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Gebhardt C. A physical map of traits of agronomic importance based on potato and tomato genome sequences. Front Genet 2023; 14:1197206. [PMID: 37564870 PMCID: PMC10411547 DOI: 10.3389/fgene.2023.1197206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/30/2023] [Indexed: 08/12/2023] Open
Abstract
Potato, tomato, pepper, and eggplant are worldwide important crop and vegetable species of the Solanaceae family. Molecular linkage maps of these plants have been constructed and used to map qualitative and quantitative traits of agronomic importance. This research has been undertaken with the vision to identify the molecular basis of agronomic characters on the one hand, and on the other hand, to assist the selection of improved varieties in breeding programs by providing DNA-based markers that are diagnostic for specific agronomic characters. Since 2011, whole genome sequences of tomato and potato became available in public databases. They were used to combine the results of several hundred mapping and map-based cloning studies of phenotypic characters between 1988 and 2022 in physical maps of the twelve tomato and potato chromosomes. The traits evaluated were qualitative and quantitative resistance to pathogenic oomycetes, fungi, bacteria, viruses, nematodes, and insects. Furthermore, quantitative trait loci for yield and sugar content of tomato fruits and potato tubers and maturity or earliness were physically mapped. Cloned genes for pathogen resistance, a few genes underlying quantitative trait loci for yield, sugar content, and maturity, and several hundred candidate genes for these traits were included in the physical maps. The comparison between the physical chromosome maps revealed, in addition to known intrachromosomal inversions, several additional inversions and translocations between the otherwise highly collinear tomato and potato genomes. The integration of the positional information from independent mapping studies revealed the colocalization of qualitative and quantitative loci for resistance to different types of pathogens, called resistance hotspots, suggesting a similar molecular basis. Synteny between potato and tomato with respect to genomic positions of quantitative trait loci was frequently observed, indicating eventual similarity between the underlying genes.
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Peters SA, Underwood CJ. Technology-driven approaches for meiosis research in tomato and wild relatives. PLANT REPRODUCTION 2023; 36:97-106. [PMID: 36149478 PMCID: PMC9957858 DOI: 10.1007/s00497-022-00450-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Meiosis is a specialized cell division during reproduction where one round of chromosomal replication is followed by genetic recombination and two rounds of segregation to generate recombined, ploidy-reduced spores. Meiosis is crucial to the generation of new allelic combinations in natural populations and artificial breeding programs. Several plant species are used in meiosis research including the cultivated tomato (Solanum lycopersicum) which is a globally important crop species. Here we outline the unique combination of attributes that make tomato a powerful model system for meiosis research. These include the well-characterized behavior of chromosomes during tomato meiosis, readily available genomics resources, capacity for genome editing, clonal propagation techniques, lack of recent polyploidy and the possibility to generate hybrids with twelve related wild species. We propose that further exploitation of genome bioinformatics, genome editing and artificial intelligence in tomato will help advance the field of plant meiosis research. Ultimately this will help address emerging themes including the evolution of meiosis, how recombination landscapes are determined, and the effect of temperature on meiosis.
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Affiliation(s)
- Sander A Peters
- Business Unit Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Charles J Underwood
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
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D'Amelia V, Staiti A, D'Orso F, Maisto M, Piccolo V, Aversano R, Carputo D. Targeted mutagenesis of StISAC stabilizes the production of anthocyanins in potato cell culture. PLANT DIRECT 2022; 6:e433. [PMID: 35949953 PMCID: PMC9352536 DOI: 10.1002/pld3.433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/15/2022] [Indexed: 05/31/2023]
Abstract
To increase the production of decorated anthocyanins in potato cell cultures, we knocked out a novel potato gene, named Inducer Silencing of Anthocyanins in Cell culture (StISAC), using CRISPR-Cas9 editing. Our results provided evidence that mutant cell lines doubled the accumulation level of anthocyanins biosynthesized. Moreover, the production of these important pigments was stabilized over time. Our study overcame important challenges in the efficient biotechnological production of these valuable pigments and reported the function of a novel anthocyanin biosynthesis repressor gene.
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Affiliation(s)
- Vincenzo D'Amelia
- Institute of Biosciences and Bioresources (IBBR)National Research Council of ItalyPorticiItaly
| | - Annalisa Staiti
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
| | - Fabio D'Orso
- Research Centre for Genomics and Bioinformatics (CREA‐GB)Council for Agricultural Research and EconomicsRomeItaly
| | - Maria Maisto
- Department of PharmacyUniversity of Naples Federico IINaplesItaly
| | - Vincenzo Piccolo
- Department of PharmacyUniversity of Naples Federico IINaplesItaly
| | - Riccardo Aversano
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
| | - Domenico Carputo
- Department of Agricultural SciencesUniversity of Naples Federico IIPorticiItaly
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Meng Z, Wang Q, Khurshid H, Raza G, Han J, Wang B, Wang K. Chromosome Painting Provides Insights Into the Genome Structure and Evolution of Sugarcane. FRONTIERS IN PLANT SCIENCE 2021; 12:731664. [PMID: 34512706 PMCID: PMC8429501 DOI: 10.3389/fpls.2021.731664] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
The genus Saccharum is composed of species with high polyploidy and highly varied chromosome numbers, laying a challenge for uncovering its genomic structure and evolution. We developed a chromosome 2 painting (CP2) probe by designing oligonucleotides covering chromosome 2 of Saccharum spontaneum (2n = 8x = 64). Fluorescence in situ hybridization (FISH) using this CP2 probe revealed six types of ploidies from twenty S. spontaneum clones, including 6x, 8x, 10x, 11x, 12x, and 13x clones. The finding of S. spontaneum clones with uneven of ploid suggested that certain S. spontaneum clones come from hybridization. It renews our knowledge that S. spontaneum is derived from autopolyploidization. Combined with a S. spontaneum-specific probe, chromosome 2-derived chromosome or fragments from either S. spontaneum or Saccharum officinarum can be identified in sugarcane modern cultivars. We revealed unexpected high level of interspecific recombination from introgressive S. spontaneum chromosomes (>50.0%) in cultivars ROC22 and ZZ1, indicating frequent chromosome exchange in cultivars. Intriguingly, we observed interspecific recombination recurring among either homoeologous or non-homoeologous chromosomes in sugarcane cultivars. These results demonstrated that chromosome painting FISH is a powerful tool in the genome dissection of sugarcane and provide new insights into the genome structure and evolution of the complex genus Saccharum.
