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Genome-editing technologies and their potential application in horticultural crop breeding.

Xiong JS, Ding J, Li Y - Hortic Res (2015)

Bottom Line: Plant breeding, one of the oldest agricultural activities, parallels human civilization.Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries.The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University , Nanjing, Jiangsu Province 210095, The People's Republic of China.

ABSTRACT
Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed.

No MeSH data available.


Schematic illustration of the ZFN structure and the principle of ZFN-mediated genomic modifications. The target site of the ZFN is recognized by the “left” and “right” half monomer that each consist of a tandem array of engineered ZFPs, and each engineered ZFP can recognize a nucleotide triplet (shown in different colors). The ZFN monomer is comprised of an N-terminal domain containing a NLS (red), a recognition domain that usually comprises tandem ZFPs (in different colors) and a C-terminal function domain that comprises the Fok I endonuclease. Recognition of the target sequence by the left and right ZFPs results in dimerization of the Fok I endonuclease, which is critical for the activity of the ZFNs. DNA cleavage takes place between the two ZFP recognition sites that contain a spacer sequence that is usually 6 bp long. Induced DSB of the target DNA are repaired either by NHEJ or HDR, resulting in gene mutation around the cleavage sites. NLS, nuclear localization signal; ZFP, zinc finger proteins; DSB, double-strand breaks; NHEJ, non-homologous end joining; HDR, homology-directed repair. Mutation#x002A;, the red color box region contains nucleotide deletion, insertion or substitution. Figure modified from Gaj et al. (2013), Figure 119 and Moore et al. (2012), Figure 1.100
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fig1: Schematic illustration of the ZFN structure and the principle of ZFN-mediated genomic modifications. The target site of the ZFN is recognized by the “left” and “right” half monomer that each consist of a tandem array of engineered ZFPs, and each engineered ZFP can recognize a nucleotide triplet (shown in different colors). The ZFN monomer is comprised of an N-terminal domain containing a NLS (red), a recognition domain that usually comprises tandem ZFPs (in different colors) and a C-terminal function domain that comprises the Fok I endonuclease. Recognition of the target sequence by the left and right ZFPs results in dimerization of the Fok I endonuclease, which is critical for the activity of the ZFNs. DNA cleavage takes place between the two ZFP recognition sites that contain a spacer sequence that is usually 6 bp long. Induced DSB of the target DNA are repaired either by NHEJ or HDR, resulting in gene mutation around the cleavage sites. NLS, nuclear localization signal; ZFP, zinc finger proteins; DSB, double-strand breaks; NHEJ, non-homologous end joining; HDR, homology-directed repair. Mutation#x002A;, the red color box region contains nucleotide deletion, insertion or substitution. Figure modified from Gaj et al. (2013), Figure 119 and Moore et al. (2012), Figure 1.100

Mentions: ZFNs are the first generation EENs that were developed following the discovery of the functional principles of the Cys2-His2 zinc finger (ZF) domains.21 Each Cys2-His2 ZF domain consists of 30 amino-acid residues that fold into a βββ configuration.21,22 Crystal structure analysis indicates that Cys2-His2 ZF proteins bind to DNA by inserting the α-helix into the major groove of the double helix.23 Each ZF protein is able to recognize 3 contiguous nucleotide bases within the DNA substrate. As shown in Figure 1, a generic ZFN monomer is fused by two functional distinct domains: an artificially prepared Cys2-His2 ZF domain at the N-terminal and a nonspecific DNA cleavage domain of the Fok I DNA restriction enzyme at the C-terminal. The dimerization of the Fok I domain is crucial for its enzymatic activity.24 Therefore, a ZFN dimer composed of two 3- or 4-ZF domains will recognize an 18- or 24-base target sequence that, statistically, forms a unique site in the genomes of most organisms. Since the first report in 1996, ZFNs have been successfully applied to gene modification mainly in animals such as human cells,25 zebrafish,26,27 and plants such as Arabidopsis,28 tobacco,29 and maize.30 However, obtaining functional ZFNs requires an extensive and time-consuming screening process.31 Further, ZFNs have other limitations, such as off-target effect22 or even toxic to the host cells. These shortcomings limit the application of ZFNs in plant genome editing. Until now, there have been no reports on ZFN applications in horticultural crops.


