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Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress

Nitika Sandhu1, Anshuman Singh1, Shalabh Dixit1, Ma Teresa Sta Cruz1, Paul Cornelio Maturan1, Rajinder Kumar Jain2 and Arvind Kumar1*

Author Affiliations

1 Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

2 Department of Molecular Biology and Biotechnology, CCS Haryana Agricultural University, Hisar 125004, India

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BMC Genetics 2014, 15:63  doi:10.1186/1471-2156-15-63

Published: 27 May 2014



Drought is one of the most important abiotic stresses that cause drastic reduction in rice grain yield (GY) in rainfed environments. The identification and introgression of QTL leading to high GY under drought have been advocated to be the preferred breeding strategy to improve drought tolerance of popular rice varieties. Genetic control of GY under reproductive-stage drought stress (RS) was studied in two BC1F4 mapping populations derived from crosses of Kali Aus, a drought-tolerant aus cultivar, with high-yielding popular varieties MTU1010 and IR64. The aim was to identify QTL for GY under RS that show a large and consistent effect for the trait. Bulk segregant analysis (BSA) was used to identify significant markers putatively linked with high GY under drought.


QTL analysis revealed major-effect GY QTL: qDTY1.2, qDTY2.2 and qDTY1.3, qDTY2.3 (DTY; Drought grain yield) under drought consistently over two seasons in Kali Aus/2*MTU1010 and Kali Aus/2*IR64 populations, respectively. qDTY1.2 and qDTY2.2 explained an additive effect of 288 kg ha−1 and 567 kg ha−1 in Kali Aus/2*MTU1010, whereas qDTY1.3 and qDTY2.3 explained an additive effect of 198 kg ha−1 and 147 kg ha−1 in Kali Aus/2*IR64 populations, respectively.

Epistatic interaction was observed for DTF (days to flowering) between regions on chromosome 2 flanked by markers RM154–RM324 and RM263–RM573 and major epistatic QTL for GY showing interaction between genomic locations on chromosome 1 at marker interval RM488–RM315 and chromosome 2 at RM324–RM263 in 2012 DS and 2013 DS RS in Kali Aus/2*IR64 mapping populations.


The QTL, qDTY1.2, qDTY1.3, qDTY2.2, and qDTY2.3, identified in this study can be used to improve GY of mega varieties MTU1010 and IR64 under different degrees of severity of drought stress through marker-aided backcrossing and provide farmers with improved varieties that effectively combine high yield potential with good yield under drought. The observed epistatic interaction for GY and DTF will contribute to our understanding of the genetic basis of agronomically important traits and enhance predictive ability at an individualized level in agriculture.

Bulk segregant analysis; Drought; Marker-assisted breeding; Rice; Quantitative trait loci