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Xiang KL, Wu SD, Lian L, He WC, Peng D, Peng HW, Zhang XN, Li HL, Xue JY, Shan HY, Xu GX, Liu Y, Wu ZQ, Wang W. Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae. SCIENCE CHINA. LIFE SCIENCES 2024; 67:803-816. [PMID: 38087029 DOI: 10.1007/s11427-023-2448-x] [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: 06/24/2023] [Accepted: 09/11/2023] [Indexed: 04/06/2024]
Abstract
Living fossils are evidence of long-term sustained ecological success. However, whether living fossils have little molecular changes remains poorly known, particularly in plants. Here, we have introduced a novel method that integrates phylogenomic, comparative genomic, and ecological niche modeling analyses to investigate the rate of molecular evolution of Eupteleaceae, a Cretaceous relict angiosperm family endemic to East Asia. We assembled a high-quality chromosome-level nuclear genome, and the chloroplast and mitochondrial genomes of a member of Eupteleaceae (Euptelea pleiosperma). Our results show that Eupteleaceae is most basal in Ranunculales, the earliest-diverging order in eudicots, and shares an ancient whole-genome duplication event with the other Ranunculales. We document that Eupteleaceae has the slowest rate of molecular changes in the observed angiosperms. The unusually low rate of molecular evolution of Eupteleaceae across all three independent inherited genomes and genes within each of the three genomes is in association with its conserved genome architecture, ancestral woody habit, and conserved niche requirements. Our findings reveal the evolution and adaptation of living fossil plants through large-scale environmental change and also provide new insights into early eudicot diversification.
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Affiliation(s)
- Kun-Li Xiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- China National Botanical Garden, Beijing, 100093, China
| | - Sheng-Dan Wu
- State Key Laboratory of Grassland Agro-Ecosystems and College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Lian Lian
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Wen-Chuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Huan-Wen Peng
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Ni Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Hong-Lei Li
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hong-Yan Shan
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Gui-Xia Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Yang Liu
- Fairylake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Zhi-Qiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Wei Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Rajpal VR, Sharma S, Sehgal D, Sharma P, Wadhwa N, Dhakate P, Chandra A, Thakur RK, Deb S, Rama Rao S, Mir BA, Raina SN. Comprehending the dynamism of B chromosomes in their journey towards becoming unselfish. Front Cell Dev Biol 2023; 10:1072716. [PMID: 36684438 PMCID: PMC9846793 DOI: 10.3389/fcell.2022.1072716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Investigated for more than a century now, B chromosomes (Bs) research has come a long way from Bs being considered parasitic or neutral to becoming unselfish and bringing benefits to their hosts. B chromosomes exist as accessory chromosomes along with the standard A chromosomes (As) across eukaryotic taxa. Represented singly or in multiple copies, B chromosomes are largely heterochromatic but also contain euchromatic and organellar segments. Although B chromosomes are derived entities, they follow their species-specific evolutionary pattern. B chromosomes fail to pair with the standard chromosomes during meiosis and vary in their number, size, composition and structure across taxa and ensure their successful transmission through non-mendelian mechanisms like mitotic, pre-meiotic, meiotic or post-meiotic drives, unique non-disjunction, self-pairing or even imparting benefits to the host when they lack drive. B chromosomes have been associated with cellular processes like sex determination, pathogenicity, resistance to pathogens, phenotypic effects, and differential gene expression. With the advancements in B-omics research, novel insights have been gleaned on their functions, some of which have been associated with the regulation of gene expression of A chromosomes through increased expression of miRNAs or differential expression of transposable elements located on them. The next-generation sequencing and emerging technologies will further likely unravel the cellular, molecular and functional behaviour of these enigmatic entities. Amidst the extensive fluidity shown by B chromosomes in their structural and functional attributes, we perceive that the existence and survival of B chromosomes in the populations most likely seem to be a trade-off between the drive efficiency and adaptive significance versus their adverse effects on reproduction.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India,*Correspondence: Vijay Rani Rajpal, , ; Soom Nath Raina,
| | - Suman Sharma
- Department of Botany, Ramjas College, University of Delhi, Delhi, India
| | - Deepmala Sehgal
- Syngenta, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Prashansa Sharma
