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Plant Cell Reports

, Volume 37, Issue 4, pp 677–687 | Cite as

QTL-Seq-based genetic analysis identifies a major genomic region governing dwarfness in rice (Oryza sativa L.)

  • Gopalakrishnamurty Kadambari
  • Lakshminarayana R. Vemireddy
  • Akkareddy Srividhya
  • Ranjithkumar Nagireddy
  • Siddhartha Swarup Jena
  • Mahendranath Gandikota
  • Santosh Patil
  • Roja Veeraghattapu
  • D. A. K. Deborah
  • G. Eswar Reddy
  • Maliha Shake
  • Aleena Dasari
  • P. V. Ramanarao
  • Ch. V. Durgarani
  • C. N. Neeraja
  • E. A. Siddiq
  • Maganti Sheshumadhav
Original Article

Abstract

Key message

A major dwarfing region for plant height, asd1, was identified employing the next-generation sequencing-based QTL-Seq approach from a dwarf mutant and is demonstrated to be responsible for the dwarf nature with least penalty on yield in rice.

Abstract

The yield plateauing of modern rice is witnessed since many decades due to the narrow genetic base owing to the usage of a single recessive gene, i.e., semi-dwarf-1 (sd-1) for development of short-statured varieties throughout the world. This calls for the searching of alternate sources for short stature in rice. To this end, we made an attempt to uncover yet another, but valuable dwarfing gene employing next-generation sequencing (NGS)-based QTL-Seq approach. Here, we have identified a major QTL governing plant height on chromosome 1, i.e., alternate semi-dwarf 1 (asd1) from an F2 mapping population derived from a cross between a dwarf mutant, LND384, and a tall landrace, INRC10192. Fine mapping of asd1 region employing sequence-based indel markers delimited the QTL region to 67.51 Kb. The sequencing of the QTL region and gene expression analysis predicted a gene that codes for IWS1 (C-terminus family protein). Furthermore, marker-assisted introgression of the asd1 into tall landrace, INRC10192, reduced its plant height substantially while least affecting the yield and its component traits. Hence, this novel dwarfing gene, asd1, has profound implications in rice breeding.

Keywords

Rice Dwarf gene QTL-Seq Plant height and semi-dwarf (sd1) gene 

Notes

Acknowledgements

This research was supported by the Department of Science and Technology (DST), India under “Fast Track scheme for young scientists” (Sanction Order: SR/FT/LS-061/2009; 13.12.2012) awarded to LR. GK is grateful to DST for providing fellowship.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

299_2018_2260_MOESM1_ESM.jpg (97 kb)
Fig. S1A Chromosomal distribution of reported dwarfing genes (JPG 97 KB)
299_2018_2260_MOESM2_ESM.jpg (66 kb)
Fig. S1B Chromosomal distribution of reported dwarfing genes (JPG 66 KB)
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Fig. S1C Chromosomal distribution of reported dwarfing genes (JPG 43 KB)
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Table S1 (DOC 41 KB)
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Table S2  (DOC 37 KB)
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Table S3 (DOC 48 KB)
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Table S4 (DOC 37 KB)
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Table S5 (DOC 31 KB)
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Table S6 (DOC 35 KB)
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Table S7 (DOC 34 KB)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Gopalakrishnamurty Kadambari
    • 1
  • Lakshminarayana R. Vemireddy
    • 1
  • Akkareddy Srividhya
    • 1
  • Ranjithkumar Nagireddy
    • 1
  • Siddhartha Swarup Jena
    • 1
  • Mahendranath Gandikota
    • 1
  • Santosh Patil
    • 1
  • Roja Veeraghattapu
    • 1
  • D. A. K. Deborah
    • 1
  • G. Eswar Reddy
    • 1
  • Maliha Shake
    • 1
  • Aleena Dasari
    • 1
  • P. V. Ramanarao
    • 1
  • Ch. V. Durgarani
    • 1
  • C. N. Neeraja
    • 2
  • E. A. Siddiq
    • 1
  • Maganti Sheshumadhav
    • 2
  1. 1.Institute of BiotechnologyAcharya NG Ranga Agricultural UniversityHyderabadIndia
  2. 2.Indian Institute of Rice ResearchHyderabadIndia

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