Artocarpus altilis (Park.) Fosberg is an important fruit vegetable tree grown in the homesteads of southern part of India. To provide reasoned scientific management practices and conservation measures, the pattern of morphological and genetic variation were investigated for six populations using Amplified Fragment Length Polymorphism (AFLP) markers and 15 morphological traits. The use of five selective primer combinations on 60 samples resulted a total of 414 bands in which 85% were polymorphic. The values of Nei's genetic distance varied from 0.0044 (PalaiPalghat) to 0.3376 (Palghat-Mangalore). Analysis of molecular variance revealed most of the variation within populations (57.45%) than (42.55%) among populations. The genetic variation by AFLP data is not reflected in quantitative morphological variables. However, the genetic and geographical distances were positively correlated which were further well supported by the PCO analysis and Dollo-parsimony tree, both show the tendency of the individuals to group according to the geographical localities.
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