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The grand challenge of breeding by design

With plentiful knowledge of gene function and the development of technologies like gene editing, breeders are fully equipped to address grand challenges and eliminate various forms of hunger.

Human society has never stop worrying about food. The recent outbreak of war in Ukraine is predicted to exacerbate famine in the global South, which receives much of the grain exported from that region, and factors like pandemics or climate change affect food supply everywhere. To feed the world, breeding is an ever important topic. In this issue ter Steeg et al. discuss breeding and factors that affect the decision-making of a commercial breeder1.

Globally, breeding is a collaborative effort among plant scientists and breeders in both public and private sectors. While there are clear biological and economic restrictions on breeding in both sectors, new opportunities and challenges also emerge that lead predictably to a new breeding landscape. Crop breeding is based on genetic variations, and while this can be created artificially, naturally occurring variations continue to be key resources.

Global institutes, like those under the Consortium of International Agricultural Research Centres (CGIAR), are constantly working to improve their germplasm collections. In this issue, Ramirez-Villegas et al. analyse the landraces of 25 major crops in ex situ repositories and identify the gaps remaining to be filled2. In a previous work, they reported the conservation status of the wild relatives of 81 crops3. Efforts like this expand the availability of natural variations and directly benefit breeders.

Artificial mutations induced by physical or chemical mutagens tend to be random and hard to use in breeding. Now, with targeted gene-editing approaches, a large number of agronomically desirable variations can be generated quickly. Many researchers have used CRISPR–Cas to target known agronomic genes, modifying coding sequences or gene expression to obtain useful mutations. For example, tomato lines have been edited for the desired architecture4 and wheat and potato varieties have been edited for better resistance to pathogens5,6. Base editing has generated new alleles for herbicide resistance in rice and wheat7,8. Gene editing can tweak not only nuclear genomes but also those of cellular organelles9,10,11. These new methods will markedly enrich the allelic spectrum that can be employed in future breeding.

Breeders are gradually abandoning the conventional breeding model — which is random and reliant on breeders’ experience — and adopting the concept of ‘prior design’. Large-scale genome sequencing and genome-wide association studies, as well as extensive functional genomic studies, have made designed breeding a realistic possibility. By stacking genes known to control grain quality and yield traits, scientists have developed high-yield and superior-quality rice varieties12. On the basis of the known function of the MLO gene in the pathogenesis of powdery mildew, mlo wheat with resistance was swiftly developed by gene editing5. Knowledge of genes controlling self-incompatibility in potato allowed the generation of diploid self-compatible potato lines, making potato breeding more efficient and propagation through seeds instead of tubers possible1,13.

In a paper published by Nature Plants last year, researchers showed in wheat breeding trials that climate change in recent decades significantly increased cross-interactions of the varieties tested across different environments, making breeders’ jobs far more difficult14. However, they also discovered that germplasm developed under heat stress was better adapted and more stable, indicating that targeting breeding to specific stress environments should help breed climate resilient varieties. Research on plant stress tolerance has identified many genes that confer resistance to environmental stresses, and thus many targets for editing to create climate-resilient crops. At the same time abundant stress-resistance alleles already exist in the wild gene pool15, highlighting the importance of landraces and crop wild relatives.

Rising labour costs are another challenge for sustainable agriculture. Although the development of mechanized technologies greatly reduces labour input, there are still many crops or crop varieties not suitable for mechanized farming. Breeding varieties more suitable for mechanized planting and harvesting is one solution; however, scientists in the perennial crop community have been working on another strategy: transforming annual crops to perennial crops. Annual crops require repetitively sowing seeds, planting and ploughing each season, while perennial agriculture is closer to natural ecological systems, minimizing the inputs of labours and fertilizers. The Land Institute in the United States has developed a perennial intermediate wheatgrass (Thinopyrum intermedium), trademark name Kernza, that has made its way to niche markets16. A group of scientists in Yunnan University, China, has developed and released perennial rice varieties that showed continuous high yield across multiple years without the need to replant each season17.

Grafting represents another route to perennialization. Recently, scientists in Huazhong Agricultural University grafted an aubergine scion to a woody Solanum root stock, making ‘eggplant trees’ that bear aubergine fruits for 3 years and achieve enhanced yield per season18.

The advantages of orphan crops have been re-recognized recently. They tend to be rich in nutrients, including micronutrients, and are able to grow in suboptimal conditions19. Without abundant genetic resources for conventional breeding, gene-editing-based approaches are particularly useful for orphan crops, especially when they are related to species that are major crops already extensively studied. More research projects have been initiated for breeding in orphan crops20,21.

There are many challenges to feeding the world; however, progress in technologies and public knowledge gives cause for optimism. There are a few factors that limit the participation of commercial breeders1, but with more genetic resources becoming available every month, the world is becoming a breeder’s oyster.


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The grand challenge of breeding by design. Nat. Plants 8, 451–452 (2022).

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