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Nayana took gold with an effort of 6.53m while Shaili settled for silver with 6.34.
Spearheaded by India's first World Championship medallist Anju Bobby George, the Foundation has been nurturing the next generation of women athletes, including the fast rising long jumper Shaili Singh.
Santhosh Kumar Tamilarnsan and Sarvesh Anil Kushare crashed out in the 400m hurdles and high jump respectively.
Among the youngest of those identified for support is swimmer Riddhima Veerendra Kumar, the 14-year-old who made waves in the senior nationals.
Shaili won a silver at the Under-20 World Championships in Nairobi on Sunday.