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Affiliation(s)
- Zhuang Meng
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinnan Wang
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Haris Khurshid
- Oilseeds Research Program, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ghulam Raza
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
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Agrawal N, Gupta M, Banga SS, Heslop-Harrison JS(P. Identification of Chromosomes and Chromosome Rearrangements in Crop Brassicas and Raphanus sativus: A Cytogenetic Toolkit Using Synthesized Massive Oligonucleotide Libraries. FRONTIERS IN PLANT SCIENCE 2020; 11:598039. [PMID: 33414797 PMCID: PMC7783396 DOI: 10.3389/fpls.2020.598039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/30/2020] [Indexed: 05/10/2023]
Abstract
Crop brassicas include three diploid [Brassica rapa (AA; 2n = 2x = 16), B. nigra (BB; 2n = 2x = 18), and B. oleracea (CC; 2n = 2x = 20)] and three derived allotetraploid species. It is difficult to distinguish Brassica chromosomes as they are small and morphologically similar. We aimed to develop a genome-sequence based cytogenetic toolkit for reproducible identification of Brassica chromosomes and their structural variations. A bioinformatic pipeline was used to extract repeat-free sequences from the whole genome assembly of B. rapa. Identified sequences were subsequently used to develop four c. 47-mer oligonucleotide libraries comprising 27,100, 11,084, 9,291, and 16,312 oligonucleotides. We selected these oligonucleotides after removing repeats from 18 identified sites (500-1,000 kb) with 1,997-5,420 oligonucleotides localized at each site in B. rapa. For one set of probes, a new method for amplification or immortalization of the library is described. oligonucleotide probes produced specific and reproducible in situ hybridization patterns for all chromosomes belonging to A, B, C, and R (Raphanus sativus) genomes. The probes were able to identify structural changes between the genomes, including translocations, fusions, and deletions. Furthermore, the probes were able to identify a structural translocation between a pak choi and turnip cultivar of B. rapa. Overall, the comparative chromosomal mapping helps understand the role of chromosome structural changes during genome evolution and speciation in the family Brassicaceae. The probes can also be used to identify chromosomes in aneuploids such as addition lines used for gene mapping, and to track transfer of chromosomes in hybridization and breeding programs.
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Affiliation(s)
- Neha Agrawal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Mehak Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder S. Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - JS (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Rommel Fuentes R, Hesselink T, Nieuwenhuis R, Bakker L, Schijlen E, van Dooijeweert W, Diaz Trivino S, de Haan JR, Sanchez Perez G, Zhang X, Fransz P, de Jong H, van Dijk ADJ, de Ridder D, Peters SA. Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:480-492. [PMID: 31820490 DOI: 10.1111/tpj.14640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Genome wide screening of pooled pollen samples from a single interspecific F1 hybrid obtained from a cross between tomato, Solanum lycopersicum and its wild relative, Solanum pimpinellifolium using linked read sequencing of the haploid nuclei, allowed profiling of the crossover (CO) and gene conversion (GC) landscape. We observed a striking overlap between cold regions of CO in the male gametes and our previously established F6 recombinant inbred lines (RILs) population. COs were overrepresented in non-coding regions in the gene promoter and 5'UTR regions of genes. Poly-A/T and AT rich motifs were found enriched in 1 kb promoter regions flanking the CO sites. Non-crossover associated allelic and ectopic GCs were detected in most chromosomes, confirming that besides CO, GC represents also a source for genetic diversity and genome plasticity in tomato. Furthermore, we identified processed break junctions pointing at the involvement of both homology directed and non-homology directed repair pathways, suggesting a recombination machinery in tomato that is more complex than currently anticipated.
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Affiliation(s)
- Roven Rommel Fuentes
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Thamara Hesselink
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Ronald Nieuwenhuis
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Linda Bakker
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Elio Schijlen
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Willem van Dooijeweert
- Centre for Genetic Resources, Wageningen University and Research, Wageningen, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sara Diaz Trivino
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jorn R de Haan
- Genetwister Technologies B.V., Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Gabino Sanchez Perez
- Genetwister Technologies B.V., Nieuwe Kanaal 7b, 6709 PA, Wageningen, The Netherlands
| | - Xinyue Zhang
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Aalt D J van Dijk
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sander A Peters
- Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Phukela B, Geeta R, Das S, Tandon R. Ancestral segmental duplication in Solanaceae is responsible for the origin of CRCa-CRCb paralogues in the family. Mol Genet Genomics 2020; 295:563-577. [PMID: 31912236 DOI: 10.1007/s00438-019-01641-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/18/2019] [Indexed: 01/03/2023]
Abstract
CRABS CLAW (CRC), a member of YABBY transcription factor family, has been previously reported to be principally involved in carpel development across angiosperms, and nectary development in core eudicots. Most of the studies suggest that CRC exists as a single copy gene, except in the Solanaceae where CRC occurs as paralogous pairs-CRCa-CRCb in Solanum lycopersicum, and CRC1-CRC2 in Petunia hybrida. In spite of their crucial role in carpel and nectary development, there is no information about the evolutionary history of the CRC paralogy in Solanaceae and whether the paralogy extends beyond Solanaceae. We analyzed homologues of CRC across angiosperms including genome sequence of fourteen species of Solanaceae available at Sol Genomics Network database, Phytozome and NCBI, to address the questions. Our phylogenetic reconstruction across angiosperms combined with comparative genomic, microsynteny and genome-fractionation analyses across the Solanaceae genomes revealed that (1) the CRCa-CRCb lineage is represented by a single copy in other flowering plants; (2) putative homologues of CRCa and CRCb are present in all the Solanaceae genomes studied; (3) the CRCa-CRCb paralogy in Solanaceae is associated with a large segmental duplication within Solanaceae (perhaps in its common ancestor), and (4) the duplicated segments have undergone different degrees of retention and loss of genes. Also, the CRC gene lineage expanded in Solanaceae following Solanaceae-α hexaploidy event and that two CRC duplicate copies were subsequently retained during the course of evolution. Besides the first detailed description of CRC evolution in Solanaceae, the study identifies potential candidate genes for future functional investigations.
