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Kumble joined training before the toss, but left the ground early at the Punjab Cricket Association Stadium and his place was taken by rookie legspinner Amit Mishra.
Kumble did not take a wicket in the first test _ for the first time in India and only the third occasion in his 131-match career _ and his role in the side has come under increased scrutiny over the past week.
This will be Dhoni's second test as captain after he led the team against South Africa in April.
Mishra has played three one-day internationals and 77 first-class games, taking 303 wickets at an average of 24.91.
Australia will bowl in clear conditions on a pitch that is expected to turn heavily as the match wears on.
Australian Fast bowler Peter Siddle will play his first test after replacing Stuart Clark, who succumbed to an elbow injury on the eve of the match. Australia retained legspinner Cameron White, who will share the slow-bowling duties with Michael Clarke.
The first test of the four-match series was drawn when India reached 177 for 4 on the final day at Bangalore after being set 299 for victory.
Teams:
Australia: Matthew Hayden, Simon Katich, Ricky Ponting (captain), Michael Hussey, Michael Clarke, Shane Watson, Brad Haddin, Cameron White, Brett Lee, Mitchell Johnson, Peter Siddle.
India: Gautam Gambhir, Virender Sehwag, Rahul Dravid, Sachin Tendulkar, V.V.S Laxman, Sourav Ganguly, Mahendra Singh Dhoni (capt), Harbhajan Singh, Zaheer Khan, Amit Mishra, Ishant Sharma.
Umpires: Asad Rauf, Pakistan, Rudi Koertzen, South Africa.
TV Umpire: Amiesh Saheba, India. Match Referee: Chris Broad, England.
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