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Liu Y, Li Y, Wang A, Xu Z, Li C, Wang Z, Guo B, Chen Y, Tang F, Li J. Enhancing cold resistance in Banana (Musa spp.) through EMS-induced mutagenesis, L-Hyp pressure selection: phenotypic alterations, biomass composition, and transcriptomic insights. BMC PLANT BIOLOGY 2024; 24:101. [PMID: 38331759 PMCID: PMC10854111 DOI: 10.1186/s12870-024-04775-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/29/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND The cultivation of bananas encounters substantial obstacles, particularly due to the detrimental effects of cold stress on their growth and productivity. A potential remedy that has gained attention is the utilization of ethyl mesylate (EMS)-induced mutagenesis technology, which enables the creation of a genetically varied group of banana mutants. This complex procedure entails subjecting the mutants to further stress screening utilizing L-Hyp in order to identify those exhibiting improved resistance to cold. This study conducted a comprehensive optimization of the screening conditions for EMS mutagenesis and L-Hyp, resulting in the identification of the mutant cm784, which exhibited remarkable cold resistance. Subsequent investigations further elucidated the physiological and transcriptomic responses of cm784 to low-temperature stress. RESULTS EMS mutagenesis had a substantial effect on banana seedlings, resulting in modifications in shoot and root traits, wherein a majority of seedlings exhibited delayed differentiation and limited elongation. Notably, mutant leaves displayed altered biomass composition, with starch content exhibiting the most pronounced variation. The application of L-Hyp pressure selection aided in the identification of cold-resistant mutants among seedling-lethal phenotypes. The mutant cm784 demonstrated enhanced cold resistance, as evidenced by improved survival rates and reduced symptoms of chilling injury. Physiological analyses demonstrated heightened activities of antioxidant enzymes and increased proline production in cm784 when subjected to cold stress. Transcriptome analysis unveiled 946 genes that were differentially expressed in cm784, with a notable enrichment in categories related to 'Carbohydrate transport and metabolism' and 'Secondary metabolites biosynthesis, transport, and catabolism'. CONCLUSION The present findings provide insights into the molecular mechanisms that contribute to the heightened cold resistance observed in banana mutants. These mechanisms encompass enhanced carbohydrate metabolism and secondary metabolite biosynthesis, thereby emphasizing the adaptive strategies employed to mitigate the detrimental effects induced by cold stress.
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Affiliation(s)
- Yumeng Liu
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yujia Li
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Anbang Wang
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Zhuye Xu
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
- College of Horticulture, Hainan University, Haikou, 571101, Hainan, China
| | - Chunfang Li
- Collage of Tropical Crop, Yunnan Agricultural University, Puer, 611101, Yunnan, China
| | - Zuo Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Borui Guo
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Chen
- Collage of Tropical Crop, Yunnan Agricultural University, Puer, 611101, Yunnan, China
| | - Fenling Tang
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Jingyang Li
- National Key Laboratory for Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya/Haikou, Hainan, 572024/571101, China.
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
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Shalini Udaya CY. Inducing mutation and ascertaining lethal dosage of in vitro cultures of banana cv. Ney Poovan to ethyl methane sulfonate. Mutat Res 2024; 828:111850. [PMID: 38160536 DOI: 10.1016/j.mrfmmm.2023.111850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
In vitro mutation breeding in vegetatively propagated crops like banana offers a benefit in screening for beneficial variants in plant cells or cultured tissues. An attempt was made to induce mutants and determine the lethal dose, as it is the prerequisite to optimize the concentration and duration of the mutagen used to recover a larger population in mutation research. Shoot tip cultures were treated for 2 and 4 h at six different EMS concentrations ranging from 80 mM to 160 mM, whereas proliferating multiple shoots were exposed for 30 and 60 min at six different EMS concentrations ranging from 8 mM to 40 mM. Survival percentage, shoot length, and number of shoots reduced linearly and significantly as concentration and duration increased in both shoot tips and proliferating multiple buds. The probit curve-based analysis of mortality of treated explants revealed that the LD50 was 155.83 mM for 2 h and 113.72 mM for 4 h, respectively for shoot tip cultures, whereas for proliferating multiple buds, the LD50 value was adjusted to 39.11 mM for 30 min and 30.41 mM for 60 min. 160 mM EMS for 4 h resulted in a shorter shoot, a longer rooting duration, a lesser number of roots, and decreased root development. In proliferating multiple shoots, the smallest shoot, longest rooting duration, least number of roots, and shortest root were observed in 40 mM EMS for 60 min. Similar reductions in growth parameters were observed in proliferating multiple shoots at higher exposure to EMS for a longer duration.
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Affiliation(s)
- C Y Shalini Udaya
- Department of Fruit Science, Horticultural College & Research Institute, TNAU, Coimbatore, Tamil Nadu, India.
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Din A, Qadri ZA, Wani MA, Iqbal S, Malik SA, Zargar SM, Banday N, Nazki IT. Comparative Analysis of Physical and Chemical Mutagenesis in Chrysanthemum cv. 'Candid': Assessing Genetic Variation and Breeding Potential. ACS OMEGA 2023; 8:43836-43849. [PMID: 38027373 PMCID: PMC10666220 DOI: 10.1021/acsomega.3c05723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/08/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
In this study, we developed a mutagenesis protocol specifically designed for chrysanthemum cv. "Candid" in order to introduce genetic variation. By subjecting chrysanthemum shoots to different doses of physical and chemical mutagens, we successfully generated a total of 24 mutants, each with unique genetic compositions. We observed that the mortality rate was lowest when the shoots were exposed to 10 Gy gamma irradiation and 1.00% EMS. To assess the diversity and relatedness among the mutants, we employed RAPD and SSR markers. The combination of these markers allowed us to construct a dendrogram that effectively categorized the mutant population into distinct clusters based on the specific mutagen treatments. Interestingly, the mutants induced by 10 Gy gamma irradiation exhibited greater genetic diversity in terms of flower colors. On the other hand, mutants created with 1.00% EMS displayed a higher level of variation and yielded more viable mutants. To determine the optimal markers for studying genetic diversity, we analyzed the polymorphic information content (PIC) of different markers. Among the tested markers, OPA-07 (RAPD) and JH47 (SSR) showed the highest PIC values, indicating their effectiveness in capturing genetic variability within the mutant population. Conversely, the PIC values of OPD-07 and JH20 demonstrated the lowest among the markers tested. Our results revealed a percentage of polymorphism ranging from 81.81% to 100% for RAPD markers and 66.66% to 100% for SSR markers. These findings indicate that physical mutation induced by 10 Gy gamma irradiation can be clearly distinguished from chemical mutation induced by EMS at concentrations of 1% and 0.75% in chrysanthemum cv. "Candid.″ Overall, this study provides valuable insights into the genetic composition of the generated mutants and highlights their potential for enhancing chrysanthemum-breeding programs. The identified markers, particularly, OPA-07 and JH47, can serve as valuable tools for future studies aimed at exploring and exploiting the genetic diversity within the chrysanthemum population.
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Affiliation(s)
- Ambreena Din
- Division
of FLA, Faculty of Horticulture, SKUAST-Kashmir, Srinagar 190001, India
| | - Zahoor Ahmad Qadri
- Division
of FLA, Faculty of Horticulture, SKUAST-Kashmir, Srinagar 190001, India
| | - Muneeb Ahmad Wani
- Division
of FLA, Faculty of Horticulture, SKUAST-Kashmir, Srinagar 190001, India
| | - Shameen Iqbal
- Division
of FLA, Faculty of Horticulture, SKUAST-Kashmir, Srinagar 190001, India
| | - Sajid Ali Malik
- Division
of FLA, Faculty of Horticulture, SKUAST-Kashmir, Srinagar 190001, India
| | - Sajad Majeed Zargar
- Division
of Plant Biotechnology, Faculty of Horticulture, SKUAST-Kashmir, Srinagar 190001, India
| | - Neelofar Banday
- Division
of FLA, Faculty of Horticulture, SKUAST-Kashmir, Srinagar 190001, India
| | - Imtiyaz Tahir Nazki
- Division
of FLA, Faculty of Horticulture, SKUAST-Kashmir, Srinagar 190001, India
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Szurman-Zubrzycka M, Kurowska M, Till BJ, Szarejko I. Is it the end of TILLING era in plant science? FRONTIERS IN PLANT SCIENCE 2023; 14:1160695. [PMID: 37674734 PMCID: PMC10477672 DOI: 10.3389/fpls.2023.1160695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023]
Abstract
Since its introduction in 2000, the TILLING strategy has been widely used in plant research to create novel genetic diversity. TILLING is based on chemical or physical mutagenesis followed by the rapid identification of mutations within genes of interest. TILLING mutants may be used for functional analysis of genes and being nontransgenic, they may be directly used in pre-breeding programs. Nevertheless, classical mutagenesis is a random process, giving rise to mutations all over the genome. Therefore TILLING mutants carry background mutations, some of which may affect the phenotype and should be eliminated, which is often time-consuming. Recently, new strategies of targeted genome editing, including CRISPR/Cas9-based methods, have been developed and optimized for many plant species. These methods precisely target only genes of interest and produce very few off-targets. Thus, the question arises: is it the end of TILLING era in plant studies? In this review, we recap the basics of the TILLING strategy, summarize the current status of plant TILLING research and present recent TILLING achievements. Based on these reports, we conclude that TILLING still plays an important role in plant research as a valuable tool for generating genetic variation for genomics and breeding projects.
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Affiliation(s)
- Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Marzena Kurowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bradley J. Till
- Veterinary Genetics Laboratory, University of California, Davis, Davis, United States
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Szurman-Zubrzycka M, Jędrzejek P, Szarejko I. How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants. Int J Mol Sci 2023; 24:ijms24032404. [PMID: 36768727 PMCID: PMC9916837 DOI: 10.3390/ijms24032404] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
DNA damage is induced by many factors, some of which naturally occur in the environment. Because of their sessile nature, plants are especially exposed to unfavorable conditions causing DNA damage. In response to this damage, the DDR (DNA damage response) pathway is activated. This pathway is highly conserved between eukaryotes; however, there are some plant-specific DDR elements, such as SOG1-a transcription factor that is a central DDR regulator in plants. In general, DDR signaling activates transcriptional and epigenetic regulators that orchestrate the cell cycle arrest and DNA repair mechanisms upon DNA damage. The cell cycle halts to give the cell time to repair damaged DNA before replication. If the repair is successful, the cell cycle is reactivated. However, if the DNA repair mechanisms fail and DNA lesions accumulate, the cell enters the apoptotic pathway. Thereby the proper maintenance of DDR is crucial for plants to survive. It is particularly important for agronomically important species because exposure to environmental stresses causing DNA damage leads to growth inhibition and yield reduction. Thereby, gaining knowledge regarding the DDR pathway in crops may have a huge agronomic impact-it may be useful in breeding new cultivars more tolerant to such stresses. In this review, we characterize different genotoxic agents and their mode of action, describe DDR activation and signaling and summarize DNA repair mechanisms in plants.
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Chen L, Duan L, Sun M, Yang Z, Li H, Hu K, Yang H, Liu L. Current trends and insights on EMS mutagenesis application to studies on plant abiotic stress tolerance and development. FRONTIERS IN PLANT SCIENCE 2023; 13:1052569. [PMID: 36684716 PMCID: PMC9846265 DOI: 10.3389/fpls.2022.1052569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Ethyl methanesulfonate (EMS)-induced mutagenesis is a powerful tool to generate genetic resource for identifying untapped genes and characterizing the function of genes to understand the molecular basis of important agronomic traits. This review focuses on application of contemporary EMS mutagenesis in the field of plant development and abiotic stress tolerance research, with particular focuses on reviewing the mutation types, mutagenesis site, mutagen concentration, mutagenesis duration, the identification and characterization of mutations responsible for altered stress tolerance responses. The application of EMS mutation breeding combined with genetic engineering in the future plant breeding and fundamental research was also discussed. The collective information in this review will provide good insight on how EMS mutagenesis is efficiently applied to improve abiotic stress tolerance of crops with the utilization of Next-generation sequencing (NGS) for mutation identification.
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Affiliation(s)
- Liuzhu Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Liu Duan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Minghui Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhuo Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Hongyu Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Keming Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Hong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Li Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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7
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Ji Y, Chen X, Lin S, Traw MB, Tian D, Yang S, Wang L, Huang J. High level of somatic mutations detected in a diploid banana wild relative Musa basjoo. Mol Genet Genomics 2023; 298:67-77. [PMID: 36283995 DOI: 10.1007/s00438-022-01959-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 09/27/2022] [Indexed: 01/10/2023]
Abstract
Plants are thought to lack an early segregating germline and often retain both asexual and sexual reproduction, both of which may allow somatic mutations to enter the gametes or clonal progeny, and thereby impact plant evolution. It is yet unclear how often these somatic mutations occur during plant development and what proportion is transmitted to their sexual or cloned offspring. Asexual "seedless" propagation has contributed greatly to the breeding in many fruit crops, such as citrus, grapes and bananas. Whether plants in these lineages experience substantial somatic mutation accumulation is unknown. To estimate the somatic mutation accumulation and inheritance among a clonal population of plant, here we assess somatic mutation accumulation in Musa basjoo, a diploid banana wild relative, using 30 whole-genome resequenced samples collected from five structures, including leaves, sheaths, panicle, roots and underground rhizome connecting three clonal individuals. We observed 18.5 high proportion de novo somatic mutations on average between each two adjacent clonal suckers, equivalent to ~ 2.48 × 10-8 per site per asexual generation, higher than the per site per sexual generation rates (< 1 × 10-8) reported in Arabidopsis and peach. Interestingly, most of these inter-ramet somatic mutations were shared simultaneously in different tissues of the same individual with a high level of variant allele fractions, suggesting that these somatic mutations arise early in ramet development and that each individual may develop only from a few apical stem cells. These results thus suggest substantial mutation accumulation in a wild relative of banana. Our work reveals the significance of somatic mutation in Musa basjoo genetics variations and contribute to the trait improvement breeding of bananas and other asexual clonal crops.
