分析,在相似系数为0.63的水平可将49个品种按A、B基因型分为2个类群,基本与形态分类结果一致,表明EST-SSR引物可应用于香蕉品种资源分类的研究。
(2)应用SAM法从香蕉AA基因组的100个克隆序列中获得83条SSR序列,得率为83%,从香蕉BB基因组的43个克隆中得到38条SSR序列,得率为88.3%,综合得率达到84.6%；并成功设计引物62对(AA组38对,BB组24对)。经过筛选,得到AA组引物26对,BB组引物19对。
(3)利用45对Genomic-SSR和24对EST-SSR引物对26个香蕉栽培品种(系)和11个芭蕉科种属材料的遗传关系进行分析表明,EST-SSR比Genomic-SSR多态性高,但二者都能很好的揭示出香蕉群体内的遗传多样性。Genomic-SSR和EST-SSR标记在11个芭蕉科种属材料上的转移扩增率分别为80%和70.83%。对4个转移扩增位点的测序结果分析表明,不同种属间的材料扩增得到的序列与原始序列具有同源性。序列间的变异主要是由SSR位点重复次数和侧翼序列的碱基的替换、插入／缺失等变化引起。
(4)利用5对香蕉SSR引物构建了56份香蕉种质的分子身份证和指纹图谱。5对引物扩增出的多态性带为11-16,平均为13.8；引物的多态信息含量(PIC)在0.8490-0.9022之间,平均0.8727,说明我们选择的引物适合于对该批样品进行指纹标记。建立的香蕉分子指纹图谱可为在分子水平上区分香蕉种质材料和知识产权保护提供依据。
(5)阿宽蕉在居群水平上,各个居群平均等位基因数(Na)为4.0个,有效等位基因数(Ne)为1.5404个,观察杂合度(Ho)和期望杂合度(He)分别为0.3038和0.2775。九架岭居群的遗传多样性水平最高(Na=3.40,Ne=1.7054,Ho=0.3043,He=0.3633),阿驼岭居群的遗传多样性水平最低(Na=2.20,Ne=1.4050,Ho=0.2296,He=0.2633)。遗传分化系数(Fst)为0.0677,即有6.77%的遗传变异存在居群之间,93.23%的遗传变异存在于居群内。利用算术加权平均数法(UPGMA)将7个居群分成2大类,地理位置较近的聚在一起。
In the study, genomic-SSRs and EST-SSRs were developed by using selectively amplified microsatellite (SAM) analysis and searching the ESTdb of NCBI. Meanwhile, those SSR markers were evaluated in a collection of 11 related species/subspecies of Musaceae about 82 banana accessions and 7 M. itinerans populations. The main results and conclusions were as follows:
(1) Analysis of 2284 ESTs identified 110 sequences containing 122 SSRs. Among them, there were 37 motifs. The overall average length of SSRs was 20 bp. The trinucelotide repeats appeared to be the most abundant SSRs (47.6%), followed by dinucelotide repeats (33.1%), whereas the tetrnucelotide repeats were less abundant. The rich repeats AG and AGG were predominant, accounting for 75.7% and 36% in dri-and tri-nucelotide repeats respectively. A total of 63 primer pairs were designed and tested against genomic DNA of brazil. Forty-one primers could be validated as usable markers. Nineteen of these primers revealed moderate to high polymorphism information content (PIC) across 49 accessions. The polymorphic bands were ranged from 4 to 12, averagely 7.58. The mean PIC value was 0.7324, ranging from 0.3572 to 0.8744. Forty-nine banana varieties were separated into two major clusters closely corresponding with the genome composition by UPGMA analysis. The results showed that the EST-SSR markers were of great value in evaluation of banana germplasms.
(2) Eighty-three and thirty-eight microsatellite sequences were cloned and sequenced from a commercial cultivar'Gongjiao' (Musa acuminate, AA froup) and'Yejiao'(M. balbisiana, BB group) respectively, using selectively amplified microsatellite (SAM) analysis. A total of 62 microsatellite primers were designed (38 from AA group and 24 from BB group). These primers were pre-screened on'Gongjiao'and'Yejiao'. From those,26 from AA group and 19 from BB group produced clear repeatable amplification patterns and were used to all the samples.
