Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange

Abstract

Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.

Detection and diversity of viruses infecting African yam (Dioscorea rotundata) in a collection and F1 progenies in Côte d'Ivoire shed light to plant‐to‐plant viral transmission

“…Total nucleic acids (TNAs) were extracted from leaf samples according to procedure 2 developed by Foissac et al ( 2005 ) and used for the detection by RT‐PCR of CMV, DMaV, YaV1, YMV, YMMV, yam macluraviruses, and yam potexviruses as described by Umber et al ( 2020 ). Details of the primers are provided in Table S3 .…”

“…Using mainly viral metagenomics, a large number of novel viruses have been identified in yam during the last 15 years. Thus far, viruses belonging to genera Ampelovirus , Aureusvirus , Badnavirus , Carlavirus , Cucumovirus , Fabavirus , Macluravirus , Potexvirus , Potyvirus , Sadwavirus , and an unknown genus belonging to the family Betaflexiviridae , have been reported in yams (Umber et al, 2020 ).…”

“…The control of viral diseases affecting crops relies primarily on the use of clean seeds and/or the breeding of resistant varieties either by conventional methods or by genetic engineering. Yam sanitation programmes have been successfully implemented, resulting in the production of clean seeds (Umber et al, 2020 ). Such programmes rely on plant regeneration from meristem culture in vitro, thermotherapy, or cryotherapy (Filloux & Girard, 2006 ).…”

“…rotundata F 1 progenies obtained from hybridizations by CNRA in Bouaké and of a diverse panel of D . rotundata accessions has been assessed using the comprehensive diagnostic scheme designed by the Biological Resources Center for Tropical Plants (BRC‐TP) located in Guadeloupe (French West Indies) (Umber et al, 2020 ). Molecular tools used for diagnosis include reverse transcription (RT)‐PCR for the detection of RNA viruses and immunocapture (IC)‐PCR for that of badnaviruses, which avoids false positives resulting from the presence of endogenous badnavirus sequences (eDBVs) in the genome of some yam species, including D .…”

“…RNA viruses targeted in this study include CMV, Dioscorea mosaic‐associated virus (DMaV; genus Sadwavirus ), yam asymptomatic virus 1 (YaV1; genus Ampelovirus ), YMV, and YMMV with specific tests. Yam potexviruses and yam macluraviruses are detected using generic tests, which are able to target several yam‐infecting viral species (Umber et al, 2020 ).…”