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Affiliation(s)
- Yilun Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaonan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Shengqiu Lin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
| | - Ju Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
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Mbo Nkoulou LF, Ngalle HB, Cros D, Adje COA, Fassinou NVH, Bell J, Achigan-Dako EG. Perspective for genomic-enabled prediction against black sigatoka disease and drought stress in polyploid species. FRONTIERS IN PLANT SCIENCE 2022; 13:953133. [PMID: 36388523 PMCID: PMC9650417 DOI: 10.3389/fpls.2022.953133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Genomic selection (GS) in plant breeding is explored as a promising tool to solve the problems related to the biotic and abiotic threats. Polyploid plants like bananas (Musa spp.) face the problem of drought and black sigatoka disease (BSD) that restrict their production. The conventional plant breeding is experiencing difficulties, particularly phenotyping costs and long generation interval. To overcome these difficulties, GS in plant breeding is explored as an alternative with a great potential for reducing costs and time in selection process. So far, GS does not have the same success in polyploid plants as with diploid plants because of the complexity of their genome. In this review, we present the main constraints to the application of GS in polyploid plants and the prospects for overcoming these constraints. Particular emphasis is placed on breeding for BSD and drought-two major threats to banana production-used in this review as a model of polyploid plant. It emerges that the difficulty in obtaining markers of good quality in polyploids is the first challenge of GS on polyploid plants, because the main tools used were developed for diploid species. In addition to that, there is a big challenge of mastering genetic interactions such as dominance and epistasis effects as well as the genotype by environment interaction, which are very common in polyploid plants. To get around these challenges, we have presented bioinformatics tools, as well as artificial intelligence approaches, including machine learning. Furthermore, a scheme for applying GS to banana for BSD and drought has been proposed. This review is of paramount impact for breeding programs that seek to reduce the selection cycle of polyploids despite the complexity of their genome.
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Affiliation(s)
- Luther Fort Mbo Nkoulou
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
- Institute of Agricultural Research for Development, Centre de Recherche Agricole de Mbalmayo (CRAM), Mbalmayo, Cameroon
| | - Hermine Bille Ngalle
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - David Cros
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche (UMR) Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, Montpellier, France
- Unité Mixte de Recherche (UMR) Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales (AGAP) Institut, University of Montpellier, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Agro, Montpellier, France
| | - Charlotte O. A. Adje
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
| | - Nicodeme V. H. Fassinou
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
| | - Joseph Bell
- Unit of Genetics and Plant Breeding (UGAP), Department of Plant Biology, Faculty of Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Enoch G. Achigan-Dako
- Genetics, Biotechnology, and Seed Science Unit (GBioS), Department of Plant Sciences, Faculty of Agronomic Sciences, University of Abomey Calavi, Cotonou, Benin
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Quiroz-Iturra LF, Simpson K, Arias D, Silva C, González-Calquin C, Amaza L, Handford M, Stange C. Carrot DcALFIN4 and DcALFIN7 Transcription Factors Boost Carotenoid Levels and Participate Differentially in Salt Stress Tolerance When Expressed in Arabidopsis thaliana and Actinidia deliciosa. Int J Mol Sci 2022; 23:ijms232012157. [PMID: 36293018 PMCID: PMC9603649 DOI: 10.3390/ijms232012157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
ALFIN-like transcription factors (ALs) are involved in several physiological processes such as seed germination, root development and abiotic stress responses in plants. In carrot (Daucus carota), the expression of DcPSY2, a gene encoding phytoene synthase required for carotenoid biosynthesis, is induced after salt and abscisic acid (ABA) treatment. Interestingly, the DcPSY2 promoter contains multiple ALFIN response elements. By in silico analysis, we identified two putative genes with the molecular characteristics of ALs, DcAL4 and DcAL7, in the carrot transcriptome. These genes encode nuclear proteins that transactivate reporter genes and bind to the carrot DcPSY2 promoter in yeast. The expression of both genes is induced in carrot under salt stress, especially DcAL4 which also responds to ABA treatment. Transgenic homozygous T3 Arabidopsis thaliana lines that stably express DcAL4 and DcAL7 show a higher survival rate with respect to control plants after chronic salt stress. Of note is that DcAL4 lines present a better performance in salt treatments, correlating with the expression level of DcAL4, AtPSY and AtDXR and an increase in carotenoid and chlorophyll contents. Likewise, DcAL4 transgenic kiwi (Actinidia deliciosa) lines show increased carotenoid and chlorophyll content and higher survival rate compared to control plants after chronic salt treatment. Therefore, DcAL4 and DcAL7 encode functional transcription factors, while ectopic expression of DcAL4 provides increased tolerance to salinity in Arabidopsis and Kiwi plants.
