The nectarine (Prunus persica var. nucipersica) is a smooth-skinned variety of the peach (Prunus persica) and not a separate species, as some people believe. Growing a nectarine tree from seed will provide you with a tree, the fruit of which may not be of the same quality, according to Penn State University's Horticulture Department. Nectarine trees need full sunlight and warm temperatures to thrive. Begin preparing your seed for germination in mid-January.
Remove all fruit pulp from the seed by scrubbing it under running water. Place the seed in a well-ventilated area until it is completely dry.
Wrap the seed in a handful of moist, not wet, peat moss, and place it in a plastic container. Seal the container and place it in the refrigerator for 130 days.
Dig a hole in the planting area in the garden that is twice the depth of the seed's longest dimension. Remove the seed from the refrigerator and place it in the hole. Cover the seed with garden soil and then 2 inches of sand. Water the area to a depth of 6 inches.
Place a square of hardware cloth over the planted seed and push the edges into the soil to a depth of at least 2 inches. This will protect the seed from squirrels and other critters.