Markers for major drought tolerance QTLs for upland and lowland rice

Product Description/Background: Molecular marker loci responding to selection under drought stress were monitored in a rice breeding population derived from a tolerant parent (Apo) crossed with IR64, a susceptible parent (Venuprasad, et al 2009 Euphytica. 167:261–269).  Genotyping the highest-yielding lines under stress and nonstress conditions obtained after two cycles of divergent selection under both revealed ten loci (Table 1) showing highly significant allele frequency differences.  Results showed that at six loci (RM572, RM6703, RM520, RM256, RM269, and RM511), Apo alleles had highly significant effects on grain yield in at least three of the four stress trials and two of these loci (RM572 and RM511) also affected grain yield under non-stress conditions.  In all cases, the effects of loci generally increased with stress level (Table 2). Large-effect quantitative trait loci (QTLs) affecting grain yield under upland drought stress have already been found previously in other populations near RM6703, RM520, and RM511 indicating the importance of these regions for explaining upland drought tolerance.














In more recent studies (Vikram et al, 2011; Venuprasad et al, 2011), further trialing and fine-mapping has increased definition of these loci.  Markers for a previously undefined QTL, qDTY1.1, were obtained from the highly tolerant Indian donor variety Moroberekan and had stable positive effects in different high yielding genetic backgrounds (Table 3). Under drought stress, qDTY1.1 explained phenotypic variance (R2) of 14.3%, 19.3%, and 13.4% in derived N22/Swarna, N22/IR64, and N22/MTU1010 populations, respectively. The additive effect of this QTL for grain yield under drought stress was 30.2%, 25.8%, and 16.9% of the respective population means in N22/Swarna, N22/IR64, and N22/MTU1010 populations.









Access/Availability:  Markers cited  are freely available for use.  Primer and other information for SSR markers may be obtained by contacting Arvind Kumar, IRRI ( or R. Venuprasad, IRRI ( or P. Vikram ( This information can be taken to any qualified laboratory for generation of markers and subsequent genotyping of germplasm materials. SNP markers have not been validated but are assumed to be diagnostic for the QTL given the proximity of these to the originals..  SNPs have been converted to the KASPar platform of LGC Genomics (KBiosciences), Herts, UK and may be accessed by direct contact ( or through the Breeding Services of the IBP platform. The Integrated Breeding Platform Genotyping Service provides a set of options for users to access different marker service laboratories in the public and private sector with clear contractual conditions. The service identifies laboratories able to provide services for genetic diversity analysis and plant breeding applications and negotiates favourable terms for IBP clients. Laboratories are selected on the basis of competitive cost, fit with quality control requirements and expeditious delivery. Click here for a list and description of laboratories and services. Click on  Service request for details of how to access genotyping services through the platform. For additional information and help on using the IBP Marker Service, contact Chunlin He.

If you need assistance in the use of these markers refer to  IBP Breeding Services or for more information contact Mark Sawkins or Chunlin He.  You may also contact Arvind Kumar, IRRI, The Philippines

Germplasm resources: Drought tolerant rice NILs in an IR64 background incorporating QTL qDTY1.1 among others with a yield advantage of 0.5 - 1.5 t/ha under drought over IR64. Contact IRRI Genebank, IRRI, The Philippines ( or

Resource Publications:

Supplementary Resources:

Contributing GCP Project: GCP Project G3007.05 - Detecting and fine-mapping QTLs with major effects on rice yield under drought stress for deployment via marker-aided breeding of which the Principal Investigator was Arvind Kumar, IRRI, The Philippines. Contact: Arvind Kumar, IRRI, The Philippines

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