101
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Mawphlang OIL, Kharshiing EV. Photoreceptor Mediated Plant Growth Responses: Implications for Photoreceptor Engineering toward Improved Performance in Crops. FRONTIERS IN PLANT SCIENCE 2017; 8:1181. [PMID: 28744290 PMCID: PMC5504655 DOI: 10.3389/fpls.2017.01181] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/20/2017] [Indexed: 05/18/2023]
Abstract
Rising temperatures during growing seasons coupled with altered precipitation rates presents a challenging task of improving crop productivity for overcoming such altered weather patterns and cater to a growing population. Light is a critical environmental factor that exerts a powerful influence on plant growth and development ranging from seed germination to flowering and fruiting. Higher plants utilize a suite of complex photoreceptor proteins to perceive surrounding red/far-red (phytochromes), blue/UV-A (cryptochromes, phototropins, ZTL/FKF1/LKP2), and UV-B light (UVR8). While genomic studies have also shown that light induces extensive reprogramming of gene expression patterns in plants, molecular genetic studies have shown that manipulation of one or more photoreceptors can result in modification of agronomically beneficial traits. Such information can assist researchers to engineer photoreceptors via genome editing technologies to alter expression or even sensitivity thresholds of native photoreceptors for targeting aspects of plant growth that can confer superior agronomic value to the engineered crops. Here we summarize the agronomically important plant growth processes influenced by photoreceptors in crop species, alongwith the functional interactions between different photoreceptors and phytohormones in regulating these responses. We also discuss the potential utility of synthetic biology approaches in photobiology for improving agronomically beneficial traits of crop plants by engineering designer photoreceptors.
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102
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Sun C, Yan K, Han JT, Tao L, Lv MH, Shi T, He YX, Wierzba M, Tax FE, Li J. Scanning for New BRI1 Mutations via TILLING Analysis. PLANT PHYSIOLOGY 2017; 174:1881-1896. [PMID: 28461403 PMCID: PMC5490892 DOI: 10.1104/pp.17.00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/27/2017] [Indexed: 05/02/2023]
Abstract
The identification and characterization of a mutational spectrum for a specific protein can help to elucidate its detailed cellular functions. BRASSINOSTEROID INSENSITIVE1 (BRI1), a multidomain transmembrane receptor-like kinase, is a major receptor of brassinosteroids in Arabidopsis (Arabidopsis thaliana). Within the last two decades, over 20 different bri1 mutant alleles have been identified, which helped to determine the significance of each domain within BRI1. To further understand the molecular mechanisms of BRI1, we tried to identify additional alleles via targeted induced local lesions in genomes. Here, we report our identification of 83 new point mutations in BRI1, including nine mutations that exhibit an allelic series of typical bri1 phenotypes, from subtle to severe morphological alterations. We carried out biochemical analyses to investigate possible mechanisms of these mutations in affecting brassinosteroid signaling. A number of interesting mutations have been isolated via this study. For example, bri1-702, the only weak allele identified so far with a mutation in the activation loop, showed reduced autophosphorylation activity. bri1-705, a subtle allele with a mutation in the extracellular portion, disrupts the interaction of BRI1 with its ligand brassinolide and coreceptor BRI1-ASSOCIATED RECEPTOR KINASE1. bri1-706, with a mutation in the extracellular portion, is a subtle defective mutant. Surprisingly, root inhibition analysis indicated that it is largely insensitive to exogenous brassinolide treatment. In this study, we found that bri1-301 possesses kinase activity in vivo, clarifying a previous report arguing that kinase activity may not be necessary for the function of BRI1. These data provide additional insights into our understanding of the early events in the brassinosteroid signaling pathway.
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Affiliation(s)
- Chao Sun
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Kan Yan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jian-Ting Han
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Liang Tao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ming-Hui Lv
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Tao Shi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Michael Wierzba
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Frans E Tax
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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103
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Daszkowska-Golec A, Skubacz A, Marzec M, Slota M, Kurowska M, Gajecka M, Gajewska P, Płociniczak T, Sitko K, Pacak A, Szweykowska-Kulinska Z, Szarejko I. Mutation in HvCBP20 ( Cap Binding Protein 20) Adapts Barley to Drought Stress at Phenotypic and Transcriptomic Levels. FRONTIERS IN PLANT SCIENCE 2017; 8:942. [PMID: 28626467 PMCID: PMC5454077 DOI: 10.3389/fpls.2017.00942] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/19/2017] [Indexed: 05/20/2023]
Abstract
CBP20 (Cap-Binding Protein 20) encodes a small subunit of the cap-binding complex (CBC), which is involved in the conserved cell processes related to RNA metabolism in plants and, simultaneously, engaged in the signaling network of drought response, which is dependent on ABA. Here, we report the enhanced tolerance to drought stress of barley mutant in the HvCBP20 gene manifested at the morphological, physiological, and transcriptomic levels. Physiological analyses revealed differences between the hvcbp20.ab mutant and its WT in response to a water deficiency. The mutant exhibited a higher relative water content (RWC), a lower stomatal conductance and changed epidermal pattern compared to the WT after drought stress. Transcriptome analysis using the Agilent Barley Microarray integrated with observed phenotypic traits allowed to conclude that the hvcbp20.ab mutant exhibited better fitness to stress conditions by its much more efficient and earlier activation of stress-preventing mechanisms. The network hubs involved in the adjustment of hvcbp20.ab mutant to the drought conditions were proposed. These results enabled to make a significant progress in understanding the role of CBP20 in the drought stress response.
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Affiliation(s)
- Agata Daszkowska-Golec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Anna Skubacz
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Marek Marzec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Michal Slota
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Marzena Kurowska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Monika Gajecka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Patrycja Gajewska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Tomasz Płociniczak
- Department of Microbiology, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Krzysztof Sitko
- Department of Plant Physiology, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Faculty of Biology, Adam Mickiewicz University in PoznanPoznań, Poland
| | | | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in KatowiceKatowice, Poland
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104
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Kohzuma K, Chiba M, Nagano S, Anai T, Ueda MU, Oguchi R, Shirai K, Hanada K, Hikosaka K, Fujii N. Mutant selection in the self-incompatible plant radish ( Raphanus sativus L. var. sativus) using two-step TILLING. BREEDING SCIENCE 2017; 67:268-276. [PMID: 28744180 PMCID: PMC5515317 DOI: 10.1270/jsbbs.16200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/15/2017] [Indexed: 05/08/2023]
Abstract
Radish (Raphanus sativus L. var. sativus), a widely cultivated root vegetable crop, possesses a large sink organ (the root), implying that photosynthetic activity in radish can be enhanced by altering both the source and sink capacity of the plant. However, since radish is a self-incompatible plant, improved mutation-breeding strategies are needed for this crop. TILLING (Targeting Induced Local Lesions IN Genomes) is a powerful method used for reverse genetics. In this study, we developed a new TILLING strategy involving a two-step mutant selection process for mutagenized radish plants: the first selection is performed to identify a BC1M1 line, that is, progenies of M1 plants crossed with wild-type, and the second step is performed to identify BC1M1 individuals with mutations. We focused on Rubisco as a target, since Rubisco is the most abundant plant protein and a key photosynthetic enzyme. We found that the radish genome contains six RBCS genes and one pseudogene encoding small Rubisco subunits. We screened 955 EMS-induced BC1M1 lines using our newly developed TILLING strategy and obtained six mutant lines for the six RsRBCS genes, encoding proteins with four different types of amino acid substitutions. Finally, we selected a homozygous mutant and subjected it to physiological measurements.
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Affiliation(s)
- Kaori Kohzuma
- Graduate School of Life Sciences, Tohoku University,
Sendai, Miyagi 980-8578,
Japan
- CREST, Japan Science and Technology Agency,
Tokyo 102-0076,
Japan
| | - Motoko Chiba
- Graduate School of Life Sciences, Tohoku University,
Sendai, Miyagi 980-8578,
Japan
- CREST, Japan Science and Technology Agency,
Tokyo 102-0076,
Japan
| | - Soichiro Nagano
- Graduate School of Life Sciences, Tohoku University,
Sendai, Miyagi 980-8578,
Japan
- CREST, Japan Science and Technology Agency,
Tokyo 102-0076,
Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University,
Saga, Saga 840-8502,
Japan
| | - Miki U. Ueda
- Graduate School of Life Sciences, Tohoku University,
Sendai, Miyagi 980-8578,
Japan
| | - Riichi Oguchi
- Graduate School of Life Sciences, Tohoku University,
Sendai, Miyagi 980-8578,
Japan
| | - Kazumasa Shirai
- Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology,
Iizuka, Fukuoka 820-8502,
Japan
- CREST, Japan Science and Technology Agency,
Tokyo 102-0076,
Japan
| | - Kousuke Hanada
- Frontier Research Academy for Young Researchers, Kyusyu Institute of Technology,
Iizuka, Fukuoka 820-8502,
Japan
- CREST, Japan Science and Technology Agency,
Tokyo 102-0076,
Japan
| | - Kouki Hikosaka
- Graduate School of Life Sciences, Tohoku University,
Sendai, Miyagi 980-8578,
Japan
- CREST, Japan Science and Technology Agency,
Tokyo 102-0076,
Japan
| | - Nobuharu Fujii
- Graduate School of Life Sciences, Tohoku University,
Sendai, Miyagi 980-8578,
Japan
- CREST, Japan Science and Technology Agency,
Tokyo 102-0076,
Japan
- Corresponding author (e-mail: )
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105
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Gilliham M, Able JA, Roy SJ. Translating knowledge about abiotic stress tolerance to breeding programmes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:898-917. [PMID: 27987327 DOI: 10.1111/tpj.13456] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 11/23/2016] [Accepted: 12/06/2016] [Indexed: 05/20/2023]
Abstract
Plant breeding and improvements in agronomic practice are making a consistent contribution to increasing global crop production year upon year. However, the rate of yield improvement currently lags behind the targets set to produce enough food to meet the demands of the predicted global population in 2050. Furthermore, crops that are exposed to harmful abiotic environmental factors (abiotic stresses, e.g. water limitation, salinity, extreme temperature) are prone to reduced yields. Here, we briefly describe the processes undertaken in conventional breeding programmes, which are usually designed to improve yields in near-optimal conditions rather than specifically breeding for improved crop yield stability under stressed conditions. While there is extensive fundamental research activity that examines mechanisms of plant stress tolerance, there are few examples that apply this research to improving commercial crop yields. There are notable exceptions, and we highlight some of these to demonstrate the magnitude of yield gains that could be made by translating agronomic, phenological and genetic solutions focused on improving or mitigating the effect of abiotic stress in the field; in particular, we focus on improvements in crop water-use efficiency and salinity tolerance. We speculate upon the reasons for the disconnect between research and research translation. We conclude that to realise untapped rapid gains towards food security targets new funding structures need to be embraced. Such funding needs to serve both the core and collaborative activities of the fundamental, pre-breeding and breeding research communities in order to expedite the translation of innovative research into the fields of primary producers.
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Affiliation(s)
- Matthew Gilliham
- ARC Centre of Excellence in Plant Energy Biology, Glen Osmond, SA, 5064, Australia
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Jason A Able
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Stuart J Roy
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
- Australian Centre for Plant Functional Genomics, Glen Osmond, SA, 5064, Australia
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106
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Li G, Jain R, Chern M, Pham NT, Martin JA, Wei T, Schackwitz WS, Lipzen AM, Duong PQ, Jones KC, Jiang L, Ruan D, Bauer D, Peng Y, Barry KW, Schmutz J, Ronald PC. The Sequences of 1504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. THE PLANT CELL 2017; 29:1218-1231. [PMID: 28576844 PMCID: PMC5502455 DOI: 10.1105/tpc.17.00154] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/16/2017] [Accepted: 06/01/2017] [Indexed: 05/19/2023]
Abstract
The availability of a whole-genome sequenced mutant population and the cataloging of mutations of each line at a single-nucleotide resolution facilitate functional genomic analysis. To this end, we generated and sequenced a fast-neutron-induced mutant population in the model rice cultivar Kitaake (Oryza sativa ssp japonica), which completes its life cycle in 9 weeks. We sequenced 1504 mutant lines at 45-fold coverage and identified 91,513 mutations affecting 32,307 genes, i.e., 58% of all rice genes. We detected an average of 61 mutations per line. Mutation types include single-base substitutions, deletions, insertions, inversions, translocations, and tandem duplications. We observed a high proportion of loss-of-function mutations. We identified an inversion affecting a single gene as the causative mutation for the short-grain phenotype in one mutant line. This result reveals the usefulness of the resource for efficient, cost-effective identification of genes conferring specific phenotypes. To facilitate public access to this genetic resource, we established an open access database called KitBase that provides access to sequence data and seed stocks. This population complements other available mutant collections and gene-editing technologies. This work demonstrates how inexpensive next-generation sequencing can be applied to generate a high-density catalog of mutations.
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Affiliation(s)
- Guotian Li
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Rashmi Jain
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Nikki T Pham
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Joel A Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Tong Wei
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Wendy S Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Anna M Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Phat Q Duong
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
| | - Kyle C Jones
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Liangrong Jiang
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Deling Ruan
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Diane Bauer
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Yi Peng
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Kerrie W Barry
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616
- Grass Genetics, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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107
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Guo H, Liu Y, Li X, Yan Z, Xie Y, Xiong H, Zhao L, Gu J, Zhao S, Liu L. Novel mutant alleles of the starch synthesis gene TaSSIVb-D result in the reduction of starch granule number per chloroplast in wheat. BMC Genomics 2017; 18:358. [PMID: 28482814 DOI: 10.1186/s12864-017-37244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/25/2017] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Transient starch provides carbon and energy for plant growth, and its synthesis is regulated by the joint action of a series of enzymes. Starch synthesis IV (SSIV) is one of the important starch synthase isoforms, but its impact on wheat starch synthesis has not yet been reported due to the lack of mutant lines. RESULTS Using the TILLING approach, we identified 54 mutations in the wheat gene TaSSIVb-D, with a mutation density of 1/165 Kb. Among these, three missense mutations and one nonsense mutation were predicted to have severe impacts on protein function. In the mutants, TaSSIVb-D was significantly down-regulated without compensatory increases in the homoeologous genes TaSSIVb-A and TaSSIVb-B. Altered expression of TaSSIVb-D affected granule number per chloroplast; compared with wild type, the number of chloroplasts containing 0-2 granules was significantly increased, while the number containing 3-4 granules was decreased. Photosynthesis was affected accordingly; the maximum quantum yield and yield of PSII were significantly reduced in the nonsense mutant at the heading stage. CONCLUSIONS These results indicate that TaSSIVb-D plays an important role in the formation of transient starch granules in wheat, which in turn impact the efficiency of photosynthesis. The mutagenized population created in this study allows the efficient identification of novel alleles of target genes and could be used as a resource for wheat functional genomics.
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Affiliation(s)
- Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Yunchuan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Xiao Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Zhihui Yan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Hongchun Xiong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China.
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108
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Guo H, Liu Y, Li X, Yan Z, Xie Y, Xiong H, Zhao L, Gu J, Zhao S, Liu L. Novel mutant alleles of the starch synthesis gene TaSSIVb-D result in the reduction of starch granule number per chloroplast in wheat. BMC Genomics 2017; 18:358. [PMID: 28482814 PMCID: PMC5422989 DOI: 10.1186/s12864-017-3724-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/25/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Transient starch provides carbon and energy for plant growth, and its synthesis is regulated by the joint action of a series of enzymes. Starch synthesis IV (SSIV) is one of the important starch synthase isoforms, but its impact on wheat starch synthesis has not yet been reported due to the lack of mutant lines. RESULTS Using the TILLING approach, we identified 54 mutations in the wheat gene TaSSIVb-D, with a mutation density of 1/165 Kb. Among these, three missense mutations and one nonsense mutation were predicted to have severe impacts on protein function. In the mutants, TaSSIVb-D was significantly down-regulated without compensatory increases in the homoeologous genes TaSSIVb-A and TaSSIVb-B. Altered expression of TaSSIVb-D affected granule number per chloroplast; compared with wild type, the number of chloroplasts containing 0-2 granules was significantly increased, while the number containing 3-4 granules was decreased. Photosynthesis was affected accordingly; the maximum quantum yield and yield of PSII were significantly reduced in the nonsense mutant at the heading stage. CONCLUSIONS These results indicate that TaSSIVb-D plays an important role in the formation of transient starch granules in wheat, which in turn impact the efficiency of photosynthesis. The mutagenized population created in this study allows the efficient identification of novel alleles of target genes and could be used as a resource for wheat functional genomics.
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Affiliation(s)
- Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Yunchuan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Xiao Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Zhihui Yan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Hongchun Xiong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Linshu Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Jiayu Gu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Shirong Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement/National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, China.
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109
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Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis. Appl Environ Microbiol 2017; 83:AEM.02990-16. [PMID: 28314725 DOI: 10.1128/aem.02990-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/07/2017] [Indexed: 12/22/2022] Open
Abstract
Lentinula edodes is a popular, cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems, such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction for Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and by using long reads by PacBio, resulting in a contig number of 1,951 and an N50 of 1 Mb. Furthermore, we predicted genes by Augustus using transcriptome sequencing (RNA-seq) data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes. This analysis revealed that Lentinula edodes lacks lignin peroxidase. To reveal genes involved in the loss of quality of Lentinula edodes postharvest fruiting bodies, transcriptome analysis was carried out using serial analysis of gene expression (SuperSAGE). This analysis revealed that many cell wall-related enzymes are upregulated after harvest, such as β-1,3-1,6-glucan-degrading enzymes in glycoside hydrolase (GH) families GH5, GH16, GH30, GH55, and GH128, and thaumatin-like proteins. In addition, we found that several chitin-related genes are upregulated, such as putative chitinases in GH family 18, exochitinases in GH20, and a putative chitosanase in GH family 75. The results suggest that cell wall-degrading enzymes synergistically cooperate for rapid fruiting body autolysis. Many putative transcription factor genes were upregulated postharvest, such as genes containing high-mobility-group (HMG) domains and zinc finger domains. Several cell death-related proteins were also upregulated postharvest.IMPORTANCE Our data collectively suggest that there is a rapid fruiting body autolysis system in Lentinula edodes The genes for the loss of postharvest quality newly found in this research will be targets for the future breeding of strains that keep fresh longer than present strains. De novoLentinula edodes genome assembly data will be used for the construction of a complete Lentinula edodes chromosome map for future breeding.
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110
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Jouanin A, Gilissen LJWJ, Boyd LA, Cockram J, Leigh FJ, Wallington EJ, van den Broeck HC, van der Meer IM, Schaart JG, Visser RGF, Smulders MJM. Food processing and breeding strategies for coeliac-safe and healthy wheat products. Food Res Int 2017; 110:11-21. [PMID: 30029701 DOI: 10.1016/j.foodres.2017.04.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 01/01/2023]
Abstract
A strict gluten-free diet is currently the only treatment for the 1-2% of the world population who suffer from coeliac disease (CD). However, due to the presence of wheat and wheat derivatives in many food products, avoiding gluten consumption is difficult. Gluten-free products, made without wheat, barley or rye, typically require the inclusion of numerous additives, resulting in products that are often less healthy than gluten-based equivalents. Here, we present and discuss two broad approaches to decrease wheat gluten immunogenicity for CD patients. The first approach is based on food processing strategies, which aim to remove gliadins or all gluten from edible products. We find that several of the candidate food processing techniques to produce low gluten-immunogenic products from wheat already exist. The second approach focuses on wheat breeding strategies to remove immunogenic epitopes from the gluten proteins, while maintaining their food-processing properties. A combination of breeding strategies, including mutation breeding and possibly genome editing, will be necessary to produce coeliac-safe wheat. Individuals suffering from CD and people genetically susceptible who may develop CD after prolonged gluten consumption would benefit from reduced CD-immunogenic wheat. Although the production of healthy and less CD-toxic wheat varieties and food products will be challenging, increasing global demand may require these issues to be addressed in the near future by food processing and cereal breeding companies.
