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Hannan Parker A, Wilkinson SW, Ton J. Epigenetics: a catalyst of plant immunity against pathogens. THE NEW PHYTOLOGIST 2022; 233:66-83. [PMID: 34455592 DOI: 10.1111/nph.17699] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/20/2021] [Indexed: 05/11/2023]
Abstract
The plant immune system protects against pests and diseases. The recognition of stress-related molecular patterns triggers localised immune responses, which are often followed by longer-lasting systemic priming and/or up-regulation of defences. In some cases, this induced resistance (IR) can be transmitted to following generations. Such transgenerational IR is gradually reversed in the absence of stress at a rate that is proportional to the severity of disease experienced in previous generations. This review outlines the mechanisms by which epigenetic responses to pathogen infection shape the plant immune system across expanding time scales. We review the cis- and trans-acting mechanisms by which stress-inducible epigenetic changes at transposable elements (TEs) regulate genome-wide defence gene expression and draw particular attention to one regulatory model that is supported by recent evidence about the function of AGO1 and H2A.Z in transcriptional control of defence genes. Additionally, we explore how stress-induced mobilisation of epigenetically controlled TEs acts as a catalyst of Darwinian evolution by generating (epi)genetic diversity at environmentally responsive genes. This raises questions about the long-term evolutionary consequences of stress-induced diversification of the plant immune system in relation to the long-held dichotomy between Darwinian and Lamarckian evolution.
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Affiliation(s)
- Adam Hannan Parker
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
| | - Samuel W Wilkinson
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jurriaan Ton
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
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Lemay MA, Malle S. A Practical Guide to Using Structural Variants for Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:161-172. [PMID: 35641764 DOI: 10.1007/978-1-0716-2237-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Structural variants (SVs) are known to have large functional impacts on phenotypes of agricultural interest, but they have yet to be routinely used for GWAS. Apart from the difficulty in obtaining high-quality SV genotype data for large populations, one of the main hurdles to using SVs for GWAS lies in formatting of genotype data for use with popular GWAS programs. This protocol describes how typical SV genotype data can be formatted for input to three GWAS programs commonly used by the plant genetics community: TASSEL, GAPIT, and mrMLM.
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Affiliation(s)
- Marc-André Lemay
- Département de phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, QC, Canada.
| | - Sidiki Malle
- Institut Polytechnique Rural de Formation et de Recherche Appliquée De Katibougou, Koulikoro, Mali
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Kirov I, Merkulov P, Dudnikov M, Polkhovskaya E, Komakhin RA, Konstantinov Z, Gvaramiya S, Ermolaev A, Kudryavtseva N, Gilyok M, Divashuk MG, Karlov GI, Soloviev A. Transposons Hidden in Arabidopsis thaliana Genome Assembly Gaps and Mobilization of Non-Autonomous LTR Retrotransposons Unravelled by Nanotei Pipeline. PLANTS (BASEL, SWITZERLAND) 2021; 10:2681. [PMID: 34961152 PMCID: PMC8704663 DOI: 10.3390/plants10122681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/26/2021] [Accepted: 12/02/2021] [Indexed: 06/12/2023]
Abstract
Long-read data is a great tool to discover new active transposable elements (TEs). However, no ready-to-use tools were available to gather this information from low coverage ONT datasets. Here, we developed a novel pipeline, nanotei, that allows detection of TE-contained structural variants, including individual TE transpositions. We exploited this pipeline to identify TE insertion in the Arabidopsis thaliana genome. Using nanotei, we identified tens of TE copies, including ones for the well-characterized ONSEN retrotransposon family that were hidden in genome assembly gaps. The results demonstrate that some TEs are inaccessible for analysis with the current A. thaliana (TAIR10.1) genome assembly. We further explored the mobilome of the ddm1 mutant with elevated TE activity. Nanotei captured all TEs previously known to be active in ddm1 and also identified transposition of non-autonomous TEs. Of them, one non-autonomous TE derived from (AT5TE33540) belongs to TR-GAG retrotransposons with a single open reading frame (ORF) encoding the GAG protein. These results provide the first direct evidence that TR-GAGs and other non-autonomous LTR retrotransposons can transpose in the plant genome, albeit in the absence of most of the encoded proteins. In summary, nanotei is a useful tool to detect active TEs and their insertions in plant genomes using low-coverage data from Nanopore genome sequencing.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Maxim Dudnikov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Ekaterina Polkhovskaya
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Roman A. Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Zakhar Konstantinov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Sofya Gvaramiya
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Aleksey Ermolaev
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia; (A.E.); (N.K.)
| | - Natalya Kudryavtseva
- Center of Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, 127550 Moscow, Russia; (A.E.); (N.K.)
| | - Marina Gilyok
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
| | - Alexander Soloviev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (P.M.); (M.D.); (E.P.); (R.A.K.); (Z.K.); (S.G.); (M.G.); (M.G.D.); (G.I.K.); (A.S.)
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Tonnessen BW, Bossa-Castro AM, Martin F, Leach JE. Intergenic spaces: a new frontier to improving plant health. THE NEW PHYTOLOGIST 2021; 232:1540-1548. [PMID: 34478160 DOI: 10.1111/nph.17706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
To more sustainably mitigate the impact of crop diseases on plant health and productivity, there is a need for broader spectrum, long-lasting resistance traits. Defense response (DR) genes, located throughout the genome, participate in cellular and system-wide defense mechanisms to stave off infection by diverse pathogens. This multigenic resistance avoids rapid evolution of a pathogen to overcome host resistance. DR genes reside within resistance-associated quantitative trait loci (QTL), and alleles of DR genes in resistant varieties are more active during pathogen attack relative to susceptible haplotypes. Differential expression of DR genes results from polymorphisms in their regulatory regions, that includes cis-regulatory elements such as transcription factor binding sites as well as features that influence epigenetic structural changes to modulate chromatin accessibility during infection. Many of these elements are found in clusters, known as cis-regulatory modules (CRMs), which are distributed throughout the host genome. Regulatory regions involved in plant-pathogen interactions may also contain pathogen effector binding elements that regulate DR gene expression, and that, when mutated, result in a change in the plants' response. We posit that CRMs and the multiple regulatory elements that comprise them are potential targets for marker-assisted breeding for broad-spectrum, durable disease resistance.
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Affiliation(s)
- Bradley W Tonnessen
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
- Western Colorado Research Center, Colorado State University, 30624 Hwy 92, Hotchkiss, CO, 81419, USA
| | - Ana M Bossa-Castro
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
- Universidad de los Andes, Bogotá, 111711, Colombia
| | - Federico Martin
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jan E Leach
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
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55
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Fuentes RR, de Ridder D, van Dijk ADJ, Peters SA. Domestication shapes recombination patterns in tomato. Mol Biol Evol 2021; 39:6379725. [PMID: 34597400 PMCID: PMC8763028 DOI: 10.1093/molbev/msab287] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Meiotic recombination is a biological process of key importance in breeding, to generate genetic diversity and develop novel or agronomically relevant haplotypes. In crop tomato, recombination is curtailed as manifested by linkage disequilibrium decay over a longer distance and reduced diversity compared with wild relatives. Here, we compared domesticated and wild populations of tomato and found an overall conserved recombination landscape, with local changes in effective recombination rate in specific genomic regions. We also studied the dynamics of recombination hotspots resulting from domestication and found that loss of such hotspots is associated with selective sweeps, most notably in the pericentromeric heterochromatin. We detected footprints of genetic changes and structural variants, among them associated with transposable elements, linked with hotspot divergence during domestication, likely causing fine-scale alterations to recombination patterns and resulting in linkage drag.
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Affiliation(s)
- Roven Rommel Fuentes
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB The Netherlands
| | - Sander A Peters
- Applied Bioinformatics, Wageningen Plant Research, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
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56
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Liu Z, Zhao H, Yan Y, Wei MX, Zheng YC, Yue EK, Alam MS, Smartt KO, Duan MH, Xu JH. Extensively Current Activity of Transposable Elements in Natural Rice Accessions Revealed by Singleton Insertions. FRONTIERS IN PLANT SCIENCE 2021; 12:745526. [PMID: 34650583 PMCID: PMC8505701 DOI: 10.3389/fpls.2021.745526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/08/2021] [Indexed: 06/01/2023]
Abstract
Active transposable elements (TEs) have drawn more attention as they continue to create new insertions and contribute to genetic diversity of the genome. However, only a few have been discovered in rice up to now, and their activities are mostly induced by artificial treatments (e.g., tissue culture, hybridization etc.) rather than under normal growth conditions. To systematically survey the current activity of TEs in natural rice accessions and identify rice accessions carrying highly active TEs, the transposon insertion polymorphisms (TIPs) profile was used to identify singleton insertions, which were unique to a single accession and represented the new insertion of TEs in the genome. As a result, 10,924 high-confidence singletons from 251 TE families were obtained, covering all investigated TE types. The number of singletons varied substantially among different superfamilies/families, perhaps reflecting distinct current activity. Particularly, eight TE families maintained potentially higher activity in 3,000 natural rice accessions. Sixty percent of rice accessions were detected to contain singletons, indicating the extensive activity of TEs in natural rice accessions. Thirty-five TE families exhibited potentially high activity in at least one rice accession, and the majority of them showed variable activity among different rice groups/subgroups. These naturally active TEs would be ideal candidates for elucidating the molecular mechanisms underlying the transposition and activation of TEs, as well as investigating the interactions between TEs and the host genome.
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Affiliation(s)
- Zhen Liu
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Han Zhao
- Jiangsu Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yan Yan
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Ming-Xiao Wei
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Yun-Chao Zheng
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Er-Kui Yue
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mohammad Shah Alam
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Kwesi Odel Smartt
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Ming-Hua Duan
- Zhejiang Zhengjingyuan Pharmacy Chain Co., Ltd., Hangzhou, China
- Hangzhou Zhengcaiyuan Pharmaceutical Co., Ltd., Hangzhou, China
| | - Jian-Hong Xu
- Hainan Institute, Zhejiang University, Sanya, China
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou, China
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57
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Qiu Y, O’Connor CH, Della Coletta R, Renk JS, Monnahan PJ, Noshay JM, Liang Z, Gilbert A, Anderson SN, McGaugh SE, Springer NM, Hirsch CN. Whole-genome variation of transposable element insertions in a maize diversity panel. G3 (BETHESDA, MD.) 2021; 11:jkab238. [PMID: 34568911 PMCID: PMC8473971 DOI: 10.1093/g3journal/jkab238] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023]
Abstract
Intact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome-wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short-read sequencing data from 509 diverse inbred lines to classify the presence/absence of 445,418 nonredundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e., LTRs, Helitrons, and TIRs) had different frequency distributions within the population. LTRs with lower LTR similarity were generally more frequent in the population than LTRs with higher LTR similarity, though high-frequency insertions with very high LTR similarity were observed. LTR similarity and frequency estimates of nested elements and the outer elements in which they insert revealed that most nesting events occurred very near the timing of the outer element insertion. TEs within genes were at higher frequency than those that were outside of genes and this is particularly true for those not inserted into introns. Many TE insertional polymorphisms observed in this population were tagged by SNP markers. However, there were also 19.9% of the TE polymorphisms that were not well tagged by SNPs (R2 < 0.5) that potentially represent information that has not been well captured in previous SNP-based marker-trait association studies. This study provides a population scale genome-wide assessment of TE variation in maize and provides valuable insight on variation in TEs in maize and factors that contribute to this variation.
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Affiliation(s)
- Yinjie Qiu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Christine H O’Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Jonathan S Renk
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Patrick J Monnahan
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Zhikai Liang
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Amanda Gilbert
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sarah N Anderson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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Fernie AR, Alseekh S, Liu J, Yan J. Using precision phenotyping to inform de novo domestication. PLANT PHYSIOLOGY 2021; 186:1397-1411. [PMID: 33848336 PMCID: PMC8260140 DOI: 10.1093/plphys/kiab160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/22/2021] [Indexed: 05/09/2023]
Abstract
An update on the use of precision phenotyping to assess the potential of lesser cultivated species as candidates for de novo domestication or similar development for future agriculture.
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Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Author for communication: (A.R.F.)
| | - Saleh Alseekh
- Max Planck Institute for Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
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Castanera R, Vendrell-Mir P, Bardil A, Carpentier MC, Panaud O, Casacuberta JM. Amplification dynamics of miniature inverted-repeat transposable elements and their impact on rice trait variability. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:118-135. [PMID: 33866641 DOI: 10.1111/tpj.15277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted-repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut-and-paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103 109 transposon insertion polymorphisms (TIPs) in 738 Oryza sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-genome-wide association studies (TIP-GWAS) to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than single nucleotide polymorphisms (SNPs) on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidence of the replicative amplification of MITEs.
