Genomewide association study (GWAS) on five panicle traits of 315 rice accessions introduced from international rice microcore germplasm bank was conducted. The panicle length (PL) and the primary rachis branch number (PBN) exhibited significant difference between the two plant locations, while grain length (GL), grain width (GW) and grain length to width ratio (GLWR) were not, indicating that PL and PBN are sensitive to environments. Totally 7, 5, 10, 8 and 6 chromosome regions or SNP (single nucleotide polymorphism) marker loci were significantly associated with PL, PBN, GL, GW and GLWR, respectively. Among them, eleven regions associated with grain shape and one region controlling PBN were consistence in two environments. Significant linear correlation was found between the average trait value and the number of favorable alleles carried by the cultivars in all associational loci. Among all associational loci, the cultivars in Aromatic (ARO) and tropical japonica (TRJ) subpopulations owned most favorable alleles, but those in temperate japonica (TEJ) subpopulation contained the least. The domestic varieties mainly harbored unfavorable alleles in 6 of associational loci detected. Totally 15 varieties from 11 different countries harbored more than 30 favorable alleles, which were fallen in TRJ subpopulation, demonstrating that the cultivars in TRJ subpopulation have high potential in rice breeding for high and stable yield. Based on these results, we discussed the approach to improve domestic rice panicle traits by using TRJ varieties.
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