This was a paper that was approved as ROI000384 and subsequently submitted and accepted by PLOS ONE with minor changes. However it was subsequently agreed that some changes would be made to emphasize the comparison with ROI000372 which has now been formally published and can be fully referenced. This has been done. A version with marked up changes that directly affect the request (to simplify matters) has been sent separately to Victoria Hatton.  

Second part of Milestone7. This paper acknowledges the results of the predicted methane paper (ROI#372). This paper compares the GWAS results from both datasets in the discussion, as appropriate due to being two different methane traits and on two different species genotype platforms. 

 Please note PLoS ONE guidelines state that funding sources should not be included in the acknowledgments or anywhere in the manuscript file. This information will be provided during the manuscript submission process. during this process I will acknowledge PGgRc, NZAGRC and GRA.

