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Cloning of an Albino Mutation of Arabidopsis thaliana Using Mapping-by-Sequencing. Int J Mol Sci 2023; 24:ijms24044196. [PMID: 36835605 PMCID: PMC9964061 DOI: 10.3390/ijms24044196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
We report the molecular characterization of an ethyl methanesulfonate (EMS)-induced mutation that causes albinism and lethality at the seedling stage in Arabidopsis thaliana. We identified the mutation using a mapping-by-sequencing approach that uses Fisher's exact tests to detect changes in allele frequencies among the seedlings of an F2 mapping population, which had been pooled according to their phenotypes (wild-type or mutant). After purifying genomic DNA from the plants of both pools, the two samples were sequenced using the Illumina HiSeq 2500 next-generation sequencing platform. The bioinformatic analysis allowed us to identify a point mutation that damages a conserved residue at the acceptor site of an intron of the At2g04030 gene, which encodes the chloroplast-localized AtHsp90.5 protein, a member of the HSP90 family of heat shock proteins. Our RNA-seq analysis demonstrates that the new allele alters the splicing of At2g04030 transcripts in multiple ways, leading to massive deregulation of genes encoding plastid-localized proteins. A search for protein-protein interactions using the yeast two-hybrid method allowed us to identify two members of the GrpE superfamily as potential interactors of AtHsp90.5, as has previously been reported for green algae.
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Lup SD, Navarro-Quiles C, Micol JL. Versatile mapping-by-sequencing with Easymap v.2. FRONTIERS IN PLANT SCIENCE 2023; 14:1042913. [PMID: 36778692 PMCID: PMC9909543 DOI: 10.3389/fpls.2023.1042913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Mapping-by-sequencing combines Next Generation Sequencing (NGS) with classical genetic mapping by linkage analysis to establish gene-to-phenotype relationships. Although numerous tools have been developed to analyze NGS datasets, only a few are available for mapping-by-sequencing. One such tool is Easymap, a versatile, easy-to-use package that performs automated mapping of point mutations and large DNA insertions. Here, we describe Easymap v.2, which also maps small insertion/deletions (InDels), and includes workflows to perform QTL-seq and variant density mapping analyses. Each mapping workflow can accommodate different experimental designs, including outcrossing and backcrossing, F2, M2, and M3 mapping populations, chemically induced mutation and natural variant mapping, input files containing single-end or paired-end reads of genomic or complementary DNA sequences, and alternative control sample files in FASTQ and VCF formats. Easymap v.2 can also be used as a variant analyzer in the absence of a mapping algorithm and includes a multi-threading option.
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3
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Rosignoli S, Cosenza F, Moscou MJ, Civolani L, Musiani F, Forestan C, Milner SG, Savojardo C, Tuberosa R, Salvi S. Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing. THE PLANT GENOME 2022; 15:e20187. [PMID: 35302294 DOI: 10.1002/tpg2.20187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Disease lesion mimic (DLM) or necrotic mutants display necrotic lesions in the absence of pathogen infections. They can show improved resistance to some pathogens and their molecular dissection can contribute to revealing components of plant defense pathways. Although forward-genetics strategies to find genes causal to mutant phenotypes are available in crops, these strategies require the production of experimental cross populations, mutagenesis, or gene editing and are time- and resource-consuming or may have to deal with regulated plant materials. In this study, we described a collection of 34 DLM mutants in barley (Hordeum vulgare L.) and applied a novel method called complementation by sequencing (CBS), which enables the identification of the gene responsible for a mutant phenotype given the availability of two or more chemically mutagenized individuals showing the same phenotype. Complementation by sequencing relies on the feasibility to obtain all induced mutations present in chemical mutants and on the low probability that different individuals share the same mutated genes. By CBS, we identified a cytochrome P450 CYP71P1 gene as responsible for orange blotch DLM mutants, including the historical barley nec3 locus. By comparative phylogenetic analysis we showed that CYP71P1 gene family emerged early in angiosperm evolution but has been recurrently lost in some lineages including Arabidopsis thaliana (L.) Heynh. Complementation by sequencing is a straightforward cost-effective approach to clone genes controlling phenotypes in a chemically mutagenized collection. The TILLMore (TM) collection will be instrumental for understanding the molecular basis of DLM phenotypes and to contribute knowledge about mechanisms of host-pathogen interaction.
