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Tan H, Guo M, Chen J, Wang J, Yu G. HetFCM: functional co-module discovery by heterogeneous network co-clustering. Nucleic Acids Res 2024; 52:e16. [PMID: 38088228 PMCID: PMC10853805 DOI: 10.1093/nar/gkad1174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/31/2023] [Accepted: 11/23/2023] [Indexed: 02/10/2024] Open
Abstract
Functional molecular module (i.e., gene-miRNA co-modules and gene-miRNA-lncRNA triple-layer modules) analysis can dissect complex regulations underlying etiology or phenotypes. However, current module detection methods lack an appropriate usage and effective model of multi-omics data and cross-layer regulations of heterogeneous molecules, causing the loss of critical genetic information and corrupting the detection performance. In this study, we propose a heterogeneous network co-clustering framework (HetFCM) to detect functional co-modules. HetFCM introduces an attributed heterogeneous network to jointly model interplays and multi-type attributes of different molecules, and applies multiple variational graph autoencoders on the network to generate cross-layer association matrices, then it performs adaptive weighted co-clustering on association matrices and attribute data to identify co-modules of heterogeneous molecules. Empirical study on Human and Maize datasets reveals that HetFCM can find out co-modules characterized with denser topology and more significant functions, which are associated with human breast cancer (subtypes) and maize phenotypes (i.e., lipid storage, drought tolerance and oil content). HetFCM is a useful tool to detect co-modules and can be applied to multi-layer functional modules, yielding novel insights for analyzing molecular mechanisms. We also developed a user-friendly module detection and analysis tool and shared it at http://www.sdu-idea.cn/FMDTool.
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Affiliation(s)
- Haojiang Tan
- School of Software, Shandong University, Jinan 250101, Shandong, China
- Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University, Jinan 250101, Shandong, China
| | - Maozu Guo
- College of Electrical and Information Engineering, Beijing Uni. of Civil Eng. and Arch., Beijing 100044, China
| | - Jian Chen
- College of Agronomy & Biotechnolog, China Agricultural University, Beijing 100193, China
| | - Jun Wang
- Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University, Jinan 250101, Shandong, China
| | - Guoxian Yu
- School of Software, Shandong University, Jinan 250101, Shandong, China
- Joint SDU-NTU Centre for Artificial Intelligence Research, Shandong University, Jinan 250101, Shandong, China
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2
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Mleziva AD, Ngumbi EN. Comparative analysis of defensive secondary metabolites in wild teosinte and cultivated maize under flooding and herbivory stress. PHYSIOLOGIA PLANTARUM 2024; 176:e14216. [PMID: 38366721 DOI: 10.1111/ppl.14216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/18/2024]
Abstract
Climate change is driving an alarming increase in the frequency and intensity of abiotic and biotic stress factors, negatively impacting plant development and agricultural productivity. To survive, plants respond by inducing changes in below and aboveground metabolism with concomitant alterations in defensive secondary metabolites. While plant responses to the isolated stresses of flooding and insect herbivory have been extensively studied, much less is known about their response in combination. Wild relatives of cultivated plants with robust stress tolerance traits provide an excellent system for comparing how diverse plant species respond to combinatorial stress, and provide insight into potential germplasms for stress-tolerant hybrids. In this study, we compared the below and aboveground changes in the secondary metabolites of maize (Zea mays) and a flood-tolerant wild relative Nicaraguan teosinte (Zea nicaraguensis) in response to flooding, insect herbivory, and their combination. Root tissue was analyzed for changes in belowground metabolism. Leaf total phenolic content and headspace volatile organic compound emission were analyzed for changes in aboveground secondary metabolism. Results revealed significant differences in the root metabolome profiles of teosinte and maize. Notably, the accumulation of the flavonoids apigenin, naringenin, and luteolin during flooding and herbivory differentiated teosinte from maize. Aboveground, terpenes, including trans-α-bergamotene and (E)-4,8-dimethylnona-1,3,7-triene, shaped compositional differences in their volatile profiles between flooding, herbivory, and their combination. Taken together, these results suggest teosinte may be more tolerant than maize due to dynamic metabolic changes during flooding and herbivory that help relieve stress and influence plant-insect interactions.
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Affiliation(s)
- Aaron D Mleziva
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Esther N Ngumbi
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL, USA
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3
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Singh R, Kumar K, Bharadwaj C, Verma PK. Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes. PLANTA 2022; 255:46. [PMID: 35076815 DOI: 10.1007/s00425-022-03827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.
