Acta Physiol Plant (2010) 32:355364 DOI 10.

1007/s11738-009-0413-1

ORIGINAL PAPER

Molecular mapping and location of QTLs for drought-resistance traits in indica rice (Oryza sativa L.) lines adapted to target environments
Selvaraj Michael Gomez N. Manikanda Boopathi S. Satheesh Kumar T. Ramasubramanian Zhu Chengsong P. Jeyaprakash A. Senthil R. Chandra Babu

Received: 19 February 2009 / Revised: 4 September 2009 / Accepted: 4 November 2009 / Published online: 3 December 2009 Franciszek Gorski Institute of Plant Physiology, Polish Academy of Sciences, Krakow 2009

Abstract Drought is a major limitation for rice production in rainfed ecosystems. Identifying quantitative trait loci (QTLs) linked to drought resistance provides opportunity to breed high yielding rice varieties suitable for drought-prone areas. Although considerable efforts were made in mapping QTLs associated with drought-resistance traits in rice, most of the studies involved indica 9 japonica crosses and hence, the drought-resistance alleles were contributed mostly by japonica ecotypes. It is desirable to look for genetic variation within indica ecotypes adapted to target environment (TE) as the alleles from japonica ecotype may not be expressed under lowland conditions. A subset of 250 recombinant inbred lines (RILs) of F8 generation derived from two indica rice lines (IR20 and Nootripathu) with contrasting drought-resistance traits were used to map the
Communicated by S. Abe. S. Michael Gomez Texas Agri Life Research, Texas A&M University System, Lubbock, TX 79403, USA e-mail: micbiotech@yahoo.co.in N. Manikanda Boopathi A. Senthil R. Chandra Babu (&) Centre for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore 641003, India e-mail: chandrarc2000@yahoo.com S. Satheesh Kumar Z. Chengsong Department of Agronomy, Throckmorton Plant Sciences Centre, Kansas State University, Manhattan, KS 66506, USA T. Ramasubramanian Central Research Institute for Jute and Allied Fibres (ICAR), Barrackpore, Kolkata, India P. Jeyaprakash Agricultural Research Station, Tamil Nadu Agricultural University, Paramakudi, India

QTLs for morpho-physiological and plant production traits under drought stress in the eld in TE. A genetic linkage map was constructed using 101 polymorphic PCR-based markers distributed over the 12 chromosomes covering a total length of 1,529 cM in 17 linkage groups with an average distance of 15.1 cM. Composite interval mapping analysis identied 22 QTLs, which individually explained 4.832.2% of the phenotypic variation. Consistent QTLs for drought-resistance traits were detected using locally adapted indica ecotypes, which may be useful for rainfed rice improvement. Keywords Recombinant inbred lines Drought resistance indica rice Genetic linkage map Quantitative trait loci

Introduction Rice is the staple food for more than 3 billion people in Asia, where more than 90% of the worlds rice is produced and consumed (Li and Xu 2007). It is grown worldwide in 154 million hectares (m ha) and more than 45% of the area is in rainfed ecosystems, where yields are seriously affected by drought (IRRI 2002). Of worlds rainfed lowland rice area of 41 m ha, 95% is in Asia (IRRI 1995). The rice yields in these ecosystems remain very low at 1.0 2.5 t ha-1 and tend to be unstable due to erratic and unpredictable rainfall. Drought mitigation, through development of drought-resistant rice varieties with higher yields suitable for water-limiting environments will be a key to improve rice production and ensure food security to 3 billion people in Asia. The increasing threat from water shortage and drought in many rice-growing areas of Asia, particularly the rainfed areas, has posed a great challenge

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to rice breeders to develop drought-tolerant and/or watersaving rice cultivars (Zhao et al. 2008). The progress in genetic improvement of rice for water-limiting environments, however, has been slow and limited (Evenson and Gollin 2003) due to poor understanding of the inheritance of tolerance and lack of efcient techniques for screening breeding materials for drought tolerance (Khush 2001). Alternatively, selection for drought-resistance traits has been suggested. Though several putative traits contributing to drought resistance in rice have been proposed (Nguyen et al. 1997; Bernier et al. 2008; Kamoshita et al. 2008), these traits are rarely selected for in breeding programs as phenotypic selection for these traits is difcult and labourintensive. The advent of molecular markers has revolutionized the genetic analysis of complex traits such as drought resistance in crop plants. Molecular markers help to track the genetic loci controlling drought-resistance traits without having to measure the phenotype, thus reducing the need for extensive eld testing over space and time (Nguyen et al. 1997). Once the tightly linked markers have been identied, the quantitative trait loci (QTLs) can be selected for in breeding programs using marker-assisted selection (MAS) strategy. QTLs for several drought-resistance traits have been mapped in rice (Li and Xu 2007; Kamoshita et al. 2008). Most of the studies were conducted employing populations derived from indica 9 japonica parental lines and majority of the positive alleles for drought-resistance traits were contributed by japonica parents. Since indica and japonica ecotypes are grown in entirely diverse environments, japonica alleles may not be expressed in lowland ecosystem (Wang et al. 1994; Redona and Mackil 1996; Yano and Sasaki 1997). Hence, it is desirable to look for genetic variation among rice accessions within indica ecotypes (Ingram et al. 1994) and map QTLs using populations derived from indica rice lines adapted to the target environments (TE). The indica 9 indica rice populations have been utilized in few QTL mapping studies till date (Ali et al. 2000; Kamoshita et al. 2002a, b; Manickavelu et al. 2006; Biji et al. 2008). The present study was conducted with the objective of mapping QTLs for drought-resistance traits using locally adapted indica rice lines under drought stress conditions in managed stress environment (MSE) and TE.

drought-sensitive. It has high yield potential, semi-dwarf stature with more tillers and good grain quality. Nootripathu, an indica landrace adapted to rainfed condition, on the other has a deep and thick root system (Babu et al. 2001) and is highly drought-tolerant. But it has low yield potential, 1.52.0 t ha-1 and poor grain quality. These two parental lines are well adapted to the TE. A cross involving these two indica rice lines (IR20/Nootripathu) was used to develop a recombinant inbred (RI) line population by single seed descent method. From the total of 397 F7 RI lines, a subset of 250 lines was randomly selected for genetic linkage map construction and drought phenotyping. Parental polymorphism and genetic linkage map construction A total of 1,151 simple sequence repeat (SSR) primers were used for parental polymorphism. Initially the polymorphism was established in polyacrylamide gel electrophoresis and then progeny screening was carried out using 3% Metaphor agarose (BioWhittaker Molecular Applications, Vallensbaek Strand, Denmark). In addition, 100 inter-simple sequence repeat (ISSR) primers, 320 randomly amplied polymorphic DNA (RAPD) primers and 78 drought stress expressed sequence tags (ESTs) (Reddy et al. 2002) were also used for parental polymorphism. The genetic linkage map was constructed using markers polymorphic between the parents and the data generated after genotyping of 250 recombinant inbred lines (RILs) were tested for v2 goodness of t against 1:1 segregation ratio. The signicantly segregated SSR markers were used for the construction of the linkage map using MAPMAKER/EXP MS-DOS 3.0 software (Lander et al. 1987) using the Haldane mapping function after all the heterozygote data had been entered as missing data (Lander et al. 1987; Lincoln et al. 1992). Calculation parameters were set for a minimum LOD threshold of 3.0 and recombination fraction of 0.5. Field trials Field trials were conducted under upland conditions in experimental elds of Tamil Nadu Agricultural University, Coimbatore, India at two locations: Coimbatore (Trial 1) during dry season (FebruaryJune 2003) and Paramakudi (Trial 2) during wet season (SeptemberFebruary 2003 2004) for QTL mapping of drought-resistance traits. The site, soil and drought stress characteristics of the two trials are summarized in Table 1. MSE: Coimbatore (Trial 1) A subset of 236 RI lines along with the parents were evaluated in randomized block design in 2.5 9 0.2 m size

Materials and methods Population development The parents of the mapping population used in this study viz., IR20 and Nootripathu differ considerably for a range of plant type, yield and quality traits. IR20, a lowland indica ecotype, has shallow and thin roots and is highly

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Acta Physiol Plant (2010) 32:355364 Table 1 Site, soil and drought characteristics of eld trials Particular Elevation (meters above sea level) Latitude and longitude Soil texture Soil pH Characterization of stress Timing of start of stress (days after sowing) Duration of the stress period (days) Rainfall during the stress period (mm) Number of continuous rain free days during stress period Rainfall during crop period (mm) Mean temperature maximum/minimum (C) Average relative humidity (%) Trial 1: Coimbatore 427 11N, 77E Clay loam 8.4 Severe 60 18 18 357 36.5/18.0 70 Trial 2: Paramakudi 40 9N, 70E Black clay 8.1 Severe 78 51 2 45 233 37.8/19.0 86.5

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cessation of rain. Days to 50% owering was also recorded in the population. Plants were harvested at maturity (120 DAS) and data on plant height, number of tillers and biomass were recorded. Statistical analysis of the phenotypic data Analysis of variance was done using the general linear model (GLM) procedure of the SAS program (SAS Institute Inc. 1990) to check the genetic variance among the RI lines for all the traits. Since there was no signicant difference between control and water stress treatments due to severe water stress in both the trials, the data on plant height, number of tillers and biomass have been considered as stress data and thus ultimately all the six replications were used for mean and covariance analysis. The frequency distributions of all the traits were performed to test the skewness of the traits towards the parents. The broad sense heritability or repeatability (H) was calculated for each trait from the covariance values using the formula, H r2 =r2 r2 =k; where r2 and r2 are the genetic and G G e G e residual variances, respectively and k is the number of replications. Phenotypic correlations among the traits within the trial were computed using the trait mean value. QTL analysis Composite interval mapping (CIM) was used to detect QTL-marker associations using WINQTLCART v.2.5 (Basten et al. 2005). Model six was selected with control marker numbers (Cofactors) of 5 and window size of 10 cM. The forward regression method was used for selecting the control markers. QTLs were searched for every 2 cM. Permutation testing of 1,000 randomizations was carried out to identify the 5% genomewide signicant threshold, which indicated that a logarithm of the odds ratio LOD score of 2.5 is suitable for this set of data.

plots under irrigated (non-stress) control and water stress treatments with three replications. Hand sowing of seeds at 100 kg ha-1 in 20 9 10 cm spacing (between and within rows, respectively) was done in dry soil. All the plots were surface irrigated to eld capacity once in a week, except in stress plots, when water stress was imposed by withholding irrigation at 60 days after sowing (DAS). In this trial, there was a continuous stress period for 18 days. Changes in soil moisture and penetration resistance were monitored periodically in stress plots with thetaprobe and penetrometer, respectively. Leaf rolling and leaf drying scores were taken at mid-day, 15 days after stress (IRRI 1996). Leaf relative water content (RWC) was determined at mid-day, 16 days after stress (Barrs and Weatherley 1962) and canopy temperature was taken 17 days after stress (Garrity and OToole 1995). Drought recovery score was made 3 days after rewatering (IRRI 1996). Following this, both control and stress plots were regularly irrigated until harvest. The plants were harvested 120 DAS and total biomass was recorded along with plant height and number of tillers. Plants were gently uprooted and basal root thickness was measured at 2 mm from the base of the node in all the RI lines using digital micrometer. TE: Paramakudi (Trial 2) A subset of 250 RI lines along with the parents was evaluated in TE under irrigated (non-stress) control and rainfed condition with three replications. The stress plots were rainfed from sowing to harvest. Canopy temperature, leaf chlorophyll (SPAD-502, Minolta Camera Co., USA), leaf rolling and leaf drying scores were recorded 14 days after

Results and discussion Variation for physio-morphological traits under water stress in eld condition Signicant variation was observed among the RI lines and the parents for various traits under stress in both the trials. Mean, variance and broad sense heritability of the RI lines in both the trials are given (Table 2). Leaf rolling and leaf drying scores across the RI lines indicated the severe drought stress experienced by the rice lines. Nootripathu had higher plant height, tiller number and biomass than IR20 in both the trials and thicker roots in Trial 1 under water stress conditions in the eld. Transgressive

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358 Table 2 Trait mean values for IR20, Nootripathu and RI lines for the two eld trials Trait Trial IR20 Nootripathu RI lines Mean Leaf rolling Leaf drying Recovery Canopy temperature (C) Relative water content (%) Plant height (cm) Number of tillers Biomass (g/m2) Basal root thickness (mm) Days to 50% owering (days) SPAD value Trial 1 Trial 2 Trial 1 Trial 2 Trial 1 Trial 1 Trial 2 Trial 1 Trial 1 Trial 2 Trial 1 Trial 2 Trial 1 Trial 2 Trial 1 Trial 2 Trial 2 6.7 5.7 7.0 4.3 6.3 43.7 35.5 42.3 27.5 43.8 5.25 7.9 32.9 148.3 0.7 35.6 4.0 5.0 4.3 3.0 3.0 39.7 34.3 61.8 49.6 56.4 7.9 7.2 157.3 185.0 1.1 86.0 38.6 6.0 6.6 5.8 4.8 4.9 43.0 32.8 59.1 40.5 62.5 5.8 7.2 177.6 627.5 0.92 82.4 36.0

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SD Range 3.07.0 3.07.0 2.37.0 2.37.0 1.07.0 39.446.6 27.640.5 34.181.4 24.972.2 42.086.5 2.412.2 5.310.3 64.61,638.0 302.21,077.0 0.61.2 64.788.1 26.645.3 0.71 0.66 0.67 0.95 1.15 1.35 2.24 8.80 7.73 10.01 1.43 0.86 119.09 128.33 0.12 5.01 3.27

0.73 0.57 0.70 0.58 0.91 0.75 0.95 0.10 0.89 0.87 0.67 0.30 0.91 0.56 0.78 0.31 0.61

SD standard deviation, H broad sense heritability

segregation was noticed for several traits, which were approximately tted to the normal distribution. Similar genetic variation and transgressive segregation for various morpho-physiological, plant phenology and production traits under water stress have been reported earlier in several rice lines (Blum et al. 1999; Babu et al. 2003; Manickavelu et al. 2006). In the present investigation, signicant difference was observed in biomass between the two trials. The broad sense heritability of this trait in Trials 1 and 2 was 0.91 and 0.56, respectively. In Trial 1, both biomass and drought recovery recorded the highest H (0.91), while the lowest H was noticed for RWC (0.10). In summary, there was signicant genotypic effect for most traits in both the trials except for RWC in Trial 1, and days to 50% owering and number of tillers in Trial 2. Similar level of low H was found earlier for percent spikelet fertility and days to heading under water stress in a DH population of rice (Babu et al. 2003). Relationship between water stress indicators and biomass under water stress Plant biomass was the only measure of plant production in the present study due to high evaporative demand and severe water stress in Trials 1 and 2. Signicant positive correlations were observed between biomass under stress and plant height, number of tillers and basal root thickness in Trial 1 (Table 3). Water stress indicators such as leaf

rolling, leaf drying and canopy temperature were negatively correlated with basal root thickness and biomass under stress. Similarly, in Trial 2, signicant positive correlation was observed between plant height and biomass under stress (Table 3). Signicant negative correlations were noticed between water stress indicators such as leaf rolling and leaf drying with biomass under stress. Negative correlations of water stress indicators with biomass and positive correlations of plant production traits with biomass have been reported in rice (Babu et al. 2003; Michael Gomez et al. 2006; Srinivasan et al. 2008). Genotyping of RILs and genetic map construction Only 197 (11.9%) of the 1,649 primers generated informative polymorphism between the parents and were used in linkage map construction. ISSR primers generated higher level of polymorphism (35.7%), followed by RAPD (14.4%), SSR (10.4%) and ESTs (1.5%). Despite a relatively large number of SSR markers used in this cross, the parents exhibited low level of polymorphism as both are indica ecotypes. Low level of polymorphism had already been noticed between the parents in the intra-sub-specic (Ali et al. 2000) and even in inter-sub-specic crosses of rice (McCouch et al. 1988; Price and Tomos 1997). Low level of polymorphism resulted in poor genome coverage and large gaps in the linkage map. All the 250 RILs were genotyped for these 197 marker loci and our analysis

