49ers set to gather for first time under Chip Kelly and with Colin Kaepernick

The San Francisco 49ers open their first offseason program under new coach Chip Kelly on Monday. Here’s where things stand with the Niners with the NFL draft just a few weeks away.

What the 49ers hope Kelly brings: Offense. Lots and lots of offense. The 49ers scored the fewest points in the league last season and ranked next to last in total offense. Kelly is synonymous with quick-strike, high-scoring offenses, from his days in college at Oregon to his star-crossed run with the Philadelphia Eagles the last three years. And as long as Colin Kaepernick is on the roster, the Niners hope Kelly can get the dual-threat quarterback back to the form he exhibited when the Niners made a Super Bowl run in 2012 and advanced to the NFC title game in 2013. But he regressed in Jim Harbaugh’s final season and was benched by Jim Tomsula last year. And if Kaepernick is indeed gone – his agents requested a trade at the combine – the Niners need Kelly to work his magic with the forgotten starter, Blaine Gabbert. And what if they draft a quarterback?

The biggest question mark about Kelly: Kelly is seen as a Quarterback Whisperer of sorts, and if Kaepernick is indeed gone by the time training camp opens in July, any time he will have spent with Kaepernick in the offseason program will have turned out to be wasted time. Especially when it could have been used on Gabbert. The biggest question, then, is: If Kaepernick sticks in Santa Clara, can Kelly “fix” him? And don’t forget that Kelly left Philadelphia with a tarnished reputation for his dealings with players, purportedly running the Eagles like a college program. Is he going to have urine tests and smoothies galore for accomplished veterans like NaVorro Bowman?

Key additions: The Niners’ lone outside free-agent signing of note is left guard Zane Beadles, who inked a three-year, $11.75 million deal. No, it was not the sexiest signing, but it may turn out to be the most important. Kaepernick and Gabbert were sacked a combined 53 times last season, and the offensive line was a leaky work in progress. The 6-foot-4, 310-pound Beadles, a Pro Bowler for the Denver Broncos in 2012 who spent the past two years with the Jacksonville Jaguars, has started 94 of his 96 games and played every snap in 79 of 80 regular-season games over the past five seasons, missing just nine snaps in that time frame, per Pro Football Focus. Still, PFF, which gave him a +17.1 grade to rank 16th among 81 guards in 2012, issued him a -14.6 grade last season with the Jaguars, when he moved away from a zone-blocking scheme and his 41 pressures allowed were the fifth-most among guards. Beadles’ addition should mean the Niners are heading to a zone-blocking scheme as well.

Key subtractions: For all of the distractions Alex Boone created off the field – first defending Harbaugh before blasting him, saying the game officials “sucked” in a tough loss to the Arizona Cardinals last season, holding out and creating instability in the trenches – Boone was an institution on the offensive line, starting in all but five games over the past four seasons. He is now the Minnesota Vikings’ issue. And while the team’s leading pass-catcher the past three seasons – Anquan Boldin – remains on the market, there is no sense the Niners are interested in re-signing him, as general manager Trent Baalke said last week at the NFL owners meetings he had not spoken to Boldin since the end of the season.