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Keywords:

  • natural selection;
  • plant breeding;
  • genomics

Summary

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Climate change threatens reduced crop production and poses major challenges to food security. The breeding of climate-resilient crop varieties is increasingly urgent. Wild plant populations evolve to cope with changes in their environment due to the forces of natural selection. This adaptation may be followed over time in populations at the same site or explored by examining differences between populations growing in different environments or across an environmental gradient. Survival in the wild has important differences to the objective of agriculture to maximize crop yields. However, understanding the nature of adaptation in wild populations at the whole genome level may suggest strategies for crop breeding to deliver agricultural production with more resilience to climate variability.


Importance of crop breeding for food security

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Agriculture faces growing global demand for food from population growth and strong growth in per capita consumption due to economic development especially in Asia (Henry, 2010). It is widely accepted that this food needs to be produced from a similar area of land to that currently under cultivation (Foley et al., 2011). This perspective establishes the need to satisfy demands for more food by increasing agricultural productivity by crop breeding and improved crop management. Recent analysis of current growth in productivity for major crop species suggests that productivity growth (Ray et al., 2013) will not be sufficient to satisfy the predicted growth in demand (Figure 1). More aggressive innovation in plant breeding is a major option that may help to close the gap between the growth rates of production and demand.

image

Figure 1. Progress in crop productivity. The estimated current rate of global productivity growth in maize, rice, wheat and soybean (Ray et al., 2013) relative to that required to deliver the required doubling in productivity predicted to be necessary by 2050.

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Threat of climate change to agricultural production

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

The threat of climate change (Lotze-Campen, 2011; Thornton and Ceamer, 2012) makes delivery of significant productivity gains more difficult. Climate change is expected to impact significantly on biodiversity in the 21st century (Dawson et al., 2011). New strategies are required to overcome this major challenge in agricultural production systems. The urgent need for development of farming systems and crop varieties (Lobell and Gourdji, 2012) that will be productive despite climate variability or change requires that we explore new approaches to crop breeding. Climate change may bring a range of related challenges. For example, higher temperatures (Cossani and Reynolds, 2012) may be associated with greater water stress in many environments (Lobell et al., 2013). Excess water resulting in flooding may be a growing challenge (Bailey-Serres et al., 2012). Adaptation of natural systems is expected to see the emergence of winners and losers among species in specific ecosystems (Hoffmann et al., 2011). This suggests that crop species distributions need to change, but some species especially those adapted to cool environments may not have anywhere to relocate to (Alsos et al., 2012). Unless human food preferences change some species will need to adapt to satisfy food demand. New species with improved environmental adaptation could be domesticated (Malory et al., 2011) and this probably should be considered as a significant complementary strategy for adapting agriculture to climate change.

Study of adaptation to climate under natural selection as a guide to plant breeding

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

One key option that may be used to understand how to adapt crop varieties to climate change is to explore how plant populations adapt to environmental change or variation under natural selection. Analysis of wild plants from different environments allows identification of genetic variation associated with adaptation to the differing environments. Natural plant populations that extend over a gradient of environmental conditions of, for example, temperature or rainfall provide a system that is ideal for this type of study. Model systems may offer a first level of insight into how plants adapt to climate (Nevo, 2001). Analysis of the adaptation of Arabidopsis thaliana to climatic conditions has been studied by analysis of genome-wide variation in accessions collected from across the native range of the species allowing the identification of adaptive alleles (Hancock et al., 2011). Growth of the accessions in different environments revealed that local adaptation may be associated with different loci and different mechanisms of adaptation in each environment (Fournier-Level et al., 2011). Cronin et al. (2007) examined the diversity in the Isa defence locus in wild barley growing in diverse environments and reported greater variation in the more stressed (dryer) sites. Biotic stress genes showed much greater diversity than abiotic stress related genes in these populations (Fitzgerald et al., 2011). Increased diversity of genes protecting against biotic stress may be important in adaptation to hotter and drier climatic conditions. Adaptation to high temperatures may require adaptation to the different (or greater) range of biotic stress (Jamieson et al., 2012) that results at higher temperatures. The important message from this study is that adapting crops to climate change may be more about adaptation to a different biotic environment than to the temperature itself.

