scholarly journals Mining for Single Nucleotide Polymorphisms and Insertions/Deletions in Maize Expressed Sequence Tag Data

2003 ◽  
Vol 132 (1) ◽  
pp. 84-91 ◽  
Author(s):  
Jacqueline Batley ◽  
Gary Barker ◽  
Helen O'Sullivan ◽  
Keith J. Edwards ◽  
David Edwards
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tag ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence

scholarly journals Confirming Single Nucleotide Polymorphisms from Expressed Sequence Tag Datasets Derived from Three Cattle cDNA Libraries

BMB Reports ◽  
2006 ◽  
Vol 39 (2) ◽  
pp. 183-188 ◽  
Author(s):  
Seung-Hwan Lee ◽  
Eung-Woo Park ◽  
Yong-Min Cho ◽  
Ji-Woong Lee ◽  
Hyoung-Yong Kim ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tag ◽  
Cdna Libraries ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Expressed Sequence

Single-nucleotide polymorphisms detected in expressed sequence tags of melon (Cucumis melo L.)

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 352-360 ◽  
Author(s):  
M Morales ◽  
E Roig ◽  
A J Monforte ◽  
P Arús ◽  
J Garcia-Mas
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Cucumis Melo ◽  
Expressed Sequence Tag ◽  
Primer Extension ◽  
Nucleotide Polymorphisms ◽  
Snp Detection ◽  
Single Nucleotide ◽  
Cucumis Melo L ◽  
Single Primer ◽  
Expressed Sequence

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.Key words: SNP, CAPS marker, single primer extension.

scholarly journals Sequence polymorphism from EST data in sugarcane: a fine analysis of 6-phosphogluconate dehydrogenase genes

2001 ◽  
Vol 24 (1-4) ◽  
pp. 161-167 ◽  
Author(s):  
L. Grivet ◽  
J.C. Glaszmann ◽  
P. Arruda
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Expressed Sequence Tag ◽  
Sequence Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Base Pairs ◽  
Est Database ◽  
Single Nucleotide ◽  
Clear Cut ◽  
Phosphogluconate Dehydrogenase ◽  
Expressed Sequence

This paper presents preliminary results demonstrating the use of the sugarcane expressed sequence tag (EST) database (SUCEST) to detect single nucleotide polymorphisms (SNPs) inside 6-phosphogluconate dehydrogenase genes (Pgds). Sixty-four Pgd-related EST sequences were identified and partitioned into two clear-cut sets of 14 and 50 ESTs, probably corresponding to two genes, A and B, respectively. Alignment of A sequences allowed the detection of a single SNP while alignment of B sequences permitted the detection of 39 reliable SNPs, 27 of which in the coding sequence of the gene. Thirty-eight SNPs were binucleotidic and a single one was trinucleotidic. Nine insertions/deletions from one to 72 base pairs long were also detected in the noncoding 3’ and 5’ sequences. The soundness and the consequences of those preliminary observations on sequence polymorphism in sugarcane are discussed.

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