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Background  Poor grain plumpness (GP) is one of the main constraints to reaching the yield potential of hybrid rice.    Results  In this study, the GP of 177 rice varieties was investigated in three locations across 2 years. By combining the genotype data of 261 simple sequence repeat (SSR) markers, association mapping was conducted to identify the marker-GP association loci. Among 31 marker-GP association loci detected in two or more environments and determined using general linear model (GLM) analyses, seven association loci were also detected using mixed linear model (MLM) analyses. The seven common loci detected by the two analytical methods were located on chromosomes 2, 3 (2), 7, 8 and 12 (2) and explained 7.24~22.28% of the variance. Of these 7 association loci, five markers linked to GP were newly detected: RM5340 on Chr2, RM5480 and RM148 on Chr3, RM1235 on Chr8, and RM5479 on Chr12.    Conclusions  Five marker-GP association loci were newly detected using both the GLM and MLM analytical methods. Elite allele RM505-170 bp had the highest average phenotypic effect on increasing the GP, and the typical carrier variety was ‘Maozitou’. Based on the distribution of the elite alleles among the carrier varieties, the top 10 parental combinations for improving the GP in rice via cross-breeding were predicted.    Electronic supplementary material  The online version of this article (10.1186/s12863-017-0559-6) contains supplementary material, which is available to authorized users.

Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping