Barnyardgrass (Echinochloa crus-galli) is a pernicious weed in agricultural fields worldwide. The molecular mechanisms underlying its success in the absence of human intervention are presently unknown. Here we report a draft genome sequence of the hexaploid species E. crus-galli, i.e., a 1.27 Gb assembly representing 90.7% of the predicted genome size. An extremely large repertoire of genes encoding cytochrome P450 monooxygenases and glutathione S-transferases associated with detoxification are found. Two gene clusters involved in the biosynthesis of an allelochemical 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and a phytoalexin momilactone A are found in the E. crus-galli genome, respectively. The allelochemical DIMBOA gene cluster is activated in response to co-cultivation with rice, while the phytoalexin momilactone A gene cluster specifically to infection by pathogenic Pyricularia oryzae. Our results provide a new understanding of the molecular mechanisms underlying the extreme adaptation of the weed.

The phylogenetic relationship among 30 accessions belonging to nine species of the genus Echinochloa Beauv. was studied on the basis of the sequence of three non-coding regions ( trn T-L, trn L-F intergenic spacers, and trn L intron) of chloroplast DNA (cpDNA). A strict consensus parsimonious tree of the three most parsimonious trees derived from 25 polymorphic sites (six indels and 19 substitutions) in the total sequences, ranging from 1715-1760 bp, represented five groups: (i) Echinochloa oryzicola Vasing. and Echinochloa stagnina Beauv. from Thailand; (ii) Echinochloa crus-galli Beauv. complex; (iii) Echinochloa crus-pavonis Schult; (iv) Echinochloa colonum Link. and Echinochloa frumentacea Link.; and (v) the African species, Echinochloa obtusiflora Stapf and Echinochloa stagnina . Japanese barnyard millet ( Echinochloa esculenta H. Scholz) and various weedy varieties of E. crus-galli and Echinochloa oryzoides Fritsch had quite similar sequences and formed the E. crus-galli complex, which was characterized by six substitutions. A cultivated form of E. oryzicola (Mosuo barnyard millet) and various morphological and agronomical forms of E. oryzicola were characterized by two indels. Indian barnyard millet ( E. frumentacea ) and its wild counterpart ( E. colonum ) were characterized by five substitutions. Domestication as millets and adaptation to paddy environments as mimic weeds might occur after the divergence of species in the Asian Echinochloa .

As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.

The frequency of hybridization through pollen flow from the cultivated soybean to the wild soybean was evaluated for the purpose of assessment of the ecological risk of genetically modified crops. The flowering habits of three soybean cultivars and one wild soybean accession were monitored on an experimental farm. A cultivar and a wild accession, both of which flowered at a similar period, were then planted alternately in 5 × 12 arrays with 50 cm spacing on the farm. The seedlings of progeny seeds gathered from individual plants of the wild accession were used for an isozyme analysis to identify whether they were hybrid or not. In 23 plants of the wild accession, four plants produced hybrids (the incidence of hybridization = 17.4%). There was no directionality in hybridization. The hybridization rate per maternal plant varied from 0 to 5.89% with a mean of 0.73% for all maternal plants. The results indicate that natural hybrids are easily produced in a certain frequency by pollen flow from the cultivated soybean to the wild soybean under their simultaneous flowering with adequate pollinators.

Barnyardgrass, hexaploid Echinochloa crus-galli, is considered to arise from the hybridization between tetraploid Echinochloa oryzicola and an unknown diploid species.The genetic relationship between E. crus-galli and E. oryzicola was examined to investigate the position of E. oryzicola in the evolutionary process of E. crus-galli, based on the nuclear DNA internal transcribed spacer (ITS) and the chloroplast cpDNA trnT-L, trnL intron, and trnL-F regions. New World E. crus-galli was clearly separated from Eurasian E. crus-galli and showed a close relationship to the American taxa, Echinochloa crus-pavonis and Echinochloa walteri, in both the ITS and chloroplast DNA. The nrDNA ITS sequences indicated no differentiation between the Eurasian E. crus-galli and E. oryzicola, in contrast to their clear divergence in the cpDNA sequence. The present results suggest that E. oryzicola is the male donor of E. crus-galli.

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.

The findings provide an improved understanding of the interspecific relationships, and ecological and geographical phylogenetic structure of the subgenus Ceratotropis. The quaternary diversification of the subgenus Ceratotropis implicates its geographical dispersal in the south-eastern part of Asia involving adaptation to climatic condition after the collision of the Indian subcontinent with the Asian plate. The phylogenetic results indicate that the epigeal germination is plesiomorphic, and the germination type evolved independently multiple times in this subgenus, implying its limited taxonomic utility.

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