Identification of Quantitative Trait Loci Associated with Grain Shape Using Cheongchenong/Nagdong Double Haploid Lines in Rice

We performed a molecular marker-based analysis of quantitative trait loci (QTLs) for the traits that determine appearance quality of the grains using 120 double haploid (DH) lines developed by anther culture from F1 hybrid of a cross between Cheongcheong (Oryza sativa L. ssp. Indica) and Nagdong (Oryza sativa L. ssp. Japonica). The traits studied included grain length, grain width, grain thickness, length to width ration and thousand grain weight. This experiment was conducted with two replications of 2013 and 2014. A linkage map with 217 DNA markers was constructed spanning across 2,067.1 centiMorgans (cM) at an average interval of 9.5 cM between markers and covering 12 rice chromosomes. Interval mapping procedure was used to identify the QTLs controlling five grain traits and QTLs detected were further confirmed using composite interval mapping. A total of 24 QTLs affecting grain appearances were identified and mapped on all the twelve chromosomes for 2 years at grain quality. Nine of the 24 QTLs were reproducibly detected in two year trials. Major QTL for grain length was detected on chromosome 5 in 2013 with a phenotypic variation of 64% and chromosome 7 in 2014 that explained 55% of the phenotypic variation. The QTL findings in this study will in future faciltate the gene isolation and breeding application for improvement of rice grain shape and yield.