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Affiliation(s)
- Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110020, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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4
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Dong H, Li H, Xue Y, Su S, Li S, Shan X, Liu H, Jiang N, Wu X, Zhang Z, Yuan Y. E183K Mutation in Chalcone Synthase C2 Causes Protein Aggregation and Maize Colorless. FRONTIERS IN PLANT SCIENCE 2021; 12:679654. [PMID: 34249050 PMCID: PMC8261305 DOI: 10.3389/fpls.2021.679654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/12/2021] [Indexed: 06/13/2023]
Abstract
Flavonoids give plants their rich colors and play roles in a number of physiological processes. In this study, we identified a novel colorless maize mutant showing reduced pigmentation throughout the whole life cycle by EMS mutagenesis. E183K mutation in maize chalcone synthase C2 (ZmC2) was mapped using MutMap strategy as the causal for colorless, which was further validated by transformation in Arabidopsis. We evaluated transcriptomic and metabolic changes in maize first sheaths caused by the mutation. The downstream biosynthesis was blocked while very few genes changed their expression pattern. ZmC2-E183 site is highly conserved in chalcone synthase among Plantae kingdom and within species' different varieties. Through prokaryotic expression, transient expression in maize leaf protoplasts and stable expression in Arabidopsis, we observed that E183K and other mutations on E183 could cause almost complete protein aggregation of chalcone synthase. Our findings will benefit the characterization of flavonoid biosynthesis and contribute to the body of knowledge on protein aggregation in plants.
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Affiliation(s)
- Haixiao Dong
- College of Plant Science, Jilin University, Changchun, China
| | - He Li
- College of Plant Science, Jilin University, Changchun, China
| | - Yingjie Xue
- College of Plant Science, Jilin University, Changchun, China
| | - Shengzhong Su
- College of Plant Science, Jilin University, Changchun, China
| | - Shipeng Li
- College of Plant Science, Jilin University, Changchun, China
| | - Xiaohui Shan
- College of Plant Science, Jilin University, Changchun, China
| | - Hongkui Liu
- College of Plant Science, Jilin University, Changchun, China
| | - Nan Jiang
- College of Plant Science, Jilin University, Changchun, China
| | - Xuyang Wu
- College of Plant Science, Jilin University, Changchun, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Yaping Yuan
- College of Plant Science, Jilin University, Changchun, China
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5
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Jia S, Yobi A, Naldrett MJ, Alvarez S, Angelovici R, Zhang C, Holding DR. Deletion of maize RDM4 suggests a role in endosperm maturation as well as vegetative and stress-responsive growth. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5880-5895. [PMID: 32667993 DOI: 10.1093/jxb/eraa325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Opaque kernels in maize may result from mutations in many genes, such as OPAQUE-2. In this study, a maize null mutant of RNA-DIRECTED DNA METHYLATION 4 (RDM4) showed an opaque kernel phenotype, as well as plant developmental delay, male sterility, and altered response to cold stress. We found that in opaque kernels, all zein proteins were reduced and amino acid content was changed, including increased lysine. Transcriptomic and proteomic analysis confirmed the zein reduction and proteomic rebalancing of non-zein proteins, which was quantitatively and qualitatively different from opaque-2. Global transcriptional changes were found in endosperm and leaf, including many transcription factors and tissue-specific expressed genes. Furthermore, of the more than 8000 significantly differentially expressed genes in wild type in response to cold, a significant proportion (25.9% in moderate cold stress and 40.8% in near freezing stress) were not differentially expressed in response to cold in rdm4, suggesting RDM4 may participate in regulation of abiotic stress tolerance. This initial characterization of maize RDM4 provides a basis for further investigating its function in endosperm and leaf, and as a regulator of normal and stress-responsive development.
