October 20, 2021, by Lexi Earl

Adaptation in the face of adversity: unlocking the secret of genomes

How can we better understand plant responses to stress through their genomes? Prof Levi Yant and Dr Guillermina Mendiondo discuss different ways to look inside the world of plants.

Life’s astonishing diversity is entirely the product of evolution. Adaptation of any organism to the environment, and the reflection of this adaptation – the evolution of genomes – has historically been viewed as a gradual process. But this is not always so: during times of rapid climate change chance mixtures of related species and genome duplication can create ‘hopeful monsters.’ These instantly created new species can then enjoy rapid adaptation in response to climate, instant genome remodelling, and sometimes, ecological invasions. How is it that certain terrestrial plant populations grow in pure seawater, while closely related populations of the same species are intolerant of salinity? What mechanisms may accelerate such adaptation? Can scientists provide breeders with plant genetic resources that are capable of better tolerating environmental stressors? Natural systems of adaptation provide powerful stories of evolutionary change, and inform crop design in the face of landscape degradation and climate change.

There are different ways to examine genomic adaptation. One is to apply population genomics to wild populations that evolved in response to definable, quantifiable challenges. Using new low-cost genome sequencing, dozens – or even hundreds – of individuals within a single plant species are genetically sequenced. This allows scientists to pinpoint differences associated with interesting changes in individual plants. Recent advances in genomics and bioinformatics allow us to clearly identify natural alleles underlying particular adaptations. Another way to examine genomic adaptation is to investigate plant-environment interactions, defining the biochemistry of how plants sense environmental change, and identifying proteins that can be manipulated genetically in agriculturally important crop species to affect crop quality and yield.

Guille stands in a field of yellow-green barley

Guillermina Mendiondo in a field of barley in mid-July

Understanding how different plant species respond to climate volatility is hugely important, as is the potential to grow crops that can withstand this volatility. It is estimated that 50% of cultivated land will be salinized by 2050 as a consequence of adverse weather events like droughts, flooding and sea incursions. Our key crops have become genetically vulnerable through modern agricultural breeding and growing methods. Scientists are therefore seeking different ways we can understand genetic adaptation in different plant species.

One method takes advantage of ‘natural laboratories’, wild areas across the UK and Europe, where a wild, diverse, naturally-evolved gene bank is accessible. We can then use cutting-edge, large-scale genomics to find out how evolution forged resilient communities over time, and test these in the field to confirm genomic signals of adaptation. We can isolate the effects of a single genetic change. Using large-scale genome sequencing we can examine what changes in the genome have occurred in response to climate change. We can then track these changes via invasive plants to understand the biological mechanisms that allowed them to succeed.

Levi Yant collecting samples

Another method combines the lab and the field. Scientists can identify and then develop plant lines that hold altered components of different novel pathways. These pathways might be cell proteins that are used by plants to sense and respond to their environments – and can therefore increase plant tolerance to abiotic stress. Once the lines have been developed, the new mutant plants can be grown in the field. We can monitor how these plants develop, testing their performance against wild types, and noticing particular phenotypic traits. Saving seeds from these field trials means we can go back and investigate desirable traits in the lab, allowing for the evolution of plants with higher tolerance to certain environmental stressors like drought.

Understanding how different genes help plants tolerate environmental stresses like increased soil salinity, droughts, or flooding, means we can apply this knowledge to other cultivars, identifying new varieties or improving existing ones. This is essential if we are going to continue to produce enough food to feed the global population.

Further reading

Levi:
Konečná V, Bray S, Vlček J, Bohutínská M, Požárová D, Choudhury R, Bollmann A, Flis P, Salt D, Parisod C, Yant L, Kolář F (2021) Serpentine adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles, Nature Communications. https://rdcu.be/cutvo

Busoms S, Paajanen P, Marburger S, Bray S, Huang X, Poschenrieder C, Yant L, and Salt D (2018) Ecological and population genomics reveals fluctuating selection on migrant adaptive sodium transporter alleles in coastal Arabidopsis thaliana. PNAS,https://doi.org/10.1073/pnas.1816964115

Guillermina:

Shayanowako AIT et. al. (2021) African Leafy Vegetables for Improved Human Nutrition and Food System Resilience in Southern Africa: A Scoping Review Int. J. Mol. Sci. 22 (2), 765. https://doi.org/10.3390/ijms22020765

*Vicente Conde J, *Mendiondo GM, Movahedi M, Peirats-Llobet, Yu-ting J, Yu-yen S, Dambire C, Smart K, Rodriguez PL, Yee-yung C, Gray J, Holdsworth MJ. (2017) The Cys-Arg/N-end rule pathway is a general sensor of abiotic stress in flowering plants. Current Biology 27(20), 3183-3190.e4. *Contributed equally to this work. http://doi.org/10.1016/j.cub.2017.09.006

Mendiondo GM, et al. (2016) Enhanced waterlogging tolerance in barley by manipulation of expression of the N-end rule pathway E3 ligase PROTEOLYSIS6. Plant Biotechnol J 14(1), 40-50. http://doi.org/10.1111/pbi.12334

 

Levi Yant is a Professor of Evolutionary Genomics and a core member of the University of Nottingham’s Future Food Beacon of Excellence. Before this he was a Project Leader at the John Innes Centre (Norwich, UK). His independent research career began in 2014 as a Project Leader at Harvard University (USA), where he had previously been a postdoctoral researcher studying the evolution of developmental mechanisms in rapidly radiating species.

Guillermina Mendiondo is an Assistant Professor in Translational Agriculture-Crop Molecular Physiology in the School of Biosciences. Before this she was a Future Food Beacon Nottingham Research Fellow. She is an applied plant biologist with a background in molecular and crop physiology. She has expertise in a variety of approaches that include plant physiology, molecular biology, biochemistry, cell biology, genetics and bioinformatics, in both genetic model systems and crops.

Follow Levi @leviyant and Guille @GuilleMendiondo on Twitter

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