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Advances in Plant Mutagenesis Research
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Advances in Plant Mutagenesis Research

A special issue of Plants (ISSN 2223-7747).

Deadline for manuscript submissions: closed (30 August 2019) | Viewed by 50934

Special Issue Editors

Dr. Rupesh Deshmukh

E-Mail Website
Guest Editor
Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, Haryana, India
Interests: aquaporins; comparative genomics; genome editing; nutrient uptake; transporter proteins
Special Issues, Collections and Topics in MDPI journals
Dr. Juhi Chaudhary

E-Mail Website
Guest Editor
College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, USA
Interests: soybean breeding; seed composition; seed oil
Dr. Humira Sonah

E-Mail Website
Guest Editor
National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), PO Manauli, S.A.S. Nagar, Mohali-140306, Punjab, India
Interests: genomics; genome editing; genetic regulation of plant disease; soybean seed composition
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Induced mutagenesis, one of the most efficient tool for the crop improvement, has been utilized extensively to create genetic variation for economically important traits.  Induced mutagenesis has also been proven to be a convenient tool for the identification of key regulatory genes and molecular mechanism involved in the trait development. Conventionally, the induced mutagenesis is performed by means of physical, chemical, and insertional mutagen treatment methods. Besides achieving numerous benefits, these methods are less preferred due to random and slow process.  In addition, localization of casual mutation using the conventional methods is tedious and costly. However, due to the recent advancements in next-generation sequencing (NGS) techniques, detection of millions of mutations in short period of time has become convenient and cost efficient. Several mutation mapping approaches utilizing NGS such as MutMap, MutChromSeq and whole genome sequencing based mapping have been recently developed. The cost-effectiveness and high applicability make these approaches a choice of method to identify desired genes in lesser time. Furthermore, induced mutagenesis coupled with whole genome sequencing has provided a robust platform for forward and reverse genetic applications. Apart from the advances in mutation mapping, excellent tools have been recently invented to induce at precise location in the genome. Increasing availability of whole genome sequence information for large number of crops have enabled target specific genome editing techniques such as ZFNs (Zinc Finger Nucleases), transcription activator like effector nucleases (TALENS), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease. The CRISPR/Cas9 has instigated paradigm shift in the entire biology field including crop science. The special issue of Plants will highlight the advances in mutagenesis techniques, high-throughput mutation mapping, identification of novel genes using mutagenesis approaches and mutation breeding efforts.

Dr. Rupesh Deshmukh
Dr. Juhi Chaudhary
Dr. Humira Sonah
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • mutation mapping
  • MutMap
  • MutChromSeq
  • induced mutagenesis
  • genome-editing

Published Papers (6 papers)

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Editorial

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4 pages, 196 KiB  
Editorial
Mutagenesis Approaches and Their Role in Crop Improvement
by Juhi Chaudhary, Rupesh Deshmukh and Humira Sonah
Plants 2019, 8(11), 467; https://doi.org/10.3390/plants8110467 - 31 Oct 2019
Cited by 44 | Viewed by 6746
Abstract
Induced mutagenesis is one of the most efficient tools that has been utilized extensively to create genetic variation as well as for identification of key regulatory genes for economically important traits toward the crop improvement. Mutations can be induced by several techniques such [...] Read more.
Induced mutagenesis is one of the most efficient tools that has been utilized extensively to create genetic variation as well as for identification of key regulatory genes for economically important traits toward the crop improvement. Mutations can be induced by several techniques such as physical, chemical, and insertional mutagen treatments; however, these methods are not preferred because of cost and tedious process. Nonetheless, with the advancements in next-generation sequencing (NGS) techniques, millions of mutations can be detected in a very short period of time and, therefore, considered as convenient and cost efficient. Furthermore, induced mutagenesis coupled with whole-genome sequencing has provided a robust platform for forward and reverse genetic applications. Moreover, the availability of whole-genome sequence information for large number of crops has enabled target-specific genome editing techniques as a preferable method to engineer desired mutations. The available genome editing approaches such as ZFNs (Zinc Finger Nucleases), transcription activator like effector nucleases (TALENS), and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated9 (Cas9) endonuclease have been utilized to perform site-specific mutations in several plant species. In particular, the CRISPR/Cas9 has transformed the genome editing because of its simplicity and robustness, therefore, have been utilized to enhance biotic and abiotic stress resistance. The Special Issue of Plants highlights the efforts by the scientific community utilizing mutagenesis techniques for the identification of novel genes toward crop improvement. Full article
(This article belongs to the Special Issue Advances in Plant Mutagenesis Research)

