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Fanelli E, Troccoli A, Tarasco E, De Luca F. Molecular Characterization and Functional Analysis of the Hb-hsp90-1 Gene in Relation to Temperature Changes in Heterorhabditis bacteriophora. Front Physiol 2021; 12:615653. [PMID: 33732162 PMCID: PMC7959791 DOI: 10.3389/fphys.2021.615653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/26/2021] [Indexed: 12/17/2022] Open
Abstract
Understanding how entomopathogenic nematodes respond to temperature changes and have adapted to the local environment is crucial to improve their potential as biocontrol agents. In order to improve understanding of Heterorhabditis bacteriophora's potential adaptability to future climate changes, full-length cDNA and the corresponding gene of heat shock protein 90 (Hsp90) were isolated and fully characterized. The reproductive potential of the Apulian strain of H. bacteriophora increased when the temperature rose from 23 to 30°C, but no reproduction was found at 12°C. Expression analyses revealed that Hb-hsp90-1 was differentially expressed in Infective Juveniles (IJs) and adults (hermaphrodites, females and males). Up-regulation of Hb-hsp90-1 was higher during the recovery process in Galleria mellonella larvae than adults, thus confirming the protective role of Hb-hsp90-1 in coping with the host environment. Silencing of Hb-hsp90-1 resulted in a significant reduction (76%) in the expression level. Silenced IJs took longer than untreated nematodes to infect G. mellonella, showing that Hb-hsp90-1 could be also involved in chemosensation. Furthermore, the number of adults and IJs recovered from G. mellonella infected with silenced nematodes and incubated at 30°C was higher than that obtained from G. mellonella infected with untreated nematodes. These data confirm the crucial role of Hb-hsp90-1 allowing acclimation to increased temperatures and modulation of the recovery process.
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Affiliation(s)
- Elena Fanelli
- Institute for Sustainable Plant Protection-CNR, Bari, Italy
| | | | - Eustachio Tarasco
- Institute for Sustainable Plant Protection-CNR, Bari, Italy
- Section of Entomology and Zoology, Department of Soil, Plant and Food Sciences, University of Bari “A. Moro”, Bari, Italy
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2
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Digital PCR: What Relevance to Plant Studies? BIOLOGY 2020; 9:biology9120433. [PMID: 33266157 PMCID: PMC7760125 DOI: 10.3390/biology9120433] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 01/01/2023]
Abstract
Simple Summary Digital PCR is a third-generation technology based on the subdivision of the analytical sample into numerous partitions that are amplified individually. This review presents the major applications of digital PCR (dPCR) technology developed so far in the field of plant science. In greater detail, dPCR assays have been developed to trace genetically modified plant components, pathogenic and non-pathogenic microorganisms, and plant species. Other applications have concerned the study of the aspects of structural and functional genetics. Abstract Digital PCR (dPCR) is a breakthrough technology that able to provide sensitive and absolute nucleic acid quantification. It is a third-generation technology in the field of nucleic acid amplification. A unique feature of the technique is that of dividing the sample into numerous separate compartments, in each of which an independent amplification reaction takes place. Several instrumental platforms have been developed for this purpose, and different statistical approaches are available for reading the digital output data. The dPCR assays developed so far in the plant science sector were identified in the literature, and the major applications, advantages, disadvantages, and applicative perspectives of the technique are presented and discussed in this review.
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Zmienko A, Marszalek-Zenczak M, Wojciechowski P, Samelak-Czajka A, Luczak M, Kozlowski P, Karlowski WM, Figlerowicz M. AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. THE PLANT CELL 2020; 32:1797-1819. [PMID: 32265262 PMCID: PMC7268809 DOI: 10.1105/tpc.19.00640] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 03/09/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for >1000 Arabidopsis (Arabidopsis thaliana) accessions focused on small variations and did not include CNVs. Here, we performed genome-wide analysis and identified large indels (50 to 499 bp) and CNVs (500 bp and larger) in these accessions. The CNVs fully overlap with 18.3% of protein-coding genes, with enrichment for evolutionarily young genes and genes involved in stress and defense. By combining analysis of both genes and transposable elements (TEs) affected by CNVs, we revealed that the variation statuses of genes and TEs are tightly linked and jointly contribute to the unequal distribution of these elements in the genome. We also determined the gene copy numbers in a set of 1060 accessions and experimentally validated the accuracy of our predictions by multiplex ligation-dependent probe amplification assays. We then successfully used the CNVs as markers to analyze population structure and migration patterns. Finally, we examined the impact of gene dosage variation triggered by a CNV spanning the SEC10 gene on SEC10 expression at both the transcript and protein levels. The catalog of CNVs, CNV-overlapping genes, and their genotypes in a top model dicot will stimulate the exploration of the genetic basis of phenotypic variation.
