1
|
Shahwar D, Ahn N, Kim D, Ahn W, Park Y. Mutagenesis-based plant breeding approaches and genome engineering: A review focused on tomato. Mutat Res Rev Mutat Res 2023; 792:108473. [PMID: 37716439 DOI: 10.1016/j.mrrev.2023.108473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/18/2023]
Abstract
Breeding is the most important and efficient method for crop improvement involving repeated modification of the genetic makeup of a plant population over many generations. In this review, various accessible breeding approaches, such as conventional breeding and mutation breeding (physical and chemical mutagenesis and insertional mutagenesis), are discussed with respect to the actual impact of research on the economic improvement of tomato agriculture. Tomatoes are among the most economically important fruit crops consumed worldwide because of their high nutritional content and health-related benefits. Additionally, we summarize mutation-based mapping approaches, including Mutmap and MutChromeSeq, for the efficient mapping of several genes identified by random indel mutations that are beneficial for crop improvement. Difficulties and challenges in the adaptation of new genome editing techniques that provide opportunities to demonstrate precise mutations are also addressed. Lastly, this review focuses on various effective and convenient genome editing tools, such as RNA interference (RNAi), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), and their potential for the improvement of numerous desirable traits to allow the development of better varieties of tomato and other horticultural crops.
Collapse
Affiliation(s)
- Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Namju Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Donghyun Kim
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Wooseong Ahn
- Daenong Seed Company, Hwasun-gun 58155, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea.
| |
Collapse
|
2
|
Sugihara Y, Young L, Yaegashi H, Natsume S, Shea DJ, Takagi H, Booker H, Innan H, Terauchi R, Abe A. High-performance pipeline for MutMap and QTL-seq. PeerJ 2022; 10:e13170. [PMID: 35321412 PMCID: PMC8935991 DOI: 10.7717/peerj.13170] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/04/2022] [Indexed: 01/12/2023] Open
Abstract
Summary Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5-8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies. Availability The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).
Collapse
Affiliation(s)
- Yu Sugihara
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan,Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Lester Young
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Hiroki Yaegashi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan
| | - Satoshi Natsume
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan
| | - Daniel J. Shea
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan
| | - Hiroki Takagi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Japan
| | - Helen Booker
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada,Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Hideki Innan
- Graduate University for Advanced Studies, Hayama, Japan
| | - Ryohei Terauchi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan,Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Akira Abe
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Japan
| |
Collapse
|
3
|
Mo Y, Howell T, Vasquez-Gross H, de Haro LA, Dubcovsky J, Pearce S. Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study. Mol Genet Genomics 2017. [PMID: 29188438 DOI: 10.1007/s00438‐017‐1401‐6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes.
Collapse
Affiliation(s)
- Youngjun Mo
- Department of Plant Sciences, University of California, Davis, CA, USA
- National Institute of Crop Science, Rural Development Administration, Wanju, South Korea
| | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Luis Alejandro de Haro
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
4
|
Mo Y, Howell T, Vasquez-Gross H, de Haro LA, Dubcovsky J, Pearce S. Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study. Mol Genet Genomics 2017; 293:463-477. [PMID: 29188438 PMCID: PMC5854723 DOI: 10.1007/s00438-017-1401-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/23/2017] [Indexed: 11/23/2022]
Abstract
Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes.
Collapse
Affiliation(s)
- Youngjun Mo
- Department of Plant Sciences, University of California, Davis, CA, USA.,National Institute of Crop Science, Rural Development Administration, Wanju, South Korea
| | - Tyson Howell
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Luis Alejandro de Haro
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Buenos Aires, Argentina
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
| |
Collapse
|
5
|
Tuncbag N, Keskin O, Nussinov R, Gursoy A. Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information. Methods Mol Biol 2017; 1558:255-270. [PMID: 28150242 PMCID: PMC7900904 DOI: 10.1007/978-1-4939-6783-4_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structural details of protein interactions are invaluable to the understanding of cellular processes. However, the identification of interactions at atomic resolution is a continuing challenge in the systems biology era. Although the number of structurally resolved complexes in the Protein Databank increases exponentially, the complexes only cover a small portion of the known structural interactome. In this chapter, we review the PRISM system that is a protein-protein interaction (PPI) prediction tool-its rationale, principles, and applications. We further discuss its extensions to discover the effect of single residue mutations, to model large protein assemblies, to improve its performance by exploiting conformational protein ensembles, and to reconstruct large PPI networks or pathway maps.