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Affiliation(s)
- Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Pol Vendrell-Mir
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex, 66860, France
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy, Perpignan Cedex, 66860, France
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona, 08193, Spain
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60
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A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome. Genes (Basel) 2021; 12:genes12060859. [PMID: 34205210 PMCID: PMC8227079 DOI: 10.3390/genes12060859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/26/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack of coding capacity, the identification of MITEs has been demanding. However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes. We mined MITEs in the carrot reference genome DH1 using MITE-hunter and developed a curated carrot MITE repository comprising 428 families. Of the 31,025 MITE copies spanning 10.34 Mbp of the carrot genome, 54% were positioned in genic regions. Stowaways and Tourists were frequently present in the vicinity of genes, while Mutator-like MITEs were relatively more enriched in introns. hAT-like MITEs were relatively more frequently associated with transcribed regions, including untranslated regions (UTRs). Some carrot MITE families were shared with other Apiaceae species. We showed that hAT-like MITEs were involved in the formation of new splice variants of insertion-harboring genes. Thus, carrot MITEs contributed to the accretion of new diversity by altering transcripts and possibly affecting the regulation of many genes.
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Baduel P, Quadrana L. Jumpstarting evolution: How transposition can facilitate adaptation to rapid environmental changes. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102043. [PMID: 33932785 DOI: 10.1016/j.pbi.2021.102043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/10/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Because of their ability to replicate across genomes, transposable elements (TEs) represent major generators of large-effect mutations. As a result, chromatin-based mechanisms have evolved to control the mutational potential of TEs at multiple levels, from the epigenetic silencing of TE sequences, through the modulation of their integration space, up to the alleviation of the impact of new insertions. Although most TE insertions are highly deleterious, some can provide key adaptive variation. Together with their remarkable sensitivity to the environment and precise integration preferences, the unique characteristics of TEs place them as potent genomic engines of adaptive innovation. Herein, we review recent works exploring the regulation and impact of transposition in nature and discuss their implications for the evolutionary response of species to drastic environmental changes.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Leandro Quadrana
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
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Alseekh S, Scossa F, Wen W, Luo J, Yan J, Beleggia R, Klee HJ, Huang S, Papa R, Fernie AR. Domestication of Crop Metabolomes: Desired and Unintended Consequences. TRENDS IN PLANT SCIENCE 2021; 26:650-661. [PMID: 33653662 DOI: 10.1016/j.tplants.2021.02.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 05/02/2023]
Abstract
The majority of the crops and vegetables of today were domesticated from their wild progenitors within the past 12 000 years. Considerable research effort has been expended on characterizing the genes undergoing positive and negative selection during the processes of crop domestication and improvement. Many studies have also documented how the contents of a handful of metabolites have been altered during human selection, but we are only beginning to unravel the true extent of the metabolic consequences of breeding. We highlight how crop metabolomes have been wittingly or unwittingly shaped by the processes of domestication, and highlight how we can identify new targets for metabolite engineering for the purpose of de novo domestication of crop wild relatives.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy
| | - Weiwei Wen
- Key laboratory of Horticultural Plant Biology (MOE),College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Hubei, Wuhan 430070, China
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China; College of Tropical Crops, Hainan University, Haikou, Hainan, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University Hubei, Wuhan 430070, China
| | - Romina Beleggia
- Council for Agricultural Research and Economics (CREA), Research Centre for Cereal and Industrial Crops (CREA-, CI), 71122 Foggia, Italy
| | - Harry J Klee
- Horticultural Sciences, University of Florida, Gainesville, FL, USA
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture - Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
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63
