Molecular identification of Echinochloa oryzicola Vasing. and E. crus‐galli (L.) Beauv. using a polymerase chain reaction–restriction fragment length polymorphism technique

Abstract

Polymerase chain reaction (PCR) and polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) techniques were applied for establishing the reliable practice in identification of Echinochloa oryzicola Vasing. and E. crus‐galli (L.) Beauv. (barnyardgrass). Total DNA was extracted from 18 accessions and 86 individuals of E. oryzicola, 33 accessions and 140 individuals of E. crus‐galli var. crus‐galli, 23 individuals of E. crus‐galli var. praticola, and six individuals of E. crus‐galli var. formosensis that were collected from Japan. A partial region of intergenetic spacer between trnT and trnL, and an intron of trnL were amplified separately using a trn‐a and trn‐b1 primer set, and a trn‐c and trn‐d primer set, respectively. All individuals of E. oryzicola showed the same fragment amplified by the trn‐a and trn‐b1 primer set. The fragment was 481 bp in length, and was undigested by EcoR I, whereas all individuals of E. crus‐galli, including three botanical varieties, showed the same fragment with a 449‐bp length. The fragment was digested by EcoR I into two fragments (178 and 271 bp). The fragment amplified by the trn‐c and trn‐d primer set in all individuals of E. oryzicola was digested by Alu I into two fragments (174 and 452 bp), but undigested by Dra I. In contrast, the fragment amplified by the trn‐c and trn‐d primer set in all individuals of E. crus‐galli was digested by Dra I into two fragments (134 and 487 bp), but undigested by Alu I. There was no intraspecific variation in these regions; thus, these two species are easily identifiable by using our method.

Genetic and morphologic diversity of Echinochloa crus-galli populations from different origins

“…Echinochloa crus-galli includes many botanical varieties and these varieties are conventionally identified on the basis of their spikelet morphological features and ecological habits (Yabuno 1996). However, this species shows different morphological features of spikelet among varieties and morphological features of spikelet overlap among species (Yasuda et al 2002). This was confirmed in our study, indicating that morphology of spikelet varies with populations.…”

Target‐site mutation associated with cross‐resistance to ALS‐inhibiting herbicides in late watergrass (Echinochloa oryzicola Vasing.)

“…Fritsch . Although some of these taxa can be conventionally identified on the basis of their spikelet morphological traits and ecological habits, a significant amount of skill is required for their accurate identification, as the morphological features of the spikelet frequently overlap within and between species/taxa …”

Using next‐generation sequencing to detect mutations endowing resistance to pesticides: application to acetolactate‐synthase (ALS)‐based resistance in barnyard grass, a polyploid grass weed

“…These species are rather difficult to distinguish on the basis of morphological traits. 45,46 The nucleotide sequences encoding ALS have been determined in both barnyard grass 37,38 and rice barnyard grass. 47 They are 99% identical between the two species, which does not enable species identification.…”

“…47 They are 99% identical between the two species, which does not enable species identification. PCR-RFLP assays targeting chloroplastic DNA sequences, allowing the differentiation of barnyard grass and rice barnyard grass, 46 were thus used to assign the plants in each population to a species.…”