Development of microsatellite markers targeting (GATA)n motifs in sorghum [Sorghum bicolor (L.) Moench]

Abstract

Microsatellite markers targeting (GATA)n motifs are known to be highly polymorphic. Genomewide development of such markers has not been reported in sorghum. The main objective of this study was to identify Class I microsatellites with (GATA)n motifs in the sorghum genome through in silico analysis and assess their potential as molecular markers. The study identified a total of 128 such motifs, of which 14, 16 and 98motifswere present in the genic, upstream and non-genic regions, respectively. The majority of the (GATA)n motifs were found in the non-genic regions of the genome while 23.44 % of them were found within the genes and upstreamof genes.About 110 PCR-based markers were developed targeting these microsatellites and 50 of them distributed across the genome were validated in 24 diverse sorghumgenotypes representing different racial groups. Thirty-eight markers were polymorphic, with average polymorphism information content value of 0.69, and the sorghumgenotypes could be grouped into two major clusters. These markers with robust amplification combined with good allelic diversity represent a new set of microsatellite markers in sorghum reported for the first time that will be highly useful for various genetics and molecular breeding applications.