Research

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18 pages, 2102 KiB  
Article
A Novel Stay-Green Mutant of Rice with Delayed Leaf Senescence and Better Harvest Index Confers Drought Tolerance
by M. K. Ramkumar, S. Senthil Kumar, Kishor Gaikwad, Rakesh Pandey, Viswanathan Chinnusamy, Nagendra Kumar Singh, Ashok Kumar Singh, Trilochan Mohapatra and Amitha Mithra Sevanthi
Plants 2019, 8(10), 375; https://doi.org/10.3390/plants8100375 - 26 Sep 2019
Cited by 21 | Viewed by 6645
Abstract
Three Ethyl methansulphonate (EMS)-induced stay-green mutants (SGM-1, SGM-2 and SGM-3) and their wild-type (WT), were tested for their Stay-Green (SG) and drought tolerance nature as the relation between these two attributes is not yet established in rice. In the dark induced senescence assay, [...] Read more.
Three Ethyl methansulphonate (EMS)-induced stay-green mutants (SGM-1, SGM-2 and SGM-3) and their wild-type (WT), were tested for their Stay-Green (SG) and drought tolerance nature as the relation between these two attributes is not yet established in rice. In the dark induced senescence assay, SGM-3 showed delayed senescence while SGM-1 and SGM-2 showed complete lack of senescence. Mutants showed stable transcript abundance over time, for 15 candidate genes (CGs) associated with senescence, compared to the WT. SGM-3 however showed moderately increasing transcript abundance over time for ATG6a, ATG4a, NYC1, NOL and NYC3. Only SGM-3 performed better than the WT for yield and harvest index under well irrigated as well as drought conditions, though all the mutants showed better performance for other agronomic traits under both the conditions and ascorbate peroxidase activity under drought. Thus, SG trait showed positive correlation with drought tolerance though only SGM-3 could convert this into higher harvest index. Sequence analysis of 80 senescence-associated genes including the 15 CGs showed non-synonymous mutations in four and six genes in SGM-1 and SGM-2 respectively, while no SNPs were found in SGM-3. Analysis of the earlier reported Quantitative Trait Loci (QTL) regions in SGM-3 revealed negligible variations from WT, suggesting it to be a novel SG mutant. Full article
(This article belongs to the Special Issue Advances in Plant Mutagenesis Research)
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22 pages, 13251 KiB  
Article
Proteome Profiling of the Mutagen-Induced Morphological and Yield Macro-Mutant Lines of Nigella sativa L.
by Ambreen Asif, Mohammad Yunus K. Ansari, Abeer Hashem, Baby Tabassum, Elsayed Fathi Abd_Allah and Altaf Ahmad
Plants 2019, 8(9), 321; https://doi.org/10.3390/plants8090321 - 02 Sep 2019
Cited by 3 | Viewed by 2872
Abstract
In the present investigation, the leaf proteome profile of the macro-mutant lines of Nigella sativa L. was analyzed to identify the key proteins involved in the expression of traits associated with the morphology, seed yield, and content of thymoquinone. In our earlier study, [...] Read more.
In the present investigation, the leaf proteome profile of the macro-mutant lines of Nigella sativa L. was analyzed to identify the key proteins involved in the expression of traits associated with the morphology, seed yield, and content of thymoquinone. In our earlier study, the macro-mutants were generated with contrasting morphological traits and seed yields through induced mutagenesis, using ethyl methyl sulfonate, gamma rays, and combinations of both. Analysis of the leaf proteome of the control and macro-mutant lines of N. sativa showed that twenty-three proteins were differentially expressed. These differentially expressed proteins were sequenced through mass spectrometry and identified using the MASCOT software. On the basis of their function, these proteins were categorized into several groups. Most proteins were found in the categories of signal transduction (18%) and carbon metabolism (18%). A total of 13% of proteins belonged to the categories of energy and metabolism. Proteins in the categories of secondary plant metabolism, stress defense, cytoskeleton, and protein synthesis were also found. The polycomb group protein (FIE1), transcription factor (PRE1), and geranyl diphosphate synthase were notable proteins, in addition to some proteins of signal transduction and carbon metabolism. Expression patterns of the differentially expressed proteins were also studied at the transcript level by using qRT-PCR. Transcriptomics analysis was consistent with the proteomics data. This study shows the changes that take place at the proteomic level through induced mutagenesis, as well as the involvement of some proteins in the expression traits associated with plant height, seed yield, and the thymoquinone content of N. sativa. The identified proteins might help elucidate the metabolic pathways involved in the expression of traits, including seed yield, and the active compounds of medicinal plants. Full article
(This article belongs to the Special Issue Advances in Plant Mutagenesis Research)
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Review

