Development and validation of class I SSR markers targeting (GATA) n repeat motifs in rice

Abstract

SSR markers targeting (GATA) n motifs are known to be highly polymorphic and useful in many organisms. (GATA) n motif specific SSR markers covering the whole rice genome are not available. The present study was carried out with an objective to identify class I rice microsatellites in the rice genome with (GATA) n motifs, in-silico, and validate their potential as molecular markers. A total of 243 such motifs were identified; 65 of these were present in the genic region, 59 were in the upstream region and the remaining motifs were found in the intergenic regions. Many of the (GATA) n motifs were found within and/or upstream of genes associated with biotic or abiotic stress tolerance. A total of 230 PCRbased markers targeting all the class I (GATA) n microsatellites were developed and 35 of these markers spread across the rice genome were validated in a set of 24 representative rice varieties belonging to five distinct cultivar groups. All the markers were polymorphic, with average polymorphism information content (PIC) value of 0.61, and the rice cultivars could be uniquely distinguished into different cultivar groups based on marker analysis. These informative markers targeting (GATA) n motifs representing a new set of markers in rice will be highly useful for genetic studies and marker-assisted selection.

Molecular diversity analysis in rice (Oryza sativa L.) using SSR markers

“…Markers with PIC values of 0.5 or above are broadly highlights for the genetic studies since they are most useful in describing the polymorphism magnitude of a specific locus (Akkaya and Buyukunal Bal 2004). The obtained results are showing close resemble to the output mentioned by Brondani et al 2008, Rajendrakumar et al 2009and Matin et al 2012; they also mentioned mean PIC Values of 0.61, 0.61 and 0.634, respectively with variable set of rice genotypes with use of SSR markers. However, the PIC values reported in this study were lower than those obtained by Sonkar et al 2016 who reported a mean PIC value of 0.92.…”

Potentiality of evenly distributed hypervariable microsatellite markers in marker‐assisted breeding of rice

“…2005, Glaszman 1987) which underscores the potentiality of hypervariable microsatellite markers (hvRMs) in studying genetic relatedness within and between species. Very recently, Rajendrakumar et al. (2009) proved that (GATA)n repeats of Class I SSR markers could be effectively used for genetic diversity studies and marker‐assisted selection.…”

“…Overall, the pattern of grouping clearly corresponds to earlier reports (Garris et al 2005, Glaszman 1987) which underscores the potentiality of hypervariable microsatellite markers (hvRMs) in studying genetic relatedness within and between species. Very recently, Rajendrakumar et al (2009) proved that (GATA)n repeats of Class I SSR markers could be effectively used for genetic diversity studies and marker-assisted selection. However, the present study offers experimental evidence for the potential use of evenly spaced hvRMs in marker-assisted selection/breeding and in genetic diversity analysis.…”

Molecular Characterization and Genetic Diversity Analysis of Rice (Oryza sativaL.) Using SSR Markers

“…The SSR markers are particularly suitable for evaluating genetic diversity and relationships among plant species, populations, or individuals (Kostova et al 2006;Tu et al 2007), studying rice germplasm for either conservation or utilization (Sharma et al 2007); marker-assisted selection breeding (Perez-Sackett et al 2011;Rani and Adilakshmi 2011); cultivar identification; hybrid purity analysis and gene mapping studies (Weising et al 1997;Altaf-Khan et al 2006;Rajendrakumar et al 2009;Sarao et al 2010). …”