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Affiliation(s)
- Aurélie Jouanin
- Wageningen University & Research, Wageningen, The Netherlands; NIAB, Cambridge CB3 0LE, UK
| | | | | | | | | | | | | | | | - Jan G Schaart
- Wageningen University & Research, Wageningen, The Netherlands
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111
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Flavell RB. Innovations continuously enhance crop breeding and demand new strategic planning. GLOBAL FOOD SECURITY 2017. [DOI: 10.1016/j.gfs.2016.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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112
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Acevedo‐Garcia J, Spencer D, Thieron H, Reinstädler A, Hammond‐Kosack K, Phillips AL, Panstruga R. mlo-based powdery mildew resistance in hexaploid bread wheat generated by a non-transgenic TILLING approach. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:367-378. [PMID: 27565953 PMCID: PMC5316926 DOI: 10.1111/pbi.12631] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 08/12/2016] [Accepted: 08/24/2016] [Indexed: 05/03/2023]
Abstract
Wheat is one of the most widely grown cereal crops in the world and is an important food grain source for humans. However, wheat yields can be reduced by many abiotic and biotic stress factors, including powdery mildew disease caused by Blumeria graminis f.sp. tritici (Bgt). Generating resistant varieties is thus a major effort in plant breeding. Here, we took advantage of the non-transgenic Targeting Induced Lesions IN Genomes (TILLING) technology to select partial loss-of-function alleles of TaMlo, the orthologue of the barley Mlo (Mildew resistance locus o) gene. Natural and induced loss-of-function alleles (mlo) of barley Mlo are known to confer durable broad-spectrum powdery mildew resistance, typically at the expense of pleiotropic phenotypes such as premature leaf senescence. We identified 16 missense mutations in the three wheat TaMlo homoeologues, TaMlo-A1, TaMlo-B1 and TaMlo-D1 that each lead to single amino acid exchanges. Using transient gene expression assays in barley single cells, we functionally analysed the different missense mutants and identified the most promising candidates affecting powdery mildew susceptibility. By stacking of selected mutant alleles we generated four independent lines with non-conservative mutations in each of the three TaMlo homoeologues. Homozygous triple mutant lines and surprisingly also some of the homozygous double mutant lines showed enhanced, yet incomplete, Bgt resistance without the occurrence of discernible pleiotropic phenotypes. These lines thus represent an important step towards the production of commercial non-transgenic, powdery mildew-resistant bread wheat varieties.
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Affiliation(s)
- Johanna Acevedo‐Garcia
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - David Spencer
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - Hannah Thieron
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - Anja Reinstädler
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - Kim Hammond‐Kosack
- Department of Plant Biology and Crop ScienceRothamsted ResearchWest CommonHarpendenHertfordshireAL5 2JQ, UK
| | - Andrew L. Phillips
- Department of Plant Biology and Crop ScienceRothamsted ResearchWest CommonHarpendenHertfordshireAL5 2JQ, UK
| | - Ralph Panstruga
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
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113
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Lamour K, Finley L. A strategy for recovering high quality genomic DNA from a large number ofPhytophthoraisolates. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832686] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Ledare Finley
- Department of Entomology and Plant Pathology, The University of Tennessee, Institute of Agriculture, Knoxville, Tennessee
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114
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Functional characterization of the powdery mildew susceptibility gene SmMLO1 in eggplant (Solanum melongena L.). Transgenic Res 2017; 26:323-330. [PMID: 28070852 DOI: 10.1007/s11248-016-0007-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 12/26/2016] [Indexed: 10/20/2022]
Abstract
Eggplant (Solanum melongena L.) is one of the most important vegetables among the Solanaceae and can be a host to fungal species causing powdery mildew (PM) disease. Specific homologs of the plant Mildew Locus O (MLO) gene family are PM susceptibility factors, as their loss of function results in a recessive form of resistance known as mlo resistance. In a previous work, we isolated the eggplant MLO homolog SmMLO1. SmMLO1 is closely related to MLO susceptibility genes characterized in other plant species. However, it displays a peculiar non-synonymous substitution that leads to a T → M amino acid change at protein position 422, in correspondence of the MLO calmodulin-binding domain. In this study, we performed the functional characterization of SmMLO1. Transgenic overexpression of SmMLO1 in a tomato mlo mutant compromised resistance to the tomato PM pathogen Oidium neolycopersici, thus indicating that SmMLO1 is a PM susceptibility factor in eggplant. PM susceptibility was also restored by the transgenic expression of a synthetic gene, named s-SmMLO1, encoding a protein identical to SmMLO1, except for the presence of T at position 422. This indicates that the T → M polymorphism does not affect the protein role as PM susceptibility factor. Overall, the results of this work are of interest for the functional characterization of MLO proteins and the introduction of PM resistance in eggplant using reverse genetics.
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115
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Hablak SG. Features of inheritance of Arabidopsis thaliana (L.) Heynh. root system: Interaction of genes CTR1 and ALF3, NPH4, and IAR2. CYTOL GENET+ 2017. [DOI: 10.3103/s009545271701008x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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116
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Mantelin S, Thorpe P, Jones JT. Translational biology of nematode effectors. Or, to put it another way, functional analysis of effectors – what’s the point? NEMATOLOGY 2017. [DOI: 10.1163/15685411-00003048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
There has been a huge amount of work put into identifying and characterising effectors from plant-parasitic nematodes in recent years. Although this work has provided insights into the mechanisms by which nematodes can infect plants, the potential translational outputs of much of this research are not always clear. This short article will summarise how developments in effector biology have allowed, or will allow, new control strategies to be developed, drawing on examples from nematology and from other pathosystems.
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Affiliation(s)
- Sophie Mantelin
- Dundee Effector Consortium, Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Peter Thorpe
- Dundee Effector Consortium, Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John T. Jones
- Dundee Effector Consortium, Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Biology Department, University of St Andrews, St Andrews, Fife KY16 9TZ, UK
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117
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Xi-ou X, Wenqiu L, Wei L, Xiaoming G, Lingling L, Feiyue M, Yuge L. The Analysis of Physiological Variations in M 2 Generation of Solanum melongena L. Mutagenized by Ethyl Methane Sulfonate. FRONTIERS IN PLANT SCIENCE 2017; 8:17. [PMID: 28154575 PMCID: PMC5243811 DOI: 10.3389/fpls.2017.00017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/04/2017] [Indexed: 05/22/2023]
Abstract
The eggplant was mutagenized with ethyl methane sulfonate (EMS) to enhance its genetic variability in our previous paper. In this article, we further analyzed the phenotype of M2 generation of mutant eggplants. A total of 325 independent M2 families were investigated for phenotypic variation. In addition to the visible phenotypic variation, chlorogenic acid (CGA) concentrations were analyzed in 26 fruits of mutants with High Performance Liquid Chromatography assay. Seventeen fruits exhibited significantly higher concentrations of CGAs than those in wild-type. The anthocyanin concentration of S9-1, the purple black mutant, was higher than WT, meanwhile, the anthocyanin concentration of L6-4 and U36-1 was lower than WT. Furthermore, our RT-PCR result demonstrated that the expression levels of anthocyanin biosynthetic genes, except for SmPAL, were increased in S9-1, and the regulator SmMYB1 was decreased in L6-4 and U36-1 mutants. Together, our data indicated that, M2 generation showed abundant phenotypic variations and the strong potential usage for next step of breeding and molecular genetic mechanisms in eggplant.
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Affiliation(s)
- Xiao Xi-ou
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS)Zhanjiang, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic ImprovementZhanjiang, China
- *Correspondence: Xiao Xi-ou,
| | - Lin Wenqiu
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS)Zhanjiang, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic ImprovementZhanjiang, China
| | - Li Wei
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS)Zhanjiang, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic ImprovementZhanjiang, China
| | - Gao Xiaoming
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS)Zhanjiang, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic ImprovementZhanjiang, China
| | - Lv Lingling
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS)Zhanjiang, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic ImprovementZhanjiang, China
| | - Ma Feiyue
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS)Zhanjiang, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic ImprovementZhanjiang, China
| | - Liu Yuge
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS)Zhanjiang, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic ImprovementZhanjiang, China
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118
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Li Z, Jiang L, Ma Y, Wei Z, Hong H, Liu Z, Lei J, Liu Y, Guan R, Guo Y, Jin L, Zhang L, Li Y, Ren Y, He W, Liu M, Htwe NMPS, Liu L, Guo B, Song J, Tan B, Liu G, Li M, Zhang X, Liu B, Shi X, Han S, Hua S, Zhou F, Yu L, Li Y, Wang S, Wang J, Chang R, Qiu L. Development and utilization of a new chemically-induced soybean library with a high mutation density . JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:60-74. [PMID: 27774740 PMCID: PMC5248594 DOI: 10.1111/jipb.12505] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/20/2016] [Indexed: 05/20/2023]
Abstract
Mutagenized populations have provided important materials for introducing variation and identifying gene function in plants. In this study, an ethyl methanesulfonate (EMS)-induced soybean (Glycine max) population, consisting of 21,600 independent M2 lines, was developed. Over 1,000 M4 (5) families, with diverse abnormal phenotypes for seed composition, seed shape, plant morphology and maturity that are stably expressed across different environments and generations were identified. Phenotypic analysis of the population led to the identification of a yellow pigmentation mutant, gyl, that displayed significantly decreased chlorophyll (Chl) content and abnormal chloroplast development. Sequence analysis showed that gyl is allelic to MinnGold, where a different single nucleotide polymorphism variation in the Mg-chelatase subunit gene (ChlI1a) results in golden yellow leaves. A cleaved amplified polymorphic sequence marker was developed and may be applied to marker-assisted selection for the golden yellow phenotype in soybean breeding. We show that the newly developed soybean EMS mutant population has potential for functional genomics research and genetic improvement in soybean.
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119
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Aslam U, Cheema HMN, Ahmad S, Khan IA, Malik W, Khan AA. COTIP: Cotton TILLING Platform, a Resource for Plant Improvement and Reverse Genetic Studies. FRONTIERS IN PLANT SCIENCE 2016; 7:1863. [PMID: 28082993 PMCID: PMC5183611 DOI: 10.3389/fpls.2016.01863] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/25/2016] [Indexed: 05/26/2023]
Abstract
Cotton is cultivated worldwide for its white fiber, of which around 90% is tetraploid upland cotton (Gossypium hirsutum L.) carrying both A and D genome. Since centuries, yield increasing efforts for the cotton crop by conventional breeding approaches have caused an extensive erosion of natural genetic variability. Mutation based improvement strategies provide an effective way of creating new allelic variations. Targeting Induced Local Lesions IN Genomes (TILLING) provides a mutation based reverse genetic strategy to create and evaluate induced genetic variability at DNA level. Here, we report development and testing of TILLING populations of allotetraploid cotton (G. hirsutum) for functional genomic studies and mutation based enrichment of cotton genetic resources. Seed of two cotton cultivars "PB-899 and PB-900" were mutagenized with 0.3 and 0.2% (v/v) ethyl methanesulfonate, respectively. The phenotyping of M1 and M2 populations presented numerous mutants regarding the branching pattern, leaf morphology, disease resistance, photosynthetic lesions and flower sterility. Molecular screening for point mutations was performed by TILLING PCR aided CEL1 mismatch cleavage. To estimate the mutation frequency in the mutant genomes, five gene classes were TILLed in 8000 M2 plants of each var. "PB-899" and "PB-900." These include actin (GhACT), Pectin Methyl Esterase (GhPME), sucrose synthase (GhSUS), resistance gene analog, and defense response gene (DRGs). The var. PB-899 was harboring 47% higher mutation induction rate than PB-900. The highest rate of mutation frequency was identified for NAC-TF5 (EU706348) of DRGs class, ranging from 1/58 kb in PB-899 to 1/105 kb in PB-900. The mutation screening assay revealed the presence of significant proportion of induced mutations in cotton TILLING populations such as 1/153 kb and 1/326 kb in var. "PB-899" and "PB-900," respectively. The establishment of a cotton TILLING platform (COTIP) and data obtained from the resource TILLING population suggest its effectiveness in widening the genetic bases of cotton for improvement and utilizing it for subsequent reverse genetic studies of various genes.