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Acta Physiol Plant (2010) 32:355364 Table 3 Correlation coefcients among canopy temperature (CT), leaf rolling (LR), leaf drying (LD), recovery (REC), relative water content (RWC), plant height (PH), number of tillers (TN), SPAD reading (SPAD), days to 50% owering (DF), basal root thickness CT CT LR LD REC RWC PH TN BRT SPAD DF BM 1.00 1.00 LR 0.41** 0.15** 1.00 1.00 LD 0.49** 0.10* 0.75** 0.41** 1.00 1.00 REC -0.52** -0.69** -0.76** 1.00 RWC 0.001 -0.05 0.04 0.03 1.00 PH -0.28** 20.17** -0.27** 20.32** -0.51** 20.18** 0.45** 0.05 1.00 1.00

359 (BRT) and biomass (BM) under drought stress in the eld in Trial 1 (Coimbatore, 2003 dry season) (values in normal letters) and in Trial 2 (Paramakudi 20032004 wet season) (values in bold letters) in a RI line population of rice TN -0.40** 20.19** -0.57** 20.20** -0.70** 20.11* 0.66** 0.07 0.38** 20.34** 1.00 1.00 BRT -0.13 -0.22** -0.27** 0.40** -0.17* 0.25** 0.25** 1.00 SPAD 20.04 20.17** 20.06 20.07 0.10* 1.00 DF 20.02 20.19** 0.01 0.10 20.03 20.01 1.00 BM -0.37** 20.01 -0.42** 20.13** -0.61** 20.11* 0.50** 0.06 0.59** 0.47** 0.61** 0.01 0.20** 0.06 0.002 1.00 1.00

data not available * Signicant at 0.05 probability level ** Signicant at 0.01 probability level

showed that there was still some residual heterozygosity in the RILs, probably due to insufcient number of self pollination cycles at the F7 generation. The polymorphic markers that showed extreme segregation distortion towards either of the parent were removed and only 122 markers that segregated in the expected ratio of 1:1 at 0.01% probability level were used for map construction with LOD of 3.0 and a minimal distance of 50 cM. This resulted in mapping of 101 markers (71 SSR, 21 RAPD, 8 ISSR and 1 EST) covering a total length of 1,529 cM in 17 linkage groups with an average distance of 15.1 cM (Fig. 1). This kind of large number of linkage groups was also reported earlier in Bala 9 Azucena (17 linkage groups) (Price and Tomos 1997) and Pusa 1,121 9 Pusa 1,342 (17 linkage groups) (Amaravathi et al. 2008) RIL populations of rice. This might be due to the large gap ([50 cM) found between the polymorphic SSR markers as seen from the published map (Temnykh et al. 2001; McCouch et al. 2002).

QTLs linked to morpho-physiological traits Results of CIM and the summary statistics for all signicant QTLs are given in Table 4. A total of 22 QTLs, signicant at LOD score of C2.5 were identied for various physio-morphological and plant production traits under drought stress in this study, which individually explained 4.832.2% of phenotypic variation. The number of QTLs per environment under stress were: 9 under MSE (1 for leaf rolling, 1 for leaf drying, 4 for canopy temperature, 2 for plant height and 1 for biomass) and 13 under TE (3 for leaf rolling, 2 for leaf drying, 1 for canopy temperature, 2 for plant height, 1 for tiller number, 3 for drought recovery and 1 for biomass). No QTL was identied for SPAD, RWC and root thickness in both the environments. The canopy temperature QTL at I12S on chromosome 4 under MSE explained the highest proportion of the phenotypic variation (32.2%). QTLs linked to various traits from the two trials were located mainly on chromosomes 1, 2 and 4