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Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | | | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
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4
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Li Z, Han Y, Niu H, Wang Y, Jiang B, Weng Y. Gynoecy instability in cucumber ( Cucumis sativus L.) is due to unequal crossover at the copy number variation-dependent Femaleness ( F) locus. HORTICULTURE RESEARCH 2020; 7:32. [PMID: 32194968 PMCID: PMC7072070 DOI: 10.1038/s41438-020-0251-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 05/06/2023]
Abstract
Cucumber, Cucumis sativus is an important vegetable crop, and gynoecy has played a critical role in yield increase of hybrid cucumber production. Cucumber has a unique genetic system for gynoecious sex expression, which is determined by the copy number variation (CNV)-based, dominant, and dosage-dependent femaleness (F) locus. However, this gynoecy expression system seems unstable since monecious plants could often be found in F-dependent gynoecious cucumber inbreds. We hypothesized that gynoecy instability (gynoecy loss) may be due to unequal crossing over (UCO) during meiosis among repeat units of the CNV. In this study, using high throughput genome resequencing, fiber-FISH and genomic qPCR analyses, we first confirmed and refined the structure of the F locus, which was a CNV of a 30.2-kb tandem repeat. Gynoecious plants contained three genes: CsACS1, CsACS1G, and CsMYB, of which CsACS1G is a duplication of CsACS1 but with a recombinant distal promoter that may contribute to gynoecy sex expression. In two large populations from self-pollinated gynoecious inbred lines, 'gynoecy loss' mutants were identified with similar mutation rates (~0.12%). We show that these monecious mutants have lost CsACS1G. In addition, we identified gynoecious lines in natural populations that carry two copies of CSACS1G. We proposed a model to explain gynoecy instability in F-dependent cucumbers, which is caused by UCO among CSACS1/G units during meiosis. The findings present a convincing case that the phenotypic variation of an economically important trait is associated with the dynamic changes of copy numbers at the F locus. This work also has important implications in cucumber breeding.
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Affiliation(s)
- Zheng Li
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Yonghua Han
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 China
| | - Huanhuan Niu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100 China
| | - Yuhui Wang
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
| | - Biao Jiang
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, Guangdong 510640 China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- USDA-ARS, Vegetable Crops Research Unit, Madison, WI 53706 USA
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Pucker B, Holtgräwe D, Stadermann KB, Frey K, Huettel B, Reinhardt R, Weisshaar B. A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLoS One 2019; 14:e0216233. [PMID: 31112551 PMCID: PMC6529160 DOI: 10.1371/journal.pone.0216233] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/16/2019] [Indexed: 01/27/2023] Open
Abstract
In addition to the BAC-based reference sequence of the accession Columbia-0 from the year 2000, several short read assemblies of THE plant model organism Arabidopsis thaliana were published during the last years. Also, a SMRT-based assembly of Landsberg erecta has been generated that identified translocation and inversion polymorphisms between two genotypes of the species. Here we provide a chromosome-arm level assembly of the A. thaliana accession Niederzenz-1 (AthNd-1_v2c) based on SMRT sequencing data. The best assembly comprises 69 nucleome sequences and displays a contig length of up to 16 Mbp. Compared to an earlier Illumina short read-based NGS assembly (AthNd-1_v1), a 75 fold increase in contiguity was observed for AthNd-1_v2c. To assign contig locations independent from the Col-0 gold standard reference sequence, we used genetic anchoring to generate a de novo assembly. In addition, we assembled the chondrome and plastome sequences. Detailed analyses of AthNd-1_v2c allowed reliable identification of large genomic rearrangements between A. thaliana accessions contributing to differences in the gene sets that distinguish the genotypes. One of the differences detected identified a gene that is lacking from the Col-0 gold standard sequence. This de novo assembly extends the known proportion of the A. thaliana pan-genome.
