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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.


The structure of TALEN and the principle of TALEN-mediated genomic modifications. The target site of TALEN is recognized by the “left” and “right” half monomer that each consist of a tandem repeat of TALE repeats. Each TALE repeat comprises a 34 amino acid (aa) unit that differs at two hypervariable aa located at the 12th and 13th position, known as RVD, which determine the recognition specificity of each repeat. The TALEN monomer consists of an N-terminal domain containing a nuclear localization signal (NLS, red), a recognition domain typically composed of tandem TALE repeats (in different colors), and a C-terminal function domain that comprises the Fok I endonuclease. Simultaneous bindings of the left and right TALE enable dimerization of the Fok I cleavage domain, resulting in DSBs of the target DNA. Induced DSBs of the target DNA are repaired either by NHEJ or HDR resulting in gene mutations that include nucleotide insertion, deletion, or substitution around the cleavage site. TALE, transcription activator-like effector; NLS, nuclear localization signal; RVD, repeat-variable di-residues; DSB, double-strand breaks; NHEJ,non-homologous end joining; HDR, homology-directed repair. Mutation*, red color box regions contain 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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fig2: The structure of TALEN and the principle of TALEN-mediated genomic modifications. The target site of TALEN is recognized by the “left” and “right” half monomer that each consist of a tandem repeat of TALE repeats. Each TALE repeat comprises a 34 amino acid (aa) unit that differs at two hypervariable aa located at the 12th and 13th position, known as RVD, which determine the recognition specificity of each repeat. The TALEN monomer consists of an N-terminal domain containing a nuclear localization signal (NLS, red), a recognition domain typically composed of tandem TALE repeats (in different colors), and a C-terminal function domain that comprises the Fok I endonuclease. Simultaneous bindings of the left and right TALE enable dimerization of the Fok I cleavage domain, resulting in DSBs of the target DNA. Induced DSBs of the target DNA are repaired either by NHEJ or HDR resulting in gene mutations that include nucleotide insertion, deletion, or substitution around the cleavage site. TALE, transcription activator-like effector; NLS, nuclear localization signal; RVD, repeat-variable di-residues; DSB, double-strand breaks; NHEJ,non-homologous end joining; HDR, homology-directed repair. Mutation*, red color box regions contain nucleotide deletion, insertion or substitution. Figure modified from Gaj et al. (2013), Figure 119 and Moore et al. (2012), Figure 1.100

Mentions: Recently, a new EEN, i.e., transcription activator-like effector nucleases (TALENs), has rapidly emerged as an alternative to ZFNs for genome editing.32 The broad applications of TALENs were based on the recognition of the functional principles of the type III transcription activator-like (TAL) effectors that are secreted by the plant pathogenic bacteria Xanthomonas.33 After been pumped into host cells, the TAL effectors enter the nucleus and bind to effector-specific sequences in the host gene promoters and activate transcription.34 AvrBs3 was the first investigated TAL effector protein found in 1989.35 However, the recognition mechanism of the TAL effectors was not deciphered until 2009 by two independent research groups.36,37 The DNA recognition property of the TAL effectors is mediated by tandem amino acid repeats (34 residues in length). Two hypervariable amino acids known as repeat-variable di-residues (RVDs) located at the 12th and 13th position in each repeat determine the binding specificity of the TAL effectors.38,39 HD, NG, NI, and NN are the four most common RVDs, accounting for each of the four nucleotides C, T, A, G, respectively. Similar to ZFN, the TALEN monomer is also fused by two independent domains: a customizable DNA-binding domain at the N-terminal and a nonspecific Fok I nuclease domain at the C-terminal (Figure 2). Due to easier manipulation, the genes modified by TALENs have been successfully used in both animal and plant species within three years of deciphering their function. These species include zebrafish,40,41 rat,42 human cells,43,44 rice,45 wheat,46Arabidopsis,47, 48, 49 and horticultural crops such as potato50 and tomato.51


