Going genomic

Using science to improve food security

Justin Borevitz, John Rivers

Environment & energy, Science and technology, Food & water | Australia, Asia, East Asia, South Asia, Southeast Asia, The Pacific, The World

30 June 2015

The rapid advances in genomic sequencing have important implications for policymakers, write Justin Borevitz and John Rivers.

A revolution is underway in the life sciences. We are now obtaining more genomic sequence information from the world’s wild and domesticated plant (and animal and microbial) species than ever before.

For plant science researchers, this is very exciting. The plummeting cost of genetic sequencing means more plant varieties and species can be studied, including ‘orphan crops’ that have previously been overlooked by breeding efforts focused on the top commercial crops.

Advances in computing have also meant genomic data is more useful than ever before. More details about genomic breeding, and specifically its impact upon plant breeding, can be found in our recent review: Genomic Breeding for Food, Environment and Livelihoods.

Genomic breeding will affect regional, national and international policies toward food production, environmental protection and rural livelihoods. With careful application, we believe genomic breeding will provide new policy options. Given our research background, we have chosen to focus on plant examples of genomic breeding. The general ideas, however, are applicable to other breeding efforts.

Using next-generation DNA-sequencing technology, we  can rapidly determine how much genetic variation there is between different crop varieties. We can apply powerful bioinformatics techniques to probe this information and determine which genetic variations are responsible for changes in plant growth. Plant breeders can then use this information to predict and select high-yielding crop varieties especially suited for specific farming or agro-environments.

What’s particularly useful about genomic breeding is its ability to predict plant performance in new environments for any combination of genes found in the plant variety. This is important, as we need to start breeding for climate-change-affected environments for which there are no analogues. We can thus anticipate, to an extent, future environments and provide crop varieties with the best chance of success.

Image by James Almond on Flickr: https://www.flickr.com/photos/jamesalmond/3075701182/

Image by James Almond on Flickr: https://www.flickr.com/photos/jamesalmond/3075701182/

Genomic breeding can increase food production, especially in neglected crops not yet optimised for their agro-environment. To realise this potential we need to understand not only the diversity of plant genomes but also the new agro-environments plants will be growing in. Plant science research programs need to emphasise the collection of genetic and environmental information along with plant growth and yield characteristics. National and international organisations will also need to support neglected regions with unique environments to fully utilise genomic breeding. These areas are often overlooked by commercial efforts, which might focus on breeding for currently profitable environments.

Genomic breeding can also change our approach to conservation. Currently, conservation programs such as reforestation have a ‘local seed is best’ philosophy. For many species, this could be a problem. If their habitats are fragmented, the existing genetic diversity is trapped, limiting adaptation by natural selection. A lack of genetic diversity in a given location, coupled with small populations and reproductive cycles, leaves species, communities and ecosystems vulnerable to sudden environmental changes.

Using genomic breeding, we can identify endangered plant varieties with the right genetic combination for a given environment, just as we would for crop plants. For example, genetic isolation may have left a population of eucalyptus in a drought-prone environment without the drought-tolerant genetic variation necessary to adapt. We can directly identify drought tolerance in other populations using genomic breeding, and re-introduce this diversity into the vulnerable population, making it more adaptable and resilient.

Policymakers need to revise nature conservation guidelines, to take genomic breeding into account, and make conservation projects more effective: genomic breeding data should be used where possible, and the ‘local is best’ policy to flora replanting should be reconsidered.

Genomic breeding could also improve farmer and rural livelihoods. As mentioned above, genomic breeding can make crops more productive and resilient to stress. This would mean less variability in crop yield: resilient crops would yield more consistently under climatic fluctuations. Farmer incomes could become less variable, especially when there are many resilient crop options to plant.

An additional opportunity is to revegetate marginal or degraded land with native trees and grasses pre-selected for diversity and climate adaptability. These landscapes can then provide services and value to the farm, such as erosion control, groundwater recharge, native pollinators, and carbon sequestration for soil fertility. Ideally, we would pay farmers for these ecosystem services as we do for crops, livestock, and timber. Making the fruits of genomic breeding available to farmers, both in Australia and our region, could increase agricultural productivity and help rural communities adapt to climate change.

Genomic breeding is an exciting scientific advance that could help us improve food security, our environments and the livelihoods of those who work the land.

To realise this potential, we need policymakers to appreciate the applications of genomic breeding, support further research, and ensure this technology reaches the farmers and conservationists that can reap its benefits. We also need a new industry applying genomic breeding to a range of new crops and new agro-environments ranging from cities to the countryside.

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