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Affiliation(s)
- Boas Pucker
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Daniela Holtgräwe
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Kai Bernd Stadermann
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Katharina Frey
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bernd Weisshaar
- Bielefeld University, Faculty of Biology & Center for Biotechnology, Bielefeld, Germany
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Castagnone‐Sereno P, Mulet K, Danchin EGJ, Koutsovoulos GD, Karaulic M, Da Rocha M, Bailly‐Bechet M, Pratx L, Perfus‐Barbeoch L, Abad P. Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant‐parasitic nematode
Meloidogyne incognita. Mol Ecol 2019; 28:2559-2572. [DOI: 10.1111/mec.15095] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 03/11/2019] [Accepted: 04/01/2019] [Indexed: 01/05/2023]
Affiliation(s)
| | - Karine Mulet
- INRAUniversité Côte d'AzurCNRSISA Sophia Antipolis France
| | | | | | | | | | | | - Loris Pratx
- INRAUniversité Côte d'AzurCNRSISA Sophia Antipolis France
| | | | - Pierre Abad
- INRAUniversité Côte d'AzurCNRSISA Sophia Antipolis France
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Krasileva KV. The role of transposable elements and DNA damage repair mechanisms in gene duplications and gene fusions in plant genomes. CURRENT OPINION IN PLANT BIOLOGY 2019; 48:18-25. [PMID: 30849712 DOI: 10.1016/j.pbi.2019.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/16/2019] [Accepted: 01/29/2019] [Indexed: 05/02/2023]
Abstract
Plant genomes are shaped by structural variation. Gene-size insertions and among most prominent events and can have significant effects on amplification of gene families as well as facilitate new gene fusions. Transposable elements as well as plant DNA repair machinery have overlapping contributions to these events, and often work in synergy. Activity of transposable elements is often lineage specific and can preferentially affect specific gene families, such as disease resistance genes. Once duplicated, genes themselves can serve templates for additional variation that can arise from non-allelic homologous recombination. Non-homologous DNA repair mechanisms contribute to additional variation and diversify the mechanisms of gene movement, such as through ligation of extra-chromosomal DNA fragments. Genomic processes that generate structural variation can be induced by stress and, therefore, can provide adaptive potential. This review describes mechanisms that contribute to gene-size structural variation in plants, result in gene duplication and generation of new plant genes through gene fusion.
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Affiliation(s)
- Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, United States.
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8
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Lye ZN, Purugganan MD. Copy Number Variation in Domestication. TRENDS IN PLANT SCIENCE 2019; 24:352-365. [PMID: 30745056 DOI: 10.1016/j.tplants.2019.01.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 05/22/2023]
Abstract
Domesticated plants have long served as excellent models for studying evolution. Many genes and mutations underlying important domestication traits have been identified, and most causal mutations appear to be SNPs. Copy number variation (CNV) is an important source of genetic variation that has been largely neglected in studies of domestication. Ongoing work demonstrates the importance of CNVs as a source of genetic variation during domestication, and during the diversification of domesticated taxa. Here, we review how CNVs contribute to evolutionary processes underlying domestication, and review examples of domestication traits caused by CNVs. We draw from examples in plant species, but also highlight cases in animal systems that could illuminate the roles of CNVs in the domestication process.
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Affiliation(s)
- Zoe N Lye
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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9
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Lambing C, Heckmann S. Tackling Plant Meiosis: From Model Research to Crop Improvement. FRONTIERS IN PLANT SCIENCE 2018; 9:829. [PMID: 29971082 PMCID: PMC6018109 DOI: 10.3389/fpls.2018.00829] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/28/2018] [Indexed: 05/04/2023]
Abstract
Genetic engineering and traditional plant breeding, which harnesses the natural genetic variation that arises during meiosis, will have key roles to improve crop varieties and thus deliver Food Security in the future. Meiosis, a specialized cell division producing haploid gametes to maintain somatic diploidy following their fusion, assures genetic variation by regulated genetic exchange through homologous recombination. However, meiotic recombination events are restricted in their total number and their distribution along chromosomes limiting allelic variations in breeding programs. Thus, modifying the number and distribution of meiotic recombination events has great potential to improve and accelerate plant breeding. In recent years much progress has been made in understanding meiotic progression and recombination in plants. Many genes and factors involved in these processes have been identified primarily in Arabidopsis thaliana but also more recently in crops such as Brassica, rice, barley, maize, or wheat. These advances put researchers in the position to translate acquired knowledge to various crops likely improving and accelerating breeding programs. However, although fundamental aspects of meiotic progression and recombination are conserved between species, differences in genome size and organization (due to repetitive DNA content and ploidy level) exist, particularly among plants, that likely account for differences in meiotic progression and recombination patterns found between species. Thus, tools and approaches are needed to better understand differences and similarities in meiotic progression and recombination among plants, to study fundamental aspects of meiosis in a variety of plants including crops and non-model species, and to transfer knowledge into crop species. In this article, we provide an overview of tools and approaches available to study plant meiosis, highlight new techniques, give examples of areas of future research and review distinct aspects of meiosis in non-model species.
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Affiliation(s)
- Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Christophe Lambing, Stefan Heckmann,
| | - Stefan Heckmann
- Independent Research Group Meiosis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- *Correspondence: Christophe Lambing, Stefan Heckmann,
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Dolatabadian A, Patel DA, Edwards D, Batley J. Copy number variation and disease resistance in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2479-2490. [PMID: 29043379 DOI: 10.1007/s00122-017-2993-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 09/27/2017] [Indexed: 05/06/2023]
Abstract
Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning. Since CNVs are likely to be associated with disease resistance in plants, an understanding of the distribution of CNVs could assist in the identification of novel plant disease-resistance genes. In this paper, we review existing information about CNVs; their importance, role and function, as well as their association with disease resistance in plants.
