Effect of pyramiding root QTLs on root morphology using several root phenotyping assays

Drought restricts the stability of rice production; a strategy to overcome drought stress is acquiring water by deep rooting. For a breeding strategy using DNA marker-assisted selection, we can use several root QTLs (DRO1, qRL6.1, qFSR4, and Sta1), which have been fine-mapped in rice, as promising gene resources. However, the effect of each QTL under different phenotyping systems and the effect of pyramiding multiple QTLs on root morphology has not been examined in detail.This study aims to clarify the effect of pyramiding root QTLs on root traits using several root phenotyping assays. We used ten near-isogenic lines, including single or multiple root QTLs in the genetic background of shallow-rooted lowland rice, IR64. Four target QTLs were derived from deeprooted upland rice, Kinandang Patong; DRO1 (root growth angle), qRL6.1 (root length), qFSR4 (root volume), and Sta1 (stele size). Five experimental setups were used to evaluate the QTL effects at different growth stages. 1) basket assay and 2) hydroponic assay in the greenhouse to evaluate root morphological traits at an early stage, 3) pot assay in a growth chamber to evaluate the root system architecture by X-ray CT scan, 4) lysimeter assay in a greenhouse and 5) field assay using rain-out shelter to determine the root distribution under well-watered and drought conditions. The effect of DRO1 on deep rooting was observed in the basket assay, lysimeter assay with drought stress, and field assay. qRL6.1 effect on maximum root length was observed in hydroponic assay when introduced alone but not when pyramided with other root QTLs. qFSR4 impact on the increase of root volume per tiller was observed in lysimeter assays in lines, including single/multiple QTLs. Sta1 effect was not observed, possibly due to the root samples being younger than previously reported. The impact of DRO1 has been reported at both early and late stages, but the result when pyramided with other root QTLs were also observed. This study clarified the effect of DRO1 for deeper rooting when introduced alone and with multiple QTLs, indicating the possibility of modifying root phenotypes by QTL pyramiding.