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Baduel P, Leduque B, Ignace A, Gy I, Gil J, Loudet O, Colot V, Quadrana L. Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana. Genome Biol 2021; 22:138. [PMID: 33957946 PMCID: PMC8101250 DOI: 10.1186/s13059-021-02348-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/09/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND How species can adapt to abrupt environmental changes, particularly in the absence of standing genetic variation, is poorly understood and a pressing question in the face of ongoing climate change. Here we leverage publicly available multi-omic and bio-climatic data for more than 1000 wild Arabidopsis thaliana accessions to determine the rate of transposable element (TE) mobilization and its potential to create adaptive variation in natural settings. RESULTS We demonstrate that TE insertions arise at almost the same rate as base substitutions. Mobilization activity of individual TE families varies greatly between accessions, in association with genetic and environmental factors as well as through complex gene-environment interactions. Although the distribution of TE insertions across the genome is ultimately shaped by purifying selection, reflecting their typically strong deleterious effects when located near or within genes, numerous recent TE-containing alleles show signatures of positive selection. Moreover, high rates of transposition appear positively selected at the edge of the species' ecological niche. Based on these findings, we predict through mathematical modeling higher transposition activity in Mediterranean regions within the next decades in response to global warming, which in turn should accelerate the creation of large-effect alleles. CONCLUSIONS Our study reveals that TE mobilization is a major generator of genetic variation in A. thaliana that is finely modulated by genetic and environmental factors. These findings and modeling indicate that TEs may be essential genomic players in the demise or rescue of native populations in times of climate crises.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Basile Leduque
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Amandine Ignace
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Isabelle Gy
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - José Gil
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
- Present Address: Institut Curie, 26 rue d'Ulm, 75005, Paris, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Vincent Colot
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
| | - Leandro Quadrana
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
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64
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Genome-Wide Variation in DNA Methylation Predicts Variation in Leaf Traits in an Ecosystem-Foundational Oak Species. FORESTS 2021. [DOI: 10.3390/f12050569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications such as DNA methylation are a potential mechanism for trees to respond to changing environments. However, it remains controversial the extent to which DNA methylation impacts ecologically important traits that influence fitness. In this study, we used reduced-representation bisulfite sequencing to associate genomic and epigenomic variation with seven phenotypic traits related to growth, leaf function, and disease susceptibility in 160 valley oak (Quercus lobata) saplings planted across two common gardens in California. We found that DNA methylation was associated with a significant fraction of phenotypic variance in plant height, leaf lobedness, powdery mildew infection, and trichome density. Two of the seven traits were significantly associated with DNA methylation in the CG context, three traits were significantly associated with CHG methylation, and two traits were significantly associated with CHH methylation. Notably, controlling for genomic variation in SNPs generally reduced the amount of trait variation explained by DNA methylation. Our results suggest that DNA methylation may serve as a useful biomarker to predict phenotypic variation in trees, though it remains unclear the degree to which DNA methylation is a causal mechanism driving phenotypic variation in forest tree species.
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65
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Li M, Noshay JM, Dong X, Springer NM, Li Q. A capture-based assay for detection and characterization of transposon polymorphisms in maize. G3-GENES GENOMES GENETICS 2021; 11:6255745. [PMID: 33905487 PMCID: PMC8495914 DOI: 10.1093/g3journal/jkab138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 04/15/2021] [Indexed: 11/14/2022]
Abstract
Transposons can create allelic diversity that affects gene expression and phenotypic diversity. The detection of transposon polymorphisms at a genome-wide scale across a large population is difficult. Here we developed a targeted sequencing approach to monitor transposon polymorphisms of interest. This approach can interrogate the presence or absence of transposons reliably across various genotypes. Using this approach, we genotyped a set of 965 transposon-related presence/absence polymorphisms in a diverse panel of 16 maize (Zea mays L.) inbred lines that are representative of the major maize breeding groups. About 70% of the selected regions can be effectively assayed in each genotype. The consistency between the capture-based assay and PCR-based assay are 98.6% based on analysis of 24 randomly selected transposon polymorphisms. By integrating the transposon polymorphisms data with gene expression data, ∼18% of the assayed transposon polymorphisms were found to be associated with variable gene expression levels. A detailed analysis of 18 polymorphisms in a larger association panel confirmed the effects of 10 polymorphisms, with one of them having stronger association with expression than nearby SNP markers. The effects of seven polymorphisms were tested using a luciferase-based expression assay, and one was confirmed. Together, this study demonstrates that the targeted sequencing assay is an effective way to explore transposon function in a high-throughput manner.