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Affiliation(s)
- Banisha Phukela
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - R Geeta
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110 007, India
| | - Rajesh Tandon
- Department of Botany, University of Delhi, Delhi, 110 007, India.
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Varré JS, D'Agostino N, Touzet P, Gallina S, Tamburino R, Cantarella C, Ubrig E, Cardi T, Drouard L, Gualberto JM, Scotti N. Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. Int J Mol Sci 2019; 20:E4788. [PMID: 31561566 PMCID: PMC6801519 DOI: 10.3390/ijms20194788] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/01/2022] Open
Abstract
Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions. Based on the relevance of the potato crop worldwide, herewith we report the complete mtDNA sequence of two S. tuberosum cultivars, namely Cicero and Désirée, and a comprehensive study of its expression, based on high-coverage RNA sequencing data. We found that the potato mitogenome has a multi-partite architecture, divided in at least three independent molecules that according to our data should behave as autonomous chromosomes. Inter-cultivar variability was null, while comparative analyses with other species of the Solanaceae family allowed the investigation of the evolutionary history of their mitogenomes. The RNA-seq data revealed peculiarities in transcriptional and post-transcriptional processing of mRNAs. These included co-transcription of genes with open reading frames that are probably expressed, methylation of an rRNA at a position that should impact translation efficiency and extensive RNA editing, with a high proportion of partial editing implying frequent mis-targeting by the editing machinery.
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Affiliation(s)
- Jean-Stéphane Varré
- Univ. Lille, CNRS, Centrale Lille, UMR 9189-CRIStAL-Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Pascal Touzet
- Univ. Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Sophie Gallina
- Univ. Lille, CNRS, UMR 8198-Evo-Eco-Paleo, F-59000 Lille, France.
| | - Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, 80055 Portici, NA, Italy.
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Elodie Ubrig
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, SA, Italy.
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - José Manuel Gualberto
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg 67084, France.
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, 80055 Portici, NA, Italy.
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Gaiero P, Vaio M, Peters SA, Schranz ME, de Jong H, Speranza PR. Comparative analysis of repetitive sequences among species from the potato and the tomato clades. ANNALS OF BOTANY 2019; 123:521-532. [PMID: 30346473 PMCID: PMC6377101 DOI: 10.1093/aob/mcy186] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/20/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS The genus Solanum includes important vegetable crops and their wild relatives. Introgression of their useful traits into elite cultivars requires effective recombination between hom(e)ologues, which is partially determined by genome sequence differentiation. In this study we compared the repetitive genome fractions of wild and cultivated species of the potato and tomato clades in a phylogenetic context. METHODS Genome skimming followed by a clustering approach was used as implemented in the RepeatExplorer pipeline. Repeat classes were annotated and the sequences of their main domains were compared. KEY RESULTS Repeat abundance and genome size were correlated and the larger genomes of species in the tomato clade were found to contain a higher proportion of unclassified elements. Families and lineages of repetitive elements were largely conserved between the clades, but their relative proportions differed. The most abundant repeats were Ty3/Gypsy elements. Striking differences in abundance were found in the highly dynamic Ty3/Gypsy Chromoviruses and Ty1/Copia Tork elements. Within the potato clade, early branching Solanum cardiophyllum showed a divergent repeat profile. There were also contrasts between cultivated and wild potatoes, mostly due to satellite amplification in the cultivated species. Interspersed repeat profiles were very similar among potatoes. The repeat profile of Solanum etuberosum was more similar to that of the potato clade. CONCLUSIONS The repeat profiles in Solanum seem to be very similar despite genome differentiation at the level of collinearity. Removal of transposable elements by unequal recombination may have been responsible for structural rearrangements across the tomato clade. Sequence variability in the tomato clade is congruent with clade-specific amplification of repeats after its divergence from S. etuberosum and potatoes. The low differentiation among potato and its wild relatives at the level of interspersed repeats may explain the difficulty in discriminating their genomes by genomic in situ hybridization techniques.
