Skip to main content
ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #343423

Research Project: Genomics and Bioinformatics Research in Agriculturally Important Organisms

Location: Genomics and Bioinformatics Research

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

Author
item ZAIDI, SYED - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item NAQVI, RUBAB - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item ASIF, MUHAMMAD - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item STRICKLER, SUSAN - Boyce Thompson Institute
item SHAKIR, SARA - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item WOLDEMARIAM, MELKAMU - Boyce Thompson Institute
item SHAFIQ, MUHAMMAD - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item KHAN, ABDUL - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item AMIN, IMRAN - National Institute Of Biotechnology And Genetic Engineering (NIBGE)
item MISHRA, BHARAT - University Of Alabama
item MUKHTAR, SHAHID - University Of Alabama
item JANDER, GEORG - Boyce Thompson Institute
item Scheffler, Brian
item Scheffler, Jodi
item MUELLER, LUKAS - Boyce Thompson Institute
item 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.