Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)
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DOI：
10.1007/s00122-002-1031-0
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发表时间：
2003-02-01
影响因子：
5.4
通讯作者：
Graner, A
中科院分区：
文献类型：
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作者：
Thiel, T;Michalek, W;Graner, A
开发了一种软件工具，用于识别大麦（Hordeum vulgare L.）EST（表示序列标签）数据库中的简单序列重复序列（SSR），该数据库包含24,595个序列。总共确定了1,856个含SSR的序列。 Trimeric SSR重复基序似乎是最丰富的类型。 SSR基因座侧面的311个引物对的子集已用于筛选六种大麦品种中的多态性，是三个地图种群的父母。结果，将76个EST衍生的SSR标记物集成到大麦遗传共识图中。观察到由二聚体构建至四聚体单元的SSR观察到的多态性与重复次数之间的相关性。 3'-最终产生的多态性SSR（64％）比5'-ests更高。估计的PIC（多态性信息内容）值为0.45 +/- 0.03。大约80％的SSR标记物在Hordeum Bulbosum中放大了DNA片段，其次是黑麦，小麦（大约60％）和大米（40％）。一个包括114个等位基因的38个EST衍生的SSR标志物的子集用于研究54种大麦品种的遗传多样性。根据以前的基于RFLP的研究，春季和冬季品种以及两行和六行的Barleys，在PCOA分析时形成了单独的进化枝。 The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic 多样性。
A software tool was developed for the identification of simple sequence repeats (SSRs) in a barley (Hordeum vulgare L.) EST (expressed sequence tag) database comprising 24,595 sequences. In total, 1,856 SSR-containing sequences were identified. Trimeric SSR repeat motifs appeared to be the most abundant type. A subset of 311 primer pairs flanking SSR loci have been used for screening polymorphisms among six barley cultivars, being parents of three mapping populations. As a result, 76 EST-derived SSR-markers were integrated into a barley genetic consensus map. A correlation between polymorphism and the number of repeats was observed for SSRs built of dimeric up to tetrameric units. 3'-ESTs yielded a higher portion of polymorphic SSRs (64%) than 5'-ESTs did. The estimated PIC (polymorphic information content) value was 0.45 +/- 0.03. Approximately 80% of the SSR-markers amplified DNA fragments in Hordeum bulbosum, followed by rye, wheat (both about 60%) and rice (40%). A subset of 38 EST-derived SSR-markers comprising 114 alleles were used to investigate genetic diversity among 54 barley cultivars. In accordance with a previous, RFLP-based, study, spring and winter cultivars, as well as two- and six-rowed barleys, formed separate clades upon PCoA analysis. The results show that: (1) with the software tool developed, EST databases can be efficiently exploited for the development of cDNA-SSRs, (2) EST-derived SSRs are significantly less polymorphic than those derived from genomic regions, (3) a considerable portion of the developed SSRs can be transferred to related species, and (4) compared to RFLP-markers, cDNA-SSRs yield similar patterns of genetic diversity.