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Affiliation(s)
- Paola Gaiero
- Laboratory of Genetics, Wageningen University & Research (WUR), Droevendaalsesteeg, PB Wageningen, The Netherlands
- Laboratorio de Evolución y Domesticación de las Plantas, Facultad de Agronomía, Universidad de la República, Garzón, Montevideo, Uruguay
| | - Magdalena Vaio
- Laboratorio de Evolución y Domesticación de las Plantas, Facultad de Agronomía, Universidad de la República, Garzón, Montevideo, Uruguay
| | - Sander A Peters
- Applied Bioinformatics, Department of Bioscience, Wageningen University & Research (WUR), Droevendaalsesteeg, PB Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research (WUR), Droevendaalsesteeg, PB Wageningen, The Netherlands
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University & Research (WUR), Droevendaalsesteeg, PB Wageningen, The Netherlands
| | - Pablo R Speranza
- Laboratorio de Evolución y Domesticación de las Plantas, Facultad de Agronomía, Universidad de la República, Garzón, Montevideo, Uruguay
- For correspondence. E-mail:
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10
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Mangal M, Srivastava A, Sharma R, Kalia P. Conservation and Dispersion of Genes Conferring Resistance to Tomato Begomoviruses between Tomato and Pepper Genomes. FRONTIERS IN PLANT SCIENCE 2017; 8:1803. [PMID: 29163560 PMCID: PMC5681951 DOI: 10.3389/fpls.2017.01803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/04/2017] [Indexed: 06/07/2023]
Abstract
In the present climate change scenario, controlling plant disease through exploitation of host plant resistance could contribute toward the sustainable crop production and global food security. In this respect, the identification of new sources of resistance and utilization of genetic diversity within the species may help in the generation of cultivars with improved disease resistance. Begomoviruses namely, Tomato yellow leaf curl virus (TYLCV) and Chilli leaf curl virus (ChLCV) are known to cause major yield losses in several economically important crop plants of the family Solanaceae. Though co-occurrence, association and synergistic interactions among these viruses in the host plants is reported, whether orthologous genetic loci in related host plants could be responsible for conferring resistance to these viruses has not been investigated yet. Several loci including Ty1, Ty2, Ty3, Ty4, and ty5 have been reported to confer resistance to leaf curl viruses in tomato. Here, we examined the pepper orthologous markers, corresponding to these QTL regions, for polymorphism between ChLCV susceptible and resistant genotypes of pepper. Further, to examine if the polymorphic markers are segregating with the disease resistance, Bulk Segregant Analysis (BSA) was performed on F2 population derived from crosses between resistant and susceptible lines. However, none of the markers showed polymorphism in BSA suggesting that the tested markers are not linked to genes/QTLs responsible for conferring resistance to ChLCV in the selected genotypes. In silico analysis was performed to study the synteny and collinearity of genes located within these QTL regions in tomato and pepper genomes, which revealed that more than 60% genes located in Ty2 and Ty4, 13.71% genes in Ty1, 23.07% in Ty3, and 44.77% genes located within ty5 QTL region in tomato are conserved in pepper genome. However, despite such a high conservation in gene content, the linkage relationship in these regions seems to be greatly affected by gross rearrangements in both the species.
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Affiliation(s)
- Manisha Mangal
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Arpita Srivastava
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rita Sharma
- Crop Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Pritam Kalia
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Kim SB, Kang WH, Huy HN, Yeom SI, An JT, Kim S, Kang MY, Kim HJ, Jo YD, Ha Y, Choi D, Kang BC. Divergent evolution of multiple virus-resistance genes from a progenitor in Capsicum spp. THE NEW PHYTOLOGIST 2017; 213:886-899. [PMID: 27612097 DOI: 10.1111/nph.14177] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/31/2016] [Indexed: 05/11/2023]
Abstract
Plants have evolved hundreds of nucleotide-binding and leucine-rich domain proteins (NLRs) as potential intracellular immune receptors, but the evolutionary mechanism leading to the ability to recognize specific pathogen effectors is elusive. Here, we cloned Pvr4 (a Potyvirus resistance gene in Capsicum annuum) and Tsw (a Tomato spotted wilt virus resistance gene in Capsicum chinense) via a genome-based approach using independent segregating populations. The genes both encode typical NLRs and are located at the same locus on pepper chromosome 10. Despite the fact that these two genes recognize completely different viral effectors, the genomic structures and coding sequences of the two genes are strikingly similar. Phylogenetic studies revealed that these two immune receptors diverged from a progenitor gene of a common ancestor. Our results suggest that sequence variations caused by gene duplication and neofunctionalization may underlie the evolution of the ability to specifically recognize different effectors. These findings thereby provide insight into the divergent evolution of plant immune receptors.
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Affiliation(s)
- Saet-Byul Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Won-Hee Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 660-701, Korea
| | - Hoang Ngoc Huy
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Seon-In Yeom
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 660-701, Korea
| | - Jeong-Tak An
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Min-Young Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Hyun Jung Kim
- Department of Eco-Friendly Horticulture, Cheonan Yonam College, Cheonan, 331-709, Korea
| | - Yeong Deuk Jo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
- Korea Atomic Energy Research Institute, Jeongeup, 580-185, Korea
| | - Yeaseong Ha
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
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12
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Gaiero P, van de Belt J, Vilaró F, Schranz ME, Speranza P, de Jong H. Collinearity between potato (Solanum tuberosum L.) and wild relatives assessed by comparative cytogenetic mapping. Genome 2016; 60:228-240. [PMID: 28169563 DOI: 10.1139/gen-2016-0150] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A major bottleneck to introgressive hybridization is the lack of genome collinearity between the donor (alien) genome and the recipient crop genome. Structural differences between the homeologs may create unbalanced segregation of chromosomes or cause linkage drag. To assess large-scale collinearity between potato and two of its wild relatives (Solanum commersonii and Solanum chacoense), we used BAC-FISH mapping of sequences with known positions on the RH potato map. BAC probes could successfully be hybridized to the S. commersonii and S. chachoense pachytene chromosomes, confirming their correspondence with linkage groups in RH potato. Our study shows that the order of BAC signals is conserved. Distances between BAC signals were quantified and compared; some differences found suggest either small-scale rearrangements or reduction/amplification of repeats. We conclude that S. commersonii and S. chacoense are collinear with cultivated Solanum tuberosum on the whole chromosome scale, making these amenable species for efficient introgressive hybridization breeding.