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Affiliation(s)
- Usman Aslam
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
| | - Hafiza M. N. Cheema
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
| | - Sheraz Ahmad
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
| | - Iqrar A. Khan
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
| | - Waqas Malik
- Genomics Lab, Department of Plant Breeding and Genetics, Bahauddin Zakariya UniversityMultan, Pakistan
| | - Asif A. Khan
- Plant Genetic Resources Lab, Department of Plant Breeding and Genetics, University of AgricultureFaisalabad, Pakistan
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Artemisia annua mutant impaired in artemisinin synthesis demonstrates importance of nonenzymatic conversion in terpenoid metabolism. Proc Natl Acad Sci U S A 2016; 113:15150-15155. [PMID: 27930305 DOI: 10.1073/pnas.1611567113] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Artemisinin, a sesquiterpene lactone produced by Artemisia annua glandular secretory trichomes, is the active ingredient in the most effective treatment for malaria currently available. We identified a mutation that disrupts the amorpha-4,11-diene C-12 oxidase (CYP71AV1) enzyme, responsible for a series of oxidation reactions in the artemisinin biosynthetic pathway. Detailed metabolic studies of cyp71av1-1 revealed that the consequence of blocking the artemisinin biosynthetic pathway is the redirection of sesquiterpene metabolism to a sesquiterpene epoxide, which we designate arteannuin X. This sesquiterpene approaches half the concentration observed for artemisinin in wild-type plants, demonstrating high-flux plasticity in A. annua glandular trichomes and their potential as factories for the production of novel alternate sesquiterpenes at commercially viable levels. Detailed metabolite profiling of leaf maturation time-series and precursor-feeding experiments revealed that nonenzymatic conversion steps are central to both artemisinin and arteannuin X biosynthesis. In particular, feeding studies using 13C-labeled dihydroartemisinic acid (DHAA) provided strong evidence that the final steps in the synthesis of artemisinin are nonenzymatic in vivo. Our findings also suggest that the specialized subapical cavity of glandular secretory trichomes functions as a location for both the chemical conversion and the storage of phytotoxic compounds, including artemisinin. We conclude that metabolic engineering to produce high yields of novel secondary compounds such as sesquiterpenes is feasible in complex glandular trichomes. Such systems offer advantages over single-cell microbial hosts for production of toxic natural products.
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121
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Saini N, Singh N, Kumar A, Vihan N, Yadav S, Vasudev S, Yadava D. Development and validation of functional CAPS markers for the FAE genes in Brassica juncea and their use in marker-assisted selection. BREEDING SCIENCE 2016; 66:831-837. [PMID: 28163599 PMCID: PMC5282766 DOI: 10.1270/jsbbs.16132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/14/2016] [Indexed: 05/25/2023]
Abstract
Low erucic acid is a major breeding target to improve the edible oil quality in Brassica juncea. The single nucleotide polymorphism (SNP) in fatty acid elongase 1 (FAE1.1 and FAE1.2) gene was exploited to expedite the breeding program. The paralogs of FAE1 gene were sequenced from low erucic acid genotype Pusa Mustard 30 and SNPs were identified through homologous alignment with sequence downloaded from NCBI GenBank. Two SNPs in FAE1.1 at position 591 and 1265 and one in FAE1.2 at 237 were found polymorphic among low and high erucic acid genotypes. These SNPs either create or change the recognition site of restriction enzymes. Transition of a single nucleotide at position 591 and 1265 in FAE1.1, and at position 237 in FAE1.2, leads to a change in the recognition site of Hpy99I, BglII and MnlI restriction enzymes, respectively. Two CAPS markers for FAE1.1 and one for FAE1.2 were developed to differentiate low and high erucic acid genotypes. The efficiency of these CAPS markers was found 100 per cent when validated in Brassica juncea, and B. nigra genotypes and used in back-cross breeding. These CAPS markers will facilitate in marker-assisted selection for improvement of oil quality in Brassica juncea.
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Affiliation(s)
- Navinder Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - Naveen Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - Anil Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - Nitika Vihan
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - Sangita Yadav
- Division of Seed Science and Technology, ICAR-IARI,
New Delhi,
India
| | - Sujata Vasudev
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - D.K. Yadava
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
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122
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Yan R, Liang C, Meng Z, Malik W, Zhu T, Zong X, Guo S, Zhang R. Progress in genome sequencing will accelerate molecular breeding in cotton (Gossypium spp.). 3 Biotech 2016; 6:217. [PMID: 28330289 PMCID: PMC5055485 DOI: 10.1007/s13205-016-0534-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 09/26/2016] [Indexed: 12/22/2022] Open
Abstract
Cotton (Gossypium spp.) is the single most important spinning fiber that has economic significance worldwide. Cotton is one of the most value-added crops and an excellent model system for the analysis of polyploidization and cell development. Thus, the Cotton Genome Consortium has made rapid and significant progress in whole genome sequencing studies in the last decade. Developments in cotton genome sequencing and assembly provide powerful tools for dissecting the genetic and molecular bases of agronomically important traits and establishing regulatory networks on these processes, which leads to molecular breeding. Here, we briefly review these advances, emphasizing their implications in the genetic improvement of cotton with a particular focus on fiber quality and yield. Moreover, major progresses in chloroplast and mitochondrial genomes have also been summarized.
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Affiliation(s)
- Rong Yan
- College of Agronomy and Biotechnology, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400715, China
- Biotechnology Research Institute, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengzhen Liang
- Biotechnology Research Institute, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhigang Meng
- Biotechnology Research Institute, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Waqas Malik
- Biotechnology Research Institute, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Tao Zhu
- Biotechnology Research Institute, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuefeng Zong
- College of Agronomy and Biotechnology, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400715, China.
| | - Sandui Guo
- Biotechnology Research Institute, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Rui Zhang
- Biotechnology Research Institute, National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Ben-Amar A, Daldoul S, Reustle GM, Krczal G, Mliki A. Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics. Curr Genomics 2016; 17:460-475. [PMID: 28217003 PMCID: PMC5282599 DOI: 10.2174/1389202917666160520102827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/12/2015] [Accepted: 01/05/2016] [Indexed: 11/22/2022] Open
Abstract
In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies. Integration of different omics platforms along with gene annotation and computational analysis may elucidate a complete view in a system biology level. Extensive investigations on reverse genetics methodologies were deployed for assigning biological function to a specific gene or gene product. We provide here an updated overview of these high throughout strategies highlighting recent advances in the knowledge of functional genomics in plants.
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Affiliation(s)
- Anis Ben-Amar
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Samia Daldoul
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
| | - Götz M. Reustle
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Gabriele Krczal
- AgroScience.GmbH, AlPlanta-Institute for Plant Research, Neustadt an der Weinstraße, Germany
| | - Ahmed Mliki
- Department of Plant Molecular Physiology, Center of Biotechnology of Borj Cedria, Tunisia
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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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125
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Fondong VN, Nagalakshmi U, Dinesh-Kumar SP. Novel Functional Genomics Approaches: A Promising Future in the Combat Against Plant Viruses. PHYTOPATHOLOGY 2016; 106:1231-1239. [PMID: 27392181 DOI: 10.1094/phyto-03-16-0145-fi] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Advances in functional genomics and genome editing approaches have provided new opportunities and potential to accelerate plant virus control efforts through modification of host and viral genomes in a precise and predictable manner. Here, we discuss application of RNA-based technologies, including artificial micro RNA, transacting small interfering RNA, and Cas9 (clustered regularly interspaced short palindromic repeat-associated protein 9), which are currently being successfully deployed in generating virus-resistant plants. We further discuss the reverse genetics approach, targeting induced local lesions in genomes (TILLING) and its variant, known as EcoTILLING, that are used in the identification of plant virus recessive resistance gene alleles. In addition to describing specific applications of these technologies in plant virus control, this review discusses their advantages and limitations.
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Affiliation(s)
- Vincent N Fondong
- First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis
| | - Ugrappa Nagalakshmi
- First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis
| | - Savithramma P Dinesh-Kumar
- First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis
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126
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A Population of Deletion Mutants and an Integrated Mapping and Exome-seq Pipeline for Gene Discovery in Maize. G3-GENES GENOMES GENETICS 2016; 6:2385-95. [PMID: 27261000 PMCID: PMC4978893 DOI: 10.1534/g3.116.030528] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To better understand maize endosperm filling and maturation, we used γ-irradiation of the B73 maize reference line to generate mutants with opaque endosperm and reduced kernel fill phenotypes, and created a population of 1788 lines including 39 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes. For molecular characterization of the mutants, we developed a novel functional genomics platform that combined bulked segregant RNA and exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. To exemplify the utility of the mutants and provide proof-of-concept for the bioinformatics platform, we present detailed characterization of line 937, an opaque mutant harboring a 6203 bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 kb intragene deletion within the Sugary-1 gene and line 916 in which an 8.6 kb deletion knocks out a Cyclin A2 gene. The publically available algorithm developed in this work improves the identification of causative deletions and its corresponding gaps within mapping peaks. This study demonstrates the utility of γ-irradiation for forward genetics in large nondense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes applicable for functional genomics when combined with state-of-the-art genomics tools.
