KASP genomic selection: improving farmers' livelihoods through better rice varieties

Status: Ongoing, since 2017

Contact person: Dr Katherine Steele

Funding sources: Innovate UK (DFID)

Background: This project directly addresses the challenge of improved food security and livelihoods for international development. This project has developed nearly 5000 new molecular technologies (called KASP) and is aiming to make them the marker of choice for rice breeders through greater choice of markers (available for any cross), reduced costs (allowing a three-fold increase in the size of the breeding programme) and increased speed and reliability. A single improved rice variety can increase harvest value by millions of pounds a year so improved rice breeding methods in all Asian countries will have great impact on improved food security and improved farmers' livelihoods.

Aims:

• Build on work carried out in feasibility study to make new KASP assays available for all rice breeders
• Generate KASP designs that can be utilised in a wider variety of rice lines
• Identify suitable SNPs and InDels to replace SSR markers and confirm association with phenotypes
• Validate 4,000 assays by genotyping lines from partners’ breeding programs
• Create database of new assays enabling customers to order them direct from LGC Biosearch

Website: https://www.youtube.com/watch?v=aYlp6_R1D6c

Collaborators: LGC Biosearch-Technologies (UK), Agri-EPI Centre (UK), NIBGE (Pakistan), NARC (Nepal, Anmolbiou PVT (Nepal), SKUAST (India)

Outputs:

• Withana W.V.E., Kularathna R.M.R., Kottearachchi N.S., Kekulandara D.S., Weerasena J., Steele K.A. 2020 In silico analysis of the fragrance gene (badh2) in Asian rice (Oryza sativa L.) germplasm and validation of allele specific markers. Plant Genetic Resources: Characterization and Utilization 2020-01-30 
• Steele K.A., Quinton-Tulloch M. J., Amgai R. B, Dhakal R., Khatiwada S. P, Vyas D., Heine M., Witcombe J. R. 2018 Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice, Molecular Breeding 38: 38. 
• TU Haq, J Akhtar, KA Steele, R Munns, J Gorham.Reliability of ion accumulation and growth components for selecting salt tolerant lines in large populations of rice. Functional Plant Biology 2014 | journal-article doi.org/10.1071/FP13158
• KA Steele, AH Price, JR Witcombe, R Shrestha, BN Singh, JM Gibbons,DS Virk. QTLs associated with root traits increase yield in upland rice when transferred through marker-assisted selection. Theoretical and Applied Genetics2013 | journal-article doi.org/10.1007/s00122-012-1963-y
• TU Haq, J Gorham, J Akhtar, N Akhtar, KA Steele. Dynamic quantitative trait loci for salt stress components on chromosome 1 of rice. Functional Plant Biology 2010 | journal-article doi.org/10.1071/FP09247
• JR Witcombe, PA Hollington, CJ Howarth, S Reader, KA Steele. Breeding for abiotic stresses for sustainable agriculture PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 2008 | journal-article doi.org/10.1098/rstb.2007.2179
• KA Steele, AH Price, HE Shashidhar, JR Witcombe, Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety. Theoretical and Applied Genetics 112 (2), 208-221

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