Mapping quantitative traits for grain physical and textural quality in Cambodian Jasmine rice PRD

Grain physical and textural traits are key parameters that are assessed in rice quality improvement programs. In order to dissect the genetic basis of the premium Cambodian quality rice Phka Rumduol (PRD), a population including more than 300 recombinant inbred lines derived from PRD and Thmar Krem was used to map quantitative trait loci (QTLs) for grain length (GL), grain width (GW), degree of chalkiness, grain translucency and texture-associated traits including amylose content (AC), gelatinisation temperature (GT), gel consistency and pasting properties derived from a rapid visco analyser. QTL analysis revealed large-effect QTLs and minor QTLs for these traits of quality, indicating a complex interplay between major and minor genes. The QTL located on chromosome 3 is the major locus for GL, and the one on chromosome 5 plays a major role in determining GW. A novel QTL for GL was identified on the short arm of chromosome 6 and explained about 20% of the phenotypic variation in GL. Grain translucency and chalkiness were largely controlled by QTLs on chromosome 5 and 6. Putative genes for texture-associated traits relate back to the starch biosynthesis pathways. Major QTLs for AC and GT colocalised to the Waxy and starch synthase IIa genes on chromosome 6, respectively. Minor QTLs on chromosomes 3 and 8 were identified for AC, setback, peak viscosity and hot-paste consistency, and on chromosomes 4 and 7 for GT and pasting temperature. This is the first QTL mapping study for the quality of Cambodian rice.