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Affiliation(s)
- Paola Gaiero
- a Department of Plant Biology, Facultad de Agronomía, Universidad de la República, Garzón 780, PC 12900, Montevideo, Uruguay.,b Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, P.O. Box 16, 6708 PB, Wageningen, the Netherlands
| | - José van de Belt
- b Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, P.O. Box 16, 6708 PB, Wageningen, the Netherlands
| | - Francisco Vilaró
- c Horticulture Unit, National Institute for Agricultural Research, Ruta 48 km 10, Las Brujas, Uruguay
| | - M Eric Schranz
- d Biosystematics Group, Wageningen University, Wageningen, the Netherlands
| | - Pablo Speranza
- a Department of Plant Biology, Facultad de Agronomía, Universidad de la República, Garzón 780, PC 12900, Montevideo, Uruguay
| | - Hans de Jong
- b Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, P.O. Box 16, 6708 PB, Wageningen, the Netherlands
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13
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Zhang L, Yang X, Tian L, Chen L, Yu W. Identification of peanut (Arachis hypogaea) chromosomes using a fluorescence in situ hybridization system reveals multiple hybridization events during tetraploid peanut formation. THE NEW PHYTOLOGIST 2016; 211:1424-39. [PMID: 27176118 DOI: 10.1111/nph.13999] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/31/2016] [Indexed: 05/17/2023]
Abstract
The cultivated peanut Arachis hypogaea (AABB) is thought to have originated from the hybridization of Arachis duranensis (AA) and Arachis ipaënsis (BB) followed by spontaneous chromosome doubling. In this study, we cloned and analyzed chromosome markers from cultivated peanut and its wild relatives. A fluorescence in situ hybridization (FISH)-based karyotyping cocktail was developed with which to study the karyotypes and chromosome evolution of peanut and its wild relatives. Karyotypes were constructed in cultivated peanut and its two putative progenitors using our FISH-based karyotyping system. Comparative karyotyping analysis revealed that chromosome organization was highly conserved in cultivated peanut and its two putative progenitors, especially in the B genome chromosomes. However, variations existed between A. duranensis and the A genome chromosomes in cultivated peanut, especially for the distribution of the interstitial telomere repeats (ITRs). A search of additional A. duranensis varieties from different geographic regions revealed both numeric and positional variations of ITRs, which were similar to the variations in tetraploid peanut varieties. The results provide evidence for the origin of cultivated peanut from the two diploid ancestors, and also suggest that multiple hybridization events of A. ipaënsis with different varieties of A. duranensis may have occurred during the origination of peanut.
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Affiliation(s)
- Laining Zhang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Xiaoyu Yang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - Lei Chen
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Weichang Yu
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
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14
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Mohan V, Pandey A, Sreelakshmi Y, Sharma R. Neofunctionalization of Chromoplast Specific Lycopene Beta Cyclase Gene (CYC-B) in Tomato Clade. PLoS One 2016; 11:e0153333. [PMID: 27070417 PMCID: PMC4829152 DOI: 10.1371/journal.pone.0153333] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 03/28/2016] [Indexed: 11/18/2022] Open
Abstract
The ancestor of tomato underwent whole genome triplication ca. 71 Myr ago followed by widespread gene loss. However, few of the triplicated genes are retained in modern day tomato including lycopene beta cyclase that mediates conversion of lycopene to β-carotene. The fruit specific β-carotene formation is mediated by a chromoplast-specific paralog of lycopene beta cyclase (CYC-B) gene. Presently limited information is available about how the variations in CYC-B gene contributed to its neofunctionalization. CYC-B gene in tomato clade contained several SNPs and In-Dels in the coding sequence (33 haplotypes) and promoter region (44 haplotypes). The CYC-B gene coding sequence in tomato appeared to undergo purifying selection. The transit peptide sequence of CYC-B protein was predicted to have a stronger plastid targeting signal than its chloroplast specific paralog indicating a possible neofunctionalization. In promoter of two Bog (Beta old gold) mutants, a NUPT (nuclear plastid) DNA fragment of 256 bp, likely derived from a S. chilense accession, was present. In transient expression assay, this promoter was more efficient than the "Beta type" promoter. CARGATCONSENSUS box sequences are required for the binding of the MADS-box regulatory protein RIPENING INHIBITOR (RIN). The loss of CARGATCONSENSUS box sequence from CYC-B promoter in tomato may be related to attenuation of its efficiency to promote higher accumulation of β-carotene than lycopene during fruit ripening.
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Affiliation(s)
- Vijee Mohan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Arun Pandey
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- * E-mail:
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15
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Wolters AMA, Caro M, Dong S, Finkers R, Gao J, Visser RGF, Wang X, Du Y, Bai Y. Detection of an inversion in the Ty-2 region between S. lycopersicum and S. habrochaites by a combination of de novo genome assembly and BAC cloning. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1987-97. [PMID: 26152571 PMCID: PMC4572051 DOI: 10.1007/s00122-015-2561-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/13/2015] [Indexed: 05/07/2023]
Abstract
A chromosomal inversion associated with the tomato Ty - 2 gene for TYLCV resistance is the cause of severe suppression of recombination in a tomato Ty - 2 introgression line. Among tomato and its wild relatives inversions are often observed, which result in suppression of recombination. Such inversions hamper the transfer of important traits from a related species to the crop by introgression breeding. Suppression of recombination was reported for the TYLCV resistance gene, Ty-2, which has been introgressed in cultivated tomato (Solanum lycopersicum) from the wild relative S. habrochaites accession B6013. Ty-2 was mapped to a 300-kb region on the long arm of chromosome 11. The suppression of recombination in the Ty-2 region could be caused by chromosomal rearrangements in S. habrochaites compared with S. lycopersicum. With the aim of visualizing the genome structure of the Ty-2 region, we compared the draft de novo assembly of S. habrochaites accession LYC4 with the sequence of cultivated tomato ('Heinz'). Furthermore, using populations derived from intraspecific crosses of S. habrochaites accessions, the order of markers in the Ty-2 region was studied. Results showed the presence of an inversion of approximately 200 kb in the Ty-2 region when comparing S. lycopersicum and S. habrochaites. By sequencing a BAC clone from the Ty-2 introgression line, one inversion breakpoint was identified. Finally, the obtained results are discussed with respect to introgression breeding and the importance of a priori de novo sequencing of the species involved.
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Affiliation(s)
- Anne-Marie A Wolters
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Myluska Caro
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Shufang Dong
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Richard Finkers
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Jianchang Gao
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Xiaoxuan Wang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Yongchen Du
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancunnandajie 12, Beijing, 100081, People's Republic of China
| | - Yuling Bai
- Wageningen UR Plant Breeding, Wageningen University & Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
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16
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Aflitos SA, Sanchez-Perez G, de Ridder D, Fransz P, Schranz ME, de Jong H, Peters SA. Introgression browser: high-throughput whole-genome SNP visualization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:174-182. [PMID: 25704554 DOI: 10.1111/tpj.12800] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 02/01/2015] [Accepted: 02/04/2015] [Indexed: 06/04/2023]
Abstract
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (iBrowser), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, multi-nucleotide polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis iBrowser makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the iBrowser in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of iBrowser makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes iBrowser a valuable breeding tool.