Genome-editing technologies and their potential application in horticultural crop breeding.

Xiong JS, Ding J, Li Y - Hortic Res (2015)

Schematic illustration of the ZFN structure and the principle of ZFN-mediated genomic modifications. The target site of the ZFN is recognized by the “left” and “right” half monomer that each consist of a tandem array of engineered ZFPs, and each engineered ZFP can recognize a nucleotide triplet (shown in different colors). The ZFN monomer is comprised of an N-terminal domain containing a NLS (red), a recognition domain that usually comprises tandem ZFPs (in different colors) and a C-terminal function domain that comprises the Fok I endonuclease. Recognition of the target sequence by the left and right ZFPs results in dimerization of the Fok I endonuclease, which is critical for the activity of the ZFNs. DNA cleavage takes place between the two ZFP recognition sites that contain a spacer sequence that is usually 6 bp long. Induced DSB of the target DNA are repaired either by NHEJ or HDR, resulting in gene mutation around the cleavage sites. NLS, nuclear localization signal; ZFP, zinc finger proteins; DSB, double-strand breaks; NHEJ, non-homologous end joining; HDR, homology-directed repair. Mutation#x002A;, the red color box region contains nucleotide deletion, insertion or substitution. Figure modified from Gaj et al. (2013), Figure 119 and Moore et al. (2012), Figure 1.100
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig1: Schematic illustration of the ZFN structure and the principle of ZFN-mediated genomic modifications. The target site of the ZFN is recognized by the “left” and “right” half monomer that each consist of a tandem array of engineered ZFPs, and each engineered ZFP can recognize a nucleotide triplet (shown in different colors). The ZFN monomer is comprised of an N-terminal domain containing a NLS (red), a recognition domain that usually comprises tandem ZFPs (in different colors) and a C-terminal function domain that comprises the Fok I endonuclease. Recognition of the target sequence by the left and right ZFPs results in dimerization of the Fok I endonuclease, which is critical for the activity of the ZFNs. DNA cleavage takes place between the two ZFP recognition sites that contain a spacer sequence that is usually 6 bp long. Induced DSB of the target DNA are repaired either by NHEJ or HDR, resulting in gene mutation around the cleavage sites. NLS, nuclear localization signal; ZFP, zinc finger proteins; DSB, double-strand breaks; NHEJ, non-homologous end joining; HDR, homology-directed repair. Mutation#x002A;, the red color box region contains nucleotide deletion, insertion or substitution. Figure modified from Gaj et al. (2013), Figure 119 and Moore et al. (2012), Figure 1.100
Mentions: ZFNs are the first generation EENs that were developed following the discovery of the functional principles of the Cys2-His2 zinc finger (ZF) domains.21 Each Cys2-His2 ZF domain consists of 30 amino-acid residues that fold into a βββ configuration.21,22 Crystal structure analysis indicates that Cys2-His2 ZF proteins bind to DNA by inserting the α-helix into the major groove of the double helix.23 Each ZF protein is able to recognize 3 contiguous nucleotide bases within the DNA substrate. As shown in Figure 1, a generic ZFN monomer is fused by two functional distinct domains: an artificially prepared Cys2-His2 ZF domain at the N-terminal and a nonspecific DNA cleavage domain of the Fok I DNA restriction enzyme at the C-terminal. The dimerization of the Fok I domain is crucial for its enzymatic activity.24 Therefore, a ZFN dimer composed of two 3- or 4-ZF domains will recognize an 18- or 24-base target sequence that, statistically, forms a unique site in the genomes of most organisms. Since the first report in 1996, ZFNs have been successfully applied to gene modification mainly in animals such as human cells,25 zebrafish,26,27 and plants such as Arabidopsis,28 tobacco,29 and maize.30 However, obtaining functional ZFNs requires an extensive and time-consuming screening process.31 Further, ZFNs have other limitations, such as off-target effect22 or even toxic to the host cells. These shortcomings limit the application of ZFNs in plant genome editing. Until now, there have been no reports on ZFN applications in horticultural crops.

Bottom Line: Plant breeding, one of the oldest agricultural activities, parallels human civilization.Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries.The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University , Nanjing, Jiangsu Province 210095, The People's Republic of China.

ABSTRACT
Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed.

No MeSH data available.