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United States Department of Agriculture

Agricultural Research Service

Research Project: MOLECULAR GENETIC TOOLS FOR POTATO AND FRUIT TREE IMPROVEMENT

Location: Crop Improvement & Utilization Research

Title: High throughput sequencing of small RNAs in Potato Leaves

Authors
item McCue, Kent
item Fofanov, Yuriy -

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: March 19, 2010
Publication Date: N/A

Technical Abstract: Understanding the role of small RNAs (sRNAs) in gene regulation, function and development is a rapidly evolving field. sRNAs result from transcript degradation and to regulatory micro RNA (miRNA) and small inhibitory RNA (siRNA) classes involved in gene regulation. The sRNAs from potato leaves were isolated and size selected for transcripts < 50 bp. The sRNA populations were sequenced using high-throughput next generation sequencing technology with the Genome Analyzer IIx that generates large datasets for the analysis of sRNAs. The 200 most abundant sequences from two cultivars were selected for further analysis. These were evaluated for identity to each other as well as to the database of tomato sRNAs and conserved miRNA families. The sRNAs and miRNAs unique to potato leaves were further examined for potential source/target sequences and precursor sRNA folding structures. At least 35% of sRNAs present in leaves were attributable to tRNA, rRNA or chloroplast in origin. In most cases, the longer sequences (>24) also belonged in one of these subgroups. The remaining sRNAs of 20-24 nucleotides were compared to the tomato sRNA database. 33% of these sRNAs were identical or single nucleotide polymorphisms tomato sRNA sequences. 26 sRNAs (24%) were identified as unique to potato with no homology at three mismatches or less. Several of the unique potato sequences share identity with potential mRNA targets.

Last Modified: 7/23/2014
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