Advances in genomics and genome editing for breeding next generation of fruit and nut crops

Savadi, Siddanna; Mangalassery, Shamsudheen; Sandesh, M.S.

doi:10.1016/j.ygeno.2021.09.001

Cited by 25 publications

(22 citation statements)

References 219 publications

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“…Phytoene desaturase ( pds ), a gene involved in carotenoid biosynthesis, has been targeted in most gene editing studies. Pds may be used as a visible marker to demonstrate specific genome editing effects ( Savadi et al., 2021 ) since its knockout in plants results in albino phenotypes due to the absence of chlorophylls. CRISPR/Cas9-mediated pds gene knock-out has been found to confer an albino phenotype in many fruit crops such as grape ( Nakajima et al., 2017 ), chestnut ( 2022 ; Pavese et al., 2021 ), strawberry ( Wilson et al., 2019 ), cavendish banana ( Naim et al., 2018 ; Ntui et al., 2020 ), apple ( Nishitani et al., 2016 ) and pear ( Charrier et al., 2019 ; Malabarba et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Knockout of phytoene desaturase gene using CRISPR/Cas9 in highbush blueberry

et al. 2022

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Among the New Plant Breeding Techniques (NPBTs), the CRISPR/Cas9 system represents a useful tool for target gene editing, improving the traits of the plants rapidly. This technology allows targeting one or more sequences simultaneously, as well as introducing new genetic variations by homology-directed recombination. However, the technology of CRISPR/Cas9 remains a challenge for some polyploid woody species, since all the different alleles for which the mutation is required must be simultaneously targeted. In this work we describe improved protocols adapting the CRISPR/Cas9 system to highbush blueberry (Vaccinium corymbosum L.), using Agrobacterium-mediated transformation. As a proof of concept, we targeted the gene encoding for phytoene desaturase, whose mutation disrupts chlorophyll biosynthesis allowing for the visual assessment of knockout efficiency. Leaf explants of in vitro-cultured blueberry cv. Berkeley has been transformed with a CRISPR/Cas9 construct containing two guide RNAs (gRNA1 and gRNA2) targeting two conserved gene regions of pds and subsequently maintained on a selection medium enriched with kanamycin. After 4 weeks in culture on the selection medium, the kanamycin-resistant lines were isolated, and the genotyping of these lines through Sanger sequencing revealed successful gene editing. Some of mutant shoot lines included albino phenotypes, even if the editing efficiencies were quite low for both gRNAs, ranging between 2.1 and 9.6% for gRNA1 and 3.0 and 23.8 for gRNA2. Here we showed a very effective adventitious shoot regeneration protocol for the commercial cultivar of highbush blueberry “Berkeley”, and a further improvement in the use of CRISPR/Cas9 system in Vaccinium corymbosum L., opening the way to the breeding mediated by biotechnological approaches.

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Section: Introductionmentioning

confidence: 99%

Knockout of phytoene desaturase gene using CRISPR/Cas9 in highbush blueberry

et al. 2022

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“…On the other hand, conventional plant breeding techniques have developed a multitude of fruit trees for their yield and quality indicators [ 12 ]. Nonetheless, trees have a long reproductive cycle and a high degree of heterozygosity [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

“…Thus, for meeting the needs of gardeners such as ameliorating the adverse impacts of abiotic stress, climate change, and global warming, or having a befitting form and phenology, e.g., dwarf, it is consequential to have a great breakthrough in the world of fruit tree breeding [ 12 ]. In terms of purpose, breeders have taken advantage of naturally occurring mutation, which has been widely used to spread an agronomical character through new varieties (e.g., late flowering or self-compatibility), and, on the other hand, developed genetically engineered material to improve fruit quality (e.g., shelf-life, color, flavor, texture, nutrient content) [ 12 ]. As an illustration, limitations such as challenges in economic, regulatory, and intellectual property hindering the progress of transgenic fruit trees are developed through mutation [ 14 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

“…Regarding the given information about mutation, genome editing is propounded as a novel technology so as to revolutionize and expedite the genetic improvement of tree crops inside the denominated new plant breeding techniques (NPBT) [ 12 , 18 ]. In such a case, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 and TALEN (Transcription activator-like effector nuclease) mediated gene-editing developed in bacteria are the latest technologies and accurate tools for editing genes and inducing mutations [ 19 , 20 , 21 ] ( Figure 1 ).…”