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Affiliation(s)
- Luis Felipe Quiroz-Iturra
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Kevin Simpson
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 7750000, Chile
| | - Daniela Arias
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile
| | - Cristóbal Silva
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile
| | - Christian González-Calquin
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile
| | - Leticia Amaza
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile
| | - Michael Handford
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile
| | - Claudia Stange
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile
- Correspondence: ; Tel.: +56-22-2978-7361
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Hou BH, Tsai YH, Chiang MH, Tsao SM, Huang SH, Chao CP, Chen HM. Cultivar-specific markers, mutations, and chimerisim of Cavendish banana somaclonal variants resistant to Fusarium oxysporum f. sp. cubense tropical race 4. BMC Genomics 2022; 23:470. [PMID: 35752751 PMCID: PMC9233791 DOI: 10.1186/s12864-022-08692-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background The selection of tissue culture–derived somaclonal variants of Giant Cavendish banana (Musa spp., Cavendish sub-group AAA) by the Taiwan Banana Research Institute (TBRI) has resulted in several cultivars resistant to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a destructive fungus threatening global banana production. However, the mutations in these somaclonal variants have not yet been determined. We performed an RNA-sequencing (RNA-seq) analysis of three TBRI Foc TR4–resistant cultivars: ‘Tai-Chiao No. 5’ (TC5), ‘Tai-Chiao No. 7’ (TC7), and ‘Formosana’ (FM), as well as their susceptible progenitor ‘Pei-Chiao’ (PC), to investigate the sequence variations among them and develop cultivar-specific markers. Results A group of single-nucleotide variants (SNVs) specific to one cultivar were identified from the analysis of RNA-seq data and validated using Sanger sequencing from genomic DNA. Several SNVs were further converted into cleaved amplified polymorphic sequence (CAPS) markers or derived CAPS markers that could identify the three Foc TR4–resistant cultivars among 6 local and 5 international Cavendish cultivars. Compared with PC, the three resistant cultivars showed a loss or alteration of heterozygosity in some chromosomal regions, which appears to be a consequence of single-copy chromosomal deletions. Notably, TC7 and FM shared a common deletion region on chromosome 5; however, different TC7 tissues displayed varying degrees of allele ratios in this region, suggesting the presence of chimerism in TC7. Conclusions This work demonstrates that reliable SNV markers of tissue culture–derived and propagated banana cultivars with a triploid genome can be developed through RNA-seq data analysis. Moreover, the analysis of sequence heterozygosity can uncover chromosomal deletions and chimerism in banana somaclonal variants. The markers obtained from this study will assist with the identification of TBRI Cavendish somaclonal variants for the quality control of tissue culture propagation, and the protection of breeders’ rights. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08692-5.
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Affiliation(s)
- Bo-Han Hou
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | - Yi-Heng Tsai
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | - Ming-Hau Chiang
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | - Shu-Ming Tsao
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan
| | | | - Chih-Ping Chao
- Taiwan Banana Research Institute, 90442, Pingtung, Taiwan
| | - Ho-Ming Chen
- Agricultural Biotechnology Research Center, Academia Sinica, 11529, Taipei, Taiwan.
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11
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Kannan G, Saraswathi MS, Thangavelu R, Kumar PS, Bathrinath M, Uma S, Backiyarani S, Chandrasekar A, Ganapathi TR. Development of fusarium wilt resistant mutants of Musa spp. cv.Rasthali (AAB, Silk subgroup) and comparative proteomic analysis along with its wild type. PLANTA 2022; 255:80. [PMID: 35249170 DOI: 10.1007/s00425-022-03860-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Induced mutagenesis using embryogenic cell suspension (ECS) explants with toxin based screening is an effective tool to create non-chimeral Fusarium wilt resistant mutants in banana. Global proteomics unravel the molecular mechanism behind resistance. Race 1 of Fusarium wilt is a serious threat to Musa spp. cv.Rasthali (AAB, Silk subgroup) which is a choice variety traditionally grown in most of the south East Asian countries. Resistant gene introgression into susceptible varieties through conventional breeding has several limitations and the predominant ones being sterility and long generation time. Under such circumstances, induced mutagenesis combined with toxin based in vitro screening remains as the viable alternative for the development of fusarium wilt resistant Rasthali. Therefore, induced mutagenesis was attempted by using ethylmethane sulfonate (EMS) in embryogenic cell suspension (ECS) of Rasthali followed by in vitro screening for fusarium wilt resistance using new generation toxins and pot screening through challenge inoculation with Foc race 1. This ultimately resulted in the identification of 15 resistant lines. Global proteomic analysis in one of the resistant mutant lines namely NRCBRM15 and its wild type revealed 37 proteins, of which 20 showed differential expression. Out of 20 proteins, nineteen were significantly abundant in NRCBRM15 and only one was abundant in wild Rasthali. A total of nine genes based on protein expression were further validated using quantitative real time polymerase chain reaction (qRT-PCR). Annotation results revealed that some of the genes namely Enolase, ATP synthase-alpha subunit, Actin 2, Actin 3,-glucanase, UTP-glucose-1-phosphate uridylyltransferase, Respiratory burst oxidase homolog, V type proton ATPase catalytic subunit A and DUF292 domain containing protein are involved in diverse functions such as carbohydrate metabolism, energy production, electron carrier, response to wounding, binding proteins, cytoskeleton organization, extracellular region, structural molecule and defense.
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Affiliation(s)
- Gandhi Kannan
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Road, Thayanur (post), Tiruchirappalli, Tamil Nadu, 620 102, India
| | - Marimuthu Somasundaram Saraswathi
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Road, Thayanur (post), Tiruchirappalli, Tamil Nadu, 620 102, India.
| | - Raman Thangavelu
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Road, Thayanur (post), Tiruchirappalli, Tamil Nadu, 620 102, India
| | - Parasuraman Subesh Kumar
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Road, Thayanur (post), Tiruchirappalli, Tamil Nadu, 620 102, India
| | - Murugesan Bathrinath
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Road, Thayanur (post), Tiruchirappalli, Tamil Nadu, 620 102, India
| | - Subbaraya Uma
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Road, Thayanur (post), Tiruchirappalli, Tamil Nadu, 620 102, India
| | - Suthanthiram Backiyarani
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Road, Thayanur (post), Tiruchirappalli, Tamil Nadu, 620 102, India
| | - Arumugam Chandrasekar
- Crop Improvement Division, ICAR, National Research Centre for Banana, Thogamalai Road, Thayanur (post), Tiruchirappalli, Tamil Nadu, 620 102, India
| | - Thumballi R Ganapathi
- Plant Cell Culture Technology Section Nuclear Agriculture and Biotechnology Division Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India
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12
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Wang X, Wang A, Li Y, Xu Y, Wei Q, Wang J, Lin F, Gong D, Liu F, Wang Y, Peng L, Li J. A Novel Banana Mutant " RF 1" ( Musa spp. ABB, Pisang Awak Subgroup) for Improved Agronomic Traits and Enhanced Cold Tolerance and Disease Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:730718. [PMID: 34630479 PMCID: PMC8496975 DOI: 10.3389/fpls.2021.730718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
Banana is a major fruit crop grown in tropical and subtropical regions worldwide. Among cultivars, "FenJiao, FJ" (Musa spp. ABB, Pisang Awak subgroup) is a popular variety of bananas, due to its better sugar-acid blend and relatively small fruit shape. However, because the traditional FJ variety grows relatively high in height, it is vulnerable to lodging and unsuitable for harvesting. In this study, we sought desirable banana mutants by carrying out ethyl methanesulfonate (EMS) mutagenesis with the FJ cultivar. After the FJ shoot tips had been treated with 0.8% (v/v) EMS for 4 h, we obtained a stably inherited mutant, here called "ReFen 1" (RF1), and also observed a semi-dwarfing phenotype. Compared with the wild type (FJ), this RF1 mutant featured consistently improved agronomic traits during 5-year field experiments conducted in three distinct locations in China. Notably, the RF1 plants showed significantly enhanced cold tolerance and Sigatoka disease resistance, mainly due to a substantially increased soluble content of sugar and greater starch accumulation along with reduced cellulose deposition. Therefore, this study not only demonstrated how a powerful genetic strategy can be used in fruit crop breeding but also provided insight into the identification of novel genes for agronomic trait improvement in bananas and beyond.