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Affiliation(s)
- Minqi Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jaclyn M Noshay
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Xiaoxiao Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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66
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Liu S, Gao G, Layer RM, Thorgaard GH, Wiens GD, Leeds TD, Martin KE, Palti Y. Identification of High-Confidence Structural Variants in Domesticated Rainbow Trout Using Whole-Genome Sequencing. Front Genet 2021; 12:639355. [PMID: 33732289 PMCID: PMC7959816 DOI: 10.3389/fgene.2021.639355] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout (Oncorhynchus mykiss), an important aquaculture species of cold freshwater. The objectives of this study were 1) to identify and validate high-confidence SVs in rainbow trout using whole-genome re-sequencing; and 2) to examine the contribution of transposable elements (TEs) to SVs in rainbow trout. A total of 96 rainbow trout, including 11 homozygous lines and 85 outbred fish from three breeding populations, were whole-genome sequenced with an average genome coverage of 17.2×. Putative SVs were identified using the program Smoove which integrates LUMPY and other associated tools into one package. After rigorous filtering, 13,863 high-confidence SVs were identified. Pacific Biosciences long-reads of Arlee, one of the homozygous lines used for SV detection, validated 98% (3,948 of 4,030) of the high-confidence SVs identified in the Arlee homozygous line. Based on principal component analysis, the 85 outbred fish clustered into three groups consistent with their populations of origin, further indicating that the high-confidence SVs identified in this study are robust. The repetitive DNA content of the high-confidence SV sequences was 86.5%, which is much higher than the 57.1% repetitive DNA content of the reference genome, and is also higher than the repetitive DNA content of Atlantic salmon SVs reported previously. TEs thus contribute substantially to SVs in rainbow trout as TEs make up the majority of repetitive sequences. Hundreds of the high-confidence SVs were annotated as exon-loss or gene-fusion variants, and may have phenotypic effects. The high-confidence SVs reported in this study provide a foundation for further rainbow trout SV studies.
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Affiliation(s)
- Sixin Liu
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | - Ryan M Layer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States.,Department of Computer Science, University of Colorado Boulder, Boulder, CO, United States
| | - Gary H Thorgaard
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Gregory D Wiens
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | - Timothy D Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | | | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
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67
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Scossa F, Alseekh S, Fernie AR. Integrating multi-omics data for crop improvement. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153352. [PMID: 33360148 DOI: 10.1016/j.jplph.2020.153352] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 05/26/2023]
Abstract
Our agricultural systems are now in urgent need to secure food for a growing world population. To meet this challenge, we need a better characterization of plant genetic and phenotypic diversity. The combination of genomics, transcriptomics and metabolomics enables a deeper understanding of the mechanisms underlying the complex architecture of many phenotypic traits of agricultural relevance. We review the recent advances in plant genomics to see how these can be integrated with broad molecular profiling approaches to improve our understanding of plant phenotypic variation and inform crop breeding strategies.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), 00178, Rome, Italy.
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476, Potsdam, Golm, Germany; Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria.
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68
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Alseekh S, Scossa F, Fernie AR. Mobile Transposable Elements Shape Plant Genome Diversity. TRENDS IN PLANT SCIENCE 2020; 25:1062-1064. [PMID: 32863103 DOI: 10.1016/j.tplants.2020.08.003] [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: 07/19/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 05/27/2023]
Abstract
The presence of various types of structural variants, including transposons, make up the major part of the genomic differences among plant species. Two recent papers, Domínguez et al. and Alonge et al. explore specifically the impact that retrotransposons and other structural variants had on several tomato phenotypes of agricultural importance.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, Plovdiv, 4000, Bulgaria
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Rome, Italy
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, Plovdiv, 4000, Bulgaria.
