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

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. 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.