Effects of phenotyping environment on identification of quantitative trait loci for rice root morphology under anaerobic conditions

In the rainfed lowlands, rice (Oryza sativa L.) develops roots under anaerobic soil conditions with ponded water, prior to exposure to aerobic soil conditions and water stress. Constitutive root system development in anaerobic soil conditions, has been reported to have a positive effect on subsequent expression of adaptive root traits and water extraction during water stress. We examined effects of phenotyping environment on identification or quantitative trait loci (QTLs) for constitutive root morphology traits using 220 doubled-haploid lines (DHLs) from the cross of 'CT9993-5-10-1-M' (CT9993; japonica, upland adapted) x 'IR62266-42-6-2' (IR62266; indica, lowland adapted) in four greenhouse experiments. Broad sense heritability (h(2)) was 75, 60, and 64% on average for shoot biomass, deep root morphology, and root thickness traits, respectively. Quantitative trait loci analysis identified 18 genomic regions associated with deep root morphology traits, but only three vs ere identified consistently across experiments. Three out of a total of eight QTLs, for root thickness traits were found in more than one experiment. The maximum genetic effects caused by a single QTL were increments of 0.05 g or deep root mass below a 30-cm soil depth, 0.9% of deep root ratio, 1.6 cm of rooting depth, and 0.09 cm of root thickness, with phenotypic variation explained by a single QTL ranging from 6.8 to 51.8%. The results demonstrate the importance of phenotyping environment and suggest prospects for selection of QTLs for deep root morphology, root thickness, and vigorous seedling growth under anaerobic conditions to improve the constitutive root system of rainfed lowland rice. There was some consistency in QTL regions identified, despite the presence of QTL X environment interactions

Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions

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 that arise later in the season. Constitutive root system development in anaerobic soil conditions 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 conditions. We examined quantitative trait loci (QTLs) for constitutive root morphology traits using a mapping population derived from a cross between two rice lines which were well-adapted to rainfed lowland conditions. The effects of phenotyping environment and genetic background on QTLs identification were examined by comparing the experimental data with published results from. four other populations. One hundred and eightyfour recombinant inbred lines (RILs) from a lowland indica cross (IR58821/IR52561) were grown under anaerobic conditions in two experiments. Seven traits, categorized into three groups (shoot biomass, deep root morphology, root thickness) were measured during the tillering stage. Though parental lines showed consistent differences in shoot biomass and root morphology traits across the two seasons, genotype-by-environment interaction (GxE) and QTL-by-environment interaction were significant among the progeny. Two, twelve, and eight QTLs for shoot biomass, deep root morphology, and root thickness, respectively, were identified, with LOD scores ranging from 2.0 to 12.8. Phenotypic variation explained by a single QTL ranged from 6% to 30%. Only two QTLs for deep root morphology, in RG256-RG151 in chromosome 2 and in PC75M3-PC11M4 in chromosome 4, were identified in both experiments. Comparison of positions of QTLs across five mapping populations (the current population plus populations from four other studies) revealed that these two QTLs for deep root morphology were only identified in populations that were phenotyped under anaerobic conditions. Fourteen and nine chromosome regions overlapped across different populations as putative QTLs for deep root morphology and root thickness, respectively. PC41M2-PC173M5 in chromosome 2 was identified as an interval that had QTLs for deep root morphology in four mapping populations. The PC75M3-PCIIM4 interval in chromosome 4 was identified as a QTL for root thickness in three mapping populations with phenotypic variation explained by a single QTL consistently as large as 20-30%. Three QTLs for deep root morphology were found only in japonica/indica populations but not in IR58821/ IR52561. The results identifying chromosome regions that had putative QTLs for deep root morphology and root thickness over different mapping populations indicate potential for marker-assisted selection for these traits