A study of transcriptome in leaf rust infected bread wheat involving seedling resistance gene Lr28
Chanchal Sharma A B * , Gautam Saripalli A * , Santosh Kumar C , Tinku Gautam A , Avneesh Kumar A D , Sushma Rani E , Neelu Jain E , Pramod Prasad F , Saurabh Raghuvanshi C , Mukesh Jain G , J. B. Sharma E , K. V. Prabhu E , P. K. Sharma A , H. S. Balyan A and P. K. Gupta A H
+ Author Affiliations
- Author Affiliations
A Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
B Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan City, Gyeongbook, 38453, South Korea.
C Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
D Department of Botany, Akal University, Bhatinda, Punjab, 151302, India.
E Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India.
F Regional Station, Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India.
G School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
H Corresponding author. Email: pkgupta36@gmail.com
Functional Plant Biology 45(10) 1046-1064 https://doi.org/10.1071/FP17326
Submitted: 18 November 2017 Accepted: 9 April 2018 Published: 11 May 2018
Abstract
Leaf rust disease causes severe yield losses in wheat throughout the world. During the present study, high-throughput RNA-Seq analysis was used to gain insights into the role of Lr28 gene in imparting seedling leaf rust resistance in wheat. Differential expression analysis was conducted using a pair of near-isogenic lines (NILs) (HD 2329 and HD 2329 + Lr28) at early (0 h before inoculation (hbi), 24 and 48 h after inoculation (hai)) and late stages (72, 96 and 168 hai) after inoculation with a virulent pathotype of pathogen Puccinia triticina. Expression of a large number of genes was found to be affected due to the presence/absence of Lr28. Gene ontology analysis of the differentially expressed transcripts suggested enrichment of transcripts involved in carbohydrate and amino acid metabolism, oxidative stress and hormone metabolism, in resistant and/or susceptible NILs. Genes encoding receptor like kinases (RLKs) (including ATP binding; serine threonine kinases) and other kinases were the most abundant class of genes, whose expression was affected. Genes involved in reactive oxygen species (ROS) homeostasis and several genes encoding transcription factors (TFs) (most abundant being WRKY TFs) were also identified along with some ncRNAs and histone variants. Quantitative real-time PCR was also used for validation of 39 representative selected genes. In the long term, the present study should prove useful in developing leaf rust resistant wheat cultivars through molecular breeding.
Additional keywords: defence, Lr28, Puccinia triticina, qRT–PCR, RNA-Seq, transcriptome, wheat.
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