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The SSR markers designed in our work are also applicable for such a study.
It inferred that 3622 ILP markers designed in this study are unique either in the foxtail millet or in the rice genome.
Two SNP markers designed in the D and SP genes, for which 'Micro-Tom' has mutant alleles, showed polymorphism between 'Ailsa Craig' and 'Micro-Tom'.
Nine markers designed in this study did not map to corresponding chromosomes, this is likely a result of errors occurring due to mismatching of chromosomes between diploid and tetraploid cottons.
The 20 highly polymorphic genic-SSR markers designed in this study were used to assess the genetic diversity in a set of 30 genotypes representing diverse cultivated genotypes, wild species of Cajanus and inter-specific derivatives.
Overall, the hypervariable Class I and UTR-derived microsatellite markers designed in this study from the TF genes provided a strategy for the rapid selection of more polymorphic markers from the huge marker database and thus would have greater utility for large-scale validation and efficient genotyping applications in chickpea.
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Informative DNA markers were downloaded from the Mouse Genome Database (DXMit114, DXMit96 and DXMit41)., Custom DNA markers were also designed in-house around novel SSLPs between CAST and SWR alleles in the region of Gct4 (Table S1 ).
Primer sequences and other information for DNA markers designed and used in this study are listed in Additional file 5: Table S2.
Sixty markers were designed in this third round of marker development with an average density of about 0.2 Mbp between the markers (Additional file 2: Table S1).
Additional homology information was obtained for some PCR markers designed from Arabidopsis sequences mapped in BnaDYDH (ACGM from Fourmann et al. [ 55] and specific PCR markers prefixed 'At', Delourme et al. [ 25]).
Overall, 58% of the markers designed from EST sequence which amplified in genomic DNA were polymorphic between the parent lines.
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