Tomato SNP discovery by EST mining and resequencing
Tomato SNP discovery by EST mining and resequencing
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DOI：
10.1007/s11032-005-1911-5
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发表时间：
2005-11-01
影响因子：
3.1
通讯作者：
Baldo, AM
中科院分区：
文献类型：
--
作者：
Labate, JA;Baldo, AM
许多经济上重要的作物物种在遗传多样性方面相对缺乏（例如，大豆、花生、番茄）。根据分子标记，栽培番茄内的DNA多态性估计是低的。通过对148，000多个公开的番茄表达序列标签（EST）和全长cDNA的挖掘，我们在15个番茄品系中发现了764个潜在的单核苷酸多态性（SNP）EST簇。通过对这些簇中的53个簇的两到三个系的区域进行测序，我们发现了丰富的核苷酸多态性（21个Unigenes中的62个SNP和12个indel），验证率为27.2%（EST簇中预测的103个SNP中有28个得到验证）。我们假设，5个地区与1.6-13倍的多样性相对于其他测试地区与野生亲属的基因渗入。鉴定番茄基因组中的多态性表达基因将有助于番茄的改良和种质资源的保存。
Many economically important crop species are relatively depauparate in genetic diversity (e.g., soybean, peanut, tomato). DNA polymorphism within cultivated tomato has been estimated to be low based on molecular markers. Through mining of more than 148,000 public tomato expressed sequence tags (ESTs) and full-length cDNAs, we identified 764 EST clusters with potential single nucleotide polymorphisms (SNPs) among more than 15 tomato lines. By sequencing regions from 53 of these clusters in two to three lines, we discovered a wealth of nucleotide polymorphism (62 SNPs and 12 indels in 21 Unigenes), resulting in a verification rate of 27.2% (28 of 103 SNPs predicted in EST clusters were verified). We hypothesize that five regions with 1.6-13-fold more diversity relative to other tested regions are associated with introgressions from wild relatives. Identifying polymorphic, expressed genes in the tomato genome will be useful for both tomato improvement and germplasm conservation.