Appleton declared after only 14 overs with his side having reached 140-3.
But the bottom-of-the-table Wigan side ran out four-wicket winners helped by an unbeaten 68 from professional Greg Stockdale.
Zimbabwe spinner Richard Sims took 5-63 before Wigan declared on 145-8 at Worsley, Matt Taylor 45. But like most of the games rain brought a halt when Worsley were 37-3.
Leigh were in trouble on 95-5 in their first ECB Premier League game of the season, as they chased Bootle's 150-8 declared.
League team skipper Dave Snellgrove, who joined Bootle from Ormskirk this season, top scored on 39 for Bootle, while Liam Zammit was unbeaten on 30 when Leigh's innings was ended. Tweet

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