Section: Introductionmentioning

confidence: 99%

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Spontaneous, Artificial, and Genome Editing-Mediated Mutations in Prunus

Prudencio

Devin

Mahdavi

et al. 2022

IJMS

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Mutation is a source of genetic diversity widely used in breeding programs for the acquisition of agronomically interesting characters in commercial varieties of the Prunus species, as well as in the rest of crop species. Mutation can occur in nature at a very low frequency or can be induced artificially. Spontaneous or bud sport mutations in somatic cells can be vegetatively propagated to get an individual with the mutant phenotype. Unlike animals, plants have unlimited growth and totipotent cells that let somatic mutations to be transmitted to the progeny. On the other hand, in vitro tissue culture makes it possible to induce mutation in plant material and perform large screenings for mutant’s selection and cleaning of chimeras. Finally, targeted mutagenesis has been boosted by the application of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 and Transcription activator-like effector nuclease (TALEN) editing technologies. Over the last few decades, environmental stressors such as global warming have been threatening the supply of global demand for food based on population growth in the near future. For this purpose, the release of new varieties adapted to such changes is a requisite, and selected or generated Prunus mutants by properly regulated mechanisms could be helpful to this task. In this work, we reviewed the most relevant mutations for breeding traits in Prunus species such as flowering time, self-compatibility, fruit quality, and disease tolerance, including new molecular perspectives in the present postgenomic era including CRISPR/Cas9 and TALEN editing technologies.

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“…While the recent increase in fruit tree crop genomic resources and database availability is regarded as a significant trigger to improving the understanding of gene function, recent advances in advanced biotechnology tools like RNAi-based gene silencing and gene editing are of paramount importance to accelerating gene function studies beyond the gene-to-traits associations inferred from most “OMICS” technologies. For the past twenty years, significant signs of progress have been made in most fruit trees for reverse and forward genetics programs ( Peña et al., 2004 ; Malnoy et al., 2009 ; Chaïb et al., 2010 ; Petri et al., 2018 ; Savadi et al., 2021 ). Thanks to more precise and advanced genetic systems, the functional characterization of key genes to essential performance traits in fruit trees is rapidly increasing.…”

Section: Introductionmentioning

confidence: 99%

Transgene-free genome editing and RNAi ectopic application in fruit trees: Potential and limitations

Gouthu

Mandelli²,

Eubanks³

et al. 2022

Front. Plant Sci.

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For the past fifteen years, significant research advances in sequencing technology have led to a substantial increase in fruit tree genomic resources and databases with a massive number of OMICS datasets (transcriptomic, proteomics, metabolomics), helping to find associations between gene(s) and performance traits. Meanwhile, new technology tools have emerged for gain- and loss-of-function studies, specifically in gene silencing and developing tractable plant models for genetic transformation. Additionally, innovative and adapted transformation protocols have optimized genetic engineering in most fruit trees. The recent explosion of new gene-editing tools allows for broadening opportunities for functional studies in fruit trees. Yet, the fruit tree research community has not fully embraced these new technologies to provide large-scale genome characterizations as in cereals and other staple food crops. Instead, recent research efforts in the fruit trees appear to focus on two primary translational tools: transgene-free gene editing via Ribonucleoprotein (RNP) delivery and the ectopic application of RNA-based products in the field for crop protection. The inherent nature of the propagation system and the long juvenile phase of most fruit trees are significant justifications for the first technology. The second approach might have the public favor regarding sustainability and an eco-friendlier environment for a crop production system that could potentially replace the use of chemicals. Regardless of their potential, both technologies still depend on the foundational knowledge of gene-to-trait relationships generated from basic genetic studies. Therefore, we will discuss the status of gene silencing and DNA-based gene editing techniques for functional studies in fruit trees followed by the potential and limitations of their translational tools (RNP delivery and RNA-based products) in the context of crop production.

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Advances in genomics and genome editing for breeding next generation of fruit and nut crops

Cited by 25 publications

References 219 publications

Knockout of phytoene desaturase gene using CRISPR/Cas9 in highbush blueberry

Knockout of phytoene desaturase gene using CRISPR/Cas9 in highbush blueberry

Spontaneous, Artificial, and Genome Editing-Mediated Mutations in Prunus

Transgene-free genome editing and RNAi ectopic application in fruit trees: Potential and limitations

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