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Atika Chandra
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Rakesh Kr. Thakur
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Sohini Deb
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Satyawada Rama Rao
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, Meghalaya, India
| | - Bilal Ahmad Mir
- Department of Botany, University of Kashmir, Srinagar, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India,*Correspondence: Vijay Rani Rajpal, , ; Soom Nath Raina,
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Cápal P, Said M, Molnár I, Doležel J. Flow Cytometric Analysis and Sorting of Plant Chromosomes. Methods Mol Biol 2023; 2672:177-200. [PMID: 37335476 DOI: 10.1007/978-1-0716-3226-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Flow cytometry offers a unique way of analyzing and manipulating plant chromosomes. During a rapid movement in a liquid stream, large populations can be classified in a short time according to their fluorescence and light scatter properties. Chromosomes whose optical properties differ from other chromosomes in a karyotype can be purified by flow sorting and used in a range of applications in cytogenetics, molecular biology, genomics, and proteomics. As the samples for flow cytometry must be liquid suspensions of single particles, intact chromosomes must be released from mitotic cells. This protocol describes a procedure for preparation of suspensions of mitotic metaphase chromosomes from meristem root tips and their flow cytometric analysis and sorting for various downstream applications.
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Affiliation(s)
- Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
| | - Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, Giza, Cairo, Egypt
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic
- Agricultural Institute, Centre for Agricultural Research, ELKH, Martonvásár, Hungary
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic.
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Tomaszewska P, Schwarzacher T, Heslop-Harrison JS(P. Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids. FRONTIERS IN PLANT SCIENCE 2022; 13:1026364. [PMID: 36483968 PMCID: PMC9725029 DOI: 10.3389/fpls.2022.1026364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Structural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C- into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.
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Affiliation(s)
- Paulina Tomaszewska
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - J. S. (Pat) Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial, Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Said M, Cápal P, Farkas A, Gaál E, Ivanizs L, Friebe B, Doležel J, Molnár I. Flow karyotyping of wheat- Aegilops additions facilitate dissecting the genomes of Ae. biuncialis and Ae. geniculata into individual chromosomes. FRONTIERS IN PLANT SCIENCE 2022; 13:1017958. [PMID: 36262648 PMCID: PMC9575658 DOI: 10.3389/fpls.2022.1017958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/09/2022] [Indexed: 06/13/2023]
Abstract
Breeding of wheat adapted to new climatic conditions and resistant to diseases and pests is hindered by a limited gene pool due to domestication and thousands of years of human selection. Annual goatgrasses (Aegilops spp.) with M and U genomes are potential sources of the missing genes and alleles. Development of alien introgression lines of wheat may be facilitated by the knowledge of DNA sequences of Aegilops chromosomes. As the Aegilops genomes are complex, sequencing relevant Aegilops chromosomes purified by flow cytometric sorting offers an attractive route forward. The present study extends the potential of chromosome genomics to allotetraploid Ae. biuncialis and Ae. geniculata by dissecting their M and U genomes into individual chromosomes. Hybridization of FITC-conjugated GAA oligonucleotide probe to chromosomes suspensions of the two species allowed the application of bivariate flow karyotyping and sorting some individual chromosomes. Bivariate flow karyotype FITC vs. DAPI of Ae. biuncialis consisted of nine chromosome-populations, but their chromosome content determined by microscopic analysis of flow sorted chromosomes indicated that only 7Mb and 1Ub could be sorted at high purity. In the case of Ae. geniculata, fourteen chromosome-populations were discriminated, allowing the separation of nine individual chromosomes (1Mg, 3Mg, 5Mg, 6Mg, 7Mg, 1Ug, 3Ug, 6Ug, and 7Ug) out of the 14. To sort the remaining chromosomes, a partial set of wheat-Ae. biuncialis and a whole set of wheat-Ae. geniculata chromosome addition lines were also flow karyotyped, revealing clear separation of the GAA-rich Aegilops chromosomes from the GAA-poor A- and D-genome chromosomes of wheat. All of the alien chromosomes represented by individual addition lines could be isolated at purities ranging from 74.5% to 96.6% and from 87.8% to 97.7%, respectively. Differences in flow karyotypes between Ae. biuncialis and Ae. geniculata were analyzed and discussed. Chromosome-specific genomic resources will facilitate gene cloning and the development of molecular tools to support alien introgression breeding of wheat.