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Affiliation(s)
- Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
- Key Laboratory of Pratacultural Science, Beijing Municipality, Beijing, China
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
| | - Abou Yobi
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Michael J Naldrett
- Proteomics and Metabolomics Core facility, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sophie Alvarez
- Proteomics and Metabolomics Core facility, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ruthie Angelovici
- Bond Life Sciences Center, Division of Biological Sciences, Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA
| | - Chi Zhang
- School of Biological Sciences, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
| | - David R Holding
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE, USA
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6
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Mapping-by-Sequencing via MutMap Identifies a Mutation in ZmCLE7 Underlying Fasciation in a Newly Developed EMS Mutant Population in an Elite Tropical Maize Inbred. Genes (Basel) 2020; 11:genes11030281. [PMID: 32155750 PMCID: PMC7140824 DOI: 10.3390/genes11030281] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022] Open
Abstract
Induced point mutations are important genetic resources for their ability to create hypo- and hypermorphic alleles that are useful for understanding gene functions and breeding. However, such mutant populations have only been developed for a few temperate maize varieties, mainly B73 and W22, yet no tropical maize inbred lines have been mutagenized and made available to the public to date. We developed a novel Ethyl Methanesulfonate (EMS) induced mutation resource in maize comprising 2050 independent M2 mutant families in the elite tropical maize inbred ML10. By phenotypic screening, we showed that this population is of comparable quality with other mutagenized populations in maize. To illustrate the usefulness of this population for gene discovery, we performed rapid mapping-by-sequencing to clone a fasciated-ear mutant and identify a causal promoter deletion in ZmCLE7 (CLE7). Our mapping procedure does not require crossing to an unrelated parent, thus is suitable for mapping subtle traits and ones affected by heterosis. This first EMS population in tropical maize is expected to be very useful for the maize research community. Also, the EMS mutagenesis and rapid mapping-by-sequencing pipeline described here illustrate the power of performing forward genetics in diverse maize germplasms of choice, which can lead to novel gene discovery due to divergent genetic backgrounds.
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7
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Jia S, Morton K, Zhang C, Holding D. An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 16:439-450. [PMID: 30743052 PMCID: PMC6411947 DOI: 10.1016/j.gpb.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/16/2018] [Accepted: 03/05/2018] [Indexed: 10/27/2022]
Abstract
Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 × Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-specific expression data to narrow down the list of candidate genes/mutations and identified deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identified in mutant 531, which occurs within a ∼200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4 (RdDM4) and AMP-binding protein, respectively. This study demonstrates the efficiency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection, providing a new option in mapping-by-sequencing for maize functional genomics studies.
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Affiliation(s)
- Shangang Jia
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA
| | - Kyla Morton
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA
| | - Chi Zhang
- School of Biological Sciences, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA
| | - David Holding
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska, Lincoln, NE 68588, USA.
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8
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Dong J, Tu M, Feng Y, Zdepski A, Ge F, Kumar D, Slovin JP, Messing J. Candidate gene identification of existing or induced mutations with pipelines applicable to large genomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:673-682. [PMID: 30417446 DOI: 10.1111/tpj.14153] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
Bulked segregant analysis (BSA) is used to identify existing or induced variants that are linked to phenotypes. Although it is widely used in Arabidopsis and rice, it remains challenging for crops with large genomes, such as maize. Moreover, analysis of huge data sets can present a bottleneck linking phenotypes to their molecular basis, especially for geneticists without programming experience. Here, we identified two genes of maize defective kernel mutants with newly developed analysis pipelines that require no programing skills and should be applicable to any large genome. In the 1970s, Neuffer and Sheridan generated a chemically induced defective kernel (dek) mutant collection with the potential to uncover critical genes for seed development. To locate such mutations, the dek phenotypes were introgressed into two inbred lines to take advantage of maize haplotype variations and their sequenced genomes. We generated two pipelines that take fastq files derived from next-generation (nextGen) paired-end DNA and cDNA sequencing as input, call on several well established and freely available genomic analysis tools to call SNPs and INDELs, and generate lists of the most likely causal mutations together with variant index plots to locate the mutation to a specific sequence position on a chromosome. The pipelines were validated with a known strawberry mutation before cloning the dek mutants, thereby enabling phenotypic analysis of large genomes by next-generation sequencing.
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Affiliation(s)
- Jiaqiang Dong
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Min Tu
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Yaping Feng
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Anna Zdepski
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Fei Ge
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Dibyendu Kumar
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Janet P Slovin
- Genetic Improvement of Fruits and Vegetables Laboratory, US Department of Agriculture - Agricultural Research Service, Beltsville, MD, 20705, USA
| | - Joachim Messing
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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A Megabase-Scale Deletion is Associated with Phenotypic Variation of Multiple Traits in Maize. Genetics 2018; 211:305-316. [PMID: 30389804 PMCID: PMC6325712 DOI: 10.1534/genetics.118.301567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/26/2018] [Indexed: 11/18/2022] Open
Abstract
Genomic deletions are pervasive in the maize (Zea mays L.) genome, and play important roles in phenotypic variation and adaptive evolution. However, little is known about the biological functions of these genomic deletions. Here, we report the biological function of a megabase-scale deletion, which we identified by position-based cloning of the multi-trait weakened (muw) mutant, which is inherited as a single recessive locus. MUW was mapped to a 5.16-Mb region on chromosome 2. The 5.16-Mb deletion in the muw mutant led to the loss of 48 genes and was responsible for a set of phenotypic abnormities, including wilting leaves, poor yield performance, reduced plant height, increased stomatal density, and rapid water loss. While muw appears to have resulted from double-stranded break repair that was not dependent on intragenomic DNA homology, extensive duplication of maize genes may have mitigated its effects and facilitated its survival.