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14 pages, 1334 KiB  
Review
Insertional Mutagenesis Approaches and Their Use in Rice for Functional Genomics
by Hasthi Ram, Praveen Soni, Prafull Salvi, Nishu Gandass, Ankita Sharma, Amandeep Kaur and Tilak Raj Sharma
Plants 2019, 8(9), 310; https://doi.org/10.3390/plants8090310 - 29 Aug 2019
Cited by 31 | Viewed by 7904
Abstract
Insertional mutagenesis is an indispensable tool for engendering a mutant population using exogenous DNA as the mutagen. The advancement in the next-generation sequencing platform has allowed for faster screening and analysis of generated mutated populations. Rice is a major staple crop for more [...] Read more.
Insertional mutagenesis is an indispensable tool for engendering a mutant population using exogenous DNA as the mutagen. The advancement in the next-generation sequencing platform has allowed for faster screening and analysis of generated mutated populations. Rice is a major staple crop for more than half of the world’s population; however, the functions of most of the genes in its genome are yet to be analyzed. Various mutant populations represent extremely valuable resources in order to achieve this goal. Here, we have reviewed different insertional mutagenesis approaches that have been used in rice, and have discussed their principles, strengths, and limitations. Comparisons between transfer DNA (T-DNA), transposons, and entrapment tagging approaches have highlighted their utilization in functional genomics studies in rice. We have also summarised different forward and reverse genetics approaches used for screening of insertional mutant populations. Furthermore, we have compiled information from several efforts made using insertional mutagenesis approaches in rice. The information presented here would serve as a database for rice insertional mutagenesis populations. We have also included various examples which illustrate how these populations have been useful for rice functional genomics studies. The information provided here will be very helpful for future functional genomics studies in rice aimed at its genetic improvement. Full article
(This article belongs to the Special Issue Advances in Plant Mutagenesis Research)
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16 pages, 1588 KiB  
Review
Expanding Avenue of Fast Neutron Mediated Mutagenesis for Crop Improvement
by Surbhi Kumawat, Nitika Rana, Ruchi Bansal, Gautam Vishwakarma, Sayaji T. Mehetre, Bikram Kishore Das, Manish Kumar, Satish Kumar Yadav, Humira Sonah, Tilak Raj Sharma and Rupesh Deshmukh
Plants 2019, 8(6), 164; https://doi.org/10.3390/plants8060164 - 10 Jun 2019
Cited by 34 | Viewed by 8447
Abstract
Fast neutron (FN) radiation mediated mutagenesis is a unique approach among the several induced mutagenesis methods being used in plant science in terms of impacted mutations. The FN mutagenesis usually creates deletions from few bases to several million bases (Mb). A library of [...] Read more.
Fast neutron (FN) radiation mediated mutagenesis is a unique approach among the several induced mutagenesis methods being used in plant science in terms of impacted mutations. The FN mutagenesis usually creates deletions from few bases to several million bases (Mb). A library of random deletion generated using FN mutagenesis lines can provide indispensable resources for the reverse genetic approaches. In this review, information from several efforts made using FN mutagenesis has been compiled to understand the type of induced mutations, frequency, and genetic stability. Concerns regarding the utilization of FN mutagenesis technique for a plant with different level of ploidy and genome complexity are discussed. We have highlighted the utility of next-generation sequencing techniques that can be efficiently utilized for the characterization of mutant lines as well as for the mapping of causal mutations. Pros and cons of mapping by mutation (MutMap), mutant chromosome sequencing (MutChromSeq), exon capture, whole genome sequencing, MutRen-Seq, and different tilling approaches that can be used for the detection of FN-induced mutation has also been discussed. Genomic resources developed using the FN mutagenesis have been catalogued wooing to meaningful utilization of the available resources. The information provided here will be helpful for the efficient exploration for the crop improvement programs and for better understanding of genetic regulations. Full article
(This article belongs to the Special Issue Advances in Plant Mutagenesis Research)
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17 pages, 891 KiB  
Review
Mutation Breeding in Tomato: Advances, Applicability and Challenges
by Juhi Chaudhary, Alisha Alisha, Vacha Bhatt, Sonali Chandanshive, Nirbhay Kumar, Zahoor Mir, Ashwini Kumar, Satish K. Yadav, S. M. Shivaraj, Humira Sonah and Rupesh Deshmukh
Plants 2019, 8(5), 128; https://doi.org/10.3390/plants8050128 - 14 May 2019
Cited by 74 | Viewed by 16950
Abstract
Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for [...] Read more.
Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research. Full article
(This article belongs to the Special Issue Advances in Plant Mutagenesis Research)
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