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Affiliation(s)
- Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Field Crops Research Institute, Agricultural Research Centre, Cairo, Egypt
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránd Kutatási Hálózat (ELKH), Martonvásár, Hungary
| | - Eszter Gaál
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránd Kutatási Hálózat (ELKH), Martonvásár, Hungary
| | - László Ivanizs
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránd Kutatási Hálózat (ELKH), Martonvásár, Hungary
| | - Bernd Friebe
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránd Kutatási Hálózat (ELKH), Martonvásár, Hungary
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100 Years of Chromosome Research in Rye, Secale L. PLANTS 2022; 11:plants11131753. [PMID: 35807704 PMCID: PMC9268793 DOI: 10.3390/plants11131753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]
Abstract
Although microscopy and genetics were still in their infancy, there are cytological results produced a hundred years ago that are still relevant today. Since the 1920s, rye has been a subject of chromosome research. It started by plotting its mitotic and meiotic chromosomes to determine genome size. After controversial evidence, it became clear that the base number is n = 7. However, structural differences exist between species within the genus Secale. Some rye populations even carry accessory chromosomes evolutionary derived from the A genome. The development of tetraploid strains significantly promoted chromosome analysis. Various techniques have tried to stabilize the disturbed chromosome pairing of the induced tetraploids. Although slight improvements could be achieved, they did not lead to a breakthrough. However, the various aneuploid derivatives of the polyploids found major advances in the genetic analysis of rye. Trisomics, telo-trisomics, and reciprocal translocation have served as important tools for gene mapping. Since the 1970s, various chromosome banding techniques have stimulated scientific progress. The seven haploid chromosomes could be diagnosed unequivocally, not only in S. cereale but also in related species. These findings led to a clear homoeologous assignment to the genomes of related grass species such as wheat, barley, rice, etc. Current applications of in situ fluorescence staining methods, such as GISH and FISH, allow even more precise results, depending on the specificity of the DNA samples. Advanced preparation techniques are supplemented by the variety of innovations in the field of molecular genome analysis. They replace complex cytological examinations. In this way, introgressions can be safely detected by DNA markers and be much more detailed. In addition, CRISPR/CAS-mediated chromosome engineering will become an important method of the future.
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Korchanová Z, Švec M, Janáková E, Lampar A, Majka M, Holušová K, Bonchev G, Juračka J, Cápal P, Valárik M. Identification, High-Density Mapping, and Characterization of New Major Powdery Mildew Resistance Loci From the Emmer Wheat Landrace GZ1. FRONTIERS IN PLANT SCIENCE 2022; 13:897697. [PMID: 35646009 PMCID: PMC9141293 DOI: 10.3389/fpls.2022.897697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Powdery mildew is one of the most devastating diseases of wheat which significantly decreases yield and quality. Identification of new sources of resistance and their implementation in breeding programs is the most effective way of disease control. Two major powdery mildew resistance loci conferring resistance to all races in seedling and adult plant stages were identified in the emmer wheat landrace GZ1. Their positions, effects, and transferability were verified using two linkage maps (1,510 codominant SNP markers) constructed from two mapping populations (276 lines in total) based on the resistant GZ1 line. The dominant resistance locus QPm.GZ1-7A was located in a 90 cM interval of chromosome 7AL and explains up to 20% of the trait variation. The recessive locus QPm.GZ1-2A, which provides total resistance, explains up to 40% of the trait variation and was located in the distal part of chromosome 2AL. The locus was saturated with 14 PCR-based markers and delimited to a 0.99 cM region which corresponds to 4.3 Mb of the cv. Zavitan reference genome and comprises 55 predicted genes with no apparent candidate for the QPm.GZ1-2A resistance gene. No recessive resistance gene or allele was located at the locus before, suggesting the presence of a new powdery mildew resistance gene in the GZ1. The mapping data and markers could be used for the implementation of the locus in breeding. Moreover, they are an ideal base for cloning and study of host-pathogen interaction pathways determined by the resistance genes.