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Fig. 1 The molecular genetic linkage map of rice based on 250 recombinant inbred lines derived from a cross between IR20/ Nootripathu. Chromosome numbers are indicated above each chromosome. Distances are given in Haldane centiMorgans. The letters before the numbers in marker names indicate the category of mapped primers as follows: RM rice microsatellites, I sufxed with number

and S inter-simple sequence repeats and other alphabets are randomly amplied polymorphic DNAs. QTLs associated with physio-morphological traits under stress at MSE and TE in IR20/Nootripathu RI lines. The positions of QTLs are indicated by vertical bars beside each marker, based on CIM analysis

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Table 4 QTLs detected for water stress indicators and plant production traits under drought stress in MSE and TE in IR20 9 Nootripathu RI lines using composite interval mapping Trait Trial Chromosome QTL position (cM) Nearest marker Leaf rolling 1 2 2 2 Leaf drying 1 2 2 Canopy temperature 1 1 1 1 2 Plant height (cm) 1 1 2 2 Tiller number Recovery score 2 2 2 2 Biomass (g/m2) 1 2
a

LOD From the top of linkage group 44.30 74.80 83.60 38.80 124.60 83.60 0.00 0.00 39.50 83.60 124.60 83.60 118.80 125.10 118.80 125.10 83.60 83.60 61.30 78.30 125.10 125.10 2.51 2.71 5.30 2.66 3.28 3.77 2.51 2.60 2.61 2.65 7.40 3.21 5.52 6.41 5.36 6.94 2.51 4.22 2.83 2.51 6.42 6.5

% Expl.

Additive effecta

11 2 2 6 4 2 4 2 2 2 4 2 1 1 1 1 2 2 4 4 1 1

L14_475 ? 0.50 RM263 ? 0.768 RM240 ? 0.835 RM6836 ? 0.448 I12S ? 1.626 RM240 ? 0.856 RM6314 ? 0.080 A11 ? 0.3801 M06 ? 0.395 RM240 ? 0.936 I12S ? 1.486 RM240 ? 0.836 RM302 ? 1.228 RM212 ? 1.311 RM302 ? 1.228 RM212 ? 1.311 RM240 ? 0.836 RM240 ? 0.836 C20 ? 0.733 RM3042 ? 0.786 RM212 ? 1.011 RM212 ? 1.211

6.2 5.2 11.6 5.0 8.9 8.1 7.7 5.0 4.8 8.9 32.2 9.1 10.8 12.23 11.4 13.8 4.8 7.6 6.9 4.9 8.7 8.9

-0.155 -0.167 -0.247 -0.166 0.234 -0.197 -0.195 0.580 0.550 -0.727 -1.393 -0.338 3.290 3.490 2.636 2.899 0.323 -0.325 -0.305 -0.242 -1.290 -1.090

% Expl. % of phenotypic variance explained by the QTL The additive effect of QTL. A positive value indicates that the IR20 genotype has a positive effect on the trait

(Fig. 1). In both the trials, for traits related to higher plant water status and production under stress, the majority of the favourable alleles came from Nootripathu, the local land race. The accession, IR20 contributed most of the alleles for plant height and tiller number under stress. Co-location of QTLs for correlated traits If QTLs, that were identied in one environment for a given trait, often mapped at the same place as QTLs affecting other traits in the same or another site can strengthen the utility of the QTL (Courtois et al. 2000). In TE (Trial 2), SSR marker RM240 on chromosome 2 was observed to be common for leaf rolling, leaf drying, canopy temperature, tiller number and drought recovery. Similarly, ISSR marker I12S was linked to leaf drying and canopy temperature and RM212 was linked to plant height and biomass production under water stress at both TE and MSE. This reveals that the chromosomal segments of the above-said markers had genes that are having pleiotropic effect on controlling these plant production traits under water stress in the eld. Similar kind of relationship

between water stress indicators (e.g., leaf rolling and leaf drying) and plant production traits under water stress had been reported in rice (Courtois et al. 2000; Michael Gomez et al. 2006). The results indicate that the major drought-resistance mechanism in these RI lines is avoidance of drought by continued absorption of water by deeper roots. Most of the positive alleles for drought-resistance traits are contributed by the landrace, Nootripathu which has deep roots. Deep roots access water from depth and help to main cooler canopy with no/less leaf rolling and drying. This helps to sustain carbon assimilation and production of biomass under stress. The phenotypic correlation coefcients obtained between root thickness, canopy temperature, leaf rolling and drying scores and biomass under stress (Table 3) also support such a drought avoidance strategy in these RI lines. Similar mechanism was reported in rice earlier (Babu et al. 2003). QTLs across the trials Consistency of QTLs across the environment is essential for effective marker-aided selection. Analysis of QTLs

