Pittsburgh Pirates top pitching prospect Paul Skenes saw his scoreless streak end at 14 innings when he allowed his first runs of the season Wednesday afternoon at Omaha.

Skenes had seven strikeouts and hit season highs by throwing 71 pitches in 4 1/3 innings in his fifth start for Triple-A Indianapolis. He allowed two runs (one earned) on five hits and one walk against the Storm Chasers.

Ranked the No. 3 overall prospect by MLB Pipeline, Skenes hadn’t allowed a run through his first four starts. The 6-foot-6 ½ right-hander, the 2023 No. 1 overall pick, topped 99 mph 21 times, hitting triple digits twice while throwing 26 four-seam fastballs that averaged 99.2 mph.

Skenes also threw 22 splinkers — a splitter-sinker hybrid — 13 sliders, five changeups, four sweepers and a curveball and generated 16 whiffs and eight called strikes. He topped his season high of 65 pitches in his previous start against St. Paul and produced his second-most efficient start of the season by throwing 50 pitches for strikes (70.4%). He threw 32 of 44 pitches for strikes (72.7%) against Memphis on April 5.

“He just keeps getting better,” Pirates general manager Ben Cherington said. “We see the pitch-mix coming into form. Working on efficiency, when he’s using the secondary and starting to build the pitch count up now.”

Skenes struck out three of the first four batters he faced before CJ Alexander hit an 87.5-mph slider over the middle for a triple to center field. Skenes struck out Cam Devanney, but Nick Eaton hit a 94.7-mph splitter for an RBI single.

Skenes gave up another single, to Brian O’Keefe, to start the third inning but got a fly out, strikeout and groundout.

Nick Loftin led off the fourth with a single, and Nick Pratto worked an eight-pitch at-bat to draw a walk and put a pair of runners on base. Skenes got Alexander to fly out to center but committed a throwing error on a Devanney grounder that allowed Loftin to score. Skenes answered by getting Nate Eaton swinging at a 99.6-mph four-seamer and O’Keefe looking at a 100.2-mph fastball to end the frame.

Skenes pitched into the fifth inning for the first time as a pro, and his outing ended after another eight-pitch at-bat, with John Rave getting a one-out single to left. Brady Feigl then replaced Skenes, who is expected to continue pitching in the minors until the Pirates feel his development is complete.

“Not surprised that he’s having success, but more underneath that just being intentional about what he’s doing,” Cherington said. “He’s working on things that will allow him to be a good major league pitcher and more than just he’s trying to be a good Triple-A pitcher.”

Kevin Gorman is a TribLive reporter covering the Pirates. A Baldwin native and Penn State graduate, he joined the Trib in 1999 and has covered high school sports, Pitt football and basketball and was a sports columnist for 10 years. He can be reached at kgorman@triblive.com.