Plant-breeding programs need to begin to utilize genome-wide analysis of adaptation genes in defining the genetic loci to be selected in breeding new varieties for a variable climate. Complex genotype by environment interactions have been revealed in studies of environmental adaptation in domesticated gene pools. Analysis of wild gene pools under natural selection may reveal clues to key adaptive paths in plant genome evolution. Genome-wide selection under natural selection has been explored in Arabidopsis (Fournier-Level et al., 2011). This provides a model system in which to study adaptation. In these studies, unexpected loci may show variations that suggest adaptive evolution to climatic factors (Shapter et al., 2012). A preliminary study of genome analysis has been conducted at ‘Evolution Canyon’ (EC) in Ricotia lunaria, an annual crucifer distant from Arabidopsis, common in EC (Brodsky et al., 2008; Kosover et al., 2009). A similar approach should be useful in many crop systems. Future studies of this type can with current and emerging technologies include consideration of the whole genome by complete analysis of whole-genome sequences (Brodsky et al., 2010).

Advances in tools suitable for analysis of genome-wide adaptation in wild populations

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Recent advances in DNA sequencing technology (Brodsky et al., 2010; Loman et al., 2012) make whole-genome analysis (Bilsborough, 2013) of plant populations more feasible. This technology is being applied to the study of genetic variation within the gene pools of cultivated crop species (Xu et al., 2012). Extending this type of analysis to wild populations will allow many key questions to be asked for the first time. For example, we can now ask which genes show variation in the populations growing in different environments and which genes have changed in populations that have been sampled over time from the same population in a changing environment. At higher taxonomic levels, we can explore how natural selection has acted within plant groups and resulted in the evolution of species with specific adaptation to different environments. Sequence-based phylogenetic analysis is widely used (Duan et al., 2007), but adoption of next-generation sequencing (Nock et al., 2010) allows major advances in the analysis of evolutionary relationships in plants. These new perspectives provide greater resolution in defining evolutionary history and reveal the detail of evolutionary changes. Fitzgerald et al. (2011) explored whole chloroplast genome diversity in populations of a distant wild relative of rice and found greater diversity at the more stressed (dryer) sites. Local adaptation to environment may be apparent in wild populations (Fournier-Level et al., 2011; Hancock et al., 2011). Analysis of nuclear genome diversity of wild populations of this type should now be possible in many more species with current next-generation sequencing techniques. Quantitative traits may show complex genetic adaptation mechanisms (Anderson et al., 2014). However, continuing advances in DNA sequencing technologies will make these strategies more effective extending plant genotyping to the whole genome level by reducing dramatically the costs and technical difficulties of genome sequencing (Henry, 2013). Analysis of whole-genome sequences is now being used to support plant breeding (Gopala et al., 2012) in ways that marker scans of genomes could not deliver because the functional significance of genes across the genome can be suggested by homology analysis.

Studies of changes in plant populations over time

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Studies of wild plant populations overtime as they adapt to a changing climate requires the availability of samples collected over a long period of time. Comparison of the genetics of plants from past collections with those of more recent collections from the same locations can provide the required information. For example, analysis of populations of wild thyme (Thymus vulgaris) has shown genetic adaptation to reduced winter freezing events in the period since the 1970s (Thompson, 2013).

Long-term collection sites have enabled the study of the effects of global warming across Israel in wild cereals collected in 1980 and again in the same sites in 2008, subjected to 28 years of global warming (Nevo et al., 2012). Wild emmer wheat (Triticum dicoccoides) populations and wild barley (Hordeum spontaneum) populations (10 populations of each) were sampled in 1980 and again in 2008 (Nevo et al., 2012). Profound adaptive changes of these cereals were identified over the 28 years, phenotypically in flowering time and genotypically in simple sequence repeat (SSR) allelic turnover. Phenotypically, both cereals had shortened flowering time, but this was significantly (< 0.01) greater in wild barley than in emmer wheat. The average shortening for each population after the 28-year period in emmer wheat was 8.5 days, whereas in wild barley, it was 10.9 days (Figure 2). Earliness may be a key trait required to adapt crops to warmer and dryer climates worldwide.

image

Figure 2. Changes in flowering time of wild cereals in response to climate change differences in FT (days) of wild emmer wheat and wild barley collected in 1980 and in 2008 (Nevo et al., 2012). (a) The FT differences in 10 wild emmer wheat populations. (b) The FT differences in 10 wild barley populations. The x-axis shows populations numbered from north to south. The y-axis shows days from germination to flowering.