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

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

The structure of TALEN and the principle of TALEN-mediated genomic modifications. The target site of TALEN is recognized by the “left” and “right” half monomer that each consist of a tandem repeat of TALE repeats. Each TALE repeat comprises a 34 amino acid (aa) unit that differs at two hypervariable aa located at the 12th and 13th position, known as RVD, which determine the recognition specificity of each repeat. The TALEN monomer consists of an N-terminal domain containing a nuclear localization signal (NLS, red), a recognition domain typically composed of tandem TALE repeats (in different colors), and a C-terminal function domain that comprises the Fok I endonuclease. Simultaneous bindings of the left and right TALE enable dimerization of the Fok I cleavage domain, resulting in DSBs of the target DNA. Induced DSBs of the target DNA are repaired either by NHEJ or HDR resulting in gene mutations that include nucleotide insertion, deletion, or substitution around the cleavage site. TALE, transcription activator-like effector; NLS, nuclear localization signal; RVD, repeat-variable di-residues; DSB, double-strand breaks; NHEJ,non-homologous end joining; HDR, homology-directed repair. Mutation*, red color box regions contain 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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Related In: Results  -  Collection

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Show All Figures
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fig2: The structure of TALEN and the principle of TALEN-mediated genomic modifications. The target site of TALEN is recognized by the “left” and “right” half monomer that each consist of a tandem repeat of TALE repeats. Each TALE repeat comprises a 34 amino acid (aa) unit that differs at two hypervariable aa located at the 12th and 13th position, known as RVD, which determine the recognition specificity of each repeat. The TALEN monomer consists of an N-terminal domain containing a nuclear localization signal (NLS, red), a recognition domain typically composed of tandem TALE repeats (in different colors), and a C-terminal function domain that comprises the Fok I endonuclease. Simultaneous bindings of the left and right TALE enable dimerization of the Fok I cleavage domain, resulting in DSBs of the target DNA. Induced DSBs of the target DNA are repaired either by NHEJ or HDR resulting in gene mutations that include nucleotide insertion, deletion, or substitution around the cleavage site. TALE, transcription activator-like effector; NLS, nuclear localization signal; RVD, repeat-variable di-residues; DSB, double-strand breaks; NHEJ,non-homologous end joining; HDR, homology-directed repair. Mutation*, red color box regions contain nucleotide deletion, insertion or substitution. Figure modified from Gaj et al. (2013), Figure 119 and Moore et al. (2012), Figure 1.100
Mentions: Recently, a new EEN, i.e., transcription activator-like effector nucleases (TALENs), has rapidly emerged as an alternative to ZFNs for genome editing.32 The broad applications of TALENs were based on the recognition of the functional principles of the type III transcription activator-like (TAL) effectors that are secreted by the plant pathogenic bacteria Xanthomonas.33 After been pumped into host cells, the TAL effectors enter the nucleus and bind to effector-specific sequences in the host gene promoters and activate transcription.34 AvrBs3 was the first investigated TAL effector protein found in 1989.35 However, the recognition mechanism of the TAL effectors was not deciphered until 2009 by two independent research groups.36,37 The DNA recognition property of the TAL effectors is mediated by tandem amino acid repeats (34 residues in length). Two hypervariable amino acids known as repeat-variable di-residues (RVDs) located at the 12th and 13th position in each repeat determine the binding specificity of the TAL effectors.38,39 HD, NG, NI, and NN are the four most common RVDs, accounting for each of the four nucleotides C, T, A, G, respectively. Similar to ZFN, the TALEN monomer is also fused by two independent domains: a customizable DNA-binding domain at the N-terminal and a nonspecific Fok I nuclease domain at the C-terminal (Figure 2). Due to easier manipulation, the genes modified by TALENs have been successfully used in both animal and plant species within three years of deciphering their function. These species include zebrafish,40,41 rat,42 human cells,43,44 rice,45 wheat,46Arabidopsis,47, 48, 49 and horticultural crops such as potato50 and tomato.51

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.