Novel expressed sequence tag- simple sequence repeats (EST-SSR) markers characterized by new bioinformatic criteria reveal high genetic similarity in sugarcane ( Saccharum spp.) breeding lines
2012
Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs selected, based on repeat patterns of n≥8 for di-, tri-, tetra- and penta-nucleotide repeat motifs verified using 15 sugarcane ( Saccharum spp.) genotypes and marker segregation using F1 progenies of a cultivated sugarcane and Saccharum spontaneum , 191 loci were identified. All new ESTSSR loci detected a total of 1,529 markers ranging from 2 to 21 markers per locus, with an average of eight markers per locus. Observed polymorphism ranged from 0.12 to 0.93 with a mean of 0.74. A total of 426 and 333 markers were putatively identified as simplex in the cultivated sugarcane and S. spontaneum , respectively and corresponding to 2.23 and 1.74 markers per primer, respectively while 167 markers were identified as double-simplex markers, with 0.87 markers per primer. Cluster analysis revealed a high genetic similarity among the sugarcane ( Saccharum spp.) breeding lines which could reduce the genetic gain in sugarcane breeding. Key words : sugarcane, expressed sequence tag- simple sequence repeats (EST-SSRs) markers, genetic similarity.
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