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The resolution in measuring genetic distance using SNPs based on allele-sharing was lower than the more polymorphic SSRs.
In this work we initiated the search for a new set of EST-SSR with the thought that given the high proportion of 5'UTR sequences in the ESTs we have obtained, there would be new classes and perhaps more polymorphic SSRs.
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As has been observed in other systems, SSRs with more repeats were more polymorphic than SSRs with fewer repeats.
Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search.
If there are more available polymorphic SSRs within the region defined by the flanking markers, use these to genotype only the recombinants and further narrow the interval.
Intron and UTR SSRs were more polymorphic than CDS SSRs due to low selective pressure in non-coding regions, which were consistent with previous reports.
To test whether the AT-repeat SSRs were more polymorphic than normal SSRs, a further upland cotton variety (Liaomian 7) and a sealand cotton variety (Hai 7124) were employed for genotyping against TM-1.
Across dinucleotide and trinucleotide loci, dinucleotide SSRs were significantly more polymorphic than trinucleotide SSRs (nA and He both P < 0.01; 2-sample t test).
Therefore, the AT-repeat SSRs selected in this study were deemed more polymorphic than normal SSRs.
EST-derived SSRs from diploid species tended to map more often to their orthologous genomes in corresponding tetraploid species [ 23], with G. raimondii-derived SSRs (43% polymorphism) being more polymorphic than G. arboreum derived SSRs (18%) in the same cross [ 24, 34].
We also expect lower PIC values for the EST-SSRs used in the present study than for the random and BAC-derived SSRs, even though we did not examine their PIC values, as the BAC-SSRs were more polymorphic than the EST-SSRs in the parental lines.
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