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Affiliation(s)
- Xiaoyi Wang
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Anbang Wang
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yujia Li
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yi Xu
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Qing Wei
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jiashui Wang
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Fei Lin
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Deyong Gong
- The Fruit Tree Research Center, Institute of Subtropical Crops, Guizhou Academy of Agricultural Sciences, Xinyi, China
| | - Fei Liu
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingyang Li
- Hainan Banana Healthy Seedling Propagation Engineering Research Center, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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13
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Maghuly F, Pabinger S, Krainer J, Laimer M. The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:524. [PMID: 29774036 PMCID: PMC5944264 DOI: 10.3389/fpls.2018.00524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/04/2018] [Indexed: 05/31/2023]
Abstract
Mutagenesis in combination with Genotyping by Sequencing (GBS) is a powerful tool for introducing variation, studying gene function and identifying causal mutations underlying phenotypes of interest in crop plant genomes. About 400 million paired-end reads were obtained from 82 ethylmethane sulfonate (EMS) induced mutants and 14 wild-type accessions of Jatropha curcas for the detection of Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletions (InDels) by two different approaches (nGBS and ddGBS) on an Illumina HiSeq 2000 sequencer. Using bioinformatics analyses, 1,452 induced SNPs and InDels were identified in coding regions, which were distributed across 995 genes. The predominantly observed mutations were G/C to A/T transitions (64%), while transversions were observed at a lower frequency (36%). Regarding the effect of mutations on gene function, 18% of the mutations were located in intergenic regions. In fact, mutants with the highest number of heterozygous SNPs were found in samples treated with 0.8% EMS for 3 h. Reconstruction of the metabolic pathways showed that in total 16 SNPs were located in six KEGG pathways by nGBS and two pathways by ddGBS. The most highly represented pathways were ether-lipid metabolism and glycerophospholipid metabolism, followed by starch and sucrose metabolism by nGBS and triterpenoid biosynthesis as well as steroid biosynthesis by ddGBS. Furthermore, high genome methylation was observed in J. curcas, which might help to understand the plasticity of the Jatropha genome in response to environmental factors. At last, the results showed that continuously vegetatively propagated tissue is a fast, efficient and accurate method to dissolve chimeras, especially for long-lived plants like J. curcas. Obtained data showed that allelic variations and in silico analyses of gene functions (gene function prediction), which control important traits, could be identified in mutant populations using nGBS and ddGBS. However, the handling of GBS data is more difficult and more challenging than the traditional TILLING strategy in mutated plants, since the Jatropha genome sequence is incomplete, which makes alignment and variant analysis of target sequence reads challenging to perform and interpret. Therefore, providing a complete Jatropha reference genome sequence with high quality should be a priority for any breeding program.
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Affiliation(s)
- Fatemeh Maghuly
- Plant Biotechnology Unit, Department of Biotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stephan Pabinger
- Molecular Diagnostics, Center for Health & Bioresources, Austrian Institute of Technology, Vienna, Austria
| | - Julie Krainer
- Molecular Diagnostics, Center for Health & Bioresources, Austrian Institute of Technology, Vienna, Austria
| | - Margit Laimer
- Plant Biotechnology Unit, Department of Biotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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14
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Datta S, Jankowicz‐Cieslak J, Nielen S, Ingelbrecht I, Till BJ. Induction and recovery of copy number variation in banana through gamma irradiation and low-coverage whole-genome sequencing. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1644-1653. [PMID: 29476650 PMCID: PMC6097122 DOI: 10.1111/pbi.12901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/02/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Traditional breeding methods are hindered in bananas due to the fact that major cultivars are sterile, parthenocarpic, triploid and thus clonally propagated. This has resulted in a narrow genetic base and limited resilience to biotic and abiotic stresses. Mutagenesis of in vitro propagated bananas is one method to introduce novel alleles and broaden genetic diversity. We previously established a method for the induction and recovery of single nucleotide mutations generated with the chemical mutagen EMS. However, officially released mutant banana varieties have been created using gamma rays, a mutagen that can produce large genomic insertions and deletions (indels). Such dosage mutations may be important for generating observable phenotypes in polyploids. In this study, we establish a low-coverage whole-genome sequencing approach in triploid bananas to recover large genomic indels caused by treatment with gamma irradiation. We first evaluated the commercially released mutant cultivar 'Novaria' and found that it harbours multiple predicted deletions, ranging from 0.3 to 3.8 million base pairs (Mbp). In total, predicted deletions span 189 coding regions. To evaluate the feasibility of generating and maintaining new mutations, we developed a pipeline for mutagenesis and screening for copy number variation in Cavendish bananas using the cultivar 'Williams'. Putative mutations were recovered in 70% of lines treated with 20 Gy and 60% of the lines treated with 40 Gy. While deletion events predominate, insertions were identified in 20 Gy-treated material. Based on these results, we believe this approach can be scaled up to support large breeding projects.