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Both wild cereals revealed remarkable genetic divergence, much more in emmer wheat than in wild barley populations (Figure 3). In emmer wheat, the total allelic count was 318 alleles in 1980 versus 290 alleles in 2008, a highly significant reduction of 28 alleles (8.8%; < 0.0001). In wild barley, the total allelic count in 1980 was 319 alleles and 309 in 2008, nearly significant (= 0.082) reduction of 10 alleles and the same reduction trend as in emmer wheat. However, some new alleles that were detected in both wild cereals may be adaptive and valuable for breeding.

image

Figure 3. Changes in diversity in wild cereal populations responding to climate change. Genetic associations of individual wild emmer wheat and wild barley plants, as revealed by the principle coordinates analysis of SSR markers (Nevo et al., 2012). (a) The associations of 143 and 149 individual samples collected in 1980 and in 2008 of the 10 wild emmer wheat populations, respectively. (b) The associations of 148 and 148 individual samples collected in 1980 and in 2008 of the 10 wild barley populations, respectively.

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These samples or measurements over time are only available for a very limited number of cases. Urgent establishment of coordinated long-term experiments to monitor future changes in wild populations is required.

Studies of plant populations growing across environmental gradients

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Changes in populations overtime may be similar to those in current populations adapted to a different environment in space. Species of plants growing across diverse environments may demonstrate genetic adaptation to the different environments encountered in different parts of their natural range (Lowry et al., 2013). Analysis of the genomes of wild plant populations growing along environmental gradients may reveal how the plants have adapted to the changed environment. Identification of the key genes that are selected by natural selection for climate change and how these genes are altered may be useful information for those attempting to breed crops to cope with altered or variable climates.

The evidence for climate adaptation in the genome of wild populations of the model plant, Arabidopsis thaliana, has been studied (Lasky et al., 2012; Stearns and Fenster, 2013) revealing patterns of parallel or convergent evolution. Analysis of functional (nonsynonymous) SNP patterns across the genome showed a stronger correlation with climate differences than with geographical distance (Lasky et al., 2012). Local adaptation to climate variation can be the result of parallel mutation (the same mutations beings selected independently) or due to convergent evolution (selection of different mutations with the same impact on phenotype). Analysis of wild populations of Arabidopsis from Asia and Europe (Stearns and Fenster, 2013) suggests that parallel mutation is most likely to explain the observed patterns of adaptation.

The ‘Evolution Canyon’ (EC) microsite (Figure 4) is probably the most studied site for this type of research (Nevo, 2011a,b). Local microcosms and natural laboratories, in the ‘EC model’, reinforce studies of regional and global macrocosm ecological theatres across life. They present sharp ecological contrasts at a microscale, permitting the pursuit of observations and experiments across diverse prokaryote and eukaryote taxa sharing a sharp microecological division (Nevo, 2001, 2011a,b). The effects of climatic change on living organisms have been shown primarily on regional and global scales. The EC microscale model could be studied as a potential life monitor of global warming (Nevo, 2011a,b). The EC model reveals evolution in action at a microscale involving biodiversity divergence, adaptation and incipient sympatric speciation across life from viruses and bacteria through fungi, plants and animals. The EC consists of two abutting slopes separated, on average, by 200 m at EC I, Mt Carmel, Israel. The tropical, xeric, savannoid, ‘African’ (AS) south-facing slope (SFS) abuts the forested ‘European’ (ES) north-facing slope (NFS). The AS receives 200%–800% higher solar radiation than the ES. The ES represents south European and East Mediterranean forested maquis. The AS and ES exhibit drought and shade stress, respectively. Major adaptive complexes on the AS are because of solar radiation, heat and drought, whereas those on the ES relate to light stress and photosynthesis. Preliminary evidence suggests the extinction of some European species on the ES and AS. Climatic change predictions could be tested in diverse species across life at EC. The EC microclimatic model is optimal to track global warming at a microscale across life from viruses and bacteria to mammals and at numerous other ECs across the planet (Nevo, 2011a,b).

