Viruses of banana in East Africa

摘要: Bananas are one of the world's most important food crops, providing sustenance and income for millions people in developing countries supporting large export industries. Viruses considered major constraints to banana production, germplasm multiplication exchange, genetic improvement through traditional breeding. In Africa, two virus diseases bunchy top, caused by Banana top (BBTV), streak disease, (BSV). BBTV is a serious production constraint number within/bordering East such as Burundi, Democratic Republic Congo, Malawi, Mozambique, Rwanda Zambia, but not present Kenya, Tanzania Uganda. Additionally, epidemics disease occurring Kenya Uganda. The rapidly growing tissue culture (TC) industry within aiming provide planting material farmers, has stimulated discussion about need indexing certify virus-free. Diagnostic methods BSV have been reported and, BBTV, PCR-based assays reliable relatively straightforward. However BSV, high levels serological variability presence endogenous sequences genome complicate diagnosis. Uganda shown contain greatest diversity isolates found anywhere world. A broad-spectrum diagnostic test detection, which can discriminate between episomal sequences, priority. This PhD project aimed establish viruses, with particular focus on development novel use these detection characterisation viruses Africa. A rolling-circle amplification (RCA) method was developed BSV. Using samples MY (BSMYV) OL (BSOLV) from Australia, this distinguish plants. The RCA assay used screen collection 56 south-west detected at least five distinct samples, including BSOLV GF (BSGFV) well three (Banana Uganda-I, -L -M virus) only partial had previously reported. These latter using immuno-capture (IC)-PCR thus were possible sequences. addition its ability detect protocol also demonstrated other family Caulimoviridae, Sugar cane bacilliform virus, Cauliflower mosaic virus. Using method, both identified characterised. complete sequenced annotated. All six characteristic badnavirus organisation open reading frames (ORFs) polyprotein encoded ORF 3 conserved amino acid motifs movement, aspartic protease, reverse transcriptase ribonuclease H activities. As well, several expression replication tRNAmet primer binding site intergenic region all badnaviruses. Based International Committee Taxonomy (ICTV) guidelines species demarcation genus Badnavirus, proposed species, named UA (BSUAV), UI (BSUIV), UL (BSULV), UM (BSUMV), CA (BSCAV) IM (BSIMV). PCR species-specific primers designed each isolate, genotypically diverse 12 virus-free cultivars tested For no observed any cultivar tested, while BSIMV, four positive B-genome component. During field visits Uganda, 143 collected assayed nine sets primers, RCA, compared detection. known counterpart (namely BSCAV, BSUAV, BSUIV, BSULV BSUMV), 30 infections samples. 96.4% positive, additional sample PCR. useful identifying infected irrespective host genotype (Musa A- or components). counterparts M. balbisiana (BSOLV, BSGFV, BSMYV BSIMV), 75 an A-only component there 96.3% agreement again demonstrating either suitable However, 45 some component, level 70.5%. suggests that, many result cases, another discriminates PCR, needed diagnose infection. Field made Malawi collect local validation assay. bananas confirmed 28 out 39 Rwanda, RCA. isolates, nucleotide determined similar published isolates. 98.1% sequence identity DNA components, similarity 96.2% 99.4% depending component. At level, similarities putative proteins DNA-R, -S, -M, - C -N range 98.8% 100%. phylogenetic analysis, African clustered together South Pacific subgroup Nucleotide comparison outside Africa India origin BBTV.