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controlling different traits involved in drought avoidance and plant production under stress had shown common QTLs for several traits across the trials. RM240 on chromosome 2 had shown to have linkage with canopy temperature in both the trials. RM212 and RM302 on chromosome 1 were identied as markers linked to plant height in both the trials. In addition, RM212 was also linked to biomass production under water stress in both the trials. These markers that consistently identied for various traits across the trials may be useful as potential markers for the transfer of these QTLs into elite background through MAS. QTLs across genetic backgrounds A comparison of QTLs detected in this present investigation with those identied in different populations (Zhang et al. 2001; Price et al. 2002; Robin et al. 2003; Nguyen et al. 2004; Zou et al. 2005; Bernier et al. 2007; Zhao et al. 2008) of rice was made. The inconsistent map distances between markers in different maps hampered precision in the comparison and the results should be considered as indicative. RM212 on chromosome 1 has been identied for plant height and biomass under water stress in this study (Fig. 1). The marker interval R2417-RM212-C813 on chromosome 1 was associated with deep root mass, deep root ratio and deep root per tiller in CT9993/IR62266 DH population of rice (Kamoshita et al. 2002a). This region was found to be linked to RWC under eld drought condition (Babu et al. 2003) and number of tillers in these DH lines (Kanbar et al. 2003). The same region was also linked to plant biomass, basal root thickness and rootshoot ratio in Bala/Azucena RI lines (Price et al. 2002) and osmotic adjustment in IR62266/IR60080 BC3F3 population (Robin et al. 2003). RM212 and RZ730 were located within 7.9 cM distance (Temnykh et al. 2001). The major gene controlling the semi-dwarf stature, sd-1, was located near RZ730 (Huang et al. 1996). This gene is known to affect many aspects of plant morphology and physiology viz, plant height (Bernier et al. 2007), stomatal conductance (Zhao et al. 2008) tillering, panicle length, responsiveness to fertilizer, biomass and harvest index through pleiotropic effects (Xia et al. 1991; Courtois et al. 1995) as well as root system development (Yadav et al. 1997). The same region was also reported to contain QTL for cold (Lou et al. 2007) and salt (Lang et al. 2008) tolerance in rice. Thus, RM212 may be linked to drought-resistance traits and plant production under water stress in the eld in rice. Similarly, RM240 on chromosome 2 is linked to leaf rolling, leaf drying, canopy temperature, tiller number and drought recovery in this study. In this region, QTLs for panicle number under stress was identied in Vandana/

Way Rarem F3 population (Bernier et al. 2007). RM263 on chromosome 2 is linked to leaf rolling in this study. The chromosomal segment RM263R3393 was identied as a QTL for osmotic adjustment in CT9993/IR62266 DH population (Zhang et al. 2001). The chromosomal segment RM263R3393 was linked to grain yield in Zhenshan97b/ IRAT109 rice lines (Zou et al. 2005). Consistent QTLs were identied in this study in both the trials and also found to be consistent across the genetic backgrounds. Thus, the genomic segments RM212RM302 on chromosome 1, marker I12S on chromosome 4 and RM240 on chromosome 2 would be reasonable candidates for the development of near isogenic lines and further genetic dissection of drought resistance by molecular ne mapping to identify tightly linked markers. Further research is also needed to determine whether QTLs identied in these active segments also impact grain yield under water stress. In conclusion, the present study has identied putative markers linked to drought resistance traits in locally adapted indica ecotypes in TE and may be useful in MAS for drought resistance improvement in rice.
Acknowledgments The research was supported by Rockefeller Foundation, New York, USA, through a research grant to RCB. The authors thank Dr. J.C. OToole for his guidance and encouragement though out the research.

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