Our hungry planet: new tools in agrigenomics are key to food security

Our hungry planet NGS blog 1 photoFood security is a major global threat and traditional methods of plant and animal breeding will not be sufficient to increase production to the level needed to sustain the growing world population. Modern genomics-driven breeding, through analysis based on technologies such as next generation sequencing (NGS) and arrays, is revolutionizing agriculture and making genomic selection a viable approach throughout the industry. In this three series blog post find out how technology is changing global food security and what the newest tools bring to the table.

The power of genomic selection

Perhaps the biggest revolution in agriculture in the last decade is the emergence of agrigenomics to enhance traditional breeding programs. Molecular techniques, such as marker assisted selection and genomic selection, have enabled selection of improved varieties without having to rely on assessing visible characteristics. Genomic selection, in particular, addresses the key factors of the breeder’s equation (2) that increase the rate of genetic gain in plant and animal breeding:

  • Reduced breeding cycles – individuals can be progressed faster when selection is based on genotype rather than phenotype alone
  • Greater selection intensity – selecting individuals based on genotype is cheaper than selecting on phenotype, so more individuals can be evaluated (increasing ‘n’)
  • Improved accuracy – the genomic estimated breeding value (GEBV) enables prediction models to select with greater accuracy based on phenotype and previous pedigree historical data and enables prediction models to be applied with greater accuracy.
  • More efficient integration of new genetic material through the development of training population, where intensive phenotyping and genotyping can be assessed

Genomic selection has been instrumental in dairy cattle breeding where it has essentially replaced progeny testing, enabling greater and faster improvements in terms of genetic gain (see, for example, reference 3). Genomic selection has, however, had a relatively slow uptake in plant breeding. Reasons include its relative complexity compared to traditional methods, the need for expensive investments, complexity of plant genomes and ability to analyse big data using bioinformatics. The divergence of plant and animal breeding has also hindered the translation of methods between these two fields, but this problem is being addressed and hopefully both animal and plant breeding of the future will gain from common insights into genomic selection (1).

Technological development powers the agrigenomics breakthrough

Genomic selection has been made more practical by a range of methods, including next generation sequencing (NGS) and microarrays for genotyping and single nucleotide polymorphism (SNP) analysis. Massive developments in NGS technology in particular have realized the potential of genotyping by sequencing, (or GBS), and promises to revolutionize the drive to develop varieties of plant crops with, for example, desirable traits such as drought tolerance, disease resistance, and higher yield.

Despite all these advances, there are still gaps to fill in the toolbox of technologies, and finding the optimal solution for genomic selection can be a demanding process. We will be looking into these issues in the next article in this series.

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About the author: Darshna ‘Dusty’ Vyas

Dusty has been with LGC for the last 6 years working as a plant genetics specialist.

Her career began at the James Hutton Institute, formerly the Scottish Crop Research Institute, developing molecular markers for disease resistance in raspberries. From there Dusty moved on to Biogemma UK Ltd for a period of 13 years, where she worked primarily with cereal crops such as wheat, maize and barley. Through her participation in the Artemisia Project, funded by the Bill and Melinda Gates Foundation, at York University, she gained a vast understanding of the requirements by breeders for varietal development using molecular markers in MAS.

Dusty’s goal is to further breeding programs for global agricultural sustainability using high throughput methods such as SeqSNP.

References

  1. Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery. J M Hickey, T Chiurugwi, I Mackay, W Powell & Implementing Genomic Selection in CGIAR Breeding Programs Workshop Participants. Nature Genetics volume 49, pages 1297–1303 (2017)
  2. Animal breeding plans 2nd J L Lush. The Iowa State College Press (1943)
  3. Genomic selection strategies in a small dairy cattle population evaluated for genetic gain and profit. J R Thomasen et al, J. Dairy Sci. 97:458–470. http://dx.doi.org/10.3168/jds.2013-6599 (2014).

 

This blog originally appeared on the LGC, Biosearch Technologies blog.

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Accelerating rice improvement in South Asia

WP_20180515_009Diversity 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.

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.

WP_20180515_007The 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.

To learn more about our KASP genotyping services click here.

 

This blog originally appeared on the Biosearch Technologies blog.