Mapping quantitative trait loci underlying the cooking and eating quality of rice using a DH population

The cooking and eating quality of rice has attracted more attention recently. In a comprehensive effort to unravel its genetic basis, we conducted a genome-wide analysis of six traits representing the cooking and eating quality of rice grain, namely, amylose content (AC), gel consistency (GC), gelatinization temperature (GT), water absorption (WA), cooked rice elongation (CRE) and volume expansion (VE) using a DH population derived from the anther culture of an F-1 hybrid between WYJ 2 (japonica) and Zhenshan 97B (indica). For each trait, one to three quantitative trait loci (QTL) were found, which were located on chromosomes 1, 2, 3, 6, 11. QTL analysis revealed a major QTL specifying GT, located at the interval RM276-RM121, which should be the same locus as the alkali degeneration gene (alk), while for each of the remaining five traits the QTL explaining the largest proportion of variance was located on the short arm of chromosome 6, centered at RM190 (found in the waxy gene). Our results, in combination with previous reports, further confirmed that either the waxy gene itself or a genomic region tightly linked to it plays a major role in determining the cooking and eating quality of rice.