Mapping of genes controlling aluminum tolerance in rice: comparison of different genetic backgrounds.

Aluminum toxicity is the main factor limiting the productivity of crop plants in acid soils, particularly in the tropics and subtropics. In this study, a doubled-haploid population derived from the rice ( Oryza sativa L.) breeding lines CT9993 and IR62266 was used to map genes controlling Al tolerance. A genetic linkage map consisting of 280 DNA markers (RFLP, AFLP and SSR) was constructed to determine the position and nature of quantitative trait loci (QTLs) affecting Al tolerance. Three characters - control root length (CRL), Al-stressed root length (SRL) and root length ratio (RR) - were evaluated for the DH lines and the parents at the seedling stage in nutrient solution. A total of 20 QTLs controlling root growth under Al stress and control conditions were detected and distributed over 10 of the 12 rice chromosomes, reflecting multigenic control of these traits. The two QTLs of largest effect, qALRR-1-1 and qALRR-8 for root length ratio (a measurement of Al tolerance) were localized on chromosomes 1 and 8, respectively. Three other QTLs in addition to qALRR-8 were apparently unique in the CT9993 x IR62266 mapping population, which may explain the high level of Al tolerance in CT9993. Comparative mapping identified a conserved genomic region on chromosome 1 associated with Al tolerance across three rice genetic backgrounds. This region provides an important starting point for isolating genes responsible for different mechanisms of aluminum tolerance and understanding the genetic nature of this trait in rice and other cereals.

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 of 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 were 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 of 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 eighty-four 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-PC11M4 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.

Classification of rice germplasm. II. Discrimination of indica from japonica via analysis of amplicon length polymorphisms.

The polymerase chain reaction (PCR) was used to survey DNA sequence variation among 12 indica and 10 japonica rice cultivars. Of the 143 primer pairs used, 37 detected amplicon length polymorphism (ALP) and 11 revealed PCR banding patterns paralleled with the indica/japonica differentiation. Thus the 11 primer pairs were used to discriminate the two rice subspecies. A collection of 116 accessions representing the breadth of rice germplasm was analyzed for ALP at the 11 loci. Rice accessions with scores of 0.3 or more were classified as indica while those with -0.3 or less were classified as japonica. Those with scores from -0.3 to 0.3 were considered intermediate. With this criterion, 70 accessions were classified as indica, 35 accessions as japonica, and 11 accessions as intermediate. The concept and the approach used here for rice should be equally applicable for classifying other plant species.

Development of pre-isogenic lines for rice blast-resistance by marker-aided selection from a recombinant inbred population.

To increase the available set of near-isogenic lines (NILs) for blast-resistance in rice, we have developed a general method for establishing NILs from populations of fixed recombinants that have been used for gene mapping. We demonstrated the application of this method by the selection of lines carrying genes from the rice cultivar Moroberekan. Moroberekan is a West African japonica cultivar that is considered to have durable resistance to rice blast. Multiple genes from Moroberekan conferring complete and partial resistance to blast have previously been mapped using a recombinant inbred (RI) population derived from a cross between Moroberekan and the highly and broadly susceptible indica cultivar CO39. To analyze individual blast-resistance genes, it is desirable to transfer them individually into a susceptible genetic background. This RI population, and the associated data sets on blast reaction and restriction fragment length polymorphism (RFLP) genotypes, were used for selection of lines likely to carry individual blast-resistance genes and a minimum number of chromosomal segments from Moroberekan. Because skewed segregation in the RI population favored CO39 (indica) alleles, resistant lines carrying 8.7-17.5% of Moroberekan alleles (the proportion expected after two or three backcrosses) could be selected. We chose three RI lines carrying different complete resistance genes to blast and two RI lines carrying partial resistance genes to blast as potential parents for the development of NILs. These lines were subjected to genetic analysis, which allowed clarification of some issues that could not be resolved during the initial gene-mapping study.

Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers.

This research was undertaken to identify and map quantitative trait loci (QTLs) associated with five parameters of rice root morphology and to determine if these QTLs are located in the same chromosomal regions as QTLs associated with drought avoidance/tolerance. Root thickness, root:shoot ratio, root dry weight per tiller, deep root dry weight per tiller, and maximum root length were measured in three replicated experiments (runs) of 203 recombinant inbred lines grown in a greenhouse. The lines were from a cross between indica cultivar Co39 andjaponica cultivar Moroberekan. The 203 RI lines were also grown in three replicated field experiments where they were drought-stressed at the seedling, early vegetative, and late-vegetative growth stage and assigned a visual rating based on leaf rolling as to their degree of drought avoidance/tolerance. The QTL analysis of greenhouse and field data was done using single-marker analysis (ANOVA) and interval analysis (Mapmaker QTL). Most QTLs that were identified were associated with root thickness, root/shoot ratio, and root dry weight per tiller, and only a few with deep root weight. None were reliably associated with maximum root depth due to genotype-by-experiment interaction. Root thickness and root dry weight per tiller were the characters found to be the least influenced by environmental differences between greenhouse runs. Correlations of root parameters measured in greenhouse experiments with field drought avoidance/tolerance were significant but not highly predictive. Twelve of the fourteen chromosomal regions containing putative QTLs associated with field drought avoidance/tolerance also contained QTLs associated with root morphology. Thus, selecting for Moroberekan alleles at marker loci associated with the putative root QTLs identified in this study may be an effective strategy for altering the root phenotype of rice towards that commonly associated with drought-resistant cultivars.