Whole genome resequencing deciphers new insight into genetic diversity and signatures of resistance in cultivated cotton Gossypium hirsutum

Authors: HUSSAIN, ATHAR - National Institute Of Biotechnology And Genetic Engineering (NIBGE); FAROOQ, MUHAMMAD - National Institute Of Biotechnology And Genetic Engineering (NIBGE); NAQVI, RUBAB - National Institute Of Biotechnology And Genetic Engineering (NIBGE); ASLAM, MUHAMMED - National Institute Of Biotechnology And Genetic Engineering (NIBGE); SIDDIQUI, HAMID - National Institute Of Biotechnology And Genetic Engineering (NIBGE); AMIN, IMRAN - National Institute Of Biotechnology And Genetic Engineering (NIBGE); LIU, CHENGCHENG - Beijing Genome Institute; LIU, XIN - Beijing Genome Institute; Scheffler, Jodi; ASIF, MUHAMMED - National Institute Of Biotechnology And Genetic Engineering (NIBGE); MANSOOR, SHAHID - National Institute Of Biotechnology And Genetic Engineering (NIBGE)

Submitted to: Molecular Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/7/2022
Publication Date: 7/1/2022
Citation: Hussain, A., Farooq, M., Naqvi, R.Z., Aslam, M.Q., Siddiqui, H.A., Amin, I., Liu, C., Liu, X., Scheffler, J., Asif, M., Mansoor, S. 2022. Whole genome resequencing deciphers new insight into genetic diversity and signatures of resistance in cultivated cotton Gossypium hirsutum. Molecular Biotechnology. 65:34-51. https://doi.org/10.1007/s12033-022-00527-8.
DOI: https://doi.org/10.1007/s12033-022-00527-8

Interpretive Summary: Cotton leaf curl disease is a serious disease caused by a virus transmitted via whiteflies. It is widespread in central Asia and is spreading globally, threatening U.S. cotton production. In order to develop better methods to mitigate the effects of this disease, it is necessary to understand the underlying mechanisms used by the virus to infect the plant and by the plant to resist being infected by the virus or preventing its spread within the plant after infection. The first step was to identify cotton lines that were able to resist the virus and those that were susceptible to the virus. These lines were sequenced and compared to detect differences between resistant and susceptible lines. Using existing databases, genes present in the locations where differences were detected were identified. Various biotechnology methods were used to identify which genes were functioning during infection of a plant with the virus. These genes may allow the plant to resist the virus and will be studied further with the ultimate goal of modifying the expression of these genes in susceptible cotton lines to make them able to resist the virus.

Technical Abstract: Cotton is an important crop that produces fiber and cottonseed oil for the textile and oil industry. However, multiple biotic stresses are limiting its yield. In this study, we sequenced the Mac7 line, a G. hirsutum source of resistance against several biotic stresses. By aligning it with the TM-1 reference genome, 4,705,110 SNPs and 1,287,199 InDels were discovered in the Mac7 genome. The identified variants were also categorized into different impact levels. Gene ontology and metabolic pathways enrichment of variant associated genes indicated their role in ATP and ADP binding, secondary metabolite synthesis and plant-pathogen interactions which are involved in plant defense mechanisms. Furthermore, the integration of expression profiling of differential genes in TM-1, Mac7 and NIAB-Karishma (a susceptible accession) under biotic and abiotic stresses also identified possible roles for individual genes in resistant and susceptible accessions. Real time quantitative expression analysis of resistance genes under cotton leaf curl disease pressure also demonstrated differential expression patterns in G. arboreum, Mac7, Coker 312 (susceptible) and NIAB-Karishma. The expression levels of these genes in resistant accessions were higher than susceptible accessions. The current resequencing results also provide data for identifying DNA markers for marker-assisted selection of Mac7 derived cotton lines resistant to biotic stresses.