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The dominance of trinucleotide SSRs compared to dinucleotide SSRs was not surprising considering that trinucleotides are abundant in coding regions of all higher eukaryotic genomes [ 31- 33].
In wheat, 9.9% polymorphism was observed for EST-derived SSRs compared to 35.5% polymorphism observed in case of genomic SSRs [ 12].
No significant differences (X; p < 0.05) was observed between genotypes with respect to tri- and tetra- repeat SSRs, while the EST-SSRs derived from the genotype NV 20F1-39 contained significantly (X; p < 0.05) more di-repeat SSRs compared to the EST-SSRs derived from the other two genotypes.
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Percentages of EST-SSR (compared to the total number of contigs) found in lily genotypes were comparable with each other (around 2.7%) except for 'Connecticut King' that showed a lower percentage (1.9%).
Given the low PIC of SNPs compared to SSRs a higher number of SNP markers are required to reach similar (PI) in genetic identification.
Sequences presented here are particularly rich in SSRs, when compared to available banana BAC end sequences in which only one SSR was observed every 13 kb [ 14].
This could result in reduced detectable deletion frequency for SSRs as compared to DArTs.
These observations coincide with previous reports suggesting a higher number of tri- and hexa- nucleotide SSRs when compared to the other categories in EST sequences.
Similarly, results using 9 SSRs were compared to those obtained using the set of 25 markers used for kinship estimation (see Material and Methods).
The present study recorded a relatively higher abundance of SSRs as compared to earlier reports in tea [ 15] and also in other plant species such as grapes [ 24], sugarcane [ 25], cereals [ 7, 22, 26] and coffee ESTs [ 23, 27].
Polymorphism, number of allele per locus and number of genotypes per locus for the 16 dinucleic and 23 trinucleic SSRs when compared to their respective position on the EST sequence (Table 3).
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