A molecular phylogeny of wild and cultivated Echinochloa in East Asia inferred from non‐coding region sequences of trnT‐L‐F

Abstract

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 .

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

“…Therefore, these results indicate that the cpDNA sequence comparison could be used for identification of conventionally classified E. crus‐galli and E. oryzicola accessions. Similar results were reported by Yamaguchi et al . who found that the nucleotide sequencing of cpDNA in 30 accessions belonging to nine species of the genus Echinochloa provided information on phylogenetic relationships and new tools for species identification.…”

“…Afterwards, the amplification products were resolved on a 1.2% agarose gel, and single bands of the expected size were observed . The bands of the trn L intron were excised from the gel, and DNA was recovered using a modified freeze‐squeeze method . Briefly, the band slice in a 1.5 mL reaction tube was frozen in liquid nitrogen and centrifuged for 5 min at maximum speed, and the liquid phase was recovered in a new DNA collection tube.…”

“…Also, chloroplast DNA (cpDNA) with a slow evolution rate and no recombination owing to the maternal inheritance of the organelle genome has been useful in examining relationships among different plant species . Molecular analysis of specific regions of the cpDNA provided useful tools for species discrimination, analysis of phylogenetic relationships and divergence among different Echinochloa species . Nucleotide sequencing of three non‐coding regions ( trn T‐L, trn L‐F intergenic spacers and trn L intron) of cpDNA in 30 accessions belonging to nine species of the genus Echinochloa provided information on phylogenetic relationships and new tools for species identification .…”

Cytogenetic Studies on Two Wild Species of Genus <i>Echinochloa</i> P. Beauv. from Saudi Arabia

“…Based on this suggestion we could conclude that this species is of allohexaploid structure (AAAABB). This suggestion was previously reported by Michael (2001), Yabuno (1966), Krahulcová (2003) and Yamaguchi et al (2005). This trend was also previously suggested by Haroun (1991Haroun ( , 1997 for some species of the tribe panicodeae of Poaceae as the open pollination system of this family may support this hypothesis where cross-pollination may have occurred between tetraploid Echinochloa and other diploid compatible or partially compatible species of the same genera.…”

“…Although earlier cytological studies suggest a range of basic chromosome number (8,9,10), it seems in fact that the majority of the species belongs to the genus based on x=9 with different ploidy levels of diploids, tetraploids and hexaploids (Yabuno 1962, 1966, 1984, Yamaguchi et al 2005, Spies et al 1991.…”