The role of conventional plant breeding in ensuring safe levels of naturally occurring toxins in food crops

Kaiser, Natalie; Douches, David S.; Dhingra, Amit; Glenn, Kevin C.; Herzig, Philip Reed; Stowe, Evan; Swarup, Shilpa

doi:10.1016/j.tifs.2020.03.042

Cited by 65 publications

(56 citation statements)

References 169 publications

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“…The best-performing line is selected for subsequent commercial release. This breeding process is common to all methods used for crop product development (Kaiser et al, 2020).…”

Section: Designing Genome Editing Protocols and Methods To Optimize Ementioning

confidence: 99%

“…However, plants frequently develop multiple independent reproductive structures, only a portion of which may be affected by any new mutations. Also, breeding to develop new lines for commercial release involves an intensive process of selection of individual plants with useful phenotypes while eliminating individuals with undesirable mutations or phenotypes (commonly known as "off-types"; ASTA, 2016; Glenn et al, 2017;Kaiser et al, 2020). For these reasons, off-target edits in crops present fewer safety concerns than those that could arise with therapeutic applications of genome editing.…”

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confidence: 99%

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Plant Genome Editing and the Relevance of Off-Target Changes

et al. 2020

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Site-directed nucleases (SDNs) used for targeted genome editing are powerful new tools to introduce precise genetic changes into plants. Like traditional approaches, such as conventional crossing and induced mutagenesis, genome editing aims to improve crop yield and nutrition. Next-generation sequencing studies demonstrate that across their genomes, populations of crop species typically carry millions of single nucleotide polymorphisms and many copy number and structural variants. Spontaneous mutations occur at rates of ;10 28 to 10 29 per site per generation, while variation induced by chemical treatment or ionizing radiation results in higher mutation rates. In the context of SDNs, an off-target change or edit is an unintended, nonspecific mutation occurring at a site with sequence similarity to the targeted edit region. SDN-mediated offtarget changes can contribute to a small number of additional genetic variants compared to those that occur naturally in breeding populations or are introduced by induced-mutagenesis methods. Recent studies show that using computational algorithms to design genome editing reagents can mitigate off-target edits in plants. Finally, crops are subject to strong selection to eliminate off-type plants through well-established multigenerational breeding, selection, and commercial variety development practices. Within this context, off-target edits in crops present no new safety concerns compared to other breeding practices. The current generation of genome editing technologies is already proving useful to develop new plant varieties with consumer and farmer benefits. Genome editing will likely undergo improved editing specificity along with new developments in SDN delivery and increasing genomic characterization, further improving reagent design and application. PLANT GENETIC VARIABILITY Genetic differences between individuals are the basis of adaptation and evolution. Plant breeding, as a form of directed evolution, has a long history of using genetic diversity for crop improvement. During the process of crop domestication, humans selected individual plants with favorable traits that resulted from novel mutations or standing variation in the ancestral species. The process of selecting plant varieties with favorable characteristics for cultivation and consumption continues to the present day. Modern plant breeding is a more directed process than the crop improvement that occurred through the history and prehistory of most

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“…The best-performing line is selected for subsequent commercial release. This breeding process is common to all methods used for crop product development (Kaiser et al, 2020).…”

Section: Designing Genome Editing Protocols and Methods To Optimize Ementioning

confidence: 99%

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confidence: 99%

Plant Genome Editing and the Relevance of Off-Target Changes

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“…In addition, it has been documented that other forms of processing potatoes for consumption, like chuño and moray, involving grounding, freezing, and drying processes have detoxification effects (Melton et al, 2020). Also, some authors have reported that gene flow from cultivated/weedy to wild potatoes may confer attributes evolved through domestication (e.g., some aspects of weedy behavior for survival in disturbed areas), among them decrease of toxicity (see Kaiser et al, 2020), and this could explain that consumption of wild potatoes is feasible. In theory, wild potatoes occurring in the neighborhood of agricultural areas would be less toxic than those occurring far away, but this hypothesis must be tested.…”

Section: Use and Management Of Potatoes And Their Gene Flowmentioning

confidence: 99%

Natural and Cultural Processes Influencing Gene Flow Among Wild (atoq papa), Weedy (araq papa and k’ipa papa), and Crop Potatoes in the Andean Region of Southern Peru

Parra

Casas

Begazo³

et al. 2021

Front. Ecol. Evol.

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The Andean region is one of the areas with the earliest signs of food production systems and highest agrobiodiversity of the world, which resulted from millennia of domestication in a context of high ecosystem heterogeneity and human cultures valuing diversity for risk management. FAO has reported nearly 4000 varieties of cultivated potatoes still grown in the Andes, 3000 of them currently occurring in Peru. Such diversity has enormous sources of variation in wild (atoq papa) and weedy (araq papa and k’ipa papa) potatoes that coexist with crops, but their variation, interactions and mechanisms influencing diversification processes still require studies. In order to have a panorama of the variation and mechanisms influencing it in a regional setting, we studied biocultural factors favoring potatoes diversity in communities of Cusco and Apurimac, Peru. Our study documented the regional variation of wild, weedy, and cultivated potatoes recognized by local Quechua people and conducted semi-structured interviews to document their use, cultural value, and strategies of gene flow management implemented. We also studied their phenology, floral biology, flower visitors, and conducted experimental crosses between the wild S. candolleanum and 30 varieties of cultivated potatoes. We identified the wild potatoes S. acaule, S. brevicaule and S. candolleanum and 53 varieties of araq papa used and managed by local people. The latter provide nearly one third of the annual consumption of tubers by people interviewed and are, therefore, highly valued, maintained and managed in crop fields (chacras). People recognized that crosses between wild, weedy, and cultivated potatoes occur, and identified flower visitors and frugivores consuming their berries. Overlap of blooming periods and flower visitors of wild, weedy, and cultivated potatoes was recorded. Almost all flower visitors are shared among the different potato species and varieties, the bumble bees being particularly relevant in pollination of all taxa studied. We recorded seed production in nearly 35% of the experimental crosses. K’ipa papas are sets of mixtures of plants resulting from remaining tubers of cultivated potatoes, but also those from seeds that may result from hybridization of wild, weedy, and cultivated potatoes. Since local people commonly use k’ipa papa varieties and some of them are kept for planting in chacras, sexual reproduction in k’ipa papas is possibly one main mechanism of variation and source of new varieties of crops. Maintaining wild and weedy potatoes, and the natural and cultural mechanisms of gene flow is crucial for in situ conservation and generation of potato variation.

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“…Conventional plant breeding methods have a long history of improving crop production, productivity, nutritional security, and food safety ( 5 ). Several nutrient dense crop varieties in different food crops have been released for cultivation world-wide.…”

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confidence: 99%

“…The screening of crop germplasm for identification of genotypes with significantly reduced or null allergen content is cumbersome and therefore, conventional breeding methods and genomics assisted breeding (GAB) efforts toward hypoallergenic varieties have been undertaken in different crops including wheat, soybean, peanut, etc. ( 5 ).…”

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confidence: 99%