Assessment of Banana Streak MY Virus-Based Infectious Clone Vectors in Musa Ssp. by Mary Nyambeki Onsarigo B. Ed. (Science)
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Assessment of banana streak MY virus-based infectious clone vectors in Musa ssp. by Mary Nyambeki Onsarigo B. Ed. (Science) 1996 M. Sc. (Agricultural Biotechnology) 2008 M. Sc. (Bioinformatics) 2010 Centre for Tropical Crops and Biocommodities Science and Engineering Faculty A thesis submitted for the degree of Doctor of Philosophy Queensland University of Technology 2017 Keywords Genotype, GFP, endogenous virus sequences, resistance © 2017 Mary Onsarigo Page i Abstract Banana streak disease, caused by a complex of different banana streak viruses (BSVs), occurs in all banana-producing countries. BSVs are genetically very diverse and can exist both as episomal forms or integrated into the host genome and both can be infectious to banana. Several field studies have assessed the infectivity of one or more BSV species on different banana genotypes with significant differences reported in virus incidence and symptom expression between and within genotypes. These studies used a severity index, based on symptom expression, to determine the resistance/susceptibility levels of the genotypes. Because of the great genetic variability amongst BSV species, symptoms of banana streak disease may vary widely and may be influenced by the cultivar and/or environmental conditions. Also this system of screening does not reflect the level of viral DNA accumulation (i.e. the viral load) within infected plants. Furthermore, there are no reports on the level of BSV DNA accumulation in different banana cultivars or Musa sp. Researchers at QUT had previously developed an infectious clone of one BSV species, Banana streak MY virus (BSMYV). Therefore, this study aimed to investigate the infectivity of the BSMYV infectious clone in a broad range of Musa genotypes and cultivars. Further to this, several modified infectious clones were assessed for their infectivity, and ability to either express a heterologous green fluorescent protein (GFP) reporter gene, or to illicit gene silencing. This PhD study addressed the use of an infectious clone of BSMYV (BSMYV-IC) to accurately screen diverse banana genotypes for resistance to BSV. A total of 24 banana accessions comprising of six different genomic groups (AAA, AA, BB, AAB, ABB, AT) were propagated and indexed for any episomal infection, or activation of endogenous BSMYV (eBSMYV) with all plants testing negative. Plants of all accessions were mechanically inoculated with the BSMYV-IC and monitored for development of disease symptoms for a period of 6 to 12 months. Banana streak disease infection was confirmed by polymerase chain reaction (PCR) and rolling-circle amplification (RCA) for A-only or B-genome bananas, respectively. Accumulation of BSMYV DNA in the different banana genotypes was quantified using quantitative PCR (qPCR) starting from the initial leaf with symptoms to the termination of the experiment. Also, a series of ten modified BSMYV infectious clones were evaluated for infectivity, expression and silencing ability in banana plants. © 2017 Mary Onsarigo Page ii Virus indexing of all plants of different banana accessions by PCR and RCA using BSYMV- specific primers confirmed that all propagated plants were free of virus infection. Following inoculation of plants with BSYMV, 22 out of the 24 accessions assessed were susceptible to BSYMV based on symptom expression and molecular diagnosis using either PCR or RCA. The susceptible accessions comprised of the AAA, AA, AAB, ABB and AT genome types. Interestingly, only two diploid BB accessions M. balbisiana and Butuhan did not express BSMYV symptoms and tested negative for infection by RCA. The BSMYV-IC was shown to be highly infectious, with up to 100% infectivity in the 22 Musa accessions confirmed to be infected. The effect of virus infection on growth was evaluated based on plant height and the rate of leaf emergence. There was a significant reduction in plant height in 8 accessions including Akondro Mainty (AA), Ma. ssp. zebrina (AA), Pahang (AA), Yesing (AAB), Pacific Plantain (AAB), Ma. ssp. banksii (AA), Calcutta 4 (AA) and Pisang Bangkahulu (AA), and rapid death of plants in accession Asupina (AT). There was no significant difference in the rate of leaf emergence between infected and non-infected plants in all the accessions tested In the current study, symptom variability was considerable with different Musa genotypes expressing distinct symptoms. Quantification of the levels of virus DNA showed that virus accumulation differs between genotypes, but also within plants of the same accession, and that severity scores do not correlate well with the viral load as measured using qPCR. Modified vectors with either ORF1 or ORF2 deleted were not infectious and the addition of a GFP ORF into two sites in the genome did not result in expression of this heterologous sequence from the constructs used in this study. Interestingly, two constructs with small inserts, initially designed for the purpose of gene silencing, were found to retain infectivity and maintain a heterologous sequence up to 110 nt. These studies confirm that BSMYV is infective in a broad range of Musa genotypes and cultivars but that further work is required to develop suitable vectors for either gene expression or gene silencing studies in banana © 2017 Mary Onsarigo Page iii Table of Contents Keywords .................................................................................................................................................. i Abstract ................................................................................................................................................... ii Table of Contents ................................................................................................................................... iv List of Figures ........................................................................................................................................ vii List of Tables ........................................................................................................................................... x List of Abbreviations .............................................................................................................................. xi Statement of Original Authorship ......................................................................................................... xv Acknowledgments ................................................................................................................................ xvi 1 CHAPTER 1: LITERATURE REVIEW ................................................................................................................ 1 1.1 Significance of banana ................................................................................................................. 1 1.2 Banana taxonomy ........................................................................................................................ 1 1.3 Banana hybridisation and diversity ............................................................................................. 2 1.1 Status of the wild diploid banana ................................................................................................... 4 1.2 Edible diploid (AA) and triploid (AAA) banana ................................................................................ 6 1.3 Intraspecific classification of banana and plantains ........................................................................ 6 1.4 Constraints to banana production ............................................................................................... 7 1.5 Plant DNA viruses ........................................................................................................................ 8 1.6 Badnaviruses ................................................................................................................................ 9 1.7 Banana streak viruses .................................................................................................................. 9 1.7.1 Transmission of BSV ....................................................................................................... 10 1.7.2 Endogenous BSV sequences in the host genome ........................................................... 12 1.7.3 BSV diagnostic tests ........................................................................................................ 13 1.7.4 Screening of banana genotypes for BSV resistance ....................................................... 14 1.7.5 Banana streak disease and effects on Musa .................................................................. 15 1.7.6 Expression of BSV symptoms by different banana genotypes ....................................... 16 1.8 Plant-viral interaction outcomes ............................................................................................... 17 1.8.1 Susceptibility .................................................................................................................. 21 1.8.2 Tolerance ........................................................................................................................ 21 1.8.3 Resistance ....................................................................................................................... 21 1.1 RNA silencing as an antiviral defence mechanism by plants ..................................................... 22 1.2 Infectious clones of plant viruses .............................................................................................