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

Abstract

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, Coˆte 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 corre-lated. 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, Coˆte 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 Coˆte d'Ivoire (over a 2-km distance), four different genotypes were found in a 4 m · 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.

Comparative analysis of genetic diversity of 8 millet genera revealed by ISSR markers

“…These genetic and morphological differences in the Echinochloa species lead to taxonomic problems. Thus, many studies have attempted to understand the population genetic structures of some Echinochloa species, and have revealed their genetic diversity by using molecular markers (Asins et al, 1999;Roy et al, 2000;Rutledge et al, 2000;Tasrif et al, 2004;Altop and Mennan, 2011;Nozawa et al, 2006;Danquah et al, 2002). As with previous studies, the Echinochloa species in the present study were differentiated, and might confirm the theory of Yabuno (1966) and Scholz (1992), that the weedy Echinochloa crus-galli has its cultivated counterpart Echinochloa esculenta.…”

Determination of Morphological and Genetic Diversity of ALS (Acetolactate Synthase)- Herbicide-Resistant Echinochloa oryzoides Biotypes in Rice

“…The molecular data obtained from the E. oryzoides populations identified a total of eight basic coordinates, and the proportion of genetic variation described by these coordinates ranged between 42.1% and 1.75%, similar to the results of Danquah et al (2002), in terms of the components and the variation. In addition, the genetic diversity ratios (0.22-0.99) obtained in our study could be confirmed by the same study (Danquah et al, 2002).…”

“…The increased gene diversity found in this study compared to that (55.6%) by Danquah et al (2002) and (37.4%) by Lee et al (2015), was probably because of sampling from far wider areas and the rate of resistance being more dramatic. The molecular data obtained from the E. oryzoides populations identified a total of eight basic coordinates, and the proportion of genetic variation described by these coordinates ranged between 42.1% and 1.75%, similar to the results of Danquah et al (2002), in terms of the components and the variation. In addition, the genetic diversity ratios (0.22-0.99) obtained in our study could be confirmed by the same study (Danquah et al, 2002).…”

“…Therefore, morphological similarity among populations ranged from 75% to 100%. In the literature, the presence or absence of awns is considered the first of the distinguishing features that differentiate E. oryzoides from other species of Echinochloa (Barret, 1983;Danquah et al, 2002;Damalas et al, 2008). In this study, length of the awn is known to have a significant negative correlation with the germination speed, number of tiller, plant stem diameter, number of spikelets and biomass parameters.…”

“…The total genomic DNA was extracted when plants reached the sixleaves stage using DNeasy Plant Mini Kits (Qiagen, Qiagen GmbH, Hilden, Germany), according to the instructions provided. The concentration and relative purity of the isolated DNA were checked using Nanodrop ND-1000 (Agricultural Genomic Laboratory) and adjusted to 30 ng μL -1 (Danquah et al, 2002;Santaella et al, 2006). A total of five simple sequence repeat (SSR) markers, including four Echinochloa spp.…”