Collapse
Affiliation(s)
- Nurcan Tuncbag
- Graduate School of Informatics, Department of Health Informatics, Middle East Technical University, 06800, Ankara, Turkey
| | - Ozlem Keskin
- Chemical and Biological Engineering, College of Engineering, Koc University, 34450, Istanbul, Turkey.
- Center for Computational Biology and Bioinformatics, Koc University, Rumelifeneri Yolu Sariyer, 34450, Istanbul, Turkey.
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, Koc University, Rumelifeneri Yolu Sariyer, 34450, Istanbul, Turkey.
- Computer Engineering, College of Engineering, Koc University, 34450, Istanbul, Turkey.
| |
Collapse
|
6
|
Bassot C, Minervini G, Leonardi E, Tosatto SC. Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain. Biochimie 2017; 132:109-20. [PMID: 27771369 DOI: 10.1016/j.biochi.2016.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/03/2016] [Indexed: 12/16/2022]
Abstract
Human pendrin (SLC26A4) is an anion transporter mostly expressed in the inner ear, thyroid and kidney. SLC26A4 gene mutations are associated with a broad phenotypic spectrum, including Pendred Syndrome and non-syndromic hearing loss with enlarged vestibular aqueduct (ns-EVA). No experimental structure of pendrin is currently available, making phenotype-genotype correlations difficult as predictions of transmembrane (TM) segments vary in number. Here, we propose a novel three-dimensional (3D) pendrin transmembrane domain model based on the SLC26Dg transporter. The resulting 14 TM topology was found to include two non-canonical transmembrane segments crucial for pendrin activity. Mutation mapping of 147 clinically validated pathological mutations shows that most affect two previously undescribed TM regions.
Collapse
|
7
|
Venken KJT, Bellen HJ. Chemical mutagens, transposons, and transgenes to interrogate gene function in Drosophila melanogaster. Methods 2014; 68:15-28. [PMID: 24583113 DOI: 10.1016/j.ymeth.2014.02.025] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 12/22/2022] Open
Abstract
The study of genetics, genes, and chromosomal inheritance was initiated by Thomas Morgan in 1910, when the first visible mutations were identified in fruit flies. The field expanded upon the work initiated by Herman Muller in 1926 when he used X-rays to develop the first balancer chromosomes. Today, balancers are still invaluable to maintain mutations and transgenes but the arsenal of tools has expanded vastly and numerous new methods have been developed, many relying on the availability of the genome sequence and transposable elements. Forward genetic screens based on chemical mutagenesis or transposable elements have resulted in the unbiased identification of many novel players involved in processes probed by specific phenotypic assays. Reverse genetic approaches have relied on the availability of a carefully selected set of transposon insertions spread throughout the genome to allow the manipulation of the region in the vicinity of each insertion. Lastly, the ability to transform Drosophila with single copy transgenes using transposons or site-specific integration using the ΦC31 integrase has allowed numerous manipulations, including the ability to create and integrate genomic rescue constructs, generate duplications, RNAi knock-out technology, binary expression systems like the GAL4/UAS system as well as other methods. Here, we will discuss the most useful methodologies to interrogate the fruit fly genome in vivo focusing on chemical mutagenesis, transposons and transgenes. Genome engineering approaches based on nucleases and RNAi technology are discussed in following chapters.
Collapse
Affiliation(s)
- Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Program in Developmental Biology, Baylor College of Medicine, TX 77030, United States.
| | - Hugo J Bellen
- Program in Developmental Biology, Departments of Molecular and Human Genetics, Department of Neuroscience, Howard Hughes Medical Institute, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, United States.
| |
Collapse
|