Quantitative trait locus (QTL) analysis of percentage grains chalkiness using AFLP in rice (Oryza sativa L.)

Chalkiness is a major concern in rice (Oryza sativa L.) breeding because it is one of the key factors in determining quality and price, which is a complicated quantitative trait and controlled by maternal, endosperm and cytoplasmic effects. In this study, we conducted grain chalkiness percentage quantitative trait locus (QTL) analysis using amplified fragment length polymorphism (AFLP) marker and bulked segregant analysis combination. The materials was an F12 recombinant inbred line population from a cross between two indica varieties, the parents of Shanyou63, the most widely grown hybrid rice in China. Three QTLs of grain chalkiness percentage were mapped in chromosome 3, 6 and 8, which were named qIPGC-3, qIPGC-6 and qIPGC-8, respectively. The conventional method of QTL analysis clearly confirmed the loci of grain chalkiness percentage. It demonstrated that, AFLP technique coupled with bulked segregant analysis (BSA) can allow us to identify the locus governing primordial germ cell (PGC) and to effectively determine QTLs chromosome location of this locus on the molecular linkage map of rice.Key words: Rice, quantitative trait locus (QTL), percentage of grain chalkiness, amplified fragment length polymorphism (AFLP)