In silico analysis of disease resistance and defence-related genes for a major sheath blight qShb 9-2 QTL in rice

Shyama Sundari Devi Chanthran, Boon Huat Cheah, Kalaivani K. Nadarajah

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Aims: Sheath blight disease (Rhizoctonia solani) is an important rice disease that causes heavy yield losses in rice annually. To date, no rice variety has been found to be completely resistant to this disease. The most desirable approach for the management of sheath blight disease is to introgress genes with major and durable resistance into the rice genome. Therefore, this study aims to identify disease resistance and defence genes within qShb 9-2, a major QTL found within moderately resistant rice population via in silico analysis. Methodology and results: The sequences of tightly linked markers of qShb 9-2 from GRAMENE database was used to derive the 10.24 Mbp QTL region that contains 1581 genes according to MSU Rice Genome Annotation Project database. BLAST results showed that 11.4% of these genes were transposable elements which may be involved in gene duplication. Through Blast2GO, fifty-four (2.9%) defence-related genes were annotated within this QTL and can be classified into 5 major defence mechanisms. Further, fifty (2.7%) disease resistance genes were identified in qShb 9-2 based on the presence of NB-ARC, LRR-receptor kinase, Ser/Thr protein kinase and protein kinase domains. Lastly, directed acyclic graphs showing the interaction between all the disease resistance and defence-related genes were generated. Conclusion, significance and impact of study: The presence of these genes indicates that qShb 9-2 region may contribute towards the defence against sheath blight disease. By deciphering the gene landscape within the QTL, it may be possible to further fine map the QTL into a smaller region for QTL pyramiding in breeding programmes. The resistance and defence genes are also a source for genetic engineering studies and a good source for marker development.

Original languageEnglish
Pages (from-to)534-546
Number of pages13
JournalMalaysian Journal of Microbiology
Volume14
Issue numberSpecialissue6
DOIs
Publication statusPublished - 1 Jan 2018

Fingerprint

Disease Resistance
Computer Simulation
Genes
Protein Kinases
Beriberi
Oryza
Genome
Databases
Rhizoctonia
AIDS-Related Complex
DNA Transposable Elements
Gene Duplication
Genetic Engineering
Breeding
Phosphotransferases

Keywords

  • Defencerelated genes
  • Disease resistance genes
  • Quantitative trait loci
  • Rhizoctonia solani Kühn
  • Sheath blight disease

ASJC Scopus subject areas

  • Microbiology (medical)
  • Infectious Diseases

Cite this

In silico analysis of disease resistance and defence-related genes for a major sheath blight qShb 9-2 QTL in rice. / Devi Chanthran, Shyama Sundari; Cheah, Boon Huat; K. Nadarajah, Kalaivani.

In: Malaysian Journal of Microbiology, Vol. 14, No. Specialissue6, 01.01.2018, p. 534-546.

Research output: Contribution to journalArticle

@article{349977db54834ef0a5c556c3996cc70b,
title = "In silico analysis of disease resistance and defence-related genes for a major sheath blight qShb 9-2 QTL in rice",
abstract = "Aims: Sheath blight disease (Rhizoctonia solani) is an important rice disease that causes heavy yield losses in rice annually. To date, no rice variety has been found to be completely resistant to this disease. The most desirable approach for the management of sheath blight disease is to introgress genes with major and durable resistance into the rice genome. Therefore, this study aims to identify disease resistance and defence genes within qShb 9-2, a major QTL found within moderately resistant rice population via in silico analysis. Methodology and results: The sequences of tightly linked markers of qShb 9-2 from GRAMENE database was used to derive the 10.24 Mbp QTL region that contains 1581 genes according to MSU Rice Genome Annotation Project database. BLAST results showed that 11.4{\%} of these genes were transposable elements which may be involved in gene duplication. Through Blast2GO, fifty-four (2.9{\%}) defence-related genes were annotated within this QTL and can be classified into 5 major defence mechanisms. Further, fifty (2.7{\%}) disease resistance genes were identified in qShb 9-2 based on the presence of NB-ARC, LRR-receptor kinase, Ser/Thr protein kinase and protein kinase domains. Lastly, directed acyclic graphs showing the interaction between all the disease resistance and defence-related genes were generated. Conclusion, significance and impact of study: The presence of these genes indicates that qShb 9-2 region may contribute towards the defence against sheath blight disease. By deciphering the gene landscape within the QTL, it may be possible to further fine map the QTL into a smaller region for QTL pyramiding in breeding programmes. The resistance and defence genes are also a source for genetic engineering studies and a good source for marker development.",
keywords = "Defencerelated genes, Disease resistance genes, Quantitative trait loci, Rhizoctonia solani K{\"u}hn, Sheath blight disease",
author = "{Devi Chanthran}, {Shyama Sundari} and Cheah, {Boon Huat} and {K. Nadarajah}, Kalaivani",
year = "2018",
month = "1",
day = "1",
doi = "10.21161/mjm.1461812",
language = "English",
volume = "14",
pages = "534--546",
journal = "Malaysian Journal of Microbiology",
issn = "1823-8262",
publisher = "Malaysian Society for Microbiology",
number = "Specialissue6",

}

TY - JOUR

T1 - In silico analysis of disease resistance and defence-related genes for a major sheath blight qShb 9-2 QTL in rice

AU - Devi Chanthran, Shyama Sundari

AU - Cheah, Boon Huat

AU - K. Nadarajah, Kalaivani

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Aims: Sheath blight disease (Rhizoctonia solani) is an important rice disease that causes heavy yield losses in rice annually. To date, no rice variety has been found to be completely resistant to this disease. The most desirable approach for the management of sheath blight disease is to introgress genes with major and durable resistance into the rice genome. Therefore, this study aims to identify disease resistance and defence genes within qShb 9-2, a major QTL found within moderately resistant rice population via in silico analysis. Methodology and results: The sequences of tightly linked markers of qShb 9-2 from GRAMENE database was used to derive the 10.24 Mbp QTL region that contains 1581 genes according to MSU Rice Genome Annotation Project database. BLAST results showed that 11.4% of these genes were transposable elements which may be involved in gene duplication. Through Blast2GO, fifty-four (2.9%) defence-related genes were annotated within this QTL and can be classified into 5 major defence mechanisms. Further, fifty (2.7%) disease resistance genes were identified in qShb 9-2 based on the presence of NB-ARC, LRR-receptor kinase, Ser/Thr protein kinase and protein kinase domains. Lastly, directed acyclic graphs showing the interaction between all the disease resistance and defence-related genes were generated. Conclusion, significance and impact of study: The presence of these genes indicates that qShb 9-2 region may contribute towards the defence against sheath blight disease. By deciphering the gene landscape within the QTL, it may be possible to further fine map the QTL into a smaller region for QTL pyramiding in breeding programmes. The resistance and defence genes are also a source for genetic engineering studies and a good source for marker development.

AB - Aims: Sheath blight disease (Rhizoctonia solani) is an important rice disease that causes heavy yield losses in rice annually. To date, no rice variety has been found to be completely resistant to this disease. The most desirable approach for the management of sheath blight disease is to introgress genes with major and durable resistance into the rice genome. Therefore, this study aims to identify disease resistance and defence genes within qShb 9-2, a major QTL found within moderately resistant rice population via in silico analysis. Methodology and results: The sequences of tightly linked markers of qShb 9-2 from GRAMENE database was used to derive the 10.24 Mbp QTL region that contains 1581 genes according to MSU Rice Genome Annotation Project database. BLAST results showed that 11.4% of these genes were transposable elements which may be involved in gene duplication. Through Blast2GO, fifty-four (2.9%) defence-related genes were annotated within this QTL and can be classified into 5 major defence mechanisms. Further, fifty (2.7%) disease resistance genes were identified in qShb 9-2 based on the presence of NB-ARC, LRR-receptor kinase, Ser/Thr protein kinase and protein kinase domains. Lastly, directed acyclic graphs showing the interaction between all the disease resistance and defence-related genes were generated. Conclusion, significance and impact of study: The presence of these genes indicates that qShb 9-2 region may contribute towards the defence against sheath blight disease. By deciphering the gene landscape within the QTL, it may be possible to further fine map the QTL into a smaller region for QTL pyramiding in breeding programmes. The resistance and defence genes are also a source for genetic engineering studies and a good source for marker development.

KW - Defencerelated genes

KW - Disease resistance genes

KW - Quantitative trait loci

KW - Rhizoctonia solani Kühn

KW - Sheath blight disease

UR - http://www.scopus.com/inward/record.url?scp=85059442541&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85059442541&partnerID=8YFLogxK

U2 - 10.21161/mjm.1461812

DO - 10.21161/mjm.1461812

M3 - Article

AN - SCOPUS:85059442541

VL - 14

SP - 534

EP - 546

JO - Malaysian Journal of Microbiology

JF - Malaysian Journal of Microbiology

SN - 1823-8262

IS - Specialissue6

ER -