The texture of your pie filling is built into apples’ DNA

Apples at Shelburne Farm in Stow.Valerie Ryan for The Boston Globe

New England offers an intriguing assortment of apples in the fall. Head to your local farm stand or to a pick-your-own orchard and you’ll be vexed with the perennial question of which variety to use for pies and crisps and which to eat out of hand.

Whether the apples in your pie bake into tender, well-defined slices or turn shapeless and mushy is built into the fruit’s DNA.

What gives apples a firm texture is the structure and thickness of the fruit cell walls, says Wesley Autio, professor of pomology and director of the Stockbridge School of Agriculture at the University of Massachusetts Amherst. Genetics determine differences in cell wall characteristics.

Cellulose gives cell walls structure, says Autio, and natural pectin in and between the walls connects them. (The thickener pectin can also be purchased to use in jams and jellies.) During ripening, pectin breaks down, loosening the apple’s structure. That’s why when you bite into an overripe apple, a fruit that was once crisp is now soft. The cells are pushed apart instead of snapping open.

Autio likens apple cells to cobblestones, and pectin to the cement that holds them together. “If the concrete between the cobblestones starts to break down, then the stones themselves are moved if you bang against them,” he says. In the same vein, cooking breaks down apple cell walls. Just how soft they get depends on the variety’s genetic code and how ripe they are going into the oven.

Every apple expert has a favorite baking variety (see accompanying list). Autio, who is giving an apple presentation at Boston Public Market later this month, says cooking completely breaks down the structure of an apple like McIntosh, making it particularly unsuitable for pies. “McIntosh apple pie is almost pushing toward applesauce,” says the scientist. But a Golden Delicious apple will stay firm and can even be tough. “That cell wall stays intact through the process of cooking; it doesn’t break down.” Autio likes Cortland for pies because they retain their shape with just the right amount of resistance. Others who use Cortland like the fact that they stay white after peeling.

When it comes to choosing a cooking apple, says Amy Traverso, senior lifestyle editor of Yankee Magazine and author of “The Apple Lover’s Cookbook,” the texture should match the dish. “Pie and crisps will cook about 45 minutes to an hour, so you would definitely want a firm apple for those,” she says. “But cooking pancakes or muffins, things that cook quickly where you don’t need that defined slice or chunk, tender apples are great.” Among the apples Traverso suggests for pies in her cookbook are Baldwin, Northern Spy, Rhode Island Greening, and Roxbury Russet. Gala perform nicely in pancakes, she writes, Mutsu in muffins.

The author recommends a mixture of apple varieties in one dish because flavor “can really range from lemony to spicy; some apples might even have a berry taste or a gingery taste.” She likes to store apples in a paper bag in the refrigerator.

Experiment, advises Traverso. “I would say that anything you make with local fresh apples is going to be really good,” she says.

Wesley Autio will give a free “All About Apples” talk and tasting at Boston Public Market on Oct. 22, 6:30-8:30 p.m., 100 Hanover St., Boston, 617-542-7696, ext. 2117, or go to www.bostonpublicmarket.org.

Related:

• Apple varieties used for baking