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Affiliation(s)
- Sneha Datta
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Joanna Jankowicz‐Cieslak
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Stephan Nielen
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Ivan Ingelbrecht
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Bradley J. Till
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
- Present address:
Department of Chromosome BiologyUniversity of ViennaA‐1030ViennaAustria
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15
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Szurman-Zubrzycka ME, Zbieszczyk J, Marzec M, Jelonek J, Chmielewska B, Kurowska MM, Krok M, Daszkowska-Golec A, Guzy-Wrobelska J, Gruszka D, Gajecka M, Gajewska P, Stolarek M, Tylec P, Sega P, Lip S, Kudełko M, Lorek M, Gorniak-Walas M, Malolepszy A, Podsiadlo N, Szyrajew KP, Keisa A, Mbambo Z, Todorowska E, Gaj M, Nita Z, Orlowska-Job W, Maluszynski M, Szarejko I. HorTILLUS-A Rich and Renewable Source of Induced Mutations for Forward/Reverse Genetics and Pre-breeding Programs in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2018; 9:216. [PMID: 29515615 PMCID: PMC5826354 DOI: 10.3389/fpls.2018.00216] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/05/2018] [Indexed: 05/23/2023]
Abstract
TILLING (Targeting Induced Local Lesions IN Genomes) is a strategy used for functional analysis of genes that combines the classical mutagenesis and a rapid, high-throughput identification of mutations within a gene of interest. TILLING has been initially developed as a discovery platform for functional genomics, but soon it has become a valuable tool in development of desired alleles for crop breeding, alternative to transgenic approach. Here we present the HorTILLUS ( Hordeum-TILLING-University of Silesia) population created for spring barley cultivar "Sebastian" after double-treatment of seeds with two chemical mutagens: sodium azide (NaN3) and N-methyl-N-nitrosourea (MNU). The population comprises more than 9,600 M2 plants from which DNA was isolated, seeds harvested, vacuum-packed, and deposited in seed bank. M3 progeny of 3,481 M2 individuals was grown in the field and phenotyped. The screening for mutations was performed for 32 genes related to different aspects of plant growth and development. For each gene fragment, 3,072-6,912 M2 plants were used for mutation identification using LI-COR sequencer. In total, 382 mutations were found in 182.2 Mb screened. The average mutation density in the HorTILLUS, estimated as 1 mutation per 477 kb, is among the highest mutation densities reported for barley. The majority of mutations were G/C to A/T transitions, however about 8% transversions were also detected. Sixty-one percent of mutations found in coding regions were missense, 37.5% silent and 1.1% nonsense. In each gene, the missense mutations with a potential effect on protein function were identified. The HorTILLUS platform is the largest of the TILLING populations reported for barley and best characterized. The population proved to be a useful tool, both in functional genomic studies and in forward selection of barley mutants with required phenotypic changes. We are constantly renewing the HorTILLUS population, which makes it a permanent source of new mutations. We offer the usage of this valuable resource to the interested barley researchers on cooperative basis.
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Affiliation(s)
- Miriam E. Szurman-Zubrzycka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Justyna Zbieszczyk
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Marek Marzec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Janusz Jelonek
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Beata Chmielewska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Marzena M. Kurowska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Milena Krok
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Agata Daszkowska-Golec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Justyna Guzy-Wrobelska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Monika Gajecka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Patrycja Gajewska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Magdalena Stolarek
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Piotr Tylec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Paweł Sega
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Sabina Lip
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Monika Kudełko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Magdalena Lorek
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Małgorzata Gorniak-Walas
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Anna Malolepszy
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Nina Podsiadlo
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Katarzyna P. Szyrajew
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Anete Keisa
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Latvia, Riga, Latvia
| | - Zodwa Mbambo
- Biosciences, Council for Scientific and Industrial Research, Pretoria, South Africa
| | | | - Marek Gaj
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Zygmunt Nita
- Seed Company Plant Breeding Strzelce Ltd., Plant Breeding and Acclimatization Institute, Błonie, Poland
| | - Wanda Orlowska-Job
- Seed Company Plant Breeding Strzelce Ltd., Plant Breeding and Acclimatization Institute, Błonie, Poland
| | - Miroslaw Maluszynski
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
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Abstract
Gene space: the final frontier in plant functional genomics. These are the voyages of TILLING, the reverse-genetics strategy that sought to boldly go where no-one had gone before by combining high-density chemical mutagenesis with high-throughput mutation discovery. Its 18-year mission has been to explore new technologies such as next generation sequencing and to seek out new strategies like in silico databases of catalogued EMS-induced mutations from entire mutant plant populations. This chapter is a clip show highlighting key milestones in the development of TILLING. Use of different technologies for the discovery of induced mutations, establishment of TILLING in different plant species, what has been learned about the effect of chemical mutagens on the plant genome, development of exome capture sequencing in wheat, and a look to the future of reverse-genetics with targeted genome editing are discussed. Graphical Abstract.
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17
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Gupta P, Reddaiah B, Salava H, Upadhyaya P, Tyagi K, Sarma S, Datta S, Malhotra B, Thomas S, Sunkum A, Devulapalli S, Till BJ, Sreelakshmi Y, Sharma R. Next-generation sequencing (NGS)-based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum) population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:495-508. [PMID: 28779536 DOI: 10.1111/tpj.13654] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 05/21/2023]
Abstract
The identification of mutations in targeted genes has been significantly simplified by the advent of TILLING (Targeting Induced Local Lesions In Genomes), speeding up the functional genomic analysis of animals and plants. Next-generation sequencing (NGS) is gradually replacing classical TILLING for mutation detection, as it allows the analysis of a large number of amplicons in short durations. The NGS approach was used to identify mutations in a population of Solanum lycopersicum (tomato) that was doubly mutagenized by ethylmethane sulphonate (EMS). Twenty-five genes belonging to carotenoids and folate metabolism were PCR-amplified and screened to identify potentially beneficial alleles. To augment efficiency, the 600-bp amplicons were directly sequenced in a non-overlapping manner in Illumina MiSeq, obviating the need for a fragmentation step before library preparation. A comparison of the different pooling depths revealed that heterozygous mutations could be identified up to 128-fold pooling. An evaluation of six different software programs (camba, crisp, gatk unified genotyper, lofreq, snver and vipr) revealed that no software program was robust enough to predict mutations with high fidelity. Among these, crisp and camba predicted mutations with lower false discovery rates. The false positives were largely eliminated by considering only mutations commonly predicted by two different software programs. The screening of 23.47 Mb of tomato genome yielded 75 predicted mutations, 64 of which were confirmed by Sanger sequencing with an average mutation density of 1/367 Kb. Our results indicate that NGS combined with multiple variant detection tools can reduce false positives and significantly speed up the mutation discovery rate.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Bodanapu Reddaiah
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Hymavathi Salava
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Pallawi Upadhyaya
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kamal Tyagi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Supriya Sarma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sneha Datta
- Plant Breeding and Genetics Laboratory, IAEA Seibersdorf Laboratories, Reaktorstrasse 1, Seibersdorf, Austria
| | - Bharti Malhotra
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sherinmol Thomas
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anusha Sunkum
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sameera Devulapalli
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Bradley John Till
- Plant Breeding and Genetics Laboratory, IAEA Seibersdorf Laboratories, Reaktorstrasse 1, Seibersdorf, Austria
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Awasthi P, Singh A, Sheikh G, Mahajan V, Gupta AP, Gupta S, Bedi YS, Gandhi SG. Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:925-931. [PMID: 29158639 PMCID: PMC5671454 DOI: 10.1007/s12298-017-0472-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 07/13/2017] [Accepted: 09/19/2017] [Indexed: 05/11/2023]
Abstract
Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.
