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Mol Breed. 2018;38(4):38. doi: 10.1007/s11032-018-0777-2. Epub 2018 Mar 7.

Accelerating public sector rice breeding with high-density KASP markers derived from whole genome sequencing of indica rice.

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1School of the Environment, Natural Resources and Geography, SENRGY, Bangor University, Bangor, Gwynedd LL57 2UW UK.
2Biotechnology Division, Nepal Agricultural Research Council, PO Box No. 1135, Kathmandu, Nepal.
Anamolbiu Private Ltd., P.O. Box 28, Jagritichok, Bharatpur-11, Chitwan, Nepal.
Present Address: LI-BIRD, PO Box 324, Gairapatan, Kaski, Pokhara, Nepal.
LGC Genomics, Units 1 & 2, Trident Industrial Estate, Pindar Road, Hoddesdon, Herts EN11 0WZ UK.
LGC Genomics, TGS Haus 8, Ostendstr. 25, 12459 Berlin, Germany.
Present Address: NuGEN Technologies Inc., 201 Industrial Road, Suite 310, San Carlos, CA 94070 USA.


Few public sector rice breeders have the capacity to use NGS-derived markers in their breeding programmes despite rapidly expanding repositories of rice genome sequence data. They rely on > 18,000 mapped microsatellites (SSRs) for marker-assisted selection (MAS) using gel analysis. Lack of knowledge about target SNP and InDel variant loci has hampered the uptake by many breeders of Kompetitive allele-specific PCR (KASP), a proprietary technology of LGC genomics that can distinguish alleles at variant loci. KASP is a cost-effective single-step genotyping technology, cheaper than SSRs and more flexible than genotyping by sequencing (GBS) or array-based genotyping when used in selection programmes. Before this study, there were 2015 rice KASP marker loci in the public domain, mainly identified by array-based screening, leaving large proportions of the rice genome with no KASP coverage. Here we have addressed the urgent need for a wide choice of appropriate rice KASP assays and demonstrated that NGS can detect many more KASP to give full genome coverage. Through re-sequencing of nine indica rice breeding lines or released varieties, this study has identified 2.5 million variant sites. Stringent filtering of variants generated 1.3 million potential KASP assay designs, including 92,500 potential functional markers. This strategy delivers a 650-fold increase in potential selectable KASP markers at a density of 3.1 per 1 kb in the indica crosses analysed and 377,178 polymorphic KASP design sites on average per cross. This knowledge is available to breeders and has been utilised to improve the efficiency of public sector breeding in Nepal, enabling identification of polymorphic KASP at any region or quantitative trait loci in relevant crosses. Validation of 39 new KASP was carried out by genotyping progeny from a range of crosses to show that they detected segregating alleles. The new KASP have replaced SSRs to aid trait selection during marker-assisted backcrossing in these crosses, where target traits include rice blast and BLB resistance loci. Furthermore, we provide the software for plant breeders to generate KASP designs from their own datasets.


Allele mining software; Bacterial blight; Genomic selection (GS); Kompetitive allele-specific PCR (KASP); Marker-assisted selection (MAS); Next-generation sequencing (NGS); Physical mapping; Rice blast; Single-nucleotide polymorphism (SNP)

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