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Affiliation(s)
- Saulo Alves Aflitos
- Applied Bioinformatics, Wageningen University and Research Centre (WUR), Wageningen, The Netherlands
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17
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Reconstructing the Evolution of Brachypodium Genomes Using Comparative Chromosome Painting. PLoS One 2014; 9:e115108. [PMID: 25493646 PMCID: PMC4262448 DOI: 10.1371/journal.pone.0115108] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/18/2014] [Indexed: 11/19/2022] Open
Abstract
Brachypodium distachyon is a model for the temperate cereals and grasses and has a biology, genomics infrastructure and cytogenetic platform fit for purpose. It is a member of a genus with fewer than 20 species, which have different genome sizes, basic chromosome numbers and ploidy levels. The phylogeny and interspecific relationships of this group have not to date been resolved by sequence comparisons and karyotypical studies. The aims of this study are not only to reconstruct the evolution of Brachypodium karyotypes to resolve the phylogeny, but also to highlight the mechanisms that shape the evolution of grass genomes. This was achieved through the use of comparative chromosome painting (CCP) which hybridises fluorescent, chromosome-specific probes derived from B. distachyon to homoeologous meiotic chromosomes of its close relatives. The study included five diploids (B. distachyon 2n = 10, B. sylvaticum 2n = 18, B. pinnatum 2n = 16; 2n = 18, B. arbuscula 2n = 18 and B. stacei 2n = 20) three allotetraploids (B. pinnatum 2n = 28, B. phoenicoides 2n = 28 and B. hybridum 2n = 30), and two species of unknown ploidy (B. retusum 2n = 38 and B. mexicanum 2n = 40). On the basis of the patterns of hybridisation and incorporating published data, we propose two alternative, but similar, models of karyotype evolution in the genus Brachypodium. According to the first model, the extant genome of B. distachyon derives from B. mexicanum or B. stacei by several rounds of descending dysploidy, and the other diploids evolve from B. distachyon via ascending dysploidy. The allotetraploids arise by interspecific hybridisation and chromosome doubling between B. distachyon and other diploids. The second model differs from the first insofar as it incorporates an intermediate 2n = 18 species between the B. mexicanum or B. stacei progenitors and the dysploidic B. distachyon.
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18
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Iorizzo M, Gao L, Mann H, Traini A, Chiusano ML, Kilian A, Aversano R, Carputo D, Bradeen JM. A DArT marker-based linkage map for wild potato Solanum bulbocastanum facilitates structural comparisons between Solanum A and B genomes. BMC Genet 2014; 15:123. [PMID: 25403706 PMCID: PMC4240817 DOI: 10.1186/s12863-014-0123-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/29/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Wild potato Solanum bulbocastanum is a rich source of genetic resistance against a variety of pathogens. It belongs to a taxonomic group of wild potato species sexually isolated from cultivated potato. Consistent with genetic isolation, previous studies suggested that the genome of S. bulbocastanum (B genome) is structurally distinct from that of cultivated potato (A genome). However, the genome architecture of the species remains largely uncharacterized. The current study employed Diversity Arrays Technology (DArT) to generate a linkage map for S. bulbocastanum and compare its genome architecture with those of potato and tomato. RESULTS Two S. bulbocastanum parental linkage maps comprising 458 and 138 DArT markers were constructed. The integrated map comprises 401 non-redundant markers distributed across 12 linkage groups for a total length of 645 cM. Sequencing and alignment of DArT clones to reference physical maps from tomato and cultivated potato allowed direct comparison of marker orders between species. A total of nine genomic segments informative in comparative genomic studies were identified. Seven genome rearrangements correspond to previously-reported structural changes that have occurred since the speciation of tomato and potato. We also identified two S. bulbocastanum genomic regions that differ from cultivated potato, suggesting possible chromosome divergence between Solanum A and B genomes. CONCLUSIONS The linkage map developed here is the first medium density map of S. bulbocastanum and will assist mapping of agronomical genes and QTLs. The structural comparison with potato and tomato physical maps is the first genome wide comparison between Solanum A and B genomes and establishes a foundation for further investigation of B genome-specific structural chromosome rearrangements.
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Affiliation(s)
- Massimo Iorizzo
- Department of Horticulture, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA.
- Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall/1991 Upper Buford Circle, St. Paul, MN, 55108, USA.
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
| | - Liangliang Gao
- Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall/1991 Upper Buford Circle, St. Paul, MN, 55108, USA.
| | - Harpartap Mann
- Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall/1991 Upper Buford Circle, St. Paul, MN, 55108, USA.
| | - Alessandra Traini
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, London, United Kingdom.
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
| | - Andrzej Kilian
- Diversity Arrays Technology, Pty. Ltd., University of Canberra, Kirinari Street, Bruce, ACT 2617, Canberra, Australia.
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy.
| | - James M Bradeen
- Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall/1991 Upper Buford Circle, St. Paul, MN, 55108, USA.
- Stakman-Borlaug Center for Sustainable Plant Health, 495 Borlaug Hall/1991 Upper Buford Circle, St. Paul, MN 55108, USA.
