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Hygromycin was used as the selection marker in rice transformation.
More recently, Collard and Mackill [ 32] developed another DNA marker in rice, the start codon targeted (SCoT) marker, based on the short conserved nucleotide sequence that flanks the start codon ATG.
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SSRs and SNPs are the two most widely used molecular markers in rice.
To date, there are no reports of using these markers in rice breeding programs.
b STS sequence-tagged site; SSR, simple sequence repeat Fig. 2 Detection of patterns of molecular markers in rice lines.
SSR markers are co-dominant, multi-allelic, easy to use and inexpensive; thus, they have been the most widely used markers in rice for a long period of time (Tautz 1989; McCouch et al. 2002).
We believe that they should be used as genetic markers in rice in the future.
To the best of our knowledge, there is no report on the development of candidate gene based SSR markers in rice.
The unrooted phylogenetic tree constructed based on molecular diversity values of a set of GNMS markers in rice genotypes clearly established molecular genetic relationships among the domesticated rice cultivar groups, thereby suggesting their utility in defining varietal identity in commerce.
Fifty-six of the 60 markers gave amplification around 55°C annealing temperature with a success rate of 93.3% that suggested the utility of genic non-coding sequences (with balanced GC content of 48%to52%2%) for developing large-scale microsatellite markers in rice.
The mean PIC value of all 18 cgSSR primers in the present study was 0.278 which is higher than the previous report describing salt responsive miRNA-SSR markers in rice [ 31].
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