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69
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Roohanitaziani R, de Maagd RA, Lammers M, Molthoff J, Meijer-Dekens F, van Kaauwen MPW, Finkers R, Tikunov Y, Visser RGF, Bovy AG. Exploration of a Resequenced Tomato Core Collection for Phenotypic and Genotypic Variation in Plant Growth and Fruit Quality Traits. Genes (Basel) 2020; 11:genes11111278. [PMID: 33137951 PMCID: PMC7692805 DOI: 10.3390/genes11111278] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/21/2020] [Indexed: 02/04/2023] Open
Abstract
A tomato core collection consisting of 122 gene bank accessions, including landraces, old cultivars, and wild relatives, was explored for variation in several plant growth, yield and fruit quality traits. The resequenced accessions were also genotyped with respect to a number of mutations or variations in key genes known to underlie these traits. The yield-related traits fruit number and fruit weight were much higher in cultivated varieties when compared to wild accessions, while, in wild tomato accessions, Brix was higher than in cultivated varieties. Known mutations in fruit size and shape genes could well explain the fruit size variation, and fruit colour variation could be well explained by known mutations in key genes of the carotenoid and flavonoid pathway. The presence and phenotype of several plant architecture affecting mutations, such as self-pruning (sp), compound inflorescence (s), jointless-2 (j-2), and potato leaf (c) were also confirmed. This study provides valuable phenotypic information on important plant growth- and quality-related traits in this collection. The allelic distribution of known genes that underlie these traits provides insight into the role and importance of these genes in tomato domestication and breeding. This resource can be used to support (precision) breeding strategies for tomato crop improvement.
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Affiliation(s)
- Raana Roohanitaziani
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
- Graduate School Experimental Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Ruud A. de Maagd
- Bioscience, Wageningen University & Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands; (R.A.d.M.); (M.L.)
| | - Michiel Lammers
- Bioscience, Wageningen University & Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands; (R.A.d.M.); (M.L.)
| | - Jos Molthoff
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Fien Meijer-Dekens
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Martijn P. W. van Kaauwen
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Richard G. F. Visser
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
| | - Arnaud G. Bovy
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (R.R.); (J.M.); (F.M.-D.); (M.P.W.v.K.); (R.F.); (Y.T.); (R.G.F.V.)
- Correspondence: ; Tel.: +31-317-480762
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70
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Kundariya H, Yang X, Morton K, Sanchez R, Axtell MJ, Hutton SF, Fromm M, Mackenzie SA. MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants. Nat Commun 2020; 11:5343. [PMID: 33093443 PMCID: PMC7582163 DOI: 10.1038/s41467-020-19140-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/24/2020] [Indexed: 12/20/2022] Open
Abstract
Plants transmit signals long distances, as evidenced in grafting experiments that create distinct rootstock-scion junctions. Noncoding small RNA is a signaling molecule that is graft transmissible, participating in RNA-directed DNA methylation; but the meiotic transmissibility of graft-mediated epigenetic changes remains unclear. Here, we exploit the MSH1 system in Arabidopsis and tomato to introduce rootstock epigenetic variation to grafting experiments. Introducing mutations dcl2, dcl3 and dcl4 to the msh1 rootstock disrupts siRNA production and reveals RdDM targets of methylation repatterning. Progeny from grafting experiments show enhanced growth vigor relative to controls. This heritable enhancement-through-grafting phenotype is RdDM-dependent, involving 1380 differentially methylated genes, many within auxin-related gene pathways. Growth vigor is associated with robust root growth of msh1 graft progeny, a phenotype associated with auxin transport based on inhibitor assays. Large-scale field experiments show msh1 grafting effects on tomato plant performance, heritable over five generations, demonstrating the agricultural potential of epigenetic variation. The meiotic transmissibility and progeny phenotypic influence of graft-mediated epigenetic changes remain unclear. Here, the authors use the msh1 mutant in the rootstock to trigger heritable enhanced growth vigor in Arabidopsis and tomato, and show it is associated with the RNA-directed DNA methylation pathway.
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Affiliation(s)
- Hardik Kundariya
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.,Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Xiaodong Yang
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Kyla Morton
- EpiCrop Technologies, Inc., Lincoln, NE, USA
| | - Robersy Sanchez
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Samuel F Hutton
- Gulf Coast Research and Education Center, IFAS, University of Florida, Wimauma, FL, USA
| | | | - Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, University Park, PA, USA.
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71
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Quadrana L. The contribution of transposable elements to transcriptional novelty in plants: the FLC affair. Transcription 2020; 11:192-198. [PMID: 32783496 PMCID: PMC7714446 DOI: 10.1080/21541264.2020.1803031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences with the ability to replicate across genomes and generate mutations with major transcriptional effects. Epigenetic silencing mechanisms that target TEs to limit their activity, including DNA methylation, add to the range of gene expression variants generated by TEs. Here, using the iconic gene flowering locus C (FLC) as a case study I discuss the multiple ways by which TEs can affect the expression of genes and contribute to the adaptation of plants to changing environments
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Affiliation(s)
- Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University , Paris, France
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