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Figure 4. Study of wild plants growing across a steep environmental gradient (Sikorsky and Nevo, 2007). (a) Schematic diagram of ‘Evolution Canyon’. (b) Cross-section view of ‘Evolution Canyon’ I, Lower Nahal Oren, Mount Carmel. (c) Air view of ‘Evolution Canyon’ I. Note the plant formation on opposite slopes. The green, lush, ‘European’, temperate, cool-mesic NFS sharply contrasts with the open park forest of warm-xeric, tropical, ‘African-Asian’ savannah on the SFS. In each ‘Evolution Canyon’, seven sampling stations are designated: three on the SFS (1–3), one at the valley bottom (4) and three on the NFS (5–7).

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Wild crop relatives

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

The use of new evolving genetic resources (Shapter et al., 2013) may bring the best hope to secure food for humans and animals in the future. Wild crop relatives provide excellent systems in which to study adaptation to climatic variation. Results from investigations of wild relatives (Nevo, 2012) can be easily transferred to agriculture by using appropriate wild relatives as genetic resources. The importance of wild genetic resources emphasizes the importance of their conservation and avoiding gene flow from domesticated to wild populations (Cornille et al., 2013) if we are to use them to study natural selection.

Wild cereals in the Near East Fertile Crescent are rich in adaptive genetic resources against abiotic (e.g. drought, cold, heat, salt and mineral scarcity) and biotic (viral, bacterial, fungal and herbicide) stresses, and with high quantity and quality storage proteins (glutenins, gliadins and hordeins), amylases and photosynthetic yield (Nevo, 2011a,b). Ren et al. (2013) assayed over 1000 SNP in wild emmer wheat from Turkey and Israel. Positive natural selection was identified as acting at 33 loci. Most of these resources are yet untapped and are valuable for crop improvement. The current rich genetic map of emmer wheat (Peng et al., 2003) and that of wild barley (Chen et al., 2010) permits the unravelling of beneficial alleles of candidate genes. Effective marker-assisted selection could enhance the introgression of useful alleles into cultivated wheat. The potential risk of losing precious genetic alleles should be balanced by using presumably adaptive novelties, which were derived from climate change during 1980–2008 (Nevo et al., 2012), in breeding programs for earliness and drought resistance. Wild barley has proved to be a useful source of drought tolerance that can be transferred to domesticated barley with marker-assisted selection (Lakew et al., 2012, 2013).

Wild relatives of cultivated rice have a pan tropical distribution and a genome species have been independently domesticated in Asia and Africa (Vaughan et al., 2006). The wild resources represent an important reservoir of genetic diversity for rice breeding. Wild rice populations in Australia may be of special value because of their isolation from the impacts of domestication in Asia and Africa (Waters et al., 2012). Sequencing of wild crop relatives (Henry, 2014) will support their use in plant improvement.

The genome sequences of wild relatives of many more species are becoming available. For example, the sequence of wild relatives of chickpea have recently been reported (Varshney et al., 2013). The availability of these sequences will allow the analysis of the contribution of processes such as speciation, domestication, genome plasticity, epigenetics, hybridization and polyploidy to climate adaptation.

Analysis of speciation

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Diversification of plants to adapt to diverse environments might also provide clues to strategies for breeding agricultural species. For example, analysis of the Oryza species should provide an opportunity to evaluate the genetics of adaptation of species across this important crop genus. High-quality genome sequences for the Oryza species are becoming available. The recent discovery of new wild close relatives of rice in northern Australia (Sotowa et al., 2013) provides an opportunity to investigate adaptation in a natural system highly relevant to agricultural production. Rice, Oryza sativa, was domesticated in Asia from Oryza rufipogon. Oryza rufipogon was thought to extend from Asia to Australia (Henry et al., 2010). However, recent molecular analysis (Waters et al., 2012) has demonstrated that the Australian populations are distinct and may represent a useful source of diversity for rice breeding.

