With bus and train fares increasing on Sunday, Metro Transit has developed a new program to help low-income riders stay on board.

The Transit Assistance Program, which was a pilot program last year, will allow qualified commuters to ride anytime for a discounted rate of $1. The $3 million annual cost will be covered in part by discontinuing the stored-value bonus for Go-To card holders, according to Metro Transit.

Losing the 10 percent bonus might be a disappointment to commuters, but Metro Transit is working at “redistributing benefits to riders,” said Howie Padilla, a Metro Transit spokesman.

“As we explored other options, if there was going to be a change in fares, we asked, ‘What can we do to help some of the folks that we have (riding Metro Transit)?’ ” Padilla said. “The TAP program is something we looked at to help some of our communities that depend on our services.”