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127
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Campbell BW, Stupar RM. Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects. ACTA ACUST UNITED AC 2016; 1:307-327. [PMID: 30775866 DOI: 10.1002/cppb.20015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic bottlenecks during domestication and modern breeding limited the genetic diversity of soybean (Glycine max (L.) Merr.). Therefore, expanding and diversifying soybean genetic resources is a major priority for the research community. These resources, consisting of natural and induced genetic variants, are valuable tools for improving soybean and furthering soybean biological knowledge. During the twentieth century, researchers gathered a wealth of genetic variation in the forms of landraces, Glycine soja accessions, Glycine tertiary germplasm, and the U.S. Department of Agriculture (USDA) Type and Isoline Collections. During the twenty-first century, soybean researchers have added several new genetic and genomic resources. These include the reference genome sequence, genotype data for the USDA soybean germplasm collection, next-generation mapping populations, new irradiation and transposon-based mutagenesis populations, and designer nuclease platforms for genome engineering. This paper briefly surveys the publicly accessible soybean genetic resources currently available or in development and provides recommendations for developing such genetic resources in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
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128
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Singh AK, Singh R, Subramani R, Kumar R, Wankhede DP. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals. Curr Genomics 2016; 17:177-92. [PMID: 27252585 PMCID: PMC4869005 DOI: 10.2174/1389202917666160202215308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/01/2023] Open
Abstract
Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer's preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains.
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Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajkumar Subramani
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajesh Kumar
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
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129
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Simmonds J, Scott P, Brinton J, Mestre TC, Bush M, del Blanco A, Dubcovsky J, Uauy C. A splice acceptor site mutation in TaGW2-A1 increases thousand grain weight in tetraploid and hexaploid wheat through wider and longer grains. THEORETICAL AND APPLIED GENETICS 2016; 129:1099-112. [PMID: 26883045 PMCID: PMC4869752 DOI: 10.1007/s00122-016-2686-2] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/23/2016] [Indexed: 05/18/2023]
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130
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Landau A, Lencina F, Pacheco MG, Prina AR. Plastome Mutations and Recombination Events in Barley Chloroplast Mutator Seedlings. J Hered 2016; 107:266-73. [PMID: 26774059 PMCID: PMC4885237 DOI: 10.1093/jhered/esw003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/04/2016] [Indexed: 11/12/2022] Open
Abstract
The barley chloroplast mutator (cpm) is an allele of a nuclear gene that when homozygous induces several types of cytoplasmically inherited chlorophyll deficiencies. In this work, a plastome Targeting Induced Local Lesions in Genomes (TILLING) strategy based on mismatch digestion was used on families that carried the cpm genotype through many generations. Extensive scanning of 33 plastome genes and a few intergenic regions was conducted. Numerous polymorphisms were detected on both genic and intergenic regions. The detected polymorphisms can be accounted for by at least 61 independent mutational events. The vast majority of the polymorphisms originated in substitutions and small indels (insertions/deletions) in microsatellites. The rpl23 and the rps16 genes were the most polymorphic. Interestingly, the variation observed in the rpl23 gene consisted of several combinations of 5 different one nucleotide polymorphisms. Besides, 4 large indels that have direct repeats at both ends were also observed, which appear to be originated from recombinational events. The cpm mutation spectrum suggests that the CPM gene product is probably involved in plastome mismatch repair. The numerous subtle molecular changes that were localized in a wide range of plastome sites show the cpm as a valuable source of plastome variability for plant research and/or plant breeding. Moreover, the cpm mutant appears to be an interesting experimental material for investigating the mechanisms responsible for maintaining the stability of plant organelle DNA.
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Affiliation(s)
- Alejandra Landau
- From the Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros s/n (1686) Hurlingham, Buenos Aires, Argentina (Landau, Lencina, Pacheco, and Prina)
| | - Franco Lencina
- From the Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros s/n (1686) Hurlingham, Buenos Aires, Argentina (Landau, Lencina, Pacheco, and Prina)
| | - María G Pacheco
- From the Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros s/n (1686) Hurlingham, Buenos Aires, Argentina (Landau, Lencina, Pacheco, and Prina)
| | - Alberto R Prina
- From the Instituto de Genética "Ewald A. Favret", CICVyA (Centro de Investigación en Ciencias Veterinarias y Agronómicas), Instituto Nacional de Tecnología Agropecuaria, Nicolás Repetto y de los Reseros s/n (1686) Hurlingham, Buenos Aires, Argentina (Landau, Lencina, Pacheco, and Prina).
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131
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Nida H, Blum S, Zielinski D, Srivastava DA, Elbaum R, Xin Z, Erlich Y, Fridman E, Shental N. Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:349-359. [PMID: 26959378 DOI: 10.1111/tpj.13161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/10/2016] [Accepted: 03/01/2016] [Indexed: 05/29/2023]
Abstract
Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next-generation sequencing to allow such large-scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large-scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost-effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis.
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Affiliation(s)
- Habte Nida
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shula Blum
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dina Zielinski
- New York Genome Center, 101 Avenue of the Americas, New York, NY, USA
| | - Dhruv A Srivastava
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Rivka Elbaum
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, US Department of Agriculture/Agricultural Research Service, Lubbock, TX, USA
| | - Yaniv Erlich
- New York Genome Center, 101 Avenue of the Americas, New York, NY, USA
- Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY, USA
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Eyal Fridman
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
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132
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Gruszka D, Gorniak M, Glodowska E, Wierus E, Oklestkova J, Janeczko A, Maluszynski M, Szarejko I. A Reverse-Genetics Mutational Analysis of the Barley HvDWARF Gene Results in Identification of a Series of Alleles and Mutants with Short Stature of Various Degree and Disturbance in BR Biosynthesis Allowing a New Insight into the Process. Int J Mol Sci 2016; 17:ijms17040600. [PMID: 27110778 PMCID: PMC4849053 DOI: 10.3390/ijms17040600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/15/2016] [Accepted: 04/18/2016] [Indexed: 11/16/2022] Open
Abstract
Brassinosteroids (BRs) are plant steroid hormones, regulating a broad range of physiological processes. The largest amount of data related with BR biosynthesis has been gathered in Arabidopsis thaliana, however understanding of this process is far less elucidated in monocot crops. Up to now, only four barley genes implicated in BR biosynthesis have been identified. Two of them, HvDWARF and HvBRD, encode BR-6-oxidases catalyzing biosynthesis of castasterone, but their relation is not yet understood. In the present study, the identification of the HvDWARF genomic sequence, its mutational and functional analysis and characterization of new mutants are reported. Various types of mutations located in different positions within functional domains were identified and characterized. Analysis of their impact on phenotype of the mutants was performed. The identified homozygous mutants show reduced height of various degree and disrupted skotomorphogenesis. Mutational analysis of the HvDWARF gene with the “reverse genetics” approach allowed for its detailed functional analysis at the level of protein functional domains. The HvDWARF gene function and mutants’ phenotypes were also validated by measurement of endogenous BR concentration. These results allowed a new insight into the BR biosynthesis in barley.
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Affiliation(s)
- Damian Gruszka
- Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Malgorzata Gorniak
- Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Ewelina Glodowska
- Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Ewa Wierus
- Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Jana Oklestkova
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic.
| | - Anna Janeczko
- Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Krakow, Poland.
| | - Miroslaw Maluszynski
- Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland.
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133
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Gauffier C, Lebaron C, Moretti A, Constant C, Moquet F, Bonnet G, Caranta C, Gallois JL. A TILLING approach to generate broad-spectrum resistance to potyviruses in tomato is hampered by eIF4E gene redundancy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:717-29. [PMID: 26850324 DOI: 10.1111/tpj.13136] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/22/2016] [Accepted: 02/01/2016] [Indexed: 05/23/2023]
Abstract
Genetic resistance to pathogens is important for sustainable maintenance of crop yields. Recent biotechnologies offer alternative approaches to generate resistant plants by compensating for the lack of natural resistance. Tomato (Solanum lycopersicum) and related species offer a model in which natural and TILLING-induced potyvirus resistance alleles may be compared. For resistance based on translation initiation factor eIF4E1, we confirm that the natural allele Sh-eIF4E1(PI24)-pot1, isolated from the wild tomato species Solanum habrochaites, is associated with a wide spectrum of resistance to both potato virus Y and tobacco etch virus isolates. In contrast, a null allele of the same gene, isolated through a TILLING strategy in cultivated tomato S. lycopersicum, is associated with a much narrower resistance spectrum. Introgressing the null allele into S. habrochaites did not extend its resistance spectrum, indicating that the genetic background is not responsible for the broad resistance. Instead, the different types of eIF4E1 mutations affect the levels of eIF4E2 differently, suggesting that eIF4E2 is also involved in potyvirus resistance. Indeed, combining two null mutations affecting eIF4E1 and eIF4E2 re-establishes a wide resistance spectrum in cultivated tomato, but to the detriment of plant development. These results highlight redundancy effects within the eIF4E gene family, where regulation of expression alters susceptibility or resistance to potyviruses. For crop improvement, using loss-of-function alleles to generate resistance may be counter-productive if they narrow the resistance spectrum and limit growth. It may be more effective to use alleles encoding functional variants similar to those found in natural diversity.
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Affiliation(s)
- Camille Gauffier
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
| | - Caroline Lebaron
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
| | - André Moretti
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
| | - Carole Constant
- Sakata Vegetables Europe, Domaine de Sablas Rue du Moulin, F-30620, Uchaud, France
| | - Frédéric Moquet
- Gautier Semences, Route d'Avignon, F-13630, Eyragues, France
| | - Grégori Bonnet
- Syngenta, 346 Route des Pasquiers, F-84260, Sarrians, France
| | - Carole Caranta
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
| | - Jean-Luc Gallois
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
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134
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Manzanares C, Yates S, Ruckle M, Nay M, Studer B. TILLING in forage grasses for gene discovery and breeding improvement. N Biotechnol 2016; 33:594-603. [PMID: 26924175 DOI: 10.1016/j.nbt.2016.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/09/2016] [Accepted: 02/12/2016] [Indexed: 01/04/2023]
Abstract
Mutation breeding has a long-standing history and in some major crop species, many of the most important cultivars have their origin in germplasm generated by mutation induction. For almost two decades, methods for TILLING (Targeting Induced Local Lesions IN Genomes) have been established in model plant species such as Arabidopsis (Arabidopsis thaliana L.), enabling the functional analysis of genes. Recent advances in mutation detection by second generation sequencing technology have brought its utility to major crop species. However, it has remained difficult to apply similar approaches in forage and turf grasses, mainly due to their outbreeding nature maintained by an efficient self-incompatibility system. Starting with a description of the extent to which traditional mutagenesis methods have contributed to crop yield increase in the past, this review focuses on technological approaches to implement TILLING-based strategies for the improvement of forage grass breeding through forward and reverse genetics. We present first results from TILLING in allogamous forage grasses for traits such as stress tolerance and evaluate prospects for rapid implementation of beneficial alleles to forage grass breeding. In conclusion, large-scale induced mutation resources, used for forward genetic screens, constitute a valuable tool to increase the genetic diversity for breeding and can be generated with relatively small investments in forage grasses. Furthermore, large libraries of sequenced mutations can be readily established, providing enhanced opportunities to discover mutations in genes controlling traits of agricultural importance and to study gene functions by reverse genetics.
