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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #248745
Title: Analysis of Abundant sRNAs from Potato Leaves

Author
item McCue, Kent
item FOFANOV, YURIY - University Of Houston

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/6/2009
Publication Date: N/A
Citation: N/A

Interpretive Summary: Potato is the world’s number one vegetable crop. The potato is in the same plant family as the tomato pepper and eggplant. Information from the International Potato Genome Sequencing Consortium will provide a backbone of understanding for the architecture of the potato genome. Efforts are also underway on the tomato by the International Tomato Genome Sequencing Project. In combination these two genome sequencing efforts will provide the background to study the cultivated potato and discover genes and processes unique to the potato. The next step is to understand the factors that regulate the expression of the genes in the potato genome. One emerging aspect of gene regulation is the recent discover of small RNAs (sRNA). We are examining the sRNA of the potato using an Ilumina Genome Analyzer Classic platform to take an initial look at potato sRNA.

Technical Abstract: The study of sRNAs (sRNAs) is a rapidly evolving field seeking to understand their role in gene regulation, function and development. Combining next generation sequencing with the analysis of sRNAs allows the generation of large data sets to explore abundant sRNAs resulting from transcript degradation as well as potential regulatory micro RNA (miRNA) and small inhibitory RNAs (siRNA) involved in gene regulation. RNA from potato leaves was isolated and size selected for transcripts < 50 bp. The sRNA population was sequenced using high throughput sequencing using the Genome Analyzer IIx. The 200 most abundant sequences were evaluated for identity to each other as well as to the database of tomato sRNAs and conserved miRNA families. Small RNAs 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 (>22) 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 SNPs of known tomato sRNA sequences. 26 sRNAs (24%) were identified as unique to potato with no homology at three mismatches or less. Several unique potato sequences share identity with potential mRNA targets.