Foxtail millet (Setaria italica L.) is an underutilized crop grown for its nutritious
grains and relative tolerance to drought or salinity stresses. However, variation in
the tolerance level exists among foxtail millet genotypes. A simple and reliable
technique for SNP genotyping, namely dot-blot SNP analysis, has been applied for
practical plant breeding programs and has a potential for accelerating foxtail millet
breeding for drought or salinity stress tolerance. The aim of this study was to
conduct SNP analysis for the SiDREB2 gene, which is associated with drought or
salinity stress tolerance in foxtail millet, using a marker based on polymorphism at
the 558th nucleotide,. Two factors that affect the allele-specific detection of the dotblot
SNP analysis i.e. hybridization temperature and competitive probe ratio were
optimized in this study. Four hybridization conditions consisting of the combination
between two hybridization temperatures (50 and 55 ºC) and two competitive probe
ratios (1:5 and 1:10) were optimized. The second hybridization condition (50 ºC
hybridization temperature and 1:10 competitive probe ratio) showed the best result
for SNP analysis. This optimum condition was then applied for genotyping 26 foxtail
millet genotypes with unknown drought or salinity stress tolerance levels. The
optimum condition of the dot-blot SNP analysis was effective for genotyping in an
allele-specific manner and used for predicting stress tolerance levels of the foxtail
millet genotypes. The results of this study are useful for accelerating foxtail millet
breeding for drought or salinity stresses in the future.