(3) A set of 45 Genomic-SSR and 24 EST-SSR markers was identified in a collection of 22 cultivated bananas and 11 related species/subspecies. The results showed that EST-SSR is more polymorphic than Genomic-SSR. But both of them can provide accurate evaluation of genetic relationship among accessions. The ratio of the cross-species/genera amplification detected by Genomic-SSR and EST-SSR were 80% and 70.83% among 11 related wild species representing 10 different species, representative of three important genus of Musaceae family. To further demonstrate the transferability of the developed SSR loci, Sequence comparison of cross-species/genus amplicons generated by four SSR loci for 9-11 related wild species was done. In general, the amplified regions were found to be homologous to the original sequences (from which the SSRs were developed) and their comparisons across species. Sequencing of PCR products confirmed the presence of microsatellite repeats at all loci. Sequencing alleles at four loci showed that, apart from microsatellite length variation, point mutations and insertion/deletions were quite abundant in the flanking region of the alleles sequenced.
(4) To well evaluate and use the cultivars, it is necessary to identify them accurately by DNA molecular markers. A total of 56 banana accessions were investigated in this study. Five pre-selected SSR primers showed ample polymorphism and could distinguish all the materials studied. The number of polymorphic bands varied between 11 and 16 among the 56 accessions with an average of 13.8. The mean of polymorphism information content (PIC) values was 0.80, ranging from 0.45 to 0.91. Due to the complex SSR patterns in banana, it is difficult to score each band with number 1 and 0. Here, we scored each SSR pattern with an alphanumeric code instead of with pairs of 1 and 0. By arranging all of pattern numbers, we can build the fingerprint code for every banana accession.
(5) On the population level, Na=4.0, Ne=1.5404, Ho=0.3038, He=0.2775. The genetic diversity of Jiujialing population was most (Na=3.40, Ne=1.7054, Ho=0.3043, He=0.3633) and Atuoling population was the least (Na=2.20, Ne=1.4050, Ho=0.2296, He=0.2633). A low level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (Fst=0.0677) and main variations was within population (93.23%). UPGMA cluster analysis based on Nei's genetic distance divided the 7 population into two main groups.
(1)从NCBI搜索的2282条香蕉EST中,发掘出含有SSR的EST序列110条,共有122个SSR位点,检出率为5.3%。SSR位点可分为37种重复单元,平均长度为20bp,其中二、三核苷酸重复单元的SSR占主导地位,其它重复类型所占比例均不足10%,而四核苷酸重复类型最少。GA和GAA是二、三核苷酸中的优势重复类型。设计引物63对,用巴西蕉DNA初筛得到41对EST-SSR功能引物,占总引物数的65.1%。应用19对高重复性和多态性好的引物对49个香蕉品种(系)进行分析,在相似系数为0.63的水平可将49个品种按A、B基因型分为2个类群,基本与形态分类结果一致,表明EST-SSR引物可应用于香蕉品种资源分类的研究。
(2)应用SAM法从香蕉AA基因组的100个克隆序列中获得83条SSR序列,得率为83%,从香蕉BB基因组的43个克隆中得到38条SSR序列,得率为88.3%,综合得率达到84.6%；并成功设计引物62对(AA组38对,BB组24对)。经过筛选,得到AA组引物26对,BB组引物19对。
(3)利用45对Genomic-SSR和24对EST-SSR引物对26个香蕉栽培品种(系)和11个芭蕉科种属材料的遗传关系进行分析表明,EST-SSR比Genomic-SSR多态性高,但二者都能很好的揭示出香蕉群体内的遗传多样性。Genomic-SSR和EST-SSR标记在11个芭蕉科种属材料上的转移扩增率分别为80%和70.83%。对4个转移扩增位点的测序结果分析表明,不同种属间的材料扩增得到的序列与原始序列具有同源性。序列间的变异主要是由SSR位点重复次数和侧翼序列的碱基的替换、插入／缺失等变化引起。
(4)利用5对香蕉SSR引物构建了56份香蕉种质的分子身份证和指纹图谱。5对引物扩增出的多态性带为11-16,平均为13.8；引物的多态信息含量(PIC)在0.8490-0.9022之间,平均0.8727,说明我们选择的引物适合于对该批样品进行指纹标记。建立的香蕉分子指纹图谱可为在分子水平上区分香蕉种质材料和知识产权保护提供依据。
(5)阿宽蕉在居群水平上,各个居群平均等位基因数(Na)为4.0个,有效等位基因数(Ne)为1.5404个,观察杂合度(Ho)和期望杂合度(He)分别为0.3038和0.2775。九架岭居群的遗传多样性水平最高(Na=3.40,Ne=1.7054,Ho=0.3043,He=0.3633),阿驼岭居群的遗传多样性水平最低(Na=2.20,Ne=1.4050,Ho=0.2296,He=0.2633)。遗传分化系数(Fst)为0.0677,即有6.77%的遗传变异存在居群之间,93.23%的遗传变异存在于居群内。利用算术加权平均数法(UPGMA)将7个居群分成2大类,地理位置较近的聚在一起。
In the study, genomic-SSRs and EST-SSRs were developed by using selectively amplified microsatellite (SAM) analysis and searching the ESTdb of NCBI. Meanwhile, those SSR markers were evaluated in a collection of 11 related species/subspecies of Musaceae about 82 banana accessions and 7 M. itinerans populations. The main results and conclusions were as follows:
(1) Analysis of 2284 ESTs identified 110 sequences containing 122 SSRs. Among them, there were 37 motifs. The overall average length of SSRs was 20 bp. The trinucelotide repeats appeared to be the most abundant SSRs (47.6%), followed by dinucelotide repeats (33.1%), whereas the tetrnucelotide repeats were less abundant. The rich repeats AG and AGG were predominant, accounting for 75.7% and 36% in dri-and tri-nucelotide repeats respectively. A total of 63 primer pairs were designed and tested against genomic DNA of brazil. Forty-one primers could be validated as usable markers. Nineteen of these primers revealed moderate to high polymorphism information content (PIC) across 49 accessions. The polymorphic bands were ranged from 4 to 12, averagely 7.58. The mean PIC value was 0.7324, ranging from 0.3572 to 0.8744. Forty-nine banana varieties were separated into two major clusters closely corresponding with the genome composition by UPGMA analysis. The results showed that the EST-SSR markers were of great value in evaluation of banana germplasms.
(2) Eighty-three and thirty-eight microsatellite sequences were cloned and sequenced from a commercial cultivar'Gongjiao' (Musa acuminate, AA froup) and'Yejiao'(M. balbisiana, BB group) respectively, using selectively amplified microsatellite (SAM) analysis. A total of 62 microsatellite primers were designed (38 from AA group and 24 from BB group). These primers were pre-screened on'Gongjiao'and'Yejiao'. From those,26 from AA group and 19 from BB group produced clear repeatable amplification patterns and were used to all the samples.
(3) A set of 45 Genomic-SSR and 24 EST-SSR markers was identified in a collection of 22 cultivated bananas and 11 related species/subspecies. The results showed that EST-SSR is more polymorphic than Genomic-SSR. But both of them can provide accurate evaluation of genetic relationship among accessions. The ratio of the cross-species/genera amplification detected by Genomic-SSR and EST-SSR were 80% and 70.83% among 11 related wild species representing 10 different species, representative of three important genus of Musaceae family. To further demonstrate the transferability of the developed SSR loci, Sequence comparison of cross-species/genus amplicons generated by four SSR loci for 9-11 related wild species was done. In general, the amplified regions were found to be homologous to the original sequences (from which the SSRs were developed) and their comparisons across species. Sequencing of PCR products confirmed the presence of microsatellite repeats at all loci. Sequencing alleles at four loci showed that, apart from microsatellite length variation, point mutations and insertion/deletions were quite abundant in the flanking region of the alleles sequenced.
(4) To well evaluate and use the cultivars, it is necessary to identify them accurately by DNA molecular markers. A total of 56 banana accessions were investigated in this study. Five pre-selected SSR primers showed ample polymorphism and could distinguish all the materials studied. The number of polymorphic bands varied between 11 and 16 among the 56 accessions with an average of 13.8. The mean of polymorphism information content (PIC) values was 0.80, ranging from 0.45 to 0.91. Due to the complex SSR patterns in banana, it is difficult to score each band with number 1 and 0. Here, we scored each SSR pattern with an alphanumeric code instead of with pairs of 1 and 0. By arranging all of pattern numbers, we can build the fingerprint code for every banana accession.
(5) On the population level, Na=4.0, Ne=1.5404, Ho=0.3038, He=0.2775. The genetic diversity of Jiujialing population was most (Na=3.40, Ne=1.7054, Ho=0.3043, He=0.3633) and Atuoling population was the least (Na=2.20, Ne=1.4050, Ho=0.2296, He=0.2633). A low level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (Fst=0.0677) and main variations was within population (93.23%). UPGMA cluster analysis based on Nei's genetic distance divided the 7 population into two main groups.
引文
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