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One of the newest methods in plant breeding programs is mapping quantitative trait loci (QTL) with molecular markers. In order to identify QTL associated with some chemical traits such as chlorine, nicotine, sugar concentrations and ash in oriental tobacco, a population of 55 recombinant inbred lines coming from the cross Basma seres 31 × SPT406 were evaluated for above mentioned traits. QTL mapping was performed using linkage map developed on 103 recombinant inbred lines by 64 molecular markers including 14 SSR, 24 ISSR and 26 retrotransposone. The linkage map is composed of 7 linkage groups (LGs). Composite interval mapping revealed 5 QTLs associated with studied traits. Phenotypic variation explained by identified QTLs varied between 0.34 and 0.70. Any QTL was not detected for sugar concentration in tobacco leaves. Common markers between some of studied traits can be due to linkage or pleiotropic effects. The common markers lead to increase the efficiency of marker-assisted selection in plant breeding programs via simultaneously selection for several traits.

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Mutagenesis has been one of the effective methods for creating genetic diversity and plant mutants can be significant bio-resources for crop breeding and functional genomics studies. The genetic and phenotypic diversity of 95 selected mutants from 17 mutant populations, obtained from an EMS mutagenized rice Hashemi variety, were phenotypically and molecularly assessed in M₃ generation. Phenotypic variation of these mutants showed that grain yield components varied among the selected mutants compared to the control plants. In parallel, genetic diversity assessed by 13 Inter-Simple Sequence Repeats )ISSR) primers showed that the number of amplified fragments per primer varied from 4 (pr1-7) to 11 (ISSR-7, ISSR-11). In general, 13 primers amplified 99 fragments, 50 of which were polymorphic (52.92%). The genetic variation created by ISSR markers within 17 populations varied from 11.11% in HM9 (Hashemi Mutant Line number 9) to 45.45% in HM2. The average molecular polymorphism value was 0.27. In the total genetic variance, 95% of differences were attributed to within-population diversity, and 5% were related to among-populations. The Unweighted Pair-Group Method with Arithmetic mean (UPGMA) trees illustrating ISSR diversity classified the rice mutant population into seven groups, which were further supported by model-based STRUCTURE analysis. In general, the studied mutant genotypes revealed desirable genetic characteristics in populations 13 and 17, with em₃h204 and em₃h280 genotypes being the most divergent.