Mapping quantitative trait loci (QTL) associated with cooking quality in rice (Oryza sativa L.)

A mapping population consisting of 236 F2:3 families derived from the cross between two rice varieties, Gharib as female parent (with good cooking quality) and Sepidroud as male parent (with poor cooking quality) was used to analyze the quantitative trait loci (QTLs) associated with amylose content (AC), gelatinisation temperature (GT) and gel consistency (GC). A total of 105 single sequence repeat (SSR) markers were used to construct a genetic linkage map, covering a total length of 1440.7 cM of the genome in rice (Oryza sativa L.) with an average distance of 13.72 cM between markers. Twelve independent QTLs were identified using composite interval mapping. These loci consisted of three QTLs for GT, eight QTLs for AC and one QTL for GC, most of which are reported here for the first time. For GT the QTL explaining the largest proportion of variance (18.4%) was located on chromosome 6, the same locus as the alkali degeneration gene (alk). For AC, four QTLs were found on chromosome 6, one of which was located at the interval RM586-RM190 explaining 19.3% of the total variation and which should coincide with the waxy region (wx) located on the short arm of this chromosome. The results using Iranian rice cultivars, in combination with previous reports further confirmed that alk and wx regions play a considerable role in determining cooking and eating quality of rice.