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Affiliation(s)
- Aria Dolatabadian
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Dhwani Apurva Patel
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia.
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Martins WFS, Subramaniam K, Steen K, Mawejje H, Liloglou T, Donnelly MJ, Wilding CS. Detection and quantitation of copy number variation in the voltage-gated sodium channel gene of the mosquito Culex quinquefasciatus. Sci Rep 2017; 7:5821. [PMID: 28725028 PMCID: PMC5517494 DOI: 10.1038/s41598-017-06080-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/07/2017] [Indexed: 01/23/2023] Open
Abstract
Insecticide resistance is typically associated with alterations to the insecticidal target-site or with gene expression variation at loci involved in insecticide detoxification. In some species copy number variation (CNV) of target site loci (e.g. the Ace-1 target site of carbamate insecticides) or detoxification genes has been implicated in the resistance phenotype. We show that field-collected Ugandan Culex quinquefasciatus display CNV for the voltage-gated sodium channel gene (Vgsc), target-site of pyrethroid and organochlorine insecticides. In order to develop field-applicable diagnostics for Vgsc CN, and as a prelude to investigating the possible association of CN with insecticide resistance, three assays were compared for their accuracy in CN estimation in this species. The gold standard method is droplet digital PCR (ddPCR), however, the hardware is prohibitively expensive for widespread utility. Here, ddPCR was compared to quantitative PCR (qPCR) and pyrosequencing. Across all platforms, CNV was detected in ≈10% of mosquitoes, corresponding to three or four copies (per diploid genome). ddPCR and qPCR-Std-curve yielded similar predictions for Vgsc CN, indicating that the qPCR protocol developed here can be applied as a diagnostic assay, facilitating monitoring of Vgsc CN in wild populations and the elucidation of association between the Vgsc CN and insecticide resistance.
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Affiliation(s)
- Walter Fabricio Silva Martins
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Departamento de Biologia, Universidade Estadual da Paraíba, Campina Grande, Brazil
| | | | - Keith Steen
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Henry Mawejje
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Triantafillos Liloglou
- Department of Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research, Liverpool, UK
| | - Martin James Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Malaria Programme, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Craig Stephen Wilding
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK.
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12
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Samelak-Czajka A, Marszalek-Zenczak M, Marcinkowska-Swojak M, Kozlowski P, Figlerowicz M, Zmienko A. MLPA-Based Analysis of Copy Number Variation in Plant Populations. FRONTIERS IN PLANT SCIENCE 2017; 8:222. [PMID: 28270823 PMCID: PMC5318451 DOI: 10.3389/fpls.2017.00222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/06/2017] [Indexed: 05/18/2023]
Abstract
Copy number variants (CNVs) are intraspecies duplications/deletions of large DNA segments (>1 kb). A growing number of reports highlight the functional and evolutionary impact of CNV in plants, increasing the need for appropriate tools that enable locus-specific CNV genotyping on a population scale. Multiplex ligation-dependent probe amplification (MLPA) is considered a gold standard in genotyping CNV in humans. Consequently, numerous commercial MLPA assays for CNV-related human diseases have been created. We routinely genotype complex multiallelic CNVs in human and plant genomes using the modified MLPA procedure based on fully synthesized oligonucleotide probes (90-200 nt), which greatly simplifies the design process and allows for the development of custom assays. Here, we present a step-by-step protocol for gene-specific MLPA probe design, multiplexed assay setup and data analysis in a copy number genotyping experiment in plants. As a case study, we present the results of a custom assay designed to genotype the copy number status of 12 protein coding genes in a population of 80 Arabidopsis accessions. The genes were pre-selected based on whole genome sequencing data and are localized in the genomic regions that display different levels of population-scale variation (non-variable, biallelic, or multiallelic, as well as CNVs overlapping whole genes or their fragments). The presented approach is suitable for population-scale validation of the CNV regions inferred from whole genome sequencing data analysis and for focused analysis of selected genes of interest. It can also be very easily adopted for any plant species, following optimization of the template amount and design of the appropriate control probes, according to the general guidelines presented in this paper.
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Affiliation(s)
- Anna Samelak-Czajka
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
| | - Malgorzata Marszalek-Zenczak
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | | | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Marek Figlerowicz
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Agnieszka Zmienko
- Institute of Computing Science, Faculty of Computing, Poznan University of TechnologyPoznan, Poland
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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