I've been wrestling with producing a 50% Whole Wheat sourdough loaf that has good flavor and an open, chewy crumb. I've described my difficulties, and, finally a successful attempt in: http://www.thefreshloaf.com/node/25804/whole-wheat-sunday
I won't repeat the details here, but I'll summarize what I've learned. I believe the comments are relevant to all lean dough sourdough breads to some extent, but the degree of importance may vary depending on the flours used.
Flavor: Flavor is developed in p1refements, and during bulk fermentation. Retarded bulk fermentation improves flavor. All of my earlier exploration flour prefermented during the levain building ranged from 15% to 25% of the flour, all whole wheat. I also experimented with retarding the doughs' bulk fermentations 0 to 15 hours at 38°F to 56°F. Most recently, I've settled on a formula that preferments 15% of the flour, all whole wheat, and retards bulk fermentation 15 hours, at, nominally, 54°F.
Crumb: Crumb development has many variables: flour types, mixing and kneading, hydration, baking temperatures, steam or no steam, and oven spring, arguably the most probable major contributors. In my 50% Whole Wheat failures I found, with dough hydrations nearly constant between 65% to 68%, the biggest influence was Whole Wheat's effect on a dough's strength. i.e., its shortening effect on gluten development. In early attempts I tried hand-mixing and post-autolyse kneading, followed by periodic S&F; and two-speed machine mixing, without post-autolyse machine kneading, followed by periodic S&F. I subsequently, tried one or two speed mixing, followed by post-autolyse machine kneading followed by periodic S&F. Not until I increased the the machine kneading time to more than twice what I use for white flour sourdoughs did I achieve the crumb we like.
Ultimately, I found mixing all ingredients (including the 2% salt) on speed 1 (Kitchenaid Pro 600, spiral dough hook), followed by a one hour autolyse, then with 7 minutes of machine kneading on speed 2, and subsequently doing 3 S&F at one hour intervals does the trick.There are pictures in the aforementioned post.
However, there is one negative side-effect from building the levain entirely with whole wheat flour. I maintain my refrigerated seed starter with KA bread flour only, and I replace my seed starter entirely every week with fresh levain, scavanged from excess intentionally into my weekly sourdough bake's levain build. Unfortunately, in weeks I build levain with other flours, I also separately build a bread flour levain to replace my seed starter.
This week, wanting to bake 50% Whole Wheat sourdough, I tried something different. I built the levain with 15% of the formula's KA bread flour, and soaked all of the formula's Whole Wheat flour in an equal amount (by weight) of the formula's water for eight hours. Subsequently, I made the dough exactly as described, and replaced my seed starter with the excess levain.
I don't know if the pre-hydrated Whole Wheat flour qualifies as a Soaker, since it was not "hydration neutral", but for lack of a better name that's what I'll call it. Soaker or otherwise, I'm pleased with the results.
Flavorwise, we didn't loose anything, It may even be a bit better than usual, and...
the crumb is everything we ask for.