Hi its very difficult task to extract DNA directly from seed since seeds have more protein and quality of DNA will be poor and you have to use lot of protenase. Hence use germinated/sprouted the seed for DNA extraction and follow this protocol
Genomic DNA extraction: DNA extraction from seedling was based on procedures outlined by Meng et. al. (1998). Seeds were kept for germination by following top of the paper (TP) method in petri plates (ISTA, 1996). 0.2 g of one week old seedlings was collected from incubated petri plates, surface sterilized with alcohol and washed with sterile distilled water. 0.2 g of seedling was homogenized in liquid nitrogen with 3.5 ml CTAB buffer and 14 L of -Mercaptoethanol and incubated at 65˚C for 15 minutes. Then 400μL 24:1 of chloroform:isoamyl alcohol mixture was added and blended thoroughly for 5 min. After centrifugation (5 min, 13 000 rpm), aqueous layer was pipetted into a new eppendorf tube and an approximately equal olume of cold ethanoll was added. After storage at -20 0C for 30–60 min, precipitated DNA was centrifuged, vacuum dried and finally stored in TE buffer.
I have followed this for tomato seedlings: http://www.researchgate.net/publication/215869955_Varietal_Characterization_of_Tomato_Cultivars_Based_on_RAPD_Markers