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10
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Datta S, Jankowicz‐Cieslak J, Nielen S, Ingelbrecht I, Till BJ. Induction and recovery of copy number variation in banana through gamma irradiation and low-coverage whole-genome sequencing. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1644-1653. [PMID: 29476650 PMCID: PMC6097122 DOI: 10.1111/pbi.12901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/02/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Traditional breeding methods are hindered in bananas due to the fact that major cultivars are sterile, parthenocarpic, triploid and thus clonally propagated. This has resulted in a narrow genetic base and limited resilience to biotic and abiotic stresses. Mutagenesis of in vitro propagated bananas is one method to introduce novel alleles and broaden genetic diversity. We previously established a method for the induction and recovery of single nucleotide mutations generated with the chemical mutagen EMS. However, officially released mutant banana varieties have been created using gamma rays, a mutagen that can produce large genomic insertions and deletions (indels). Such dosage mutations may be important for generating observable phenotypes in polyploids. In this study, we establish a low-coverage whole-genome sequencing approach in triploid bananas to recover large genomic indels caused by treatment with gamma irradiation. We first evaluated the commercially released mutant cultivar 'Novaria' and found that it harbours multiple predicted deletions, ranging from 0.3 to 3.8 million base pairs (Mbp). In total, predicted deletions span 189 coding regions. To evaluate the feasibility of generating and maintaining new mutations, we developed a pipeline for mutagenesis and screening for copy number variation in Cavendish bananas using the cultivar 'Williams'. Putative mutations were recovered in 70% of lines treated with 20 Gy and 60% of the lines treated with 40 Gy. While deletion events predominate, insertions were identified in 20 Gy-treated material. Based on these results, we believe this approach can be scaled up to support large breeding projects.
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Affiliation(s)
- Sneha Datta
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Joanna Jankowicz‐Cieslak
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Stephan Nielen
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Ivan Ingelbrecht
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
| | - Bradley J. Till
- Plant Breeding and Genetics LaboratoryJoint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureIAEA Laboratories SeibersdorfInternational Atomic Energy AgencyVienna International CentreViennaAustria
- Present address:
Department of Chromosome BiologyUniversity of ViennaA‐1030ViennaAustria
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11
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Jia S, Li A, Zhang C, Holding D. Deletion Mutagenesis and Identification of Causative Mutations in Maize. Methods Mol Biol 2018; 1676:97-108. [PMID: 28986905 DOI: 10.1007/978-1-4939-7315-6_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
We describe a method for gamma-irradiation of mature maize seeds to generate mutants with opaque endosperm and reduced kernel fill phenotypes. We also describe methods for mapping mutants and identifying causal gene mutations. Using this method, a population of 1788M2 families and 47 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes was developed. For molecular characterization of the mutants, we utilized a novel functional genomics platform that combines separate Bulked Segregant RNA and exome sequencing data sets (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. We also describe the use of exome capture sequencing of F2 mutant and normal pools to perform mapping and candidate gene identification without the need for separate RNA-seq (BSEx-seq). To exemplify the utility of the deletion mutants for functional genomics and provide proof-of-concept for the bioinformatics platform, we summarize the identification of the causative deletion in two mutants. Mutant 937, which was characterized by BSREx-seq, harbors a 6203-bp in-frame deletion covering six exons within the Opaque-1 gene on chromosome 4. Preliminary investigation of opaque mutant 1486 with BSEx-seq shows a tight mapping interval and associated deletion on chromosome 10.
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Affiliation(s)
- Shangang Jia
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska - Lincoln, 1901 Vine Street, P.O. Box 880665, Lincoln, NE, 68588-0665, USA
| | - Aixia Li
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska - Lincoln, 1901 Vine Street, P.O. Box 880665, Lincoln, NE, 68588-0665, USA
| | - Chi Zhang
- School of Biological Sciences, Center for Plant Science and Innovation, Beadle Center for Biotechnology, University of Nebraska - Lincoln, 1901 Vine Street, P.O. Box 880665, Lincoln, NE, 68588-0665, USA
| | - David Holding
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, Beadle Center for Biotechnology, University of Nebraska - Lincoln, 1901 Vine Street, P.O. Box 880665, Lincoln, NE, 68588-0665, USA.
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