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Affiliation(s)
- Serena Rosignoli
- Dep. of Agricultural and Food Sciences, Univ. of Bologna, Viale G. Fanin 44, Bologna, Italy, 40127
| | - Francesco Cosenza
- Dep. of Agricultural and Food Sciences, Univ. of Bologna, Viale G. Fanin 44, Bologna, Italy, 40127
- The Sainsbury Laboratory, Univ. of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK
| | - Matthew J Moscou
- The Sainsbury Laboratory, Univ. of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK
| | - Laura Civolani
- Dep. of Agricultural and Food Sciences, Univ. of Bologna, Viale G. Fanin 44, Bologna, Italy, 40127
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Dep. of Pharmacy and Biotechnology, Univ. of Bologna, Via Belmeloro 6, Bologna, Italy, 40126
| | - Cristian Forestan
- Dep. of Agricultural and Food Sciences, Univ. of Bologna, Viale G. Fanin 44, Bologna, Italy, 40127
| | - Sara Giulia Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, D
| | - Castrense Savojardo
- Biocomputing Group, Dep. of Pharmacy and Biotechnology, Univ. of Bologna, Via Belmeloro 6, Bologna, Italy, 40126
| | - Roberto Tuberosa
- Dep. of Agricultural and Food Sciences, Univ. of Bologna, Viale G. Fanin 44, Bologna, Italy, 40127
| | - Silvio Salvi
- Dep. of Agricultural and Food Sciences, Univ. of Bologna, Viale G. Fanin 44, Bologna, Italy, 40127
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Lup SD, Wilson-Sánchez D, Micol JL. Mapping-by-Sequencing of Point and Insertional Mutations with Easymap. Methods Mol Biol 2022; 2484:343-361. [PMID: 35461462 DOI: 10.1007/978-1-0716-2253-7_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Random mutagenesis followed by screening for phenotypes of interest is a widely used strategy for genetic dissection of biological pathways; however, identifying the causal gene traditionally required time-consuming mapping approaches based on iterative linkage analysis. Mapping-by-sequencing accelerates this process, efficiently linking the phenotype of a mutant to a narrow candidate genomic region, using next-generation sequencing (NGS) data from a mapping population segregating for the mutant phenotype. To enable researchers at any bioinformatics skill level to conduct mapping-by-sequencing, we developed the Easymap mapping software. In this protocol we break down the steps involved in mapping-by-sequencing. First, we describe different ways of obtaining a mapping population and the steps used to generate NGS data. Next, we show how to analyze the NGS data using Easymap and how to obtain a list of candidate mutations, along with comprehensive information for assessing the potential causality of each candidate. Thus, this protocol enables the user to conduct mapping-by-sequencing using Easymap, facilitating the identification of causal loci for a mutant phenotype of interest.
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Affiliation(s)
- Samuel Daniel Lup
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - David Wilson-Sánchez
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain.
