• The cultivars growing in different orchards in the three states namely J & K, H.P. and Uttaranchal will be identified. About 500-600 genotypes will be used for the present investigation.
• Passport data will be collected on all these cultivars especially with regard to morphological traits.
• Cytological studies, especially meiosis, will be conducted. This study will help in determining the ploidy status and residual homology.
• DNA will be isolated from all the genotypes and purified for further use.
• For molecular characterization, 40-50 SSR markers will be used. These markers will be selected out of the markers already developed by other workers in apple and as reported in the literature.
• In case some of the genotypes are difficult to differentiate using SSRs, AFLP analysis will be carried out in such cases.
• The entire data will be integrated to create a National Database on all the available germplasm of apple along with passport details on tree and fruit morphology, cytology and DNA fingerprinting. The database will be web-enabled which can be assessed by the stakeholders using specific queries.
• For association studies, the DNA variation data will be generated using multiplex marker sets. RAPD and AFLP markers will be applied to subsets of germplasm selected from the total germplasm representing contrasting types of identified traits of interest.

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Component - II: Creation of a reference molecular linkage map of apple and QTL analysis for fruit quality and growth patterns

• Selection of material for use as parents; suggested candidates are Maharaji, Delicious, Shireen and Ambri
• Reciprocal crosses will be made and a psudo-test cross type of mapping population will be developed.
• Populations of 200 – 300 plants, clonally propagated will be established.
• Collection of samples for DNA studies.
• Survey of parents using microsatellites, AFLP and RAPD markers.
• Phenotyping of mapping populations in three agro-climatic regions.

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