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Alliums are the most popular for their culinary usage and nutraceutical benefits. Their productions are greatly affected by the multiple biotic and abiotic stresses. Poor characterizations of genetic resources are the major bottleneck in genetic improvement of alliums. Chloroplast derived simple sequence repeat (cpSSR) have recently gained much popularity due to their maternal inheritance and low recombination along with their hypervariable nature. In this study, 22 chloroplast-derived SSR markers were produced from chloroplast genomes of A. cepa and A. sativum. Repeat comparison revealed tri nucleotide repeats were in higher proportion (50%) compared to other repeat motifs. The number of alleles ranged from 2 to 4, heterozygosity from 0.009 to 0.540, and PIC from 0.007 to 0.427. The polymorphism survey and clustering of twenty-two cpSSR markers of twenty-five alliums, lead to three groups (groups I, II, and III), indicated the usefulness of these cpSSR markers. This demonstrated that cultivated A. cepa and A. sativum belong to different groups II than most wild alliums, confirming the usefulness of the AccpSSR and AscpSSR markers that will allow introduction of desirable biotic and abiotic tolerance traits from various wild alliums to selected cultivated alliums. In addition, these cpSSRs were validated in 79 alliums, divided them into three groups using Jaccard dissimilarity and Bayesian model-based structure analysis. Subsequent clustering allowed us to identify diverse alliums, for constructing core collection of germplasm resource. The study will be useful for molecular breeding and genomic selection based crop improvement. |
