I am building a small horizontal fence. The facing is batu and matches my front entryway deck.
I put penofin penetrating oil on the fence boards. Do I need to seal the end of the hardwood fence boards? With what?
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Yes you absolutely want to treat the ends of fence boards, even if they don't face upwards but especially if they do.
Typically you wouldn't use anything different on them, just coat with the same product you use to protect the faces of the boards. However, an additional coat (or two) is advisable since the end grain is very much more absorbent than the face grain. So much so in fact that prior to installation some people even go to the trouble of standing their fence boards (and posts) in a shallow pool of the protective coating, letting the end grain soak it up for some time (how long varies, at least 10-15 minutes but sometimes over an hour) so that it penetrates deeply. Note however that this can leave a tell-tale darker colouring at the ends of the boards or posts.
Actual research based finishing outdoor wood - processes and products http://www.fpl.fs.fed.us/products/publications/specific_pub.php?posting_id=1020&header_id=p
There additional links in the pdf.
The service life of a Water Resistant Preservative (WRP) finish is about 1 year on the exposed surfaces of wood decks; however, a WRP is the easiest finish to reapply. It absorbs readily into the end grain of lumber and can prevent water absorption into the end grain much longer than 1 year.