Oryza sh4 gene homologue represents homoeologous genomic copies in polyploid Echinochloa.

The coding region sequence of the Oryza sh4 gene homologue in Echinochloa was analyzed in relation to the shattering nature of spikelets and the phylogeny of homologue copies in the Asian annual polyploidy Echinochloa. The Sh4 homoeologue copies were detected in Echinochloa oryzicola, Echinochloa crus-galli, Echinochloa stagnina, Echinochloa colona, and Echinochloa crus-pavonis. Amino acid sequence differences did not lead to a functional change in the sh4 gene between the shattering and non-shattering types in E. crus-galli, E. oryzicola, and E. colona. A phylogenetic analysis of the homoeologous copy sequences indicated a genomic relationship between the Asian Echinochloa species and supported that the allohexaploid E. crus-galli shares two genomes with its parental donor, E. oryzicola. The Asian perennial tetraploid species, E. stagnina, shares one genome with E. oryzicola and possesses an unknown genome. Echinochloa crus-pavonis, from the New World, shows a close affinity of two genomes with E. crus-galli and E. oryzicola. Echinochloa colona showed distant affinities in all homoeologous copies.