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The present study was conducted on different accessions of Moraceae to evaluate the genetic variation in them on the basis of morphological and biochemical attributes as well as by using molecular markers (SSR and ISSR). The developmental genes cup shaped cotyledons (CUC2) were also studied in order to confirm their functional status. For morphological, biochemical and molecular studies mulberry fresh leaves were taken and all the parameters were taken in replicates. Morphologically leaves of the majority of the accessions had light green color, acute tip, and soft surface along with cordate shaped leaves.The others had lobed shape, dark color, doubly serrate or dentate, acuminate and coarse leaves. There were significant differences in means of lamina length, lamina width and leaf area index. In biochemical analysis, the carbohydrates content was the highest in Korean subni (3.7626±0.204 cm) followed by Morus nigra(3.728±0.1795 cm), Morus latefolia (3.643±0.2458 cm) and P.F.I (3.568±0.3057 cm). Punjab II (1.704±0.1695 cm) showed the lowest carbohydrates content. The protein contents of Kanmasi Japan (1.7007±0.0049 cm) were higher as compared to Punjab-II-punjab (1.4030±0.0455 cm). The higher values of carbohydrate and protein content revealed that the leaves had the more palatability for silkworms. Lun-40-punjab showed the highest total phenolic content. Phenolic play a key role in traditional medicines. The maximum IC50 value was of Morus indica(172.21 mg/g) followed by Morus alba(152.7 mg/g) and PFI (122.4 mg/g). Punjab II Punjab (11.6), Kanmasi Japan (11.5) showed the minimum and same amount of anti-oxidant activity. One of the developmental genes CUC2 was observed in seven Morus strains. This strategy produced good-quality sequences, which were analyzed and compared to each other and to theCUC2c sequence of the reference M. notabilis strain.The sequencing results showed that the mean distance present in the overall sequence pairs xvii was 0.017. Molecular diversity between thirty accessions was checked through DNA markers i.e. SSR and ISSRs by the use of different softwares (NTSYS PC 2.2, Minitab, Statista, R) The SSRs produced 15 polymorphic bands out of 25 (60%) SS18 and MULSTR1 showed best results with the highest PIC and hundred percent polymorphism while the least was shown by SS04. It was also obvious that pic of SSR was somehow less than ISSR. The analysis of molecular variance (AMOVA) gave P value of 0.6434. The ISSR markers showed more polymorphism with more PIC value. The P value obtained from the results was 0.1089, while CV was 35.7. Our diversity results proved that all group were somewhat distant
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