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19
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Slater AT, Cogan NOI, Hayes BJ, Schultz L, Dale MFB, Bryan GJ, Forster JW. Improving breeding efficiency in potato using molecular and quantitative genetics. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2279-92. [PMID: 25186170 DOI: 10.1007/s00122-014-2386-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 08/23/2014] [Indexed: 05/24/2023]
Abstract
Potatoes are highly heterozygous and the conventional breeding of superior germplasm is challenging, but use of a combination of MAS and EBVs can accelerate genetic gain. Cultivated potatoes are highly heterozygous due to their outbreeding nature, and suffer acute inbreeding depression. Modern potato cultivars also exhibit tetrasomic inheritance. Due to this genetic heterogeneity, the large number of target traits and the specific requirements of commercial cultivars, potato breeding is challenging. A conventional breeding strategy applies phenotypic recurrent selection over a number of generations, a process which can take over 10 years. Recently, major advances in genetics and molecular biology have provided breeders with molecular tools to accelerate gains for some traits. Marker-assisted selection (MAS) can be effectively used for the identification of major genes and quantitative trait loci that exhibit large effects. There are also a number of complex traits of interest, such as yield, that are influenced by a large number of genes of individual small effect where MAS will be difficult to deploy. Progeny testing and the use of pedigree in the analysis can provide effective identification of the superior genetic factors that underpin these complex traits. Recently, it has been shown that estimated breeding values (EBVs) can be developed for complex potato traits. Using a combination of MAS and EBVs for simple and complex traits can lead to a significant reduction in the length of the breeding cycle for the identification of superior germplasm.
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Affiliation(s)
- Anthony T Slater
- Department of Environment and Primary Industries, Biosciences Research Division, AgriBio, Centre for AgriBioscience, Bundoora, Melbourne, VIC, 3083, Australia,
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20
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Aflitos S, Schijlen E, de Jong H, de Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L, Bakker F, Dirks R, Breit T, Gravendeel B, Huits H, Struss D, Swanson-Wagner R, van Leeuwen H, van Ham RCHJ, Fito L, Guignier L, Sevilla M, Ellul P, Ganko E, Kapur A, Reclus E, de Geus B, van de Geest H, Te Lintel Hekkert B, van Haarst J, Smits L, Koops A, Sanchez-Perez G, van Heusden AW, Visser R, Quan Z, Min J, Liao L, Wang X, Wang G, Yue Z, Yang X, Xu N, Schranz E, Smets E, Vos R, Rauwerda J, Ursem R, Schuit C, Kerns M, van den Berg J, Vriezen W, Janssen A, Datema E, Jahrman T, Moquet F, Bonnet J, Peters S. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:136-48. [PMID: 25039268 DOI: 10.1111/tpj.12616] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 05/20/2023]
Abstract
We explored genetic variation by sequencing a selection of 84 tomato accessions and related wild species representative of the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon groups, which has yielded a huge amount of precious data on sequence diversity in the tomato clade. Three new reference genomes were reconstructed to support our comparative genome analyses. Comparative sequence alignment revealed group-, species- and accession-specific polymorphisms, explaining characteristic fruit traits and growth habits in the various cultivars. Using gene models from the annotated Heinz 1706 reference genome, we observed differences in the ratio between non-synonymous and synonymous SNPs (dN/dS) in fruit diversification and plant growth genes compared to a random set of genes, indicating positive selection and differences in selection pressure between crop accessions and wild species. In wild species, the number of single-nucleotide polymorphisms (SNPs) exceeds 10 million, i.e. 20-fold higher than found in most of the crop accessions, indicating dramatic genetic erosion of crop and heirloom tomatoes. In addition, the highest levels of heterozygosity were found for allogamous self-incompatible wild species, while facultative and autogamous self-compatible species display a lower heterozygosity level. Using whole-genome SNP information for maximum-likelihood analysis, we achieved complete tree resolution, whereas maximum-likelihood trees based on SNPs from ten fruit and growth genes show incomplete resolution for the crop accessions, partly due to the effect of heterozygous SNPs. Finally, results suggest that phylogenetic relationships are correlated with habitat, indicating the occurrence of geographical races within these groups, which is of practical importance for Solanum genome evolution studies.
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21
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Kirov I, Van Laere K, De Riek J, De Keyser E, Van Roy N, Khrustaleva L. Anchoring linkage groups of the Rosa genetic map to physical chromosomes with tyramide-FISH and EST-SNP markers. PLoS One 2014; 9:e95793. [PMID: 24755945 PMCID: PMC3995938 DOI: 10.1371/journal.pone.0095793] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 03/31/2014] [Indexed: 11/29/2022] Open
Abstract
In order to anchor Rosa linkage groups to physical chromosomes, a combination of the Tyramide-FISH technology and the modern molecular marker system based on High Resolution Melting (HRM) is an efficient approach. Although, Tyramide-FISH is a very promising technique for the visualization of short DNA probes, it is very challenging for plant species with small chromosomes such as Rosa. In this study, we successfully applied the Tyramide-FISH technique for Rosa and compared different detection systems. An indirect detection system exploiting biotinylated tyramides was shown to be the most suitable technique for reliable signal detection. Three gene fragments with a size of 1100 pb–1700 bp (Phenylalanine Ammonia Lyase, Pyrroline-5-Carboxylate Synthase and Orcinol O-Methyl Transferase) have been physically mapped on chromosomes 7, 4 and 1, respectively, of Rosa wichurana. The signal frequency was between 25% and 40%. HRM markers of these 3 gene fragments were used to include the gene fragments on the existing genetic linkage map of Rosa wichurana. As a result, three linkage groups could be anchored to their physical chromosomes. The information was used to check for synteny between the Rosa chromosomes and Fragaria.
