¹ International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.

² Texas Tech University, Lubbock TX 79409-2122, USA.

In the rainfed lowlands, rice (Oryza sativa L.) develops roots under anaerobic soil conditions with ponded water, prior to exposure to water stress and aerobic soil conditions later in the season. Constitutive root system development in anaerobic soil has been reported to have a positive effect on subsequent expression of adaptive root traits and water extraction during progressive water stress in aerobic soil. We examined QTLs for constitutive root traits using 220 DHLs from a japonica/indica cross (CT9993/IR62266) and using 184 RILs from a lowland indica cross (IR58821/IR52561) in 4 and 2 greenhouse experiments, respectively. Comparison of positions of QTLs across 5 mapping populations revealed that 2 QTLs for deep root morphology, RG256-RG151 in chromosome 2 and PC75M3-PC11M4 in chromosome 4, were only identified in populations that were phenotyped under anaerobic conditions. PC41M2-PC173M5 in chromosome 2 was identified as an interval that had QTLs for deep root morphology in 4 mapping populations. The PC75M3-PC11M4 interval in chromosome 4 was identified as a QTL for root thickness in 3 mapping populations. Three QTLs for deep root morphology were found only in japonica/indica populations, but not in IR58821/IR52561. The results demonstrate the importance of phenotyping environment and suggest prospects for selection of QTLs for root traits. Despite the presence of QTL by environment interactions, some consistent QTL regions were identified.