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This study established phylogenetic relationships among mango varieties collected from NIHORT, Ogbomosho, Saki, Oyo, Isehin and Ibadan using Simple Sequence Repeat (SSR) markers with a view of determining their polymorphism, gene and allelic diversities. Sweet Mango UI Acc-3 had the highest total genomic DNA of 1379.00µl, while OYOM ACC-5 had the lowest concentration of 0.9 gl from total genomic DNA of 0.25. The number of alleles ranged from 2 to 4 with an average of 2.50 alleles per locus in which the highest allelic frequency of 0.97 was recorded for EF 592217 and EF 59210 primers. However, Primer SSR20 had the highest information of polymorphic at 57.57% and highest gene diversity of 0.64. The result from the dendrogram showed that out of the three major clusters generated, the second delineated the highest number of 12 varieties in which Ogbomosho Mango Acc-2 (OGBM ACC-2) branched out at a distance of 0.15 from other varieties. Sweet Mango UI 3, Ogbomosho Mango Acc-2 (OGBM ACC-2), Julie Mango are potential future breeding accessions while Primer SSR20 could therefore be considered for further molecular breeding of other mango varieties and other tree crops in the Mangifera family.
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