Diversity is the spice of life and is also key to breeding rice that delivers increased yields. Rice is a crucial staple food for about half a billion people in Asia, but it suffers from diseases that reduce yields, destroy harvests and put food security and livelihoods at risk. But there is hope – by tracking DNA markers of natural genetic variants through generations of crosses, breeders can identify better combinations that enrich crop vitality and resilience leading to more reliable and sustainable rice production.
A collaborative project between Bangor University and LGC with a university partner in India (SKUAST), a research institute in Pakistan (NIBGE) and, in Nepal, a government research centre (NARC) and a private seed company (Anamolbiou) is addressing this challenge and has already identified over a million new markers in rice. They can reveal linkage to genes and patterns of diversity that help rice breeders select for a wide range of resistance genes to improve many different varieties. The project continues to develop these markers into more KASP assays that will be made available in publicly searchable databases.
Modern disease-resistant varieties are not always well adapted to specific environments, so breeders aim to incorporate markers for both biotic and abiotic stress resistance as well as yield components into locally accepted varieties that may already possess value traits, such as aroma. Molecular markers such as Simple Sequence Repeats (SSRs) in rice were developed in the 1990s for marker-assisted selection (MAS) and these are still used by some rice breeders in Asia to improve selection efficiency. Smaller breeding companies do not have all the resources (i.e. trained personnel, instrumentation for extraction or genotyping) to use such markers in-house. They can benefit from a service-based approach such as LGC Genomics’ genotyping service using KASP technology that offers a lower cost per data point and is faster to implement or use in their own lab. KASP assays offer greater sensitivity, speed, and safety than the older techniques, such as SSRs, when carried out in breeders’ own labs.
The collaboration with Bangor University and partners has already developed new methods to identify suitable SNP and InDel markers that can replace existing SSRs in target breeding crosses which have been adopted by Nepalese breeders. Now, a broader survey of suitable SNPs and InDel markers, across a set of 130 publically available rice genome sequences selected for geographic diversity, is discovering novel markers that are relevant to both Indica and Japonica rice backgrounds.
Before the research team started this project there was a choice of 2055 useful KASP assays that breeders could use, depending on their breeding strategy, but this project has increased the choice to over 245,000 potential markers that should benefit a wider range of rice breeding programs. This increase in the number of KASP assays enables the project and research community to utilize KASP technology on a scale that was only available to big breeding companies before this project. It’s exciting times for rice breeding!
Bangor University and partners plan to make thousands of the rice markers from this project available in the form of a searchable database so that rice breeders can easily find the most suitable options to replace their target SSRs in existing programs or to identify the appropriate loci for a range of possible new crosses. LGC will also offer them as validated KASP assays on its website. The large database of validated KASP assays produced by this project will thus give rice breeders the ability to carry out genomic selection (GS) with many thousands of loci across their populations, enabling smaller breeders to benefit from the same genomic scale technologies that generally require significant resource investment to develop on their own. The availability of this marker set to the public sector, and the services provided by LGC Genomics, will enable rice breeders of all sizes to apply genomic tools to accelerate their MAS and GS breeding programs to develop new rice varieties that will improve food security.
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This blog originally appeared on the Biosearch Technologies blog.