A collection of 360 indica elite breeding lines phenotyped for grain yield and ten related traits in eight environments was used to test the usefulness of 39 well characterized yield related genes/QTL in breeding for irrigated ecosystems.
Using the 53 random SSR markers identified two major subpopulations.
All the target genes/QTL were associated with two or more measured traits including traits unreported previously.
Significant gene-by-environment interaction was present for all the target genes/QTL.
GY could not be well predicted using the markers significantly associated with the 11 measured traits or all target markers based on stepwise multiple linear regression analysis.