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Affiliation(s)
- Ilya Kirov
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
| | - Katrijn Van Laere
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
- * E-mail:
| | - Jan De Riek
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
| | - Ellen De Keyser
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Melle, Belgium
| | - Nadine Van Roy
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Ludmila Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Moscow, Russia
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22
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Lou Q, Zhang Y, He Y, Li J, Jia L, Cheng C, Guan W, Yang S, Chen J. Single-copy gene-based chromosome painting in cucumber and its application for chromosome rearrangement analysis in Cucumis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:169-79. [PMID: 24635663 DOI: 10.1111/tpj.12453] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 01/13/2014] [Accepted: 01/20/2014] [Indexed: 05/04/2023]
Abstract
Chromosome painting based on fluorescence in situ hybridization (FISH) has played an important role in chromosome identification and research into chromosome rearrangements, diagnosis of chromosome abnormalities and evolution in human and animal species. However, it has not been applied widely in plants due to the large amounts of dispersed repetitive sequences in chromosomes. In the present work, a chromosome painting method for single-copy gene pools in Cucumis sativus was successfully developed. Gene probes with sizes above 2 kb were detected consistently. A cucumber karyotype was constructed based on FISH using a cocktail containing chromosome-specific gene probes. This single-copy gene-based chromosome painting (ScgCP) technique was performed by PCR amplification, purification, pooling, labeling and hybridization onto chromosome spreads. Gene pools containing sequential genes with an interval less than 300 kb yielded painting patterns on pachytene chromosomes. Seven gene pools corresponding to individual chromosomes unambiguously painted each chromosome pair of C. sativus. Three mis-aligned regions on chromosome 4 were identified by the painting patterns. A probe pool comprising 133 genes covering the 8 Mb distal end of chromosome 4 was used to evaluate the potential utility of the ScgCP technique for chromosome rearrangement research through cross-species FISH in the Cucumis genus. Distinct painting patterns of this region were observed in C. sativus, C. melo and C. metuliferus species. A comparative chromosome map of this region was constructed between cucumber and melon. With increasing sequence resources, this ScgCP technique may be applied on any other sequenced species for chromosome painting research.
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Affiliation(s)
- Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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23
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Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps. G3-GENES GENOMES GENETICS 2013; 3:2031-47. [PMID: 24062527 PMCID: PMC3815063 DOI: 10.1534/g3.113.007153] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker−based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”.
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24
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D’Agostino N, Golas T, van de Geest H, Bombarely A, Dawood T, Zethof J, Driedonks N, Wijnker E, Bargsten J, Nap JP, Mariani C, Rieu I. Genomic analysis of the native European Solanum species, S. dulcamara. BMC Genomics 2013; 14:356. [PMID: 23713999 PMCID: PMC3680029 DOI: 10.1186/1471-2164-14-356] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Solanum dulcamara (bittersweet, climbing nightshade) is one of the few species of the Solanaceae family native to Europe. As a common weed it is adapted to a wide range of ecological niches and it has long been recognized as one of the alternative hosts for pathogens and pests responsible for many important diseases in potato, such as Phytophthora. At the same time, it may represent an alternative source of resistance genes against these diseases. Despite its unique ecology and potential as a genetic resource, genomic research tools are lacking for S. dulcamara. We have taken advantage of next-generation sequencing to speed up research on and use of this non-model species. RESULTS In this work, we present the first large-scale characterization of the S. dulcamara transcriptome. Through comparison of RNAseq reads from two different accessions, we were able to predict transcript-based SNP and SSR markers. Using the SNP markers in combination with genomic AFLP and CAPS markers, the first genome-wide genetic linkage map of bittersweet was generated. Based on gene orthology, the markers were anchored to the genome of related Solanum species (tomato, potato and eggplant), revealing both conserved and novel chromosomal rearrangements. This allowed a better estimation of the evolutionary moment of rearrangements in a number of cases and showed that chromosomal breakpoints are regularly re-used. CONCLUSION Knowledge and tools developed as part of this study pave the way for future genomic research and exploitation of this wild Solanum species. The transcriptome assembly represents a resource for functional analysis of genes underlying interesting biological and agronomical traits and, in the absence of the full genome, provides a reference for RNAseq gene expression profiling aimed at understanding the unique biology of S. dulcamara. Cross-species orthology-based marker selection is shown to be a powerful tool to quickly generate a comparative genetic map, which may speed up gene mapping and contribute to the understanding of genome evolution within the Solanaceae family.
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Affiliation(s)
- Nunzio D’Agostino
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
- Consiglio per la ricerca e la sperimentazione in agricoltura, Centro di ricerca per l’orticoltura, via Cavalleggeri 25, Pontecagnano, SA, 84098, Italy
| | - Tomek Golas
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
- Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, Wageningen, 6700 AB, The Netherlands
| | - Henri van de Geest
- Applied Bioinformatics, Bioscience, Plant Research International, Wageningen University & Research Centre, PO Box 619, Wageningen, 6700 AP, The Netherlands
- Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, Wageningen, 6700 AB, The Netherlands
| | - Aureliano Bombarely
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York, 14853-1801, USA
| | - Thikra Dawood
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Jan Zethof
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Nicky Driedonks
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Erik Wijnker
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands
| | - Joachim Bargsten
- Applied Bioinformatics, Bioscience, Plant Research International, Wageningen University & Research Centre, PO Box 619, Wageningen, 6700 AP, The Netherlands
| | - Jan-Peter Nap
- Applied Bioinformatics, Bioscience, Plant Research International, Wageningen University & Research Centre, PO Box 619, Wageningen, 6700 AP, The Netherlands
- Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, Wageningen, 6700 AB, The Netherlands
| | - Celestina Mariani
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
- Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, Wageningen, 6700 AB, The Netherlands
| | - Ivo Rieu
- IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
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25
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Interstitial telomeric repeats are enriched in the centromeres of chromosomes in Solanum species. Chromosome Res 2012; 21:5-13. [PMID: 23250588 DOI: 10.1007/s10577-012-9332-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Revised: 11/27/2012] [Accepted: 12/06/2012] [Indexed: 01/05/2023]
Abstract
Interstitial telomeric repeats (ITRs) were reported in a number of animal and plant species. Most ITRs are organized as short tandem arrays and are likely evolutionary relics derived from chromosomal rearrangements and DNA repairs. However, megabase-sized ITR arrays were reported in Solanum species. Here, we report a fluorescence in situ hybridization (FISH) survey of ITRs in all representative diploid Solanum species, including potato, tomato, and eggplant. FISH revealed massive amplification of ITRs in the centromeric regions of chromosomes from the Solanum species containing the B and P genomes. A significant proportion of the ITR FISH signals was mapped within the primary constrictions of the pachytene chromosomes of Solanum pinnatisectum (B genome). In addition, some ITR sites overlapped with St49, a satellite repeat enriched in centromeric DNA sequences associated with CENH3 nucleosomes, in both A and B genome Solanum species. These results show that some ITR subfamilies have been amplified and invaded in the functional centromeres of chromosomes in Solanum species.
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