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Affiliation(s)
- Praveen Awasthi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
| | - Ashish Singh
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
| | - Gulfam Sheikh
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Vidushi Mahajan
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Ajai Prakash Gupta
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
| | - Suphla Gupta
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Yashbir S. Bedi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Sumit G. Gandhi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
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Valdiani A, Talei D, Lattoo SK, Ortiz R, Rasmussen SK, Batley J, Rafii MY, Maziah M, Sabu KK, Abiri R, Sakuanrungsirikul S, Tan SG. Genoproteomics-assisted improvement of Andrographis paniculata: toward a promising molecular and conventional breeding platform for autogamous plants affecting the pharmaceutical industry. Crit Rev Biotechnol 2017; 37:803-816. [PMID: 28049346 DOI: 10.1080/07388551.2016.1260525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Andrographis paniculata (Burm. f.) Wall. ex Nees. (AP) is a hermaphroditic, self-compatible, and habitual inbreeding plant. Its main bioactive component is andrographolide, which is capable of inducing autophagic cell death in some human cancer cells and helps fight HIV/AIDS. Increasing the andrographolide content by investigating the genetic mechanisms controlling its biosynthesis in order to improve and develop high-yielding cultivars are the main breeding targets for AP. However, there might exist some limitations or barriers for crossability within AP accessions. Recently, this problem was addressed in AP by using a combination of crossbreeding and biotechnology-aided genetic methods. This review emphasizes that development of a breeding platform in a hard-to-breed plant, such as AP, requires the involvement of a broad range of methods from classical genetics to molecular breeding. To this end, a phenological stage (for example, flowering and stigma development) can be simplified to a quantitative morphological trait (for example, bud or stigma length) to be used as an index to express the highest level of receptivity in order to manage outcrossing. The outcomes of the basic crossability research can be then employed in diallel mating and crossbreeding. This review explains how genomic data could produce useful information regarding genetic distance and its influence on the crossability of AP accessions. Our review indicates that co-dominant DNA markers, such as microsatellites, are also capable of resolving the evolutionary pathway and cryptic features of plant populations and such information can be used to select the best breeding strategy. This review also highlights the importance of proteomic analysis as a breeding tool. In this regard, protein diversification, as well as the impact of normal and stress-responsive proteins on morphometric and physiological behaviors, could be used in breeding programs. These findings have immense potential for improving plant production and, therefore, can be regarded as prospective breeding platforms for medicinal plants that have an autogamous mode of reproduction. Finally, this review suggests that novel site-directed genome editing approaches such as TALENs (Transcription Activator-Like Effector Nucleases) and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein-9 nuclease) systems together with other new plant breeding technologies (NPBT) should simultaneously be taken into consideration for improvement of pharmaceutical plants.
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Affiliation(s)
- Alireza Valdiani
- a Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences , Universiti Putra Malaysia , Selangor , Malaysia
| | - Daryush Talei
- b Medicinal Plants Research Center , Shahed University , Tehran , Iran
| | - Surrinder K Lattoo
- c Plant Biotechnology Division , CSIR - Indian Institute of Integrative Medicine , Jammu , India
| | - Rodomiro Ortiz
- d Department of Plant Breeding , Swedish University of Agricultural Sciences (SLU) , Alnarp , Sweden
| | - Søren Kjærsgaard Rasmussen
- e Department of Plant and Environmental Science, Faculty of Sciences , University of Copenhagen , Copenhagen , Denmark
| | - Jacqueline Batley
- f School of Plant Biology , University of Western Australia , Crawley , WA , Australia
| | - Mohd Yusop Rafii
- g Institute of Tropical Agriculture , Universiti Putra Malaysia , Selangor , DE , Malaysia
| | - Mahmood Maziah
- a Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences , Universiti Putra Malaysia , Selangor , Malaysia.,g Institute of Tropical Agriculture , Universiti Putra Malaysia , Selangor , DE , Malaysia.,h Institute of Bioscience , Universiti Putra Malaysia , Selangor , Malaysia
| | - Kallevettankuzhy K Sabu
- i Jawaharlal Nehru Tropical Botanic Garden and Research Institute , Palode, Thiruvananthapuram , India
| | - Rambod Abiri
- a Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences , Universiti Putra Malaysia , Selangor , Malaysia
| | - Suchirat Sakuanrungsirikul
- j Khon Kaen Field Crops Research Center, Field and Energy Renewable Crops Research, Institute , Department of Agriculture, Ministry of Agriculture and Cooperatives , Khon Kaen , Thailand
| | - Soon Guan Tan
- k Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences , Universiti Putra Malaysia , Selangor , Malaysia
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Jankowicz-Cieslak J, Till BJ. Chemical Mutagenesis of Seed and Vegetatively Propagated Plants Using EMS. CURRENT PROTOCOLS IN PLANT BIOLOGY 2016; 1:617-635. [PMID: 31725963 DOI: 10.1002/cppb.20040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chemical mutagenesis provides an inexpensive and straightforward way to generate a high density of novel nucleotide diversity in the genomes of plants and animals. Mutagenesis therefore can be used for functional genomic studies and also for plant breeding. The most commonly used chemical mutagen in plants is ethyl methanesulfonate (EMS). EMS has been shown to induce primarily single base point mutations. Hundreds to thousands of heritable mutations can be induced in a single plant line. A relatively small number of plants, therefore, are needed to produce populations harboring deleterious alleles in most genes. EMS mutagenized plant populations can be screened phenotypically (forward-genetics), or mutations in genes can be identified in advance of phenotypic characterization (reverse-genetics). Reverse-genetics using chemically induced mutations is known as Targeting Induced Local Lesions IN Genomes (TILLING). This unit gives information on EMS treatment of seed and vegetative propagules. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Joanna Jankowicz-Cieslak
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria
| | - Bradley J Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, IAEA Laboratories Seibersdorf, International Atomic Energy Agency, Vienna International Centre, Vienna, Austria
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Tadele Z. Mutagenesis and TILLING to Dissect Gene Function in Plants. Curr Genomics 2016; 17:499-508. [PMID: 28217006 PMCID: PMC5282601 DOI: 10.2174/1389202917666160520104158] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/01/2015] [Accepted: 12/05/2015] [Indexed: 11/22/2022] Open
Abstract
Mutagenesis can be random or targeted and occur by nature or artificially by humans. However, the bulk of mutagenesis employed in plants are random and caused by physical agents such as x-ray and gamma-ray or chemicals such as ethyl-methane sulfonate (EMS). Researchers are interested in first identifying these mutations and/or polymorphisms in the genome followed by investigating their effects in the plant function as well as their application in crop improvement. The high-throughput technique called TILLING (Targeting Induced Local Lesion IN Genomes) has been already established and become popular for identifying candidate mutant individuals harboring mutations in the gene of interest. TILLING is a non-transgenic and reverse genetics method of identifying a single nucleotide changes. The procedure of TILLING comprises traditional mutagenesis using optimum type and concentration of mutagen, development of a non-chimeric population, DNA extraction and pooling, mutation detection as well as validation of results. In general, TILLING has proved to be robust in identifying useful mutant lines in diverse economically important crops of the world. The main goal of the current mini-review is to show the significance role played by mutagenesis and TILLING in the discovery of DNA lesions which are to be used in the improvement of crops for the trait of interest.
