Employing CRISPR/Cas Technology for the Improvement of Potato and Other Tuber Crops

New breeding technologies have not only revolutionized biological science, but have also been employed to generate transgene-free products. Genome editing is a powerful technology that has been used to modify genomes of several important crops. This review describes the basic mechanisms, advantages and disadvantages of genome editing systems, such as ZFNs, TALENs, and CRISPR/Cas. Secondly, we summarize in detail all studies of the CRISPR/Cas system applied to potato and other tuber crops, such as sweet potato, cassava, yam, and carrot. Genes associated with self-incompatibility, abiotic-biotic resistance, nutrient–antinutrient content, and post-harvest factors targeted utilizing the CRISPR/Cas system are analyzed in this review. We hope that this review provides fundamental information that will be useful for future breeding of tuber crops to develop novel cultivars.

Single nucleotide replacement in the Atlantic salmon genome using CRISPR/Cas9 and asymmetrical oligonucleotide donors

Background New breeding technologies (NBT) using CRISPR/Cas9-induced homology directed repair (HDR) has the potential to expedite genetic improvement in aquaculture. The long generation time in Atlantic salmon makes breeding an unattractive solution to obtain homozygous mutants and improving the rates of perfect HDR in founder (F0) fish is thus required. Genome editing can represent small DNA changes down to single nucleotide replacements (SNR). This enables edits such as premature stop codons or single amino acid changes and may be used to obtain fish with traits favorable to aquaculture, e.g. disease resistance. A method for SNR has not yet been demonstrated in salmon. Results Using CRISPR/Cas9 and asymmetrical ODNs, we were able to perform precise SNR and introduce a premature stop codon in dnd in F0 salmon. Deep sequencing demonstrated up to 59.2% efficiency in single embryos. In addition, using the same asymmetrical ODN design, we inserted a FLAG element into slc45a2 and dnd, showing high individual perfect HDR efficiencies (up to 36.7 and 32.7%, respectively). Conclusions In this work, we demonstrate that precise SNR and knock-in (KI) can be performed in F0 salmon embryos using asymmetrical oligonucleotide (ODN) donors. We suggest that HDR-induced SNR can be applied as a powerful NBT, allowing efficient introgression of favorable alleles and bypassing challenges associated with traditional selective breeding.

Open Intellectual Property Models for Plant Innovations in the Context of New Breeding Technologies

Plant related innovations are critical to enable of food security and mitigate climate change. New breeding technologies (NBTs) based on emerging genome editing technologies like CRISPR/Cas will facilitate “breeding-by-editing” and enable complex breeding targets—like climate resilience or water use efficiency—in shorter time and at lower costs. However, NBTs will also lead to an unprecedented patent complexity. This paper discusses implications and potential solutions for open innovation models.

Essentially Derived Varieties in View of New Breeding Technologies – Plant Breeders’ Rights at a Crossroads

Plant breeders’ rights (PBR) within the framework of the International Convention for the Protection of New Varieties of Plants (UPOV) are the sui generis intellectual property (IP) system of choice for plant varieties. It achieves a balance between the protection of new varieties and access to protected breeding material for further improvement. The extension of the protection to essentially derived varieties (EDVs) in the UPOV 1991 Convention1 was controversial from the beginning as it creates a tension with the breeders’ exemption. The 2017 UPOV Explanatory Notes on EDVs further fueled the debate as they were seen to limit the EDV extension, while some argue that the EDV scope should extend to all predominantly derived varieties merely on the basis of genetic conformity. With the rise of new breeding technologies (NBTs), legal certainty on the EDV definition is of fundamental importance to avoid a chilling effect on these promising technologies. Not only would a broad EDV definition block critical innovation and restrict the full potential of NBTs to a few multinational companies,2 it would also substantially limit the scope of protection of NBT-derived varieties, as an EDV itself is not entitled to the EDV extension: Valuable NBT-derived varieties would become easy prey for plagiarism. This article shows that the legislative intent of the EDV provision does not limit innovative breeding to conventional crossing and that there is no basis for extending EDV protection to new, innovative varieties which do not retain the essential characteristics of the initial variety (IV) even if there is a high genetic conformity. By analogy with the doctrine of equivalents under the patent system, a derived variety cannot qualify as an EDV if it (i) does not retain all the essential characteristic of the IV and (ii) is ‘non-obvious’ and causes a ‘significant technical progress of considerable economic interest’. The article finally suggests guidelines and processes to overcome the current EDV dilemma.

Integrating Gene Editing Techniques into Modern Cereal Breeding

New breeding technologies are revolutionizing plant and animal improvement programs [...]

The state-of-the-art of grapevine biotechnology and new breeding technologies (NBTS)

Context of the review: The manipulation of the genetic basis controlling grapevine adaptation and phenotypic plasticity can be performed either by classical genetics or biotechnologies. In the last 15 years, considerable knowledge has accumulated about the grapevine genome as well as the mechanisms involved in the interaction of the vine with the environment, pests and diseases. Despite the difficulties associated with genetic mapping in this species (allele diversity, chimerism, long generation intervals...), several major controlling important vegetative or reproductive traits have been identified. Considering the huge genotypic and phenotypic diversities existing in Vitis, breeding offers a substantial range of options to improve the performances of cultivars. However, even if marker-assisted selection was largely developed to shorten breeding programs, the selection of improved cultivars, whether for agronomic traits or disease tolerances, is still long and uncertain. Moreover, breeding by crossing does not preserve cultivar genetic background, when the wine industry and market are still based on varietal wines.Significance of the review: In grapevine, pioneering biotechnologies were set up in the 1960s to propagate and/or clean the material from micro-organisms. In the 1990s, the basis of genetic engineering was primary established through biolistic or Agrobacterium with several derived technologies refined in the last 10 years. The latest advance is represented by a group of technologies based on genome editing which allows a much more precise modification of the genome. These technologies, so-called NBTs (new breeding technologies), which theoretically do not deconstruct the phenotype of existing cultivars, could be potentially better accepted by the wine industry and consumers than previous GMO (genetically modified organism) approaches. This paper reviews the current state-of-the-art of the biotechnologies available for grapevine genome manipulation and future prospects for genetic improvement.