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Affiliation(s)
- Zuzana Korchanová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Miroslav Švec
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Eva Janáková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Adam Lampar
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Maciej Majka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Kateřina Holušová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Georgi Bonchev
- Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Jakub Juračka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Computer Science, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Miroslav Valárik
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
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Wu C, Wei X, Men X, Zhang X, Yu YL, Xu ZR, Chen ML, Wang JH. Two-Dimensional Cytometry Platform for Single-Particle/Cell Analysis with Laser-Induced Fluorescence and ICP-MS. Anal Chem 2021; 93:8203-8209. [PMID: 34077198 DOI: 10.1021/acs.analchem.1c00484] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A two-dimensional cytometry platform (CytoLM) with high sensitivity and high temporal resolution is developed for single-particle and single-cell sampling and analysis. First, a Dean flow-assisted vortex capillary cell sampling (VCCS) unit confines the sample stream in curved flow and drives to focus and align the particles or cells in a small probe volume. By coupling VCCS to a laser-induced fluorescence (LIF) detector with data acquisition and processing capability, a high-throughput single-particle/cell analysis system (VCCS-LIF) was established. The particle analysis throughput of 119.42/s and a detection recovery of 78.20 ± 1.75% were achieved at a density of 9.16 × 104/mL for fluorescent particles, and the cell analysis throughput is 48.20/s at a density of 1.5 × 105/mL. Second, the CytoLM platform is constructed by hyphenating VCCS-LIF with inductively coupled plasma mass spectrometry (ICP-MS). In the analysis of HepG2 cells by Ag+ incubation and AO staining, 10,760 fluorescence bursts and 3068 MS events were observed in 240 s. Invalid signals due to undispersed cells were controlled at 3.80% for LIF and 1.01% for MS, with a proportion of effective signal of >96.20%. After peak identification and integral processing of the original data, the statistical results including peak area, height, width, and spacing are obtained concurrently and the information on concentration and elemental quantification of single cells is evaluated. CytoLM facilitates high-throughput, multi-dimensional, and multi-parameter characterization of particles and cells, and it may provide vast potential in life science analysis.
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Affiliation(s)
- Chengxin Wu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Xing Wei
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Xue Men
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Xuan Zhang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Zhang-Run Xu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Ming-Li Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
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Doležel J, Lucretti S, Molnár I, Cápal P, Giorgi D. Chromosome analysis and sorting. Cytometry A 2021; 99:328-342. [PMID: 33615737 PMCID: PMC8048479 DOI: 10.1002/cyto.a.24324] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Flow cytometric analysis and sorting of plant mitotic chromosomes has been mastered by only a few laboratories worldwide. Yet, it has been contributing significantly to progress in plant genetics, including the production of genome assemblies and the cloning of important genes. The dissection of complex genomes by flow sorting into the individual chromosomes that represent small parts of the genome reduces DNA sample complexity and streamlines projects relying on molecular and genomic techniques. Whereas flow cytometric analysis, that is, chromosome classification according to fluorescence and light scatter properties, is an integral part of any chromosome sorting project, it has rarely been used on its own due to lower resolution and sensitivity as compared to other cytogenetic methods. To perform chromosome analysis and sorting, commercially available electrostatic droplet sorters are suitable. However, in order to resolve and purify chromosomes of interest the instrument must offer high resolution of optical signals as well as stability during long runs. The challenge is thus not the instrumentation, but the adequate sample preparation. The sample must be a suspension of intact mitotic metaphase chromosomes and the protocol, which includes the induction of cell cycle synchrony, accumulation of dividing cells at metaphase, and release of undamaged chromosomes, is time consuming and laborious and needs to be performed very carefully. Moreover, in addition to fluorescent staining chromosomal DNA, the protocol may include specific labelling of DNA repeats to facilitate discrimination of particular chromosomes. This review introduces the applications of chromosome sorting in plants, and discusses in detail sample preparation, chromosome analysis and sorting to achieve the highest purity in flow-sorted fractions, and their suitability for downstream applications.
