Identification and analysis of QTLs for grain quality traits in rice using an introgression lines population

The demand for superior grain quality represents a major issue in rice (Oryza sativa L.) breeding. To study the genetic basis of rice grain quality, including traits specifying grain dimension and percentage of grains with chalkiness, quantitative genetic analysis was conducted in a population of 37 introgression lines (ILs) of indica elite variety Habataki in the background of japonica cultivar Sasanishiki across two different environments. The ILs showed transgressive segregation for all of the investigated traits, including percentage of grains with chalkiness, brown grain length, width, thickness, length/width ratio, length/thickness ratio, volume and 1,000-brown grain weight, the result indicated that these rice grain quality traits were polygenic phenomenon. Fifty-four QTLs were identified on eleven chromosomes, and 44 QTLs were associated with more than one trait, as a cause of the observed phenotypic correlations between different traits. Five stable QTLs, namely QPGWC.NH-1.1, QPGWC.NH-1.2, QGW.NH-3.1, QLW.NH-7.1 and QGV.NH-8.2, were identified in this study. This study provides useful information for marker-aided improvement of grain quality (grain dimension and percentage of grains with chalkiness) in rice; moreover, ILs carrying these QTLs constitute good candidates for future fine mapping and positional cloning projects.