Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis

Serba, Desalegn D.; Uppalapati, Srinivasa Rao; Mukherjee, Shreyartha; Krom, Nick; Tang, Yuhong; Mysore, Kirankumar S.; Saha, Malay C.

doi:10.3835/plantgenome2014.10.0075

Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis

Journal Article · Mon Mar 16 00:00:00 EDT 2015 · The Plant Genome

DOI:https://doi.org/10.3835/plantgenome2014.10.0075· OSTI ID:1334446

Serba, Desalegn D. ^[1]; Uppalapati, Srinivasa Rao ^[2]; Mukherjee, Shreyartha ^[3]; Krom, Nick ^[3]; Tang, Yuhong ^[4]; Mysore, Kirankumar S. ^[5]; Saha, Malay C. ^[1]

Samuel Roberts Noble Foundation, Ardmore, OK (United States). Forage Improvement Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Dept. of Energy
Samuel Roberts Noble Foudnation, Ardmore, OK (United States). Plant Biology Division; Dupont Knowledge Center, Telangana (India). Dupont Pioneer
Samuel Roberts Noble Foundation, Ardmore, OK (United States). Computing Services
Samuel Roberts Noble Foudnation, Ardmore, OK (United States). Plant Biology Division; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Dept. of Energy
Samuel Roberts Noble Foudnation, Ardmore, OK (United States). Plant Biology Division

Switchgrass rust caused by Puccinia emaculata is a major limiting factor for switchgrass (Panicum virgatum L.) production, especially in monoculture. Natural populations of switchgrass displayed diverse reactions to P. emaculata when evaluated in an Ardmore, OK, field. In order to identify the differentially expressed genes during the rust infection process and the mechanisms of switchgrass rust resistance, transcriptome analysis using RNA-Seq was conducted in two pseudo-F 1 parents ('PV281' and 'NFGA472'), and three moderately resistant and three susceptible progenies selected from a three-generation, four-founder switchgrass population (K5 x A4) x (AP13 x VS16). On average, 23.5 million reads per sample (leaf tissue was collected at 0, 24, and 60 h post-inoculation (hpi)) were obtained from paired-end (2 x 100 bp) sequencing on the Illumina HiSeq2000 platform. Furthermore, mapping of the RNA-Seq reads to the switchgrass reference genome (AP13 ver. 1.1 assembly) constructed a total of 84,209 transcripts from 98,007 gene loci among all of the samples. Further analysis revealed that host defense- related genes, including the nucleotide binding site-leucinerich repeat domain containing disease resistance gene analogs, play an important role in resistance to rust infection. Rust-induced gene (RIG) transcripts inherited across generations were identified. The rust-resistant gene transcripts can be a valuable resource for developing molecular markers for rust resistance. Finally we identified the rust-resistant genotypes and gene transcripts which can expedite rust-resistant cultivar development in switchgrass.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1334446

Journal Information:: The Plant Genome, Journal Name: The Plant Genome Journal Issue: 2 Vol. 8; ISSN 1940-3372

Publisher:: Alliance of Crop, Soil, and Environmental Science SocietiesCopyright Statement

Country of Publication:: United States

Language:: English

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Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars Palmer, Nathan A.; Chowda-Reddy, R. V.; Muhle, Anthony A. PLOS ONE, Vol. 14, Issue 9 https://doi.org/10.1371/journal.pone.0222080	journal	September 2019
De novo Transcriptome Sequencing to Dissect Candidate Genes Associated with Pearl Millet-Downy Mildew (Sclerospora graminicola Sacc.) Interaction Kulkarni, Kalyani S.; Zala, Harshvardhan N.; Bosamia, Tejas C. Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.00847	journal	June 2016
Mapping of a dominant rust resistance gene revealed two R genes around the major Rust_QTL in cultivated peanut (Arachis hypogaea L.) Mondal, Suvendu; Badigannavar, Anand M. Theoretical and Applied Genetics, Vol. 131, Issue 8 https://doi.org/10.1007/s00122-018-3106-6	journal	May 2018
New insight into the species diversity and life cycles of rust fungi (Pucciniales) affecting bioenergy switchgrass (Panicum virgatum) in the Eastern and Central United States Kenaley, Shawn C.; Quan, Menchus; Aime, M. Catherine Mycological Progress, Vol. 17, Issue 11 https://doi.org/10.1007/s11557-018-1434-1	journal	October 2018
Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources Jaiswal, Sarika; Antala, Tushar J.; Mandavia, M. K. Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-21560-1	journal	February 2018
Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass Frazier, Taylor P.; Palmer, Nathan A.; Xie, Fuliang BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3201-5	journal	November 2016
Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency Serba, Desalegn D.; Uppalapati, Srinivasa Rao; Krom, Nick BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3377-8	journal	December 2016
Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.) Ayyappan, Vasudevan; Sripathi, Venkateswara R.; Kalavacharla, Venu BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6038-x	journal	August 2019
Fall armyworm (Spodoptera frugiperda Smith) feeding elicits differential defense responses in upland and lowland switchgrass Palmer, Nathan A.; Basu, Saumik; Heng-Moss, Tiffany PLOS ONE, Vol. 14, Issue 6 https://doi.org/10.1371/journal.pone.0218352	journal	June 2019

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