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Li M, Guo G, Pidon H, Melzer M, Prina AR, Börner T, Stein N. ATP-Dependent Clp Protease Subunit C1, HvClpC1, Is a Strong Candidate Gene for Barley Variegation Mutant luteostrians as Revealed by Genetic Mapping and Genomic Re-sequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:664085. [PMID: 33936155 PMCID: PMC8086601 DOI: 10.3389/fpls.2021.664085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Implementation of next-generation sequencing in forward genetic screens greatly accelerated gene discovery in species with larger genomes, including many crop plants. In barley, extensive mutant collections are available, however, the causative mutations for many of the genes remains largely unknown. Here we demonstrate how a combination of low-resolution genetic mapping, whole-genome resequencing and comparative functional analyses provides a promising path toward candidate identification of genes involved in plastid biology and/or photosynthesis, even if genes are located in recombination poor regions of the genome. As a proof of concept, we simulated the prediction of a candidate gene for the recently cloned variegation mutant albostrians (HvAST/HvCMF7) and adopted the approach for suggesting HvClpC1 as candidate gene for the yellow-green variegation mutant luteostrians.
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Affiliation(s)
- Mingjiu Li
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hélène Pidon
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Alberto R. Prina
- Institute of Genetics ‘Ewald A. Favret’ (IGEAF), INTA CICVyA/Argentina, Hurlingham, Buenos Aires, Argentina
| | - Thomas Börner
- Molecular Genetics, Institute of Biology, Humboldt University, Berlin, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University, Göttingen, Germany
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Lup SD, Wilson-Sánchez D, Andreu-Sánchez S, Micol JL. Easymap: A User-Friendly Software Package for Rapid Mapping-by-Sequencing of Point Mutations and Large Insertions. FRONTIERS IN PLANT SCIENCE 2021; 12:655286. [PMID: 34040621 PMCID: PMC8143052 DOI: 10.3389/fpls.2021.655286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/18/2021] [Indexed: 05/15/2023]
Abstract
Mapping-by-sequencing strategies combine next-generation sequencing (NGS) with classical linkage analysis, allowing rapid identification of the causal mutations of the phenotypes exhibited by mutants isolated in a genetic screen. Computer programs that analyze NGS data obtained from a mapping population of individuals derived from a mutant of interest to identify a causal mutation are available; however, the installation and usage of such programs requires bioinformatic skills, modifying or combining pieces of existing software, or purchasing licenses. To ease this process, we developed Easymap, an open-source program that simplifies the data analysis workflows from raw NGS reads to candidate mutations. Easymap can perform bulked segregant mapping of point mutations induced by ethyl methanesulfonate (EMS) with DNA-seq or RNA-seq datasets, as well as tagged-sequence mapping for large insertions, such as transposons or T-DNAs. The mapping analyses implemented in Easymap have been validated with experimental and simulated datasets from different plant and animal model species. Easymap was designed to be accessible to all users regardless of their bioinformatics skills by implementing a user-friendly graphical interface, a simple universal installation script, and detailed mapping reports, including informative images and complementary data for assessment of the mapping results. Easymap is available at http://genetics.edu.umh.es/resources/easymap; its Quickstart Installation Guide details the recommended procedure for installation.
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Sahu PK, Sao R, Mondal S, Vishwakarma G, Gupta SK, Kumar V, Singh S, Sharma D, Das BK. Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review. PLANTS 2020; 9:plants9101355. [PMID: 33066352 PMCID: PMC7602136 DOI: 10.3390/plants9101355] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022]
Abstract
The recent advancements in forward genetics have expanded the applications of mutation techniques in advanced genetics and genomics, ahead of direct use in breeding programs. The advent of next-generation sequencing (NGS) has enabled easy identification and mapping of causal mutations within a short period and at relatively low cost. Identifying the genetic mutations and genes that underlie phenotypic changes is essential for understanding a wide variety of biological functions. To accelerate the mutation mapping for crop improvement, several high-throughput and novel NGS based forward genetic approaches have been developed and applied in various crops. These techniques are highly efficient in crop plants, as it is relatively easy to grow and screen thousands of individuals. These approaches have improved the resolution in quantitative trait loci (QTL) position/point mutations and assisted in determining the functional causative variations in genes. To be successful in the interpretation of NGS data, bioinformatics computational methods are critical elements in delivering accurate assembly, alignment, and variant detection. Numerous bioinformatics tools/pipelines have been developed for such analysis. This article intends to review the recent advances in NGS based forward genetic approaches to identify and map the causal mutations in the crop genomes. The article also highlights the available bioinformatics tools/pipelines for reducing the complexity of NGS data and delivering the concluding outcomes.
