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Breeding by Design in Rice: Multi Trait Plant Type Modifications for Sustainable Agriculture

  1. Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India; PlantNura Consulting & Solutions, Hyderabad, Telangana 500081, India; Punjab Agricultural University, Ludhiana 141004, India; Department of Plant Breeding & Genetics, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India; North Dakota State University, Fargo, North Dakota 58108, USA; Texas A&M University, AgriLife Research Center, Beaumont, Texas 77713, USA; #These authors contributed equally to this work
  • Contact: Sonali HABDE; Gurjeet SINGH

Abstract: Rice (Oryza sativa L.) must produce higher grain yields while using fewer resources such as water, nutrients, and pesticides to meet global food demand. We propose a breeding-by-design (BBD) framework comprising three ideotypes: new plant type (NPT), Green Super Rice (GSR), and C4-ready rice to deliver step changes in global productivity and sustainability. Deployed at scale, BBD can increase rice yield by 15%‒25% under normal conditions and by 10%‒20% under biotic and abiotic stress conditions, while reducing water and nitrogen fertilizer use by 20%‒30% and shortening breeding cycles by 1‒2 years. NPT focuses on plant architecture and source-to-sink regulation via gene networks: sd1 (plant height), NAL1 (leaf anatomy), IPA1/OsSPL14 and DEP1 (branching/panicle size), and Gn1a/OsCKX2 (cytokinin sink). GSR enhances stress resilience and input-use efficiency using DRO1 (deep roots), qDTY1.1/ qDTY3.1 (drought and yield), OsNRT1.1B/OsNLP4 (nitrogen use), Pup1/PSTOL1 (phosphorus uptake), Sub1A-1 (flood), and Saltol/HKT1;5 (salinity). Broad spectrum disease resistance can be achieved by pyramiding blast (Pi9/Pigm and Pik), bacterial blight (Xa21, xa5, xa13, and SWEET11/13/14), and brown planthopper (Bph3/Bph32 and Bph14) resistance genes. C4-readiness addresses anatomy and biochemistry via NAL1 (vein density/mesophyll layers), OsHXK1 edits (photosynthesis), and photorespiration bypasses as near-term gains toward multi-gene C4 modules. Across ideotypes, we can integrate multi-omics approaches with marker-assisted selection and genomic selection, haplotype breeding, genome editing, and rapid generation advancement. This toolbox delivers climate-smart, high-yielding rice cultivars with excellent grain quality traits.

Key words: breeding by design, new plant type, Green Super Rice, genomic selection, genome editing, multi-omics, C4 rice