Morales M, Roig E, Monforte A J, Arús P, Garcia-Mas J
Laboratori CSIC-IRTA de Genètica Molecular Vegetal, Cabrils, Barcelona, Spain.
Genome. 2004 Apr;47(2):352-60. doi: 10.1139/g03-139.
A search was performed for single-nucleotide polymorphisms (SNP) and short insertions-deletions (indels) in 34 melon (Cucumis melo L.) expressed sequence tag (EST) fragments between two distantly related melon genotypes, a group Inodorus 'Piel de sapo' market class breeding line T111 and the Korean accession PI 161375. In total, we studied 15 kb of melon sequence. The average frequency of SNPs between the two genotypes was one every 441 bp. One indel was also found every 1666 bp. Seventy-five percent of the polymorphisms were located in introns and the 3'untranslated regions. On average, there were 1.26 SNPs plus indels per amplicon. We explored three different SNP detection systems to position five of the SNPs in a melon genetic map. Three of the SNPs were mapped using cleaved amplified polymorphic sequence (CAPS) markers, one SNP was mapped using the single primer extension reaction with fluorescent-labelled dideoxynucleotides, and one indel was mapped using polyacrilamide gel electrophoresis separation. The discovery of SNPs based on ESTs and a suitable system for SNP detection has broad potential utility in melon genome mapping.
在两个亲缘关系较远的甜瓜基因型（甜瓜市场分类育种系T111‘Piel de sapo’和韩国种质PI 161375）之间的34个甜瓜（Cucumis melo L.）表达序列标签（EST）片段中搜索单核苷酸多态性（SNP）和短插入缺失（indel）。我们总共研究了15 kb的甜瓜序列。两种基因型之间SNP的平均频率为每441 bp出现一个。每1666 bp也发现一个indel。75%的多态性位于内含子和3'非翻译区。每个扩增子平均有1.26个SNP加indel。我们探索了三种不同的SNP检测系统，以便将其中五个SNP定位到甜瓜遗传图谱中。其中三个SNP使用酶切扩增多态性序列（CAPS）标记进行定位，一个SNP使用荧光标记双脱氧核苷酸的单引物延伸反应进行定位，一个indel使用聚丙烯酰胺凝胶电泳分离进行定位。基于EST发现SNP以及合适的SNP检测系统在甜瓜基因组图谱构建中具有广泛的潜在用途。
