QTL mapping for anthocyanin and proanthocyanidin content in red rice

Anthocyanins and proanthocyanidins are the primary pigments of red rice and are also important functional nutrients for human health. To identify novel quantitative trait loci (QTLs) underlying anthocyanins and proanthocyanidins (ANC and PAC) in rice, a recombinant inbred line (RIL) derived from a cross of red rice ‘Hong Xiang 1’ (‘HX1’) and white rice ‘Song 98-131’ (‘S98-131’) was cultivated in six environments. A genetic map containing 126 markers covering 1833.4 cM with an average of 14.55 cM between markers was constructed. A total of 21 additive QTLs (A-QTLs) for ANC and PAC were identified from six environments using the IciMapping v3.3 software. Two new QTLs, qANC3 and qPAC12 - 4 , were detected in several environments, and explained significant phenotypic variance. Nine QTLs of ANC and PAC were detected with additive × environmental interaction effects (AE effects) by QTLNetwork 2.1 software, but no epistatic and epistatic × environmental interaction effects (AA and AAE effects) were detected. The information obtained in this study could be useful for fine mapping and molecular marker-assisted selection of ANC and PAC in rice.