Transcriptomics reveals multiple resistance mechanisms against cotton leaf curl disease in a naturally immune cotton species, Gossypium arboreum

Rubab Zahra Naqvi,Brian E Scheffler,M Shahid Mukhtar,Khalid Pervaiz Akhtar,Bharat Mishra,Georg Jander,Melkamu Woldemariam,Muhammad Asif,Shahid Mansoor,Jodi A Scheffler,Lukas A Mueller,Susan Strickler,Syed Shan-E-Ali Zaidi

doi:10.1038/s41598-017-15963-9

Abstract

Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. While the widely cultivated cotton species Gossypium hirsutum is generally susceptible, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the influence of CLCuD on the G. arboreum transcriptome and the interaction of CLCuD with G. arboreum remains to be elucidated. Here we have used an RNA-Seq based study to analyze differential gene expression in G. arboreum under CLCuD infestation. G. arboreum plants were infested by graft inoculation using a CLCuD infected scion of G. hirsutum. CLCuD infested asymptomatic and symptomatic plants were analyzed with RNA-seq using an Illumina HiSeq. 2500. Data analysis revealed 1062 differentially expressed genes (DEGs) in G. arboreum. We selected 17 genes for qPCR to validate RNA-Seq data. We identified several genes involved in disease resistance and pathogen defense. Furthermore, a weighted gene co-expression network was constructed from the RNA-Seq dataset that indicated 50 hub genes, most of which are involved in transport processes and might have a role in the defense response of G. arboreum against CLCuD. This fundamental study will improve the understanding of virus-host interaction and identification of important genes involved in G. arboreum tolerance against CLCuD.

Highlights

Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton
Whitefly is the vector that transmits CLCuD in tetraploid cotton, but G. arboreum remains unaffected when infected with viruliferous whiteflies
Recent studies have revealed evidence that G. arboreum plants support CLCuD replication and its long-distance spread only if CLCuD is transmitted by graft inoculation

Summary

Introduction

Cotton leaf curl disease (CLCuD), caused by cotton leaf curl viruses (CLCuVs), is among the most devastating diseases in cotton. A weighted gene co-expression network was constructed from the RNA-Seq dataset that indicated 50 hub genes, most of which are involved in transport processes and might have a role in the defense response of G. arboreum against CLCuD This fundamental study will improve the understanding of virus-host interaction and identification of important genes involved in G. arboreum tolerance against CLCuD. Viruses causing CLCuD, collectively referred to as cotton leaf curl viruses (CLCuVs), belong to the family Geminiviridae and the genus Begomovirus, which is the most important genera of this family[9] Other members of this genus infect important crops including tomato, beans, chillies, cucurbits, mungbean and other vegetables[10,11,12]. CLCuD is among the most devastating of viral diseases, responsible for serious crop losses annually that negatively impact a country’s economy[14]

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