Genetic diversity in Echinochloa spp. collected from different geographic origins and within rice fields in Cote d'Ivoire

Diversity studies of Echinochloa spp. are complicated by problems in taxonomy and species identification, caused by the existence of morphologically intergrading types. Six amplified fragment length polymorphism (AFLP) primer combinations and five microsatellites were used to assess variation in 24 samples morphologically identified as E. crus-galli, E. colona and E. crus-pavonis , from Bangladesh, India, Colombia, Costa Rica, Cote d'Ivoire and Philippines. Out of 909 AFLP bands generated, 775 were polymorphic. Genotype diversity for the microsatellites ranged from 0.28 to 0.72. Similarity matrices were calculated using Jaccard coefficient, and input into cluster and principal coordinates analyses. AFLP and microsatellite results were highly correlated. Echinochloa crus-pavonis and E. crus-galli were intermixed, consistent with the view that E. crus-galli occurs as numerous intergrading races in the four countries (Bangladesh, India, Cote d'Ivoire and Philippines). The E. colona samples clustered as a distinct group. In 15 samples of E. crus-pavonis collected from rice fields in a valley in Cote d'Ivoire (over a 2-km distance), four different genotypes were found in a 4 m x 4 m area. These results suggest that AFLPs and SSRs may be useful not only for discriminating genotypes and studying population structure but also for helping to resolve taxonomic relationships in Echinochloa spp.