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Insights into the recent outbreaks of potato bacterial wilt in Madagascar highlands: genotyping of the Ralstonia solanacearum species complex by MLVA

Ravelomanantsoa S., Boyer K., Cheron J.J., Javegny S., Costet L., Chiroleu F., Vernière C., Raveloson A., Cellier G., Ravigné V., Pruvost O., Poussier S., Guérin F., Robene I., Prior P.. 2016. In : Book of abstracts of the 6th International Bacterial Wilt Symposium. Toulouse : INRA, p. 43-43. International Bacterial Wilt Symposium. 6, 2016-07-03/2016-07-07, Toulouse (France).

The Ralstonia solanacearum species complex (Rssc) is a highly diverse cluster of strains, many of which proved destructive worldwide causing bacterial wilt (BW) on a wide plant host range. Potato BW has been described for nearly 30 years in Madagascar highlands (phylotype I and Ill) without major impact on production. Recently, potato production was dramatically devastated by severe outbreaks. Controlling this disease is crucial for Malagasy potato producers and a first important step to achieve this goal is the identification of the strains involved and of their putative origin. Consequently, the genetic diversity and population structure of the Rssc was investigated in the major potato production areas in the highlands. By using different molecular tools we characterized a large collection of strains (n=1224; 75 sites) collected from potato production areas in 2013, April (n=763; 41 sites) and December (n=461; 33 sites). Present for a long time in Madagascar, Phylotypes I and Ill strains were little associated with potato BW outbreaks, while surprisingly, most outbreaks were associated with brown rot strains IIB-1. This constitutes the first report of phylotype IIB-1 strains in Madagascar. Along with reference strains, epidemic IIB-1 strains (n=285) were genotyped through the MLVA RS2-MLVA9 implemented from existing schemes (1, 2]. Malagasy phylotype Il strains separated into two clonal complexes (CC) including one major CCl grouping also most of the worldwide genotypes that distributed in wide agro-ecological areas. Fine scale genetic investigation of the outbreak suggested that the clonal expansion of this IIB- lineage affected potato production in Madagascar after being introduced and massively spread through propagation of latently infected potato-seeds. The survey also allowed the first study about the population structure of phylotype Ill strains. Two hundreds and seventeen phylotype Ill strains were genotyped with the highly discriminatory MLVA scheme RS3-MLVA16 that we newly developed [3]. MLVA distinguished a high genetic diversity in Malagasy population of phylotype Ill strains producing 117 haplotypes grouped in 11 clonal complexes. Malagasy strains were distinct from continental African strains, suggesting little recent immigration from the continent. Many CC a long with the large genetic diversity supported the endemic character of the phylotype Ill population in Madagascar. At an agro-ecological scale, phylotype Ill mostly structured in small clonal complexes associated with a single geographic origin each. But two major CCs grouped some haplotypes shared between individuals from different highland areas, and the remainder made of haplotypes derived from a unique origin supporting long distance dispersal most probably through human activities. Although the most popular Malagasy potato cultivars developed by CIP and FIFAMANOR were apparently developing resistance to phylotype Ill strains in the field, we reported no bacterial wilt resistance properties under artificial environment (growth chambers). As expected, the same potato cultivars were highly susceptible to expanding phylotype IIB-1 lineage....

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