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Affiliation(s)
- Zerihun Tadele
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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Muthusamy A, Jayabalan N. Radiation and chemical mutagen induced somaclonal variations through in vitro organogenesis of cotton (Gossypium hirsutum L.). Int J Radiat Biol 2014; 90:1229-39. [PMID: 24831496 DOI: 10.3109/09553002.2014.923589] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE The purpose of the investigation was to induce somaclonal variations by gamma rays (GR), ethylmethane sulphonate (EMS) and sodium azide (SA) during in vitro organogenesis of cotton. MATERIALS AND METHODS The shoot tip explants were irradiated with 5-50 Gray (Gy) GR (Cobalt 60), 0.5-5.0 mM EMS and SA separately, and inoculated on Murashige and Skoog (MS) medium fortified with plant growth regulator (PGR) for organogenesis. The plantlets with well-developed root systems were acclimatized and transferred into the experimental field to screen the somaclonal variations during growth and development. RESULTS The number of somaclonal variations was observed in growth of irradiated/treated shoot tips, multiplication, plantlet regeneration and growth in vitro and ex vitro. The lower doses/concentrations of mutagenic treatments showed significant enhancement in selected agronomical characters and they showed decreased trends with increasing doses/concentrations of mutagenic agents. CONCLUSIONS The results of the present study revealed the influence of lower doses/concentrations of mutagenic treatments on in vitro and ex vitro growth of cotton plantlets and their significant improvement in agronomical characters which needs further imperative stability analysis. The present observations showed the platform to use lower doses/concentrations of mutagenic agents to induce variability for enhanced agronomical characters, resistant and tolerant cotton varieties.
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Affiliation(s)
- Annamalai Muthusamy
- Department of Plant Science, School of Life Sciences, Bharathidasan University , Tiruchirappalli, Tamil Nadu , India
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Swarupa V, Ravishankar KV, Rekha A. Plant defense response against Fusarium oxysporum and strategies to develop tolerant genotypes in banana. PLANTA 2014; 239:735-51. [PMID: 24420701 DOI: 10.1007/s00425-013-2024-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/30/2013] [Indexed: 05/23/2023]
Abstract
Soil-borne fungal pathogen, Fusarium oxysporum causes major economic losses by inducing necrosis and wilting symptoms in many crop plants. Management of fusarium wilt is achieved mainly by the use of chemical fungicides which affect the soil health and their efficiency is often limited by pathogenic variability. Hence understanding the nature of interaction between pathogen and host may help to select and improve better cultivars. Current research evidences highlight the role of oxidative burst and antioxidant enzymes indicating that ROS act as an important signaling molecule in banana defense response against Fusarium oxysporum f.sp. cubense. The role of jasmonic acid signaling in plant defense against necrotrophic pathogens is well recognized. But recent studies show that the role of salicylic acid is complex and ambiguous against necrotrophic pathogens like Fusarium oxysporum, leading to many intriguing questions about its relationship between other signaling compounds. In case of banana, a major challenge is to identify specific receptors for effector proteins like SIX proteins and also the components of various signal transduction pathways. Significant progress has been made to uncover the role of defense genes but is limited to only model plants such as Arabidopsis and tomato. Keeping this in view, we review the host response, pathogen diversity, current understanding of biochemical and molecular changes that occur during host and pathogen interaction. Developing resistant cultivars through mutation, breeding, transgenic and cisgenic approaches have been discussed. This would help us to understand host defenses against Fusarium oxysporum and to formulate strategies to develop tolerant cultivars.
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Affiliation(s)
- V Swarupa
- Division of Biotechnology, Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bengaluru, 560089, India
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Ortiz R, Swennen R. From crossbreeding to biotechnology-facilitated improvement of banana and plantain. Biotechnol Adv 2014; 32:158-69. [DOI: 10.1016/j.biotechadv.2013.09.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/16/2013] [Accepted: 09/24/2013] [Indexed: 12/30/2022]
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Hofinger BJ, Huynh OA, Jankowicz-Cieslak J, Müller A, Otto I, Kumlehn J, Till BJ. Validation of doubled haploid plants by enzymatic mismatch cleavage. PLANT METHODS 2013; 9:43. [PMID: 24220637 PMCID: PMC3831592 DOI: 10.1186/1746-4811-9-43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/01/2013] [Indexed: 05/25/2023]
Abstract
BACKGROUND Doubled haploidy is a fundamental tool in plant breeding as it provides the fastest way to generate populations of meiotic recombinants in a genetically fixed state. A wide range of methods has been developed to produce doubled haploid (DH) plants and recent advances promise efficient DH production in otherwise recalcitrant species. Since the cellular origin of the plants produced is not always certain, rapid screening techniques are needed to validate that the produced individuals are indeed homozygous and genetically distinct from each other. Ideal methods are easily implemented across species and in crops where whole genome sequence and marker resources are limited. RESULTS We have adapted enzymatic mismatch cleavage techniques commonly used for TILLING (Targeting Induced Local Lesions IN Genomes) for the evaluation of heterozygosity in parental, F1 and putative DH plants. We used barley as a model crop and tested 26 amplicons previously developed for TILLING. Experiments were performed using self-extracted single-strand-specific nuclease and standard native agarose gels. Eleven of the twenty-six tested primers allowed unambiguous assignment of heterozygosity in material from F1 crosses and loss of heterozygosity in the DH plants. Through parallel testing of previously developed Simple Sequence Repeat (SSR) markers, we show that 3/32 SSR markers were suitable for screening. This suggests that enzymatic mismatch cleavage approaches can be more efficient than SSR based screening, even in species with well-developed markers. CONCLUSIONS Enzymatic mismatch cleavage has been applied for mutation discovery in many plant species, including those with little or no available genomic DNA sequence information. Here, we show that the same methods provide an efficient system to screen for the production of DH material without the need of specialized equipment. This gene target based approach further allows discovery of novel nucleotide polymorphisms in candidate genes in the parental lines.
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Affiliation(s)
- Bernhard J Hofinger
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
| | - Owen A Huynh
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
| | - Joanna Jankowicz-Cieslak
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
| | - Andrea Müller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Ingrid Otto
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Plant Reproductive Biology, Corrensstrasse 3, D-06466 Seeland, OT Gatersleben, Germany
| | - Bradley J Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400, Vienna, Austria
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Induced Mutations Unleash the Potentials of Plant Genetic Resources for Food and Agriculture. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3010200] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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