Merlin clocked 11.35secs to win the semifinals heat number three as she bettered the earlier national record of 11.38secs in the name of Rachita Mistry set in 2000 in Trivandrum.
Merlin, however, finished third in the final race later in the day, clocking 11.95secs. Dutee Chand of ONGC won the gold in 11.73secs while H M Jyothi of Karnataka bagged the silver on a rain-marred day.
In a biggest upset of the day, Ankit Sharma of LIC pocketed the gold in men's long jump with a 7.73m ahead of Railways' Kumaravel Prem Kumar who had a hamstring injury during the finals and finished with his first round leap of 7.62m.
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Half-milers Tintu Luka and Sajeesh Joseph, both of Railways, lived up to their billings. Tintu retained her gold while Sajeesh made a 'hat-trick' of wins in 800m.
It was the fifth title at the National Open for Sajeesh and fourth for Tintu. Unlike Tintu, who got the gold in her own style in 2:01.87, Sajeesh had to fight it out with ONGC runner Manjeet Singh right up to the wire as just one-hundredth of a second decided the victor.
"I am satisfied with her performance as rain marred the event, and also it is the season ending Championship," Usha said when asked why her protege failed to clock sub two minutes.