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I am running dual boot on my iMac. I upgraded my OS to OS X Yosemite yesterday,and now I can't boot into Ubuntu. How can I fix my issue?

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If your Ubuntu partition is still there, you probably need to install a rEFIt (or an equivalent) so you can choose your Ubuntu partition.

http://refit.sourceforge.net

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This gives the simplest solution for me. 

diskutil list

and you will see something like:

$diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *251.0 GB   disk0
   1:                        EFI                         209.7 MB   disk0s1
   2:          Apple_CoreStorage                         175.6 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3
   4:       Microsoft Basic Data                         70.3 GB    disk0s4
   5:                 Linux Swap                         4.2 GB     disk0s5
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS Macintosh HD           *175.3 GB   disk1
                             Logical Volume on disk0s2
                             41AF7850-5594-4959-A135-582BF79FDE46
                             Unencrypted

Then use: 

diskutil corestorage revert /dev/disk1

And reboot, refind now works again.

I got the solution from the related question here: https://unix.stackexchange.com/questions/150670/install-refind-on-os-x-10-10-yosemite/164614, you can try other solutions there if this one fails.

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