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Prevalence of Sugarcane yellow leaf virus in sugarcane producing regions in Kenya revealed by reverse transcription loop-mediated isothermal amplification method

Amata R.L., Fernandez E., Filloux D., Martin D.P., Rott P., Roumagnac P.. 2016. Plant Disease, 100 (2) : p. 260-268.

DOI: 10.1094/PDIS-05-15-0602-RE

Yellow leaf (YL) is a disease of sugarcane that is currently widespread throughout most American and Asian sugarcane-producing countries. However, its actual distribution in Africa remains largely unknown. A reverse-transcription loop-mediated isothermal amplification (RT- LAMP) assay was developed to facilitate and improve the detection of Sugarcane yellow leaf virus (SCYLV), the causal agent of YL. The RT-LAMP assay was found to be comparable with or superior to conven- tional RT-polymerase chain reaction (PCR) for the detection of SCYLV genotypes CUB and BRA in infected sugarcane ' C132-81 ' and ' SP71- 6163 ' , respectively. Additionally, 68 sugarcane samples that tested neg- ative by RT-PCR were found positive by RT-LAMP, whereas the RT-LAMP assay failed to detect SCYLV in only 5 samples that tested positive by RT-PCR. Combining RT-PCR and RT-LAMP data enabled the detection of SCYLV in 86 of 183 Kenyan sugarcane plants, indicat- ing high SCYLV prevalence throughout the country (ranging from 36 to 64% in individual counties). Seminested PCR assays were developed that enabled the amplification of a fragment encompassing the capsid protein coding region gene and its flanking 5 ¢ and 3 ¢ genomic regions. Sequences of this fragment for four Kenyan SCYLV isolates indicated that they shared 99.2 to 99.6% pairwise identity with one another and clearly clus- tered phylogenetically with SCYLV-BRA genotype isolates. To our knowledge, this is the first report of SCYLV in Kenya.

Mots-clés : saccharum officinarum; virus des végétaux; variété; technique analytique; pcr; test biologique; transcription génique; identification; kenya; sugarcane yellow leaf virus

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