Characterization of Claviceps species pathogenic on sorghum by sequence analysis of the β-tubulin gene intron 3 region and EF-l α gene intron 4

The intron 3 region of the β-tubulin gene, and intron 4 of the translation elongation factor gene were PCR-amplified, cloned, and sequenced to determine relationships among Claviceps species and characterize isolates of Claviceps causing ergot of sorghum in the USA and other countries. The β-tubulin gene intron 3 region and intron 4 of the EF-lα gene allowed clear differentiation of five species (C. africana, C. sorghicola, C. purpurea, C. fusiformis, and C. paspali), two of which (C. africana and C. sorghicola) are pathogens of sorghum, with almost no intraspecific variation observed among isolates. Claviceps isolates obtained from sorghum in the USA contained β-tubulin gene intron 3 region sequences identical to those of C. africana isolates from India, Australia, and South Africa. PCR primers were designed from unique sequences within the β-tubulin intron 3 region that can differentiate the five Claviceps species used in this study. We describe primers that allow direct PCR detection of C. africana from honeydew produced on infected sorghum plants, providing a useful tool for analysis of field samples. The β-tubulin gene intron 3 region and EF-1α intron 4 should prove useful in phylogenetic and epidemiological studies of additional Claviceps species.