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Abstract Detail



Genomics / Proteomics

Opitz , Elizabeth A. [1], Nepal, Madhav P. [2], Andersen , Ethan J.  [3], Benson, Benjamin V. [1].

Undergraduate Research Project on Indentification of Disease Resistance Genes in Foxtail Millet (Seteria italica; Poaceae) Genome.

Foxtail millet (Setaria italica) is the second most-widely cultivated species of millet which is a common staple food in East Asia. S. italica reference genome was published in 2012 and many important genes including disease resistance genes are yet to be identified. Disease resistance genes (R-genes) encode proteins involved in plant’s detection and response to pathogen attacks. The main objectives of this project were to use in-silico approaches to identify S. italica CNL (Coiled-Coil Nucleotide binding site Leucine rich region) group of R-genes and elucidate their evolutionary relationships.  We searched S. italica CNL genes available at Phytozome (http://www.phytozome.net/foxtailmillet.php) and 40,599 protein sequences were used to construct a local database for further in-silico analysis. We performed Hidden Markov Model (HMM) search resulting into 465 CNL gene sequences, and with domain analyses we identified 237 CNL genes in S. italica.  Model based phylogenetic analysis showed that 237 CNL genes nested into four distinct clades consistent to other plant species. Further bioinformatic analyses of gene clustering, GC content and expression profiles are underway and will be discussed in our presentation.  Identification of the disease resistance genes is vital for the foxtail millet crop improvement and the results would increase our understanding of R-gene evolution in plants.


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Related Links:
Nepal Lab at SDSU


1 - South Dakota State University, Biology and Microbiology, Brookings, SD, 57006, USA
2 - South Dakota State University, Biology And Microbiology, Northern Plain Biostress Laboratory, Brookings, SD, 57007, USA
3 - South Dakota State University, Biology and Microbiology, Brookings, 57006, SD, USA

Keywords:
Disease Resistance Genes or R-genes
genomics
Foxtail Millet
Setaria italica
CNL Genes
Bioinformatics.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Eyrie/Boise Centre
Date: Monday, July 28th, 2014
Time: 5:30 PM
Number: PGP002
Abstract ID:292
Candidate for Awards:None


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