Difference in SSR variations between Japanese Barnyard Millet (Echinochloa esculenta) and its wild relative E. crus-galli

Abstract

Simple sequence repeat (SSR) variations were investigated in the Japanese barnyard millet, Echinochloa esculenta, its wild relative, E. crus-galli var. crus-galli and the rice-mimicking weed E. crus-galli var. formosensis. E. esculenta showed less average gene diversity (H) based on observed SSR allele frequency (0.37) than either E. crus-galli var. crus-galli (0.56) or E. crus-galli var. formosensis (0.55). Accessions of the three Echinochloa taxa were categorized into 13 phenotypes from the combinations of SSR alleles. Only two phenotypes, phenotypes 1 and 4, were detected in 49 accessions of E. esculenta, whereas 12 phenotypes were observed in 94 accessions of E. crus-galli var. crus-galli, and six phenotypes in 12 accessions of E. crus-galli var. formosensis. The H′ value (Shannon's information index) for SSR phenotypes was 0.69 in E. esculenta, 1.47 in E. crus-galli var. formosensis and 1.90 in E. crus-galli var. crus-galli respectively. In cultivated barnyard millet, two phenotypes aggregated in particular areas of Japan; phenotype 4 was found in the central and northeastern part of Japan, while phenotype 1 in the northern and southern parts of Japan.