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The Swede is the only player in red figures after rain and strong winds made for tough scoring conditions at Royal Troon, with Holmqvist following an opening-round 71 with a one-under 70 to head into the weekend with a one-shot advantage.
Austin Ernst and Germany's Sophia Popov are a shot back in a share of second, with Lee and Ko in the group of five players on one over after rounds of 69 and 71 respectively.
"It definitely has been a strange year," Holmqvist said. "I'm coming off an injury and still injured, so for me this break has been kind of good to just be able to focus more, rehab and kind of just heal and get a little bit stronger so I can be out here to perform again."
Holmqvist took advantage of the par-five fourth and sixth but posted back-to-back bogeys from the eighth to turn in 36, before following successive gains from the 13th by dropping a shot at the par-four 15th.
Lee finished with back-to-back birdies to get to one over for the tournament alongside Ko, Jasmine Suwannapura, Emily Kristine Pedersen and American Lindsey Weaver, who was using a malfunctioning trolley to pull her own clubs around the course.
World No 4 Nelly Korda is tied-ninth and three back with Japan's Haru Nomura, while seven-time major champion Inbee Park moved within five of the lead after a joint-low round-of-the-day 69.
Bronte Law bounced back from an opening-round 80 to post a one-under 70 and get into the ผลบอลสด7m on eight over that includes world No 2 Danielle Kang, the highest-ranked player in the field, while defending champion Hinako Shibuno missed the cut after rounds of 76 and 78.
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