Microsatellite diversity analysis and QTL identification among progenies derived from aerobic × basmati rice (Oryza sativa) cross under direct-seeded conditions

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  • RAHUL KUMAR MEENA Technical Assistant and corresponding author, ICAR-National Dairy Research Institute, Kalyani, West Bengal India and Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar,Haryana 125004, India
  • KULDEEP KUMAR Research Scholar, National Research Centre for Plant Biotechnology, New Delhi, India
  • NABIN BHUSAL Assistant Professor, Department of Genetics and Plant Breeding, Agriculture and Forestry University, Rampur, Chitwan, Nepal
  • RAJINDER KUMAR JAIN Ex-Dean, Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, Haryana 125004, India
  • SUNITA JAIN Retaired Professor, Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, Haryana 125004, India



Aerobic rice, Basmati, QTL, Root traits, SSR markers


The present investigation was designed to identify QTL associated with various traits under aerobic condition using F3 and F4 population derived from the cross MASARB25 (aerobic rice) and IB370 (basmati rice). The phenotyping was done in both field and net house conditions during the kharif seasons of 2013-14 and 2014-15. The result indicated high variation among the population for studied traits and parabolic frequency distribution was recorded for panicle length, effective number of tillers/plant, 1000-grain weight while, for grain length/breadth ratio and root thickness, frequency distribution curve were skewed toward MASARB25. Composite interval mapping identified total 16 QTLs on chromosomes 1, 2, 3, 4, 6, 9, 10 and 12 during both the years. Maximum QTL were detected for grain lengthbreadth ratio. LOD score of these QTLs ranged from 2.88 (qENT12.1) to 5.51 (qLB3.1) and explained 61.63% and 69.04% variance, respectively. The QTL mapped for grain yield/plant (qGYP6.1) on chromosome 6 had LOD score of 2.90 and explained 28.4% phenotypic variation. The identified QTL in present investigation showed high phenotypic variation, hence after validation these QTLs could be used for the improvement of rice under aerobic condition.


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How to Cite

MEENA, R. K., KUMAR, K., BHUSAL, N., JAIN, R. K., & JAIN, S. (2020). Microsatellite diversity analysis and QTL identification among progenies derived from aerobic × basmati rice (Oryza sativa) cross under direct-seeded conditions. The Indian Journal of Agricultural Sciences, 90(8), 1411-1418. https://doi.org/10.56093/ijas.v90i8.105905