Association mapping of grain quality and flowering time in elite japonica rice germplasm

Grain quality traits play an important role in the economic prosperity of commercial rice markets. The objective of our research was to identify candidate molecular markers associated with three grain quality and flowering traits in a collection of elite rice japonica inbred lines evaluated in five U.S. states. Candidate marker effects were associated with the traits mapped within regions reported from previous QTL analyses while several new allelic interactions were also detected. Common markers for each trait were observed across two or more locations, and two-way interactions unique to a single location were also found. Significant genotype x location interactions were detected while broad-sense heritability estimates were low for all characters. All but one selected marker effect was associated with a reduction in apparent amylose content. A reduction in heading date at three locations was observed with one marker as a main effect or as a component of two-way interactions that mapped similar to 5 cM from the Hd3a flowering locus. The majority of selected effects for head rice were associated with modest to substantial increases in value. Marker loci and their interactions identified in this study highlighted targeted regions for future association studies and marker-assisted breeding efforts of grain quality traits. (C) 2010 Elsevier Ltd. All rights reserved.