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Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population

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Abstract

A doubled haploid (DH) population consisting of 125 DHLs derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R) was utilized for Quantitative Trait Loci (QTL) mapping to identify novel genomic regions associated with yield related traits. A genetic map was constructed with 126 polymorphic SSR and EST derived markers, which were distributed across rice genome. QTL analysis using inclusive composite interval mapping (ICIM) method identified a total of 24 major and minor effect QTLs. Among them, twelve major effect QTLs were identified for days to fifty percent flowering (qDFF12-1), total grain yield/plant (qYLD3-1 and qYLD6-1), test (1,000) grain weight (qTGW6-1 and qTGW7-1), panicle weight (qPW9-1), plant height (qPH12-1), flag leaf length (qFLL6-1), flag leaf width (qFLW4-1), panicle length (qPL3-1 and qPL6-1) and biomass (qBM4-1), explaining 29.95–56.75% of the phenotypic variability with LOD scores range of 2.72–16.51. Chromosomal regions with gene clusters were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1) and on chromosome 6 for total grain yield/plant (qYLD6-1), flag leaf length (qFLL6-1) and panicle length (qPL6-1). Majority of the QTLs identified were observed to be co-localized with the previously reported QTL regions. Five novel, major effect QTLs associated with panicle weight (qPW9-1), plant height (qPH12-1), flag leaf width (qFLW4-1), panicle length (qPL3-1) and biomass (qBM4-1) and three novel minor effect QTLs for panicle weight (qPW3-1 and qPW8-1) and fertile grains per panicle (qFGP5-1) were identified. These QTLs can be used in breeding programs aimed to yield improvement after their validation in alternative populations.

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Acknowledgements

First author is grateful to DST INSPIRE Fellowship Division, New Delhi for providing the financial assistance (Grant # DST/INSPIRE Fellowship/2013/1146, February 2014-March 2019). All authors are grateful to the Director, ICAR-IIRR for providing the infrastructural facilities for carrying out this research work.

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  1. Swapnil Ravindra Kulkarni, S. M. Balachandran and R. M. Sundaram contributed equally

Authors and Affiliations

  1. Biotechnology Department, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, Telangana State (TS), 500030, India

    Swapnil Ravindra Kulkarni, S. M. Balachandran, Divya Balakrishnan, A. S. Hari Prasad, G. Rekha, M. B. V. N. Kousik, S. K. Hajira, Ravindra Ramarao Kale, D. Aleena, M. Anila, E. Punniakoti, T. Dilip, K. Pranathi, M. Ayyappa Das, Mastanbee Shaik, K. Chaitra, Pragya Sinha & R. M. Sundaram

  2. Centre for Plant Molecular Biology (CPMB), Osmania University, Hyderabad, 500007, India

    K. Ulaganathan

Authors
  1. Swapnil Ravindra Kulkarni
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  2. S. M. Balachandran
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  3. K. Ulaganathan
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  4. Divya Balakrishnan
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  5. A. S. Hari Prasad
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  6. G. Rekha
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  7. M. B. V. N. Kousik
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  8. S. K. Hajira
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  9. Ravindra Ramarao Kale
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  10. D. Aleena
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  19. R. M. Sundaram
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Contributions

SMB, RMS, SRK, conceptualized the study; SMB, RMS, DB guided with methodology; SRK, DB carried out the investigation and completed the formal analysis; SRK prepared the original draft of the manuscript; SMB, RMS, DB, KU, guided with the critical review and editing of the manuscript; ASHP provided with the initial material for the development of doubled haploid population; GR, MBVNK, SKH, RRK, DA, MA, EP, TD, KP, MAD, MS, KC, PS helped with the recording of agro-morphological data of the doubled haploid data in the field for three consecutive seasons.

Corresponding author

Correspondence to S. M. Balachandran.

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Kulkarni, S.R., Balachandran, S.M., Ulaganathan, K. et al. Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population. 3 Biotech 11, 513 (2021). https://doi.org/10.1007/s13205-021-03045-7

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  • DOI: https://doi.org/10.1007/s13205-021-03045-7

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