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Affiliation(s)
- Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Sergio Lucretti
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA)Division of Biotechnology and AgroindustryRomeItaly
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Debora Giorgi
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA)Division of Biotechnology and AgroindustryRomeItaly
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Sánchez-Martín J, Widrig V, Herren G, Wicker T, Zbinden H, Gronnier J, Spörri L, Praz CR, Heuberger M, Kolodziej MC, Isaksson J, Steuernagel B, Karafiátová M, Doležel J, Zipfel C, Keller B. Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins. NATURE PLANTS 2021; 7:327-341. [PMID: 33707738 PMCID: PMC7610370 DOI: 10.1038/s41477-021-00869-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/01/2021] [Indexed: 05/07/2023]
Abstract
Crop breeding for resistance to pathogens largely relies on genes encoding receptors that confer race-specific immunity. Here, we report the identification of the wheat Pm4 race-specific resistance gene to powdery mildew. Pm4 encodes a putative chimeric protein of a serine/threonine kinase and multiple C2 domains and transmembrane regions, a unique domain architecture among known resistance proteins. Pm4 undergoes constitutive alternative splicing, generating two isoforms with different protein domain topologies that are both essential for resistance function. Both isoforms interact and localize to the endoplasmatic reticulum when co-expressed. Pm4 reveals additional diversity of immune receptor architecture to be explored for breeding and suggests an endoplasmatic reticulum-based molecular mechanism of Pm4-mediated race-specific resistance.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
| | - Victoria Widrig
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Gerhard Herren
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Helen Zbinden
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Julien Gronnier
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Laurin Spörri
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Coraline R Praz
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- Unité de Recherche Résistance Induite et BioProtection des Plantes, UFR Sciences Exactes et Naturelles, Université de Reims-Champagne-Ardenne, Reims, France
| | - Matthias Heuberger
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Markus C Kolodziej
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Jonatan Isaksson
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | | | - Miroslava Karafiátová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Cyril Zipfel
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Beat Keller
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
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11
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Kolodziej MC, Singla J, Sánchez-Martín J, Zbinden H, Šimková H, Karafiátová M, Doležel J, Gronnier J, Poretti M, Glauser G, Zhu W, Köster P, Zipfel C, Wicker T, Krattinger SG, Keller B. A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat. Nat Commun 2021; 12:956. [PMID: 33574268 PMCID: PMC7878491 DOI: 10.1038/s41467-020-20777-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/18/2020] [Indexed: 01/30/2023] Open
Abstract
Plasma membrane-associated and intracellular proteins and protein complexes play a pivotal role in pathogen recognition and disease resistance signaling in plants and animals. The two predominant protein families perceiving plant pathogens are receptor-like kinases and nucleotide binding-leucine-rich repeat receptors (NLR), which often confer race-specific resistance. Leaf rust is one of the most prevalent and most devastating wheat diseases. Here, we clone the race-specific leaf rust resistance gene Lr14a from hexaploid wheat. The cloning of Lr14a is aided by the recently published genome assembly of ArinaLrFor, an Lr14a-containing wheat line. Lr14a encodes a membrane-localized protein containing twelve ankyrin (ANK) repeats and structural similarities to Ca2+-permeable non-selective cation channels. Transcriptome analyses reveal an induction of genes associated with calcium ion binding in the presence of Lr14a. Haplotype analyses indicate that Lr14a-containing chromosome segments were introgressed multiple times into the bread wheat gene pool, but we find no variation in the Lr14a coding sequence itself. Our work demonstrates the involvement of an ANK-transmembrane (TM)-like type of gene family in race-specific disease resistance in wheat. This forms the basis to explore ANK-TM-like genes in disease resistance breeding.
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Affiliation(s)
- Markus C Kolodziej
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Jyoti Singla
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Javