eprintid: 11269
rev_number: 13
eprint_status: archive
userid: 1305
dir: disk0/00/01/12/69
datestamp: 2019-08-28 06:36:48
lastmod: 2019-12-12 08:17:56
status_changed: 2019-08-28 06:36:48
type: article
metadata_visibility: show
creators_name: Garg, V
creators_name: Khan, A W
creators_name: Kudapa, H
creators_name: Kale, S M
creators_name: Chitikineni, A
creators_name: Qiwei, S
creators_name: Sharma, M
creators_name: Li, C
creators_name: Zhang, B
creators_name: Xin, L
creators_name: Kavi Kishor, P B
creators_name: Varshney, R K
creators_gender: Female
creators_gender: Female
creators_gender: Female
creators_gender: Female
icrisatcreators_name: Garg, V
icrisatcreators_name: Khan, A W
icrisatcreators_name: Kudapa, H
icrisatcreators_name: Kale, S M
icrisatcreators_name: Chitikineni, A
icrisatcreators_name: Sharma, M
icrisatcreators_name: Varshney, R K
affiliation: ICRISAT (Patancheru)
affiliation: Department of Genetics, Osmania University (Hyderabad)
affiliation: BGI-Shenzhen (Shenzhen)
affiliation: Department of Biology, East Carolina University (Greenville)
country: India
country: China
country: USA
title: Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea
ispublished: pub
subjects: Bio
subjects: s1.1
subjects: s2.13
divisions: CRPS2
divisions: CRPS3
crps: CG1
full_text_status: public
keywords: miRNA, differentially expressed genes, fungal stress, mRNA targets, Ascochyta blight resistance, miRNA-mRNA, cleavage, Chickpea, Ascochyta blight, biotic stress
note: Vanika Garg acknowledges the award of Research Fellowship
from Department of Science and Technology, Government of
India. The authors are thankful to Mr. Jaipal Goud for technical
assistance. Authors are also grateful to the Bill & Melinda Gates
Foundation for partially supporting the study. This work has been
undertaken as part of the CGIAR Research Program on Grain
Legumes & Dryland Cereals. ICRISAT is a member of CGIAR
Consortium.
abstract: Ascochyta blight (AB) is one of the major biotic stresses known to limit the chickpea production worldwide. To dissect the complex mechanisms of AB resistance in chickpea, three approaches,namely, transcriptome, small RNA and degradome sequencing were used. The transcriptome
sequencing of 20 samples including two resistant genotypes, two susceptible genotypes and one introgression line under control and stress conditions at two time points (3rd and 7th day post inoculation) identified a total of 6767 differentially expressed genes (DEGs). These DEGs were
mainly related to pathogenesis-related proteins, disease resistance genes like NBS-LRR, cell wall biosynthesis and various secondary metabolite synthesis genes. The small RNA sequencing of the samples resulted in the identification of 651 miRNAs which included 478 known and 173 novel
miRNAs. A total of 297 miRNAs were differentially expressed between different genotypes, conditions and time points. Using degradome sequencing and in silico approaches, 2131 targets were predicted for 629 miRNAs. The combined analysis of both small RNA and transcriptome
datasets identified 12 miRNA-mRNA interaction pairs that exhibited contrasting expression in resistant and susceptible genotypes and also, a subset of genes that might be posttranscriptionally silenced during AB infection. The comprehensive integrated analysis in the study provides better insights into the transcriptome dynamics and regulatory network components
associated with AB stress in chickpea and, also offers candidate genes for chickpea improvement.
date: 2019-05
date_type: published
publication: Plant Biotechnology Journal (TSI)
volume: 17
number: 5
publisher: Wiley
pagerange: 914-931
id_number: 10.1111/pbi.13026
refereed: TRUE
issn: 1467-7644
official_url: https://doi.org/10.1111/pbi.13026
related_url_url: https://scholar.google.co.in/scholar?hl=en&as_sdt=0%2C5&q=Integrated+transcriptome%2C+small+RNA+and+degradome+sequencing+approaches+provide+insights+into+Ascochyta+blight+resistance+in+chickpea&btnG=
related_url_type: pub
funders: Bill & Melinda Gates Foundation
citation:   Garg, V and Khan, A W and Kudapa, H and Kale, S M and Chitikineni, A and Qiwei, S and Sharma, M and Li, C and Zhang, B and Xin, L and Kavi Kishor, P B and Varshney, R K  (2019) Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea.  Plant Biotechnology Journal (TSI), 17 (5).  pp. 914-931.  ISSN 1467-7644     
document_url: http://oar.icrisat.org/11269/1/pbi.13026.pdf