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Affiliation(s)
- Chloe Manzanares
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Steven Yates
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Michael Ruckle
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Michelle Nay
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland.
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135
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Colasuonno P, Incerti O, Lozito ML, Simeone R, Gadaleta A, Blanco A. DHPLC technology for high-throughput detection of mutations in a durum wheat TILLING population. BMC Genet 2016; 17:43. [PMID: 26884094 PMCID: PMC4756519 DOI: 10.1186/s12863-016-0350-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 02/08/2016] [Indexed: 11/17/2022] Open
Abstract
Background Durum wheat (Triticum turgidum L.) is a cereal crop widely grown in the Mediterranean regions; the amber grain is mainly used for the production of pasta, couscous and typical breads. Single nucleotide polymorphism (SNP) detection technologies and high-throughput mutation induction represent a new challenge in wheat breeding to identify allelic variation in large populations. The TILLING strategy makes use of traditional chemical mutagenesis followed by screening for single base mismatches to identify novel mutant loci. Although TILLING has been combined to several sensitive pre-screening methods for SNP analysis, most rely on expensive equipment. Recently, a new low cost and time saving DHPLC protocol has been used in molecular human diagnostic to detect unknown mutations. Results In this work, we developed a new durum wheat TILLING population (cv. Marco Aurelio) using 0.70-0.85 % ethyl methane sulfonate (EMS). To investigate the efficiency of the mutagenic treatments, a pilot screening was carried out on 1,140 mutant lines focusing on two target genes (Lycopene epsilon-cyclase, ε-LCY, and Lycopene beta-cyclase, β-LCY) involved in carotenoid metabolism in wheat grains. We simplify the heteroduplex detection by two low cost methods: the enzymatic cleavage (CelI)/agarose gel technique and the denaturing high-performance liquid chromatography (DHPLC). The CelI/agarose gel approach allowed us to identify 31 mutations, whereas the DHPLC procedure detected a total of 46 mutations for both genes. All detected mutations were confirmed by direct sequencing. The estimated overall mutation frequency for the pilot assay by the DHPLC methodology resulted to be of 1/77 kb, representing a high probability to detect interesting mutations in the target genes. Conclusion We demonstrated the applicability and efficiency of a new strategy for the detection of induced variability. We produced and characterized a new durum wheat TILLING population useful for a better understanding of key gene functions. The availability of this tool together with TILLING technique will expand the polymorphisms in candidate genes of agronomically important traits in wheat. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0350-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pasqualina Colasuonno
- Department of Soil, Plant and Food Sciences, section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126, Bari, Italy.
| | - Ornella Incerti
- Department of Soil, Plant and Food Sciences, section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126, Bari, Italy.
| | - Maria Luisa Lozito
- Department of Soil, Plant and Food Sciences, section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126, Bari, Italy.
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences, section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126, Bari, Italy.
| | - Agata Gadaleta
- Department of Soil, Plant and Food Sciences, section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126, Bari, Italy.
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, section of Genetic and Plant Breeding, University of Bari "Aldo Moro", Via G. Amendola 165/A, 70126, Bari, Italy.
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Okabe Y, Ariizumi T. Mutant Resources and TILLING Platforms in Tomato Research. BIOTECHNOLOGY IN AGRICULTURE AND FORESTRY 2016. [DOI: 10.1007/978-3-662-48535-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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137
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Lu Y, Dai S, Gu A, Liu M, Wang Y, Luo S, Zhao Y, Wang S, Xuan S, Chen X, Li X, Bonnema G, Zhao J, Shen S. Microspore Induced Doubled Haploids Production from Ethyl Methanesulfonate (EMS) Soaked Flower Buds Is an Efficient Strategy for Mutagenesis in Chinese Cabbage. FRONTIERS IN PLANT SCIENCE 2016; 7:1780. [PMID: 28018368 PMCID: PMC5147456 DOI: 10.3389/fpls.2016.01780] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/11/2016] [Indexed: 05/03/2023]
Abstract
Chinese cabbage buds were soaked with Ethyl methanesulfonate (EMS) to induce mutagenesis. The influence of different EMS concentrations and treatment durations on microspore development, embryo production rate and seedling rate were evaluated in five Chinese cabbage genotypes. Mutations in four color-related genes were identified using high resolution melting (HRM) curves of their PCR products. The greatest embryo production and seedling rates were observed when buds were treated with 0.03 to 0.1% EMS for 5 to 10 min, while EMS concentrations greater than 0.1% were lethal to the microspores. In total, 142 mutants with distinct variations in leaf shape, leaf color, corolla size, flower color, bolting time and downy mildew resistance were identified from 475 microspore culture derived Doubled Haploids. Our results demonstrate that microspore derived Doubled Haploids from EMS soaked buds represents an efficient approach to rapidly generate homozygous Chinese cabbage mutants.
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Affiliation(s)
- Yin Lu
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Shuangyan Dai
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Aixia Gu
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Mengyang Liu
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Yanhua Wang
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Shuangxia Luo
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Yujing Zhao
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Shan Wang
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Shuxin Xuan
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Xueping Chen
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Xiaofeng Li
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
| | - Guusje Bonnema
- Plant Breeding, Wageningen University & ResearchWageningen, Netherlands.
| | - Jianjun Zhao
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
- *Correspondence: Jianjun Zhao, Shuxing Shen,
| | - Shuxing Shen
- Key Laboratory of Vegetable Germplasm and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Agricultural University of HebeiBaoding, China
- *Correspondence: Jianjun Zhao, Shuxing Shen,
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Abstract
Coeliac disease is an intolerance triggered by the ingestion of wheat gluten proteins. It is of increasing concern to consumers and health professionals as its incidence appears to be increasing. The amino acid sequences in gluten proteins that are responsible for triggering responses in sensitive individuals have been identified showing that they vary in distribution among and between different groups of gluten proteins. Conventional breeding may therefore be used to select for gluten protein fractions with lower contents of coeliac epitopes. Molecular breeding approaches can also be used to specifically down-regulate coeliac-toxic proteins or mutate coeliac epitopes within individual proteins. A combination of these approaches may therefore be used to develop a “coeliac-safe” wheat. However, this remains a formidable challenge due to the complex multigenic control of gluten protein composition. Furthermore, any modified wheats must retain acceptable properties for making bread and other processed foods. Not surprisingly, such coeliac-safe wheats have not yet been developed despite over a decade of research. Coeliac disease is of increasing concern as its incidence appears to be increasing. Over 30 amino acid sequences (coeliac epitopes) have been defined. Coeliac epitopes differ in their distribution between wheat gluten proteins. Transgenesis can be used to reduce coeliac-toxic proteins and coeliac epitopes. This can be exploited to develop “coeliac-safe” wheats.
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Affiliation(s)
- Peter R Shewry
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK; University of Reading, Whiteknights, Reading, Berkshire RG6 6AH, UK
| | - Arthur S Tatham
- Cardiff School of Heath Sciences, Cardiff Metropolitan University, Llandaff Campus, Western Avenue, Cardiff CF5 2YB, UK
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139
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Parant JM, Yeh JRJ. Approaches to Inactivate Genes in Zebrafish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:61-86. [PMID: 27165349 DOI: 10.1007/978-3-319-30654-4_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Animal models of tumor initiation and tumor progression are essential components toward understanding cancer and designing/validating future therapies. Zebrafish is a powerful model for studying tumorigenesis and has been successfully exploited in drug discovery. According to the zebrafish reference genome, 82 % of disease-associated genes in the Online Mendelian Inheritance in Man (OMIM) database have clear zebrafish orthologues. Using a variety of large-scale random mutagenesis methods developed to date, zebrafish can provide a unique opportunity to identify gene mutations that may be associated with cancer predisposition. On the other hand, newer technologies enabling targeted mutagenesis can facilitate reverse cancer genetic studies and open the door for complex genetic analysis of tumorigenesis. In this chapter, we will describe the various technologies for conducting genome editing in zebrafish with special emphasis on the approaches to inactivate genes.
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Affiliation(s)
- John M Parant
- Department of Pharmacology and Toxicology, UAB Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35294, USA.
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, 02129, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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140
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Chen F, Zhu Z, Zhou X, Yan Y, Dong Z, Cui D. High-Throughput Sequencing Reveals Single Nucleotide Variants in Longer-Kernel Bread Wheat. FRONTIERS IN PLANT SCIENCE 2016; 7:1193. [PMID: 27551288 PMCID: PMC4976665 DOI: 10.3389/fpls.2016.01193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/25/2016] [Indexed: 05/09/2023]
Abstract
The transcriptomes of bread wheat Yunong 201 and its ethyl methanesulfonate derivative Yunong 3114 were obtained by next-sequencing technology. Single nucleotide variants (SNVs) in the wheat strains were explored and compared. A total of 5907 and 6287 non-synonymous SNVs were acquired for Yunong 201 and 3114, respectively. A total of 4021 genes with SNVs were obtained. The genes that underwent non-synonymous SNVs were significantly involved in ATP binding, protein phosphorylation, and cellular protein metabolic process. The heat map analysis also indicated that most of these mutant genes were significantly differentially expressed at different developmental stages. The SNVs in these genes possibly contribute to the longer kernel length of Yunong 3114. Our data provide useful information on wheat transcriptome for future studies on wheat functional genomics. This study could also help in illustrating the gene functions of the non-synonymous SNVs of Yunong 201 and 3114.
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141
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Iovieno P, Andolfo G, Schiavulli A, Catalano D, Ricciardi L, Frusciante L, Ercolano MR, Pavan S. Structure, evolution and functional inference on the Mildew Locus O (MLO) gene family in three cultivated Cucurbitaceae spp. BMC Genomics 2015; 16:1112. [PMID: 26715041 PMCID: PMC4696115 DOI: 10.1186/s12864-015-2325-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 12/15/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The powdery mildew disease affects thousands of plant species and arguably represents the major fungal threat for many Cucurbitaceae crops, including melon (Cucumis melo L.), watermelon (Citrullus lanatus L.) and zucchini (Cucurbita pepo L.). Several studies revealed that specific members of the Mildew Locus O (MLO) gene family act as powdery mildew susceptibility factors. Indeed, their inactivation, as the result of gene knock-out or knock-down, is associated with a peculiar form of resistance, referred to as mlo resistance. RESULTS We exploited recently available genomic information to provide a comprehensive overview of the MLO gene family in Cucurbitaceae. We report the identification of 16 MLO homologs in C. melo, 14 in C. lanatus and 18 in C. pepo genomes. Bioinformatic treatment of data allowed phylogenetic inference and the prediction of several ortholog pairs and groups. Comparison with functionally characterized MLO genes and, in C. lanatus, gene expression analysis, resulted in the detection of candidate powdery mildew susceptibility factors. We identified a series of conserved amino acid residues and motifs that are likely to play a major role for the function of MLO proteins. Finally, we performed a codon-based evolutionary analysis indicating a general high level of purifying selection in the three Cucurbitaceae MLO gene families, and the occurrence of regions under diversifying selection in candidate susceptibility factors. CONCLUSIONS Results of this study may help to address further biological questions concerning the evolution and function of MLO genes. Moreover, data reported here could be conveniently used by breeding research, aiming to select powdery mildew resistant cultivars in Cucurbitaceae.
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Affiliation(s)
- Paolo Iovieno
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Giuseppe Andolfo
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Adalgisa Schiavulli
- Institute of Biosciences and Bioresources, Italian National Council of Research, Via Amendola 165/A, 70126, Bari, Italy.
| | - Domenico Catalano
- Institute of Biosciences and Bioresources, Italian National Council of Research, Via Amendola 165/A, 70126, Bari, Italy.
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
| | - Luigi Frusciante
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Maria Raffaella Ercolano
- Department of Agriculture Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Via Amendola 165/A, 70126, Bari, Italy.
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Tsuda M, Kaga A, Anai T, Shimizu T, Sayama T, Takagi K, Machita K, Watanabe S, Nishimura M, Yamada N, Mori S, Sasaki H, Kanamori H, Katayose Y, Ishimoto M. Construction of a high-density mutant library in soybean and development of a mutant retrieval method using amplicon sequencing. BMC Genomics 2015; 16:1014. [PMID: 26610706 PMCID: PMC4662035 DOI: 10.1186/s12864-015-2079-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 10/13/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Functions of most genes predicted in the soybean genome have not been clarified. A mutant library with a high mutation density would be helpful for functional studies and for identification of novel alleles useful for breeding. Development of cost-effective and high-throughput protocols using next generation sequencing (NGS) technologies is expected to simplify the retrieval of mutants with mutations in genes of interest. RESULTS To increase the mutation density, seeds of the Japanese elite soybean cultivar Enrei were treated with the chemical mutagen ethyl methanesulfonate (EMS); M2 seeds produced by M1 plants were treated with EMS once again. The resultant library, which consisted of DNA and seeds from 1536 plants, revealed large morphological and physiological variations. Based on whole-genome re-sequencing analysis of 12 mutant lines, the average number of base changes was 12,796 per line. On average, 691 and 35 per line were missense and nonsense mutations, respectively. Two screening strategies for high resolution melting (HRM) analysis and indexed amplicon sequencing were designed to retrieve the mutants; the mutations were confirmed by Sanger sequencing as the final step. In comparison with HRM screening of several genes, indexed amplicon sequencing allows one to scan a longer sequence range and skip screening steps and to know the sequence information of mutation because it uses systematic DNA pooling and the index of NGS reads, which simplifies the discovery of mutants with amino acid substitutions. CONCLUSIONS A soybean mutant library with a high mutation density was developed. A high mutation density (1 mutation/74 kb) was achieved by repeating the EMS treatment. The mutation density of our library is sufficiently high to obtain a plant in which a gene is nonsense mutated. Thus, our mutant library and the indexed amplicon sequencing will be useful for functional studies of soybean genes and have a potential to yield useful mutant alleles for soybean breeding.
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Affiliation(s)
- Mai Tsuda
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Present address: Gene Research Center, Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Ten-nodai, Tsukuba, Ibaraki, 305-8574, Japan.
| | - Akito Kaga
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, 840-8502, Japan.
| | - Takehiko Shimizu
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Takashi Sayama
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Kyoko Takagi
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Present Address: Soil Science and Plant Nutrition Division, National Agriculture and Food Research Organization Agricultural Research Center, 3-1-1, Kannondai, Tsukuba, Ibaraki, 305-8666, Japan.
| | - Kayo Machita
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Satoshi Watanabe
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, 840-8502, Japan.
| | - Minoru Nishimura
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
- Present Address: Faculty of Agriculture, Niigata University, 8050, Ikarashi 2-no-cho, Nishi-ku, Niigata, 950-2181, Japan.
| | - Naohiro Yamada
- Nagano Vegetable and Ornamental Crops Experiment Station, 1066-1, Soga, Shiojiri, Nagano, 399-6461, Japan.
| | - Satomi Mori
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Harumi Sasaki
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Hiroyuki Kanamori
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Yuichi Katayose
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Masao Ishimoto
- Agronomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
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143
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Definition und Design hypoallergener Nahrungsmittel. ALLERGO JOURNAL 2015. [DOI: 10.1007/s15007-015-0942-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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144
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Appiano M, Catalano D, Santillán Martínez M, Lotti C, Zheng Z, Visser RGF, Ricciardi L, Bai Y, Pavan S. Monocot and dicot MLO powdery mildew susceptibility factors are functionally conserved in spite of the evolution of class-specific molecular features. BMC PLANT BIOLOGY 2015; 15:257. [PMID: 26499889 PMCID: PMC4620714 DOI: 10.1186/s12870-015-0639-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/07/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Specific members of the plant Mildew Locus O (MLO) protein family act as susceptibility factors towards powdery mildew (PM), a worldwide-spread fungal disease threatening many cultivated species. Previous studies indicated that monocot and dicot MLO susceptibility proteins are phylogenetically divergent. METHODS A bioinformatic approach was followed to study the type of evolution of Angiosperm MLO susceptibility proteins. Transgenic complementation tests were performed for functional analysis. RESULTS Our results show that monocot and dicot MLO susceptibility proteins evolved class-specific conservation patterns. Many of them appear to be the result of negative selection and thus are likely to provide an adaptive value. We also tested whether different molecular features between monocot and dicot MLO proteins are specifically required by PM fungal species to cause pathogenesis. To this aim, we transformed a tomato mutant impaired for the endogenous SlMLO1 gene, and therefore resistant to the tomato PM species Oidium neolycopersici, with heterologous MLO susceptibility genes from the monocot barley and the dicot pea. In both cases, we observed restoration of PM symptoms. Finally, through histological observations, we demonstrate that both monocot and dicot susceptibility alleles of the MLO genes predispose to penetration of a non-adapted PM fungal species in plant epidermal cells. CONCLUSIONS With this study, we provide insights on the evolution and function of MLO genes involved in the interaction with PM fungi. With respect to breeding research, we show that transgenic complementation assays involving phylogenetically distant plant species can be used for the characterization of novel MLO susceptibility genes. Moreover, we provide an overview of MLO protein molecular features predicted to play a major role in PM susceptibility. These represent ideal targets for future approaches of reverse genetics, addressed to the selection of loss-of-function resistant mutants in cultivated species.
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Affiliation(s)
- Michela Appiano
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Domenico Catalano
- Institute of Biosciences and Bioresources, Italian National Research Council, via Amendola 165/A, 70126, Bari, Italy
| | - Miguel Santillán Martínez
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Concetta Lotti
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Via Napoli 25, 71100, Foggia, Italy
| | - Zheng Zheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 Zhongguan Cun Nan Da Jie, 100081, Beijing, China
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Yuling Bai
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
| | - Stefano Pavan
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari, Via Amendola 165/A, 70126, Bari, Italy.
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145
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Appiano M, Catalano D, Santillán Martínez M, Lotti C, Zheng Z, Visser RGF, Ricciardi L, Bai Y, Pavan S. Monocot and dicot MLO powdery mildew susceptibility factors are functionally conserved in spite of the evolution of class-specific molecular features. BMC PLANT BIOLOGY 2015; 15:257. [PMID: 26499889 DOI: 10.1186/s12870-015-0639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/07/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND Specific members of the plant Mildew Locus O (MLO) protein family act as susceptibility factors towards powdery mildew (PM), a worldwide-spread fungal disease threatening many cultivated species. Previous studies indicated that monocot and dicot MLO susceptibility proteins are phylogenetically divergent. METHODS A bioinformatic approach was followed to study the type of evolution of Angiosperm MLO susceptibility proteins. Transgenic complementation tests were performed for functional analysis. RESULTS Our results show that monocot and dicot MLO susceptibility proteins evolved class-specific conservation patterns. Many of them appear to be the result of negative selection and thus are likely to provide an adaptive value. We also tested whether different molecular features between monocot and dicot MLO proteins are specifically required by PM fungal species to cause pathogenesis. To this aim, we transformed a tomato mutant impaired for the endogenous SlMLO1 gene, and therefore resistant to the tomato PM species Oidium neolycopersici, with heterologous MLO susceptibility genes from the monocot barley and the dicot pea. In both cases, we observed restoration of PM symptoms. Finally, through histological observations, we demonstrate that both monocot and dicot susceptibility alleles of the MLO genes predispose to penetration of a non-adapted PM fungal species in plant epidermal cells. CONCLUSIONS With this study, we provide insights on the evolution and function of MLO genes involved in the interaction with PM fungi. With respect to breeding research, we show that transgenic complementation assays involving phylogenetically distant plant species can be used for the characterization of novel MLO susceptibility genes. Moreover, we provide an overview of MLO protein molecular features predicted to play a major role in PM susceptibility. These represent ideal targets for future approaches of reverse genetics, addressed to the selection of loss-of-function resistant mutants in cultivated species.
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Affiliation(s)
- Michela Appiano
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Domenico Catalano
- Institute of Biosciences and Bioresources, Italian National Research Council, via Amendola 165/A, 70126, Bari, Italy
| | - Miguel Santillán Martínez
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Concetta Lotti
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Via Napoli 25, 71100, Foggia, Italy
| | - Zheng Zheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 Zhongguan Cun Nan Da Jie, 100081, Beijing, China
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Yuling Bai
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
| | - Stefano Pavan
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari, Via Amendola 165/A, 70126, Bari, Italy.
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Biazzi E, Carelli M, Tava A, Abbruscato P, Losini I, Avato P, Scotti C, Calderini O. CYP72A67 Catalyzes a Key Oxidative Step in Medicago truncatula Hemolytic Saponin Biosynthesis. MOLECULAR PLANT 2015; 8:1493-506. [PMID: 26079384 DOI: 10.1016/j.molp.2015.06.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/05/2015] [Accepted: 06/07/2015] [Indexed: 05/23/2023]
Abstract
In the Medicago genus, triterpenic saponins are bioactive secondary metabolites constitutively synthesized in the aerial and subterranean parts of plants via the isoprenoid pathway. Exploitation of saponins as pharmaceutics, agrochemicals and in the food and cosmetic industries has raised interest in identifying the enzymes involved in their synthesis. We have identified a cytochrome P450 (CYP72A67) involved in hemolytic sapogenin biosynthesis by a reverse genetic TILLING approach in a Medicago truncatula ethylmethanesulfonate (EMS) mutagenized collection. Genetic and biochemical analyses, mutant complementation, and expression of the gene in a microsome yeast system showed that CYP72A67 is responsible for hydroxylation at the C-2 position downstream of oleanolic acid synthesis. The affinity of CYP72A67 for substrates with different substitutions at multiple carbon positions was investigated in the same in vitro yeast system, and in relation to two other CYP450s (CYP72A68) responsible for the production of medicagenic acid, the main sapogenin in M. truncatula leaves and roots. Full sib mutant and wild-type plants were compared for their sapogenin profile, expression patterns of the genes involved in sapogenin synthesis, and response to inoculation with Sinorhizobium meliloti. The results obtained allowed us to revise the hemolytic sapogenin pathway in M. truncatula and contribute to highlighting the tissue specificities (leaves/roots) of sapogenin synthesis.
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Affiliation(s)
- Elisa Biazzi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA), Centro di Ricerche per le Produzioni Foraggere e Lattiero Casearie, 26900 Lodi, Italy
| | - Maria Carelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA), Centro di Ricerche per le Produzioni Foraggere e Lattiero Casearie, 26900 Lodi, Italy
| | - Aldo Tava
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA), Centro di Ricerche per le Produzioni Foraggere e Lattiero Casearie, 26900 Lodi, Italy
| | | | | | - Pinarosa Avato
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Carla Scotti
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA), Centro di Ricerche per le Produzioni Foraggere e Lattiero Casearie, 26900 Lodi, Italy.
| | - Ornella Calderini
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Bioscienze e Biorisorse, 06128 Perugia, Italy
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147
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Appiano M, Pavan S, Catalano D, Zheng Z, Bracuto V, Lotti C, Visser RGF, Ricciardi L, Bai Y. Identification of candidate MLO powdery mildew susceptibility genes in cultivated Solanaceae and functional characterization of tobacco NtMLO1. Transgenic Res 2015; 24:847-58. [PMID: 25947088 PMCID: PMC4569668 DOI: 10.1007/s11248-015-9878-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/10/2015] [Indexed: 01/03/2023]
Abstract
Specific homologs of the plant Mildew Locus O (MLO) gene family act as susceptibility factors towards the powdery mildew (PM) fungal disease, causing significant economic losses in agricultural settings. Thus, in order to obtain PM resistant phenotypes, a general breeding strategy has been proposed, based on the selective inactivation of MLO susceptibility genes across cultivated species. In this study, PCR-based methodologies were used in order to isolate MLO genes from cultivated solanaceous crops that are hosts for PM fungi, namely eggplant, potato and tobacco, which were named SmMLO1, StMLO1 and NtMLO1, respectively. Based on phylogenetic analysis and sequence alignment, these genes were predicted to be orthologs of tomato SlMLO1 and pepper CaMLO2, previously shown to be required for PM pathogenesis. Full-length sequence of the tobacco homolog NtMLO1 was used for a heterologous transgenic complementation assay, resulting in its characterization as a PM susceptibility gene. The same assay showed that a single nucleotide change in a mutated NtMLO1 allele leads to complete gene loss-of-function. Results here presented, also including a complete overview of the tobacco and potato MLO gene families, are valuable to study MLO gene evolution in Solanaceae and for molecular breeding approaches aimed at introducing PM resistance using strategies of reverse genetics.
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Affiliation(s)
- Michela Appiano
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Stefano Pavan
- Department of Plant, Soil and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Domenico Catalano
- Institute of Biosciences and Bioresources, Italian National Research Council, Via Amendola 165/A, 70126, Bari, Italy
| | - Zheng Zheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, No. 12 Zhongguan Cun Nan Da Jie, Beijing, 100081, China
| | - Valentina Bracuto
- Department of Plant, Soil and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Concetta Lotti
- Department of Agro-Environmental Science, Chemistry and Crop Protection, University of Foggia, Via Napoli 25, 71100, Foggia, Italy
| | - Richard G F Visser
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Luigi Ricciardi
- Department of Plant, Soil and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Yuling Bai
- Laboratory of Plant Breeding, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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148
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Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing. PLoS One 2015; 10:e0137549. [PMID: 26335335 PMCID: PMC4559439 DOI: 10.1371/journal.pone.0137549] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/18/2015] [Indexed: 12/31/2022] Open
Abstract
Targeted Induced Local Lesions in Genomes (TILLING) is a reverse genetics approach to identify novel sequence variation in genomes, with the aims of investigating gene function and/or developing useful alleles for breeding. Despite recent advances in wheat genomics, most current TILLING methods are low to medium in throughput, being based on PCR amplification of the target genes. We performed a pilot-scale evaluation of TILLING in wheat by next-generation sequencing through exon capture. An oligonucleotide-based enrichment array covering ~2 Mbp of wheat coding sequence was used to carry out exon capture and sequencing on three mutagenised lines of wheat containing previously-identified mutations in the TaGA20ox1 homoeologous genes. After testing different mapping algorithms and settings, candidate SNPs were identified by mapping to the IWGSC wheat Chromosome Survey Sequences. Where sequence data for all three homoeologues were found in the reference, mutant calls were unambiguous; however, where the reference lacked one or two of the homoeologues, captured reads from these genes were mis-mapped to other homoeologues, resulting either in dilution of the variant allele frequency or assignment of mutations to the wrong homoeologue. Competitive PCR assays were used to validate the putative SNPs and estimate cut-off levels for SNP filtering. At least 464 high-confidence SNPs were detected across the three mutagenized lines, including the three known alleles in TaGA20ox1, indicating a mutation rate of ~35 SNPs per Mb, similar to that estimated by PCR-based TILLING. This demonstrates the feasibility of using exon capture for genome re-sequencing as a method of mutation detection in polyploid wheat, but accurate mutation calling will require an improved genomic reference with more comprehensive coverage of homoeologues.
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149
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Tohge T, Fernie AR. Metabolomics-Inspired Insight into Developmental, Environmental and Genetic Aspects of Tomato Fruit Chemical Composition and Quality. PLANT & CELL PHYSIOLOGY 2015; 56:1681-96. [PMID: 26228272 DOI: 10.1093/pcp/pcv093] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 06/12/2015] [Indexed: 05/20/2023]
Abstract
Tomato was one of the first plant species to be evaluated using metabolomics and remains one of the best characterized, with tomato fruit being both an important source of nutrition in the human diet and a valuable model system for the development of fleshy fruits. Additionally, given the broad habitat range of members of the tomato clade and the extensive use of exotic germplasm in tomato genetic research, it represents an excellent genetic model system for understanding both metabolism per se and the importance of various metabolites in conferring stress tolerance. This review summarizes technical approaches used to characterize the tomato metabolome to date and details insights into metabolic pathway structure and regulation that have been obtained via analysis of tissue samples taken under different developmental or environmental circumstance as well as following genetic perturbation. Particular attention is paid to compounds of importance for nutrition or the shelf-life of tomatoes. We propose furthermore how metabolomics information can be coupled to the burgeoning wealth of genome sequence data from the tomato clade to enhance further our understanding of (i) the shifts in metabolic regulation occurring during development and (ii) specialization of metabolism within the tomato clade as a consequence of either adaptive evolution or domestication.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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150
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Olsen A, Lütken H, Hegelund JN, Müller R. Ethylene resistance in flowering ornamental plants - improvements and future perspectives. HORTICULTURE RESEARCH 2015; 2:15038. [PMID: 26504580 PMCID: PMC4591681 DOI: 10.1038/hortres.2015.38] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 05/20/2023]
Abstract
Various strategies of plant breeding have been attempted in order to improve the ethylene resistance of flowering ornamental plants. These approaches span from conventional techniques such as simple cross-pollination to new breeding techniques which modify the plants genetically such as precise genome-editing. The main strategies target the ethylene pathway directly; others focus on changing the ethylene pathway indirectly via pathways that are known to be antagonistic to the ethylene pathway, e.g. increasing cytokinin levels. Many of the known elements of the ethylene pathway have been addressed experimentally with the aim of modulating the overall response of the plant to ethylene. Elements of the ethylene pathway that appear particularly promising in this respect include ethylene receptors as ETR1, and transcription factors such as EIN3. Both direct and indirect approaches seem to be successful, nevertheless, although genetic transformation using recombinant DNA has the ability to save much time in the breeding process, they are not readily used by breeders yet. This is primarily due to legislative issues, economic issues, difficulties of implementing this technology in some ornamental plants, as well as how these techniques are publically perceived, particularly in Europe. Recently, newer and more precise genome-editing techniques have become available and they are already being implemented in some crops. New breeding techniques may help change the current situation and pave the way toward a legal and public acceptance if products of these technologies are indistinguishable from plants obtained by conventional techniques.
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Affiliation(s)
- Andreas Olsen
- Faculty of Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 9-13, 2630 Taastrup, Denmark
| | - Henrik Lütken
- Faculty of Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 9-13, 2630 Taastrup, Denmark
| | - Josefine Nymark Hegelund
- Faculty of Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 9-13, 2630 Taastrup, Denmark
| | - Renate Müller
- Faculty of Science, Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegård Alle 9-13, 2630 Taastrup, Denmark
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