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

Amata Ruth Lodenyi, Fernandez Emmanuel, Filloux Denis, Martin Darren Patrick, Rott Philippe, Roumagnac Philippe. 2016. Prevalence of Sugarcane yellow leaf virus in sugarcane producing regions in Kenya revealed by reverse transcription loop-mediated isothermal amplification method. Plant Disease, 100 (2) : pp. 260-268.

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Quartile : Q1, Sujet : PLANT SCIENCES

Additional Information : Jeux de données enregistrés dans la base GenBank : accession numbers KEN192: KR608791, KEN193: KR608792, KEN7: KR608793, and KEN8: KR608794

Abstract : 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. (Résumé d'auteur)

Mots-clés Agrovoc : Saccharum officinarum, Virus des végétaux, Variété, Technique analytique, PCR, Test biologique, Transcription génique, Identification

Mots-clés géographiques Agrovoc : Kenya

Mots-clés complémentaires : Sugarcane yellow leaf virus

Classification Agris : H20 - Plant diseases
F30 - Plant genetics and breeding
U30 - Research methods

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Auteurs et affiliations

  • Amata Ruth Lodenyi, KARI (KEN)
  • Fernandez Emmanuel, CIRAD-BIOS-UMR BGPI (FRA)
  • Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
  • Martin Darren Patrick, Montpellier SupAgro (FRA)
  • Rott Philippe, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-6085-6159
  • Roumagnac Philippe, CIRAD-BIOS-UMR BGPI (ZAF) ORCID: 0000-0001-5002-6039

Source : Cirad-Agritrop (

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