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Affiliation(s)
- Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India; (P.K.S.); (R.S.)
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India; (P.K.S.); (R.S.)
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Gautam Vishwakarma
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Sudhir Kumar Gupta
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Vinay Kumar
- ICAR-National Institute of Biotic Stress Management, Baronda, Raipur 493225, Chhattisgarh, India;
| | - Sudhir Singh
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, Chhattisgarh, India; (P.K.S.); (R.S.)
- Correspondence: (D.S.); (B.K.D.)
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; (S.M.); (G.V.); (S.K.G.); (S.S.)
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
- Correspondence: (D.S.); (B.K.D.)
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Yang H, Geng X, Zhao S, Shi H. Genomic diversity analysis and identification of novel SSR markers in four tobacco varieties by high-throughput resequencing. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 150:80-89. [PMID: 32126511 DOI: 10.1016/j.plaphy.2020.02.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Genome resequencing was carried out on two varieties of flue-cured tobacco (LY1306 and Qinyan 96), one variety of sun-cured tobacco (Wanmao 3), and one variety of air-cured Maryland tobacco (Wufeng 1), for a comparative analysis of genomic variation across the four varieties. Single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), structural variations (SVs), and copy-number variations (CNVs) were then identified in each tobacco variety. Furthermore, a functional analysis of mutated genes was carried out. Through in-depth comparative analysis of genomes of different tobacco varieties, we identified genome variations in a number of SNPs, InDels, SVs, and CNVs, respectively. Computational analysis to predict the function of mutated genes containing these differential SNPs, InDels, SVs, and CNVs showed that they were mainly involved in different functions, such as carbohydrate metabolism and secondary metabolites biosynthesis. We mainly focused on genes that were involved in the biosynthesis of secondary metabolites and nicotine metabolism. In addition, we identified five simple sequence repeat (SSR)-based markers and verified them by PCR amplification in 10 tobacco varieties. Taken together, our study increases the understanding of genetic differences between tobacco types or varieties and identifies five SSR markers to classify tobacco varieties or types.
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Affiliation(s)
- Huijuan Yang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan Province, 450002, China.
| | - Xinqi Geng
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan Province, 450002, China.
| | - Shimin Zhao
- Luoyang Tobacco Company, Luoyang, Henan Province, 471000, China
| | - Hongzhi Shi
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, Henan Province, 450002, China.
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Ponce MR, Micol JL. A cornucopia of mutants for understanding plant embryo development. THE NEW PHYTOLOGIST 2020; 226:289-291. [PMID: 32077508 DOI: 10.1111/nph.16343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
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Zhang Y, Liu Q, Zhang Y, Chen Y, Yu N, Cao Y, Zhan X, Cheng S, Cao L. LMM24 Encodes Receptor-Like Cytoplasmic Kinase 109, Which Regulates Cell Death and Defense Responses in Rice. Int J Mol Sci 2019; 20:ijms20133243. [PMID: 31269643 PMCID: PMC6651581 DOI: 10.3390/ijms20133243] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 11/16/2022] Open
Abstract
Lesion mimic mutants are excellent models for research on molecular mechanisms of cell death and defense responses in rice. We identified a new rice lesion mimic mutant lmm24 from a mutant pool of indica rice cultivar “ZhongHui8015”. The LMM24 gene was identified by MutMap, and LMM24 was confirmed as a receptor-like cytoplasmic kinase 109 by amino acid sequence analysis. The lmm24 mutant displayed dark brown lesions in leaves and growth retardation that were not observed in wild-type ZH8015. The results of histochemical staining and TUNEL assays showed enhanced ROS accumulation and cell death in lmm24. Chloroplast degradation was observed in lmm24 leaves, with decreased expression of photosynthesis-related genes and increased expression of the senescence-induced STAYGREEN (SGR) gene and other senescence-associated genes. Furthermore, lmm24 exhibited enhanced resistance to rice blast fungus Magnaporthe oryzae (M. oryzae) and up-regulation of defense response genes. Our data demonstrate that LMM24 regulates cell death and defense responses in rice.
