Simple sequence repeat markers reveal multiple loci governing grain-size variations in a japonica rice (Oryza sativa L.) mutant induced by cosmic radiation during space flight

Abstract

Quantitative trait locus (QTL) for grain size traits that include grain length (GL), grain width (GW), grain thickness (GT) as well as thousand grain weight (TGW) were identified using F2 population derived from a cross between a japonica cultivar Nongken58 and its large grain-sized mutant, ‘Dali’, which was selected in SP2 generation of plants from Nongken58 seeds exposed to cosmic radiation upon space-flight, and then advanced it over eight successive generations by bagging the panicles to ensure self pollination. ‘Dali’ had similar GW and GT but 4.8 mm longer in GL, and 18.1 g heavier in TGW than those of Nongken58. Seven main-effect QTLs (M-QTLs) were identified for the grain size and weight traits. Among them, three M-QTLs, QGs3a and QGs3b for both GL and TGW, and QGs5 for GW, GT and TGW, which had strong additive effects on grain shape and grain weight, were validated in the two F2 plant-derived F3 populations. The three M-QTLs were found to be non-allelic to the cloned genes GS3, GL3.1, qSW5 and QGs5 by comparative mapping. However, there was only one pair of digenic epistasis involving QGs3b for TGW detected in this population. Interestingly, homozygous ‘Dali’ alleles at the QGs3a, QGs3b and QGs5 showed significant increase in the grain size and weight, suggesting these novel alleles of ‘Dali’ at the above three loci may be a very useful for marker-assisted improvement of grain quality for japonica cultivars.