Development of Cross-specific Microsatellite Markers for Echinochloa spp. (Poaceae)

Jeongran  Lee1,*   Jin-Won Kim1   In-Yong Lee1   

1National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea


Echinochloa spp. is one of the most problematic weeds, especially in rice fields. Therefore, most of the studies on this genus have been focused on chemical control. Its genetic diversity using molecular markers was not widely studied because of a few markers available. Microsatellite markers were developed in this study to evaluate the genetic diversity of a cross-specific troublesome weed Echinochloa species (Poaceae). Illumina sequencing identified a total of 44,257 di-/tri-nucleotide repeat motifs. Finally, thirteen microsatellite markers were identified for Echinochloa crus-galli. All markers were polymorphic and cross amplified in E. oryzicola. The average number of alleles per locus was 8.0 and polymorphism information content was 0.611. Observed and expected heterozygosity ranged from 0.00 to 0.98 and from 0.06 to 0.86, respectively. The 13 polymorphic markers identified in this study will be useful for assessing the genetic diversity of E. crus-galli along with E. oryzicola and for predicting the dispersal pattern of these weeds in agricultural fields.

Figures & Tables

Fig. 1. Principal coordinates of spp. spp.were grouped in cluster as expected. The two species were separated along the coordinate 1, which explained 71.5% of variance. Red blocks are and empty blocks are .