Development of SSR for foxtail millet (Setaria italica (L.) P. Beauv.) and its utility in genetic discrimination of a core set

Foxtail millet (Setaria italica (L.) P. Beauv.) is an underutilized food and forage crop with immense potential in improving global food security. In this study sequence data were mined at the database of NCBI with the aim of developing polymorphic nucleotide and expressed sequence tags (ESTs) simple sequence repeat markers. Successful amplification was visualized on 3 % agarose gel. The selected 12 candidate markers were further used to characterize available 155 core collections. A total number of 198 alleles with an average of 16.5 alleles per loci were discovered. Heterozygosity (H) ranged between 0.05 (UH-Si-173) to 0.23 (UH-Si-487) with a mean average of 0.16. Gene diversity ranged from 0.15 (UHSi-766) to 0.96 (UH-Si-500), with an average value of 0.80 across the populations. The polymorphic information content (PIC) ranged from 0.15 (UH-Si-766) to 0.96 (UH-Si-500) with a mean value of 0.79. A positive correlation (r = 0.720; P < 0.01) was found between the PIC and the number of alleles. Weighted neighbor joining dendrogram generated seven major clusters. More polymorphism was detected with the nucleotides derived microsatellites when compared to the ESTs derived microsatellites. This result shows that the morphological and phenotypic descriptors used for the development of the 155 core collections of foxtail millet was optimal enough to capture as much diversity. The newly developed markers in this study are quite informative and recommended for future genetic studies in the species and close related genera.