QTL mapping for rice grain quality: a strategy to detect more QTLs within sub-populations

Abstract

Wx is considered to be the most important gene controlling eating and cooking qualities and pasting properties in rice (Oryza sativa L.). In this study, a recombinant inbred line population derived from indica rice parents differing in apparent amylose content (AAC) was used to detect quantitative trait loci (QTLs) for ten grain quality parameters for rice quality improvement. QTL mapping was performed on the whole population and on two sub-populations based on Wx genotypes. A total of 29 QTLs were found in the whole population. Ten QTLs for 7 traits were detected in the two sub-populations, four of which (qPRO3.1, qPV9, qHPV9, and qCS7) were also detected in the whole population, whereas the other six were QTLs with minor effects that might be covered by the Wx locus. Besides the Wx locus with the largest effect on AAC and most pasting properties, there were another six QTL clusters contributing to grain quality located on chromosomes 2, 3, 5, 6 and 9. It was also found that some QTLs for peak viscosity, breakdown and consistency were closely linked to rice grain shape related QTLs on chromosome 3. A QTL cluster on chromosome 9 for peak viscosity, hot paste viscosity and cold paste viscosity was detectable in the whole population, which was close to the isoamylase 3 (ISA3) locus. A QTL cluster for both peak time and pasting temperature on chromosome 6 was near to the starch synthase I locus, and was potentially a new QTL with minor effect for peak time and pasting temperature. These findings will promote better understanding of the genetic regulation of rice eating and cooking qualities.