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GrainGenes Reference Report: PMB-48-501

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Reference	PMB-48-501
Title	Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat
Journal	Plant Molecular Biology
Year	2002
Volume	48
Pages	501-510
Author	Kantety RV La Rota M Matthews DE Sorrells ME
Abstract	Summary: Plant genomics projects involving model species and many agriculturally important crops are resulting in a rapidly increasing database of genomic and expressed DNA sequences. The publicly available collection of expressed sequence tags (ESTs) from several grass species can be used in the analysis of both structural and functional relationships in these genomes. We analyzed over 260000 EST sequences from five different cereals for their potential use in developing simple sequence repeat (SSR) markers. The frequency of SSR-containing ESTs (SSR-ESTs) in this collection varied from 1.5% for maize to 4.7% for rice. In addition, we identified several ESTs that are related to the SSR-ESTs by BLAST analysis. The SSR-ESTs and the related sequences were clustered within each species in order to reduce the redundancy and to produce a longer consensus sequence. The consensus and singleton sequences from each species were pooled and clustered to identify cross-species matches. Overall a reduction in the redundancy by 85% was observed when the resulting consensus and singleton sequences (3569) were compared to the total number of SSR-EST and related sequences analyzed (24606). This information can be useful for the development of SSR markers that can amplify across the grass genera for comparative mapping and genetics. Functional analysis may reveal their role in plant metabolism and gene evolution
Probe	AB009307 [ Show all 6818 ]
Keyword	[ Hide all but 1 of 49 ] addition allele variation barley blast cag/ctg repeats collection comparative genomics comparative mapping crop database dinucleotide dna dna marker dna sequence est est clustering evolution expressed dna sequences expressed sequence tags frequencies functional-analysis gene genera genetic diversity genome genomics hexaploid bread wheat information linkage map maize mapping marker metabolism microsatellite model order project reduction redundancy relationships repeat rice sequence sequence tags simple sequence repeat sorghum ssr ssr marker trinucleotide

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