‘Evolution Canyon’ is an ideal model for studying incipient sympatric speciation across life in soil bacteria, wild barley, Drosophila and spiny mice (Nevo, 2006). Whole-genome sequencing will again provide a key tool to advance our understanding of speciation in adaptation of plants to different environments. Sequence data can help identify new species of wild crop relatives not previously identified from morphological data (Sotowa et al., 2013). Species divergence and domestication both involve the development of distinct gene pools. The gene pools represent distinct options for use in breeding better adapted crops.

Studies of domestication

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Domestication of plants results (Purugganan and Fuller, 2009) in the establishment of a distinct gene pool that is under human as opposed to natural selection. However, significant gene flow between these two systems may continue in some systems. Knowledge of the key genes selected in domestication allows targeted selection to facilitate rapid introduction of genes from wild germplasm into the domesticated crop. Further whole-genome analysis of domesticated and wild population will greatly increase knowledge of these genes and improve the potential to utilize wild diversity. Rice quality traits in domesticated rice have been subject to significant human selection (Kharabian-Masouleh et al., 2012) relative to that found in wild species (Kasem et al., 2012). Human selection may in some cases result in reduced fitness of the domesticated populations. For example, selection for the highly desirable trait of fragrance in aromatic rice, as found in Basmati and Jasmine rice, has been achieved by selecting for loss of function of a gene (Bradbury et al., 2005) in a stress response pathway (proline metabolism) that increases susceptibility to abiotic stress (Fitzgerald et al., 2010). Increased knowledge of these conflicts can allow plant breeding to compensate for or avoid these genetic options and help to ensure better performance of crops under adverse environmental conditions. Studies of the genetic basis of adaptation in wild populations can be used to ensure resilience that is retained in crop varieties while domestication traits are being selected. The evolution of adaptation, incipient speciation, possible domestication and improvement of wild barley, Hordeum spontaneum, has been reviewed (Nevo, 2014). Advances in DNA sequencing are revealing the basis of domestication in ways that should allow accelerated domestication of new species by being more deliberate in selecting for the required alleles at domestication loci in the transfer of genes from wild relatives into domesticated crops (Henry, 2012). These insights will be critical in using wild genetic resources to breed crops for climate adaptation.

Genome plasticity

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Plants may respond to climate variation by varying their phenotype in ways that allows them to cope with diverse environments (Nicotra et al., 2010; Thompson, 2013). The breeding of climate-resilient crops may be achieved by using genes for genome plasticity (Anderson et al., 2012). These genes may provide the plant with an ability to radically alter phenotype in response to environmental signals. Genomics research may allow the genes responsible for this response to be better understood and made available for exploitation in plant breeding.

Epigenetics

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Plant adaptation to climate may involve epigenetic changes (Schmitz et al., 2013) that can allow rapid adaptation in plant populations. Whole-genome and epi-genome analysis will be needed for a full explanation of adaptation in many systems. Noncoding sequences may also provide adaptation to environmental change (Eckardt, 2007). Whole epi-genome analysis of wild populations will allow improved understanding of how this knowledge can be exploited in plant breeding.

Contribution of hybrid and polyploidy plant performance to climate adaptation

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Hybrid and polyploidy plants often demonstrate enhanced productivity. Highly polyploid plants such as wheat and sugarcane have been very successful in agriculture and polyploidiztion events have been common in the evolution of flowering plants (Soltis et al., 2009). Hybrid plants are widely used in agriculture due to the greater productivity resulting from hybrid vigour (heterosis). The basis of this enhanced growth is now being analysed at the whole genome level in hybrid (Gopala et al., 2012) and polyploid (Bundock et al., 2012) plants. The analysis of the mechanisms of hybrid and polyploidy plant performance in wild populations may demonstrate the contribution of heterosis or polyploidy to adaptation to variations in climate over short or long time periods. This approach may ultimately reveal key explanation of heterosis or superior polyploidy plant performance that has application in plant breeding for agriculture. The ability of wild plants to hybridize with closely related species has been identified as an important mechanism for survival in a changing environment. Becker et al. (2013) argue that reproductive barriers that isolate plant populations in the wild limit the ability of plant populations to adapt to climate or other environmental change. Rare interspecific hybrid individuals may have a selective advantage in responding to new environments.

Analysis of gene banks

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Plant breeders may make use of genotypes selected for the desired environment by natural selection by considering the environment from which the germplasm they use is sourced. The identification of plant genotypes suitable for current or future environments may be achieved by searching in gene banks for accessions that have been sourced from wild or domesticated populations that are from environments that match the target production environment. This approach has been demonstrated to be useful in finding new sources of disease resistance in wheat genetic resource collections (Bhullar, 2009). This focused identification of germplasm strategy (FIGS) is designed to allow appropriate germplasm to be efficiently found in large collections. This approach should greatly increase the utilization of germplasm in seed banks, much of which has not been exploited to date because it is so poorly characterized and usually of unknown value especially in relation to potential contribution to environmental adaptation traits. Much of the resistance to abiotic stress that has been exploited in the past by plant breeders has come from wild sources. New tools will allow the process of finding the required genes to be more deliberate and efficient.

Conclusions and future prospects

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References

Whole-genome analysis of more wild plant systems should greatly enhance our knowledge of the mechanisms of adaptation to climate in plants. Once identified as contributing to adaptation in wild populations, genetic variation in these loci can be studied in both wild and domesticated populations to enhance understanding of their role in environmental adaptation. Selection for validated advantageous alleles at these loci could then be adopted in crop breeding. Studies of specific loci have suggested that adaptation to higher temperatures may be found to relate more to adaptation to the reduced availability of water at high temperature rather than to adaptation to the temperature. These studies also indicate that adaptation to additional pest and disease pressures found at a higher temperature may be more critical than adaptation to the temperature itself. Adapting to climate change is not only about adapting to the changes in the abiotic environment but also to a new biotic environment (Garrett et al., 2006). Studies of wild populations at the whole genome level are required to extend and generalize these observations. However, adaptation to climate in the wild may be associated with selection for survival as distinct from traits ensuring high crop yield in an agricultural context. Slow growth and avoidance of environmental stress may be an effective strategy delivering climate resilience in wild populations. Adaptation may involve drought avoidance in Arabidopsis with rapid growth, low water use efficiency and early flowering (Lovell et al., 2013). In contrast, agricultural productivity requires the sustained production of the harvestable parts of the plants when under stress. Careful analysis of genome-adaptation mechanisms will be required to distinguish these selective processes. Remaining populations of wild crop relatives that have been isolated from the genetic impact of domestication represent especially valuable resources for understanding crop adaptation to climate variation. Long-term studies of these populations will be key tools in delivering the agricultural productivity gains required to ensure food security. Capture of genes from wild populations is an important mechanism for crop improvement (Bansal et al., 2014; Xiao et al., 1996) that is made more feasible and efficient by advancing genomic tools. Greater emphasis on climate adaptation and more targeted exploitation of genes for adaptation will be a key to delivering the agricultural productivity gains required for food security. Specific environmental adaptations such as the evolution of C4 photosynthesis may also be better understood as a result of more complete analysis at the whole genome level (von Caemmerer et al., 2013).

References

  1. Top of page
  2. Summary
  3. Importance of crop breeding for food security
  4. Threat of climate change to agricultural production
  5. Study of adaptation to climate under natural selection as a guide to plant breeding
  6. Advances in tools suitable for analysis of genome-wide adaptation in wild populations
  7. Studies of changes in plant populations over time
  8. Studies of plant populations growing across environmental gradients
  9. Wild crop relatives
  10. Analysis of speciation
  11. Studies of domestication
  12. Genome plasticity
  13. Epigenetics
  14. Contribution of hybrid and polyploidy plant performance to climate adaptation
  15. Analysis of gene banks
  16. Conclusions and future prospects
  17. Acknowledgements
  18. References
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