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Abstract Detail



Genomics / Proteomics

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

Undergraduate Research Project on Genome-wide Identification of Disease Resistance Genes in Cultivated Barley (Hordeum vulgare; Poaceae).

Cultivated barley (Hordeum vulgare), with a diploid genome of about 5.1 Gb on seven pairs of chromosomes, is the 4th most commonly cultivated cereal species. Reference genome of H. vulgare has been recently published and many important disease resistance genes are still unidentified. Proteins encoded by the disease resistance genes (R-genes) are involved in plant’s defense against pathogens. The major objectives of this project were to identify H. vulgare CNL (Coiled-Coil Nucleotide binding site Leucine rich region) group of R-genes and assess their evolutionary relationships. We explored the barley genome available at NCBI GenBank and selected 62,236 protein sequences for in-silico analyses. We performed Hidden Markov Model (HMM) search that yielded 237 CNL genes. It was  followed by domain analyses that allowed us to confirm the presence of 65 CNL R-genes in barley genome. For the species of such enormous genome size, the number of CNL genes seems much smaller compared to previously studied plant genomes. Maximum Likelihood analysis revealed that barley CNL genes were nested into four distinct clades consistent to other plant species. Analyses of the CNL gene-clustering, GC content and expression profiles are underway and we plan to discuss these results in our presentation. Identification of the barley CNL genes is essential for barley crop improvement for disease resistance and insights from our results would help us understand R-gene evolution.


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Related Links:
Nepal Lab at SDSU


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

Keywords:
Disease Resistance Genes
Barley Genome
Hordeum vulgare
CNL Genes
Barley Genomics.

Presentation Type: Poster:Posters for Topics
Session: P
Location: Eyrie/Boise Centre
Date: Monday, July 28th, 2014
Time: 5:30 PM
Number: PGP003
Abstract ID:295
Candidate for Awards:None


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