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Boro held on to second spot in the Championship in a tense tussle at the Riverside.
They took control in the first half and deservedly took the lead as Lee Tomlin sent Albert Adomah to slot home.
But as the game wore on the nerves set in and edgy Boro retreated and dug in and let Bolton back into the game then had to scramble clear from their box several time in an anxious finale.
They had chances to seal it as shot flew high and wide and Tomlin rattled the crossbar with a free-kick but it was far from a polished display,
But Boro won't mind. They won a crucial game on a night when all their promotion rivals also picked up full points.
Boro made four changes as they looked to bounce back from a frustrating 1-0 home defeat to Leeds on Saturday.
Dimi Konstantopoulos returned from a ban in place of Tomas Mejias, Ryan Fredericks was back for Emilio Nsue and up from Patrick Bamford and Lee Tomlin started in place of Kike and concussed Jelle Vossen.
Jet-heeled winger Mustapha Carayol was back on the bench after almost a year out with a cruciate injury.
After a scrappy start there was an early scare for Boro on four minutes when an under-hit Kalas back-pass sent Emile Heskey trundling into the box but Konstantopoulos was quickly out to clear the danger with a sliding tackle.
Boro started to take a grip on the game with a long spell of possession and some patient probing passing.
And they almost made the breakthrough on eight minutes as after a crisp move Patrick Bamford swept a ball down the left for Adam Reach to burst to the byline and drill a low ball in tha tBolton man Bannon deflected it just outside the near post.
From Grant Leadbitter's corner, Tomlin connected with a shot on the turn but it fizzed wide.
And soon after Reach went on a weaving run down the flank and wriggled into the box past two defenders but he stumbled and went sprawling as he tried to cut inside to find an angle for a shot.
Then Bamford laid a pass out wide for Albert Adomah and burst to the edge of the box for the return but the bal lgot stuck between his feet and Danns poked it away.
Bolton threatened on 18 minutes as they won a free-kick wide on the left and when Bannon whipped it in, defender Dervite climbed highest but headed well over.
Boro responded with a good chance as Friend sent Reach on a surging run down the left to cut the ball back to the edge of the box where unmarked Bamford blazed over the bar.
Then on 22 minutes Reach again scythed in from the left to get into the box but his angled effort was turned behind by a blocking tackle from Dervite.
Bolton probed as a long diagonal ball was nodded on by Heskey for Janko to collect by the corner flag but his ball back in towards the striker at the near post was easily cleared.
Then Janko stole a ball of Friend and sprinted towards the box but his square ball towards Heskey but Konstantopoulos dived in to intercept.
But Boro almost broke through on the half-hour as a perceptive Leadbitter back-heel split the defence and sent Bamford breaking into the box to drill in an angled 12 yards effort that was well saved by keeper Amos.
Then after a tussle in the centre-circle Bamford broke free and darted between two defenders to get into the box before being crowded out by two more.
And Boro finally broke the deadlock on 33 minutes as Tomlin shaped to send a ball out wide then deftly steer it forward between two sluggish defenders to send ALBERT ADOMAH darting to the edge of the box to slot calmly under the advancing keeper.
Bolton had a quick chance to respond on 38 minutes as Clayton failed to clear his lines and Janko stole a loose ball 25 yards out then skipped into the box to lash in a low shot that Konstantopoulos saved at the foot of his near post.
Boro may have had a second in a furious scramble on 44 minutes. Friend cut back a ball into a crowded box for Tomlin to barge through a tackle and his stabbed effort was deflected then Adomah drilled the loose ball goalwards and it was charged down but fell to Bamford who scooped over the bar from close range although the flag had already gone up.
Bolton's Vela was booked for a foul on Friend on 45 minutes.
HALF-TIME: BORO 1 BOLTON 0
Boro were quickly on the attack after the restart as Tomlin sent Bamford racing to the edge of the box on 50 minutes but former Boro man David Wheater came sliding in to tackle.
And Boro almost got a second as Friend did well to cut out a wayward pass outside the Bolton box then wriggle into box to cut the ball back for Bamford in space 12 yards out but he drilled his low shot a foot wide.
Bolton hit back with a couple of corners and from the second on 62 minutes when Heskey nodded down it bounced to Janko but with a defender on his back he could only shrug it wide off his chest.
And from another Heskey put a weak 10 yard looping header straight at keeper Konstantopoulos.
On 67 minutes Bolton's Dervite was booked for a foul on Bamford.
From the dead-ball Friend headed back across the face of goal and it appeared to be blocked by a defender's hand but penalty appeals were waved away.
On 68 minutes Bolton's Janko was booked for a foul on Kalas.
On 71 minutes Bolton put on Clough for Gudjohnsen.
There was a nervous scramble in the Boro box on 73 minutes as Bannon chipped into a crowd and bounced around and fell to Feeney before Kalas cleared.
Boro put Kike on for Bamford and Adam Forshaw for Reach on 75 minutes.
There was scare on 81 minutes as a sloppy back-pass was cut out by alert Bannon just outside the box and he darted forward and got to the byline then tried to squeeze in an angled effort but keeper Konstantopolus at the near post.
On 83 minutes Bolton put on Le Fondre for Janko.
There was another nervous scene in the Boro box on 85 minutes as Bannon crossed to the far post that bounced past Friend but although Feeney peeled off his man and stretched to make contact he could only hook it wide.
Boro had to soak up a lot of scrappy presure then broke out on 88 minutes as a long diagonal forward found Kike who held it up then slotted inside for Tomlin to scoop up and race to the edge of the box where he was bundled over.
From the free-kick a foot outside the box on 89 minutes Tomlin lofted a shot over the wall but with the keeper rooted it came back off the crossbar.
Bolton piled forward in stoppage time and had a hopeful penalty appeal waved away after a chaotic scramble in the box then after a corner Heskey was allowed to turn but then poked a weak shot that was charged down by Gibson and scrambled away.
In stoppage time Kike was booked for a foul on Dervite.
Then Bolton won a corner and their keeper came up but when it was headed down into the crowd Kike chested it down and then hooked clear.
And in the fifth minute of added time from another corner keeper Amos put in a looping header that Konstantopoulos saved and Heskey was booked for dissent in the aftermath.
BORO: Konstantopoulos, Fredericks, Kalas, Gibson, Friend; Leadbitter, Clayton; Adomah, Tomlin, Reach (Forshaw 75); Bamford (Kike 75). Subs: Mejias, Omeruo, Whitehead, Carayol, Wildschut.
BOLTON: Amos, Vela, Dervite, Wheater, Moxey, Danns, Bannan, Feeney, Janko (Le Fondre 83), Gudjohnsen (Clough 71), Heskey. Subs: Fitzsimons, Twardzik, Threlkeld, Slavchev, Walker
Ref: Andrew Madley (West Yorkshire)
Att: 16,569