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Affiliation(s)
- Yue Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Qunen Liu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yingxin Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yuyu Chen
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Ning Yu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yongrun Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiaodeng Zhan
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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Zhang J, Zhao P, Zhao J, Chen G. Synteny-based mapping of causal point mutations relevant to sand rice (Agriophyllum squarrosum) trichomeless1 mutant by RNA-sequencing. JOURNAL OF PLANT PHYSIOLOGY 2018; 231:86-95. [PMID: 30240969 DOI: 10.1016/j.jplph.2018.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 09/06/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
Sand rice (Agriophyllum squarrosum), a diploid Amaranthaceae species within the order Caryophyllalles, has potential as a crop in response to concerns about ongoing climate change and future food security. Modifying the weedy traits, such as dense trichomes, is important for the domestication of sand rice. In this study, an ethyl methanesulfonate (EMS) induced Agriophyllum squarrosum trichomeless mutant (astcl1) was isolated and genetic analysis revealed that this mutant was controlled by a single recessive locus. RNA sequencing was employed to analyze sequence variations between the mutant and wild-type individuals based on allele frequencies. Synteny-based mapping against two closely related and sequenced species finally delimited the causal mutations into an approximately 18.97 mega base pair (Mb) interval on the top portion of the chromosome 6 (Bv6) of sugar beet (Beta vulgaris) and two intervals (5.56 and 2.69 Mb) on the chromosomes 14 (CqA14) and 6 (CqB06) of quinoa (Chenopodium quinoa). These two quinoa intervals were located in the orthologous chromosomal regions against sugar beet Bv6. Differential expression analysis revealed that the astcl1 mutation only affects the expression of a small subset of genes. Most significantly, 17 lipid transport and metabolism related genes, such as GDSL esterases and very-long-chain 3-oxoacyl-CoA reductase 1, and two R2R3 MYB genes, MYB39 and RAX3, were down-regulated in astcl1 mutants. These results imply that the Astcl1 protein coordinately regulates trichome initiation and cuticle biosynthesis in sand rice.
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Affiliation(s)
- Jiwei Zhang
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China; Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Jiecai Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China; Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.
| | - Guoxiong Chen
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China; Shapotou Desert Research & Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.
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Shoko R, Manasa J, Maphosa M, Mbanga J, Mudziwapasi R, Nembaware V, Sanyika WT, Tinago T, Chikwambi Z, Mawere C, Matimba A, Mugumbate G, Mufandaedza J, Mulder N, Patterton H. Strategies and opportunities for promoting bioinformatics in Zimbabwe. PLoS Comput Biol 2018; 14:e1006480. [PMID: 30496170 PMCID: PMC6264469 DOI: 10.1371/journal.pcbi.1006480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Ryman Shoko
- Department of Biology, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- * E-mail:
| | - Justen Manasa
- African Institute of Biomedical Science & Technology, Harare, Zimbabwe
| | - Mcebisi Maphosa
- Department of Crop and Soil Science, School of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Joshua Mbanga
- Department of Applied Biology and Biochemistry, Faculty of Applied Sciences, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Reagan Mudziwapasi
- Department of Crop and Soil Science, School of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Victoria Nembaware
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Walter T. Sanyika
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Tawanda Tinago
- Department of Biology, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Zedias Chikwambi
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Cephas Mawere
- Department of Biotechnology, School of Industrial Science and Technology, Harare Institute of Technology, Harare, Zimbabwe
| | - Alice Matimba
- Department of Clinical Pharmacology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Grace Mugumbate
- Department of Chemistry, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | | | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hugh Patterton
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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Yu H, Shahid MQ, Li R, Li W, Liu W, Ghouri F, Liu X. Genome-Wide Analysis of Genetic Variations and the Detection of Rich Variants of NBS-LRR Encoding Genes in Common Wild Rice Lines. PLANT MOLECULAR BIOLOGY REPORTER 2018; 36:618-630. [PMID: 30363818 PMCID: PMC6182389 DOI: 10.1007/s11105-018-1103-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Common wild rice (Oryza rufipogon Griff.) is invaluable genetic resource for rice resistance breeding. Whole-genome re-sequencing was conducted to systematically analyze the variations in two new inbred lines (Huaye 3 and Huaye 4) developed from a common wild rice. A total of 4,841,127 SNPs, 1,170,479 InDels, 24,080 structural variations (SVs), and 298 copy number variations (CNVs) were identified in three materials. Approximately 16.24 and 5.64% of the total SNPs and InDels of Huaye 3 and Huaye 4 were located in genic regions, respectively. Together, 12,486 and 15,925 large-effect SNPs, and 12,417 and 14,513 large-effect InDels, which affect the integrity of the encoded protein, were identified in Huaye 3 and Huaye 4, respectively. The distribution map of 194 and 245 NBS-LRR encoding homologs was constructed across 12 rice chromosomes. Further, GO enrichment analysis of the homologs with identical genotype variations in Huaye 3 and Huaye 4 revealed 67, 82, and 58 homologs involved in cell death, response to stress, and both terms, respectively. Comparative analysis displayed that 550 out of 652 SNPs and 129 out of 147 InDels were present in a widely used blast-susceptible rice variety (LTH). Protein-protein interaction analysis revealed a strong interaction between NBS-LRR candidates and several known R genes. One homolog of disease resistance protein (RPM1) was involved in the plant-pathogen interaction pathway. Artificial inoculation of disease/insect displayed resistance phenotypes against rice blast and brown planthopper in two lines. The results will provide allele-specific markers for rice molecular breeding.
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Affiliation(s)
- Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530004 China
| | - Wei Li
- College of Agronomy, Guangdong Ocean University, Zhanjiang, 524000 China
| | - Wen Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Department of Tropical Crops, Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, 510507 China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
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Hu Z, Deng G, Mou H, Xu Y, Chen L, Yang J, Zhang M. A re-sequencing-based ultra-dense genetic map reveals a gummy stem blight resistance-associated gene in Cucumis melo. DNA Res 2017; 25:1-10. [PMID: 28985339 PMCID: PMC5824858 DOI: 10.1093/dnares/dsx033] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/11/2017] [Indexed: 12/30/2022] Open
Abstract
The melon (Cucumis melo) genome and genetic maps with hundreds to thousands of single nucleotide polymorphism markers were recently released. However, a high-resolution genetic map was lacking. Gummy stem blight (Gsb) is a destructive disease responsible for considerable economic losses during melon production. We herein describe the development of an ultra-dense genetic map consisting of 12,932 recombination bin markers covering 1,818 cM, with an average distance of 0.17 cM between adjacent tags. A comparison of the genetic maps for melon, watermelon, and cucumber revealed chromosome-level syntenic relationships and recombination events among the three Cucurbitaceae species. Our genetic map was useful for re-anchoring the genome scaffolds of melon. More than 92% assembly was anchored to 12 pseudo-chromosomes and 90% of them were oriented. Furthermore, 1,135 recombination hotspots revealed an unbalanced recombination rate across the melon genome. Genetic analyses of the Gsb-resistant and -susceptible lines indicated the resistance phenotype is mediated by a single dominant gene. We identified Gsb-resistance gene candidates in a 108-kb region on pseudo-chromosome 4. Our findings verify the utility of an ultra-dense genetic map for mapping a gene of interest, and for identifying new disease resistant genes.
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Affiliation(s)
- Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Guancong Deng
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Haipeng Mou
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Yuhui Xu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Li Chen
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.,Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China.,Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.,Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou 310058, China
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15
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Huo H, Henry IM, Coppoolse ER, Verhoef-Post M, Schut JW, de Rooij H, Vogelaar A, Joosen RVL, Woudenberg L, Comai L, Bradford KJ. Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:345-360. [PMID: 27406937 DOI: 10.1111/tpj.13267] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 05/07/2023]
Abstract
Lettuce (Lactuca sativa) seeds exhibit thermoinhibition, or failure to complete germination when imbibed at warm temperatures. Chemical mutagenesis was employed to develop lettuce lines that exhibit germination thermotolerance. Two independent thermotolerant lettuce seed mutant lines, TG01 and TG10, were generated through ethyl methanesulfonate mutagenesis. Genetic and physiological analyses indicated that these two mutations were allelic and recessive. To identify the causal gene(s), we applied bulked segregant analysis by whole genome sequencing. For each mutant, bulked DNA samples of segregating thermotolerant (mutant) seeds were sequenced and analyzed for homozygous single-nucleotide polymorphisms. Two independent candidate mutations were identified at different physical positions in the zeaxanthin epoxidase gene (ABSCISIC ACID DEFICIENT 1/ZEAXANTHIN EPOXIDASE, or ABA1/ZEP) in TG01 and TG10. The mutation in TG01 caused an amino acid replacement, whereas the mutation in TG10 resulted in alternative mRNA splicing. Endogenous abscisic acid contents were reduced in both mutants, and expression of the ABA1 gene from wild-type lettuce under its own promoter fully complemented the TG01 mutant. Conventional genetic mapping confirmed that the causal mutations were located near the ZEP/ABA1 gene, but the bulked segregant whole genome sequencing approach more efficiently identified the specific gene responsible for the phenotype.
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Affiliation(s)
- Heqiang Huo
- Seed Biotechnology Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, CA, 95616, USA
| | | | | | - Johan W Schut
- Rijk Zwaan Breeding B.V., 2678, ZG De Lier, The Netherlands
| | - Han de Rooij
- Rijk Zwaan Breeding B.V., 2678, ZG De Lier, The Netherlands
| | - Aat Vogelaar
- Rijk Zwaan Breeding B.V., 2678, ZG De Lier, The Netherlands
| | | | - Leo Woudenberg
- Rijk Zwaan Breeding B.V., 2678, ZG De Lier, The Netherlands
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California, Davis, CA, 95616, USA
| | - Kent J Bradford
- Seed Biotechnology Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA
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16
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Scossa F, Brotman Y, de Abreu E Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:47-64. [PMID: 26566824 DOI: 10.1016/j.plantsci.2015.05.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 05/08/2023]
Abstract
Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Rome, Italy.
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | | | - Lothar Willmitzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
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Abstract
Until recently, bioinformatics, an important discipline in the biological sciences, was largely limited to countries with advanced scientific resources. Nonetheless, several developing countries have lately been making progress in bioinformatics training and applications. In Africa, leading countries in the discipline include South Africa, Nigeria, and Kenya. However, one country that is less known when it comes to bioinformatics is Ghana. Here, I provide a first description of the development of bioinformatics activities in Ghana and how these activities contribute to the overall development of the discipline in Africa. Over the past decade, scientists in Ghana have been involved in publications incorporating bioinformatics analyses, aimed at addressing research questions in biomedical science and agriculture. Scarce research funding and inadequate training opportunities are some of the challenges that need to be addressed for Ghanaian scientists to continue developing their expertise in bioinformatics.
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Affiliation(s)
- Thomas K. Karikari
- Department of Science Laboratory Technology, School of Applied Science and Technology, Wa Polytechnic, Wa, Ghana
- * E-mail:
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