Association mapping for flag leaf thickness in an indica rice population from South China

Abstract

Flag leaf is the most important source of photosynthate for developing rice grains, and flag leaf thickness is an important morphological trait in rice plant-type breeding programs. In the present study, we carried out association mapping for flag leaf thickness in a local rice population which consisted of 86 cultivars derived from breeding programs and planted in large areas in South China. Phenotyping was conducted in the field using nondestructive leaf thickness measurements. Two hundred and thirtysix SSR markers covering 12 chromosomes were employed to genotype the accessions. The association analysis was carried out using a unified mixed-model approach. The Q+K model was selected for investigating marker-trait associations. A total of eleven marker-trait pairs with significant marker-trait associations were identified which were distributed on eight chromosomes. Four of these loci had already been identified as related to flag leaf thickness in previous studies, while the other seven were novel QTLs. The locus PSM163 had the highest r 2 -marker value of the seven novel loci, explaining 21.54 and 18.49% of the phenotypic variation in 2008 and 2009, respectively. Three of four QTLs, which were detected in a F 2 mapping population in the validation study, could correspond to a significant locus in AM, respectively. The six alleles which had the highest phenotypic values at their respective loci should be considered as favored alleles in breeding programs. Pyramiding the favored alleles for flag leaf thickness identified in the study might be a valuable approach to construct an ideal plant architecture in rice breeding.