Vol.:(0123456789) 1 3 Plant Cell Reports https://doi.org/10.1007/s00299-018-2260-2 ORIGINAL ARTICLE QTL-Seq-based genetic analysis identifes a major genomic region governing dwarfness in rice (Oryza sativa L.) 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 Received: 14 November 2017 / Accepted: 16 January 2018 © Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Key message A major dwarfing region for plant height, asd1, was identified employing the next-generation sequenc- ing-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 dwarfng gene employing next-generation sequencing (NGS)-based QTL-Seq approach. Here, we have identifed a major QTL governing plant height on chromosome 1, i.e., alternate semi-dwarf 1 (asd1) from an F 2 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 afecting the yield and its component traits. Hence, this novel dwarfng gene, asd1, has profound implications in rice breeding. Keywords Rice · Dwarf gene · QTL-Seq · Plant height and semi-dwarf (sd1) gene Introduction The plant height is one of the key agronomic traits, which determine the yield in rice, a major staple food for over half of the planet. Introduction of short-statured rice varie- ties revolutionized the plant breeding in the 1960s, widely regarded as ‘Green revolution’. Since then, the frst released semi-dwarf varieties in rice, i.e., TN-1 and IR8 have been continuously used in rice breeding as donors for lodging resistant and fertilizer responsiveness thereby high yields. Using these initial semi-dwarf varieties as donors, until today, more than 90% of the varieties were released in Asia and other rice-growing countries. The gene-mapping analysis revealed that the semi-dwarf- ism is majorly governed by a single recessive sd1 (semi- dwarf-1) gene that encodes Gibberellic acid 20 oxidase-2 (OsGA20ox2), a key enzyme involved in the penultimate step of gibberellic acid (GA) biosynthetic pathway. The sd1 Communicated by Prakash P. Kumar. Gopalakrishnamurty Kadambari, Lakshminarayana R. Vemireddy, and Akkareddy Srividhya contributed equally. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00299-018-2260-2) contains supplementary material, which is available to authorized users. * Lakshminarayana R. Vemireddy drvlnreddy@gmail.com 1 Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, Andhra Pradesh 500030, India 2 Indian Institute of Rice Research, Rajendranagar, Hyderabad, Andhra Pradesh 500030, India