Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum)

Authors: ZAIDI, SYED - NATIONAL INSTITUTE OF BIOTECHNOLOGY AND GENETIC ENGINEERING (NIBGE); NAQVI, RUBAB - NATIONAL INSTITUTE OF BIOTECHNOLOGY AND GENETIC ENGINEERING (NIBGE); ASIF, MUHAMMAD - NATIONAL INSTITUTE OF BIOTECHNOLOGY AND GENETIC ENGINEERING (NIBGE); STRICKLER, SUSAN - BOYCE THOMPSON INSTITUTE; SHAKIR, SARA - NATIONAL INSTITUTE OF BIOTECHNOLOGY AND GENETIC ENGINEERING (NIBGE); WOLDEMARIAM, MELKAMU - BOYCE THOMPSON INSTITUTE; SHAFIQ, MUHAMMAD - NATIONAL INSTITUTE OF BIOTECHNOLOGY AND GENETIC ENGINEERING (NIBGE); KHAN, ABDUL - NATIONAL INSTITUTE OF BIOTECHNOLOGY AND GENETIC ENGINEERING (NIBGE); AMIN, IMRAN - NATIONAL INSTITUTE OF BIOTECHNOLOGY AND GENETIC ENGINEERING (NIBGE); MISHRA, BHARAT - UNIVERSITY OF ALABAMA; MUKHTAR, SHAHID - UNIVERSITY OF ALABAMA; JANDER, GEORG - BOYCE THOMPSON INSTITUTE; Scheffler, Brian; Scheffler, Jodi; MUELLER, LUKAS - BOYCE THOMPSON INSTITUTE; MANSOOR, SHAHID - NATIONAL INSTITUTE OF BIOTECHNOLOGY AND GENETIC ENGINEERING (NIBGE)

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/15/2019
Publication Date: 8/26/2019
Citation: Zaidi, S., Naqvi, R., Asif, M., Strickler, S., Shakir, S., Woldemariam, M., Shafiq, M., Khan, A.M., Amin, I., Mishra, B., Mukhtar, S., Jander, G., Scheffler, B.E., Scheffler, J.A., Mueller, L.A., Mansoor, S. 2019. Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum). Plant Biotechnology Journal. Volume 18, Issue 3.
DOI: https://doi.org/10.1111/pbi.13236

Interpretive Summary: Cotton production is severely affected by cotton leaf curl virus disease (CLCuD) in the Indian subcontinent. Local cultivated cotton (Gossypium hirsutum) is either highly susceptible or shows a very low level of tolerance to CLCuD. This study screened exotic germplasm and the accession Mac7 was identified as CLCuD resistant in field trials over four consecutive years from 2013-2016. Illumina sequencing and qPCR results indicated that while begomoviruses and alphasatellites were maintained by Mac7, the pathogenicity determinant betasatellite was absent in this source of resistance against CLCuD. The transcriptome of Mac7 was then sequenced and analyzed. After confirmation for high quality and qPCR validation, RNA-seq data was analyzed for co-expression networks, gene ontology enrichment, pathway analysis and regulation of geminivirus/betasatellite interacting genes. The co-expression network analysis identified nine novel modules and degree distribution revealed 52 hubs with =25 connections within the co-expression network. Gene ontology analysis of these highly connected hubs indicated regulation of pathways involved in response to auxin stimulus and cellular localization. Genes involved in plant defense like heat shock proteins, pathogenesis related PR1, and hypersensitive responsive genes are differentially regulated in Mac7. Begomovirus infection inducing ubiquitin activating enzyme UBC3, transcription factor NAC1, ring finger protein RPK, NSP interacting GTPase NIG and shaggy-related kinase SK are downregulated while begomovirus infection suppressing plant receptor-like kinases (RLKs), ribosomal protein RPL10 and S-adenosyl homocysteine hydrolase SAHH are upregulated. Based on these analyses, we predicted a possible CLCuD resistance mechanism in Mac7. These results have important implications for developing durable resistance against CLCuD.

Technical Abstract: Cotton production is severely affected by cotton leaf curl virus disease (CLCuD) in the Indian subcontinent. Local cultivated cotton (Gossypium hirsutum) is either highly susceptible or shows a very low level of tolerance to CLCuD. This study screened exotic germplasm and the accession Mac7 was identified as CLCuD resistant in field trials over four consecutive years from 2013-2016. Illumina sequencing and qPCR results indicated that while begomoviruses and alphasatellites were maintained by Mac7, the pathogenicity determinant betasatellite was absent in this source of resistance against CLCuD. The transcriptome of Mac7 was then sequenced and analyzed. After confirmation for high quality and qPCR validation, RNA-seq data was analyzed for co-expression networks, gene ontology enrichment, pathway analysis and regulation of geminivirus/betasatellite interacting genes. The co-expression network analysis identified nine novel modules and degree distribution revealed 52 hubs with =25 connections within the co-expression network. Gene ontology analysis of these highly connected hubs indicated regulation of pathways involved in response to auxin stimulus and cellular localization. Genes involved in plant defense like heat shock proteins, pathogenesis related PR1, and hypersensitive responsive genes are differentially regulated in Mac7. Begomovirus infection inducing ubiquitin activating enzyme UBC3, transcription factor NAC1, ring finger protein RPK, NSP interacting GTPase NIG and shaggy-related kinase SK are downregulated while begomovirus infection suppressing plant receptor-like kinases (RLKs), ribosomal protein RPL10 and S-adenosyl homocysteine hydrolase SAHH are upregulated. Based on these analyses, we predicted a possible CLCuD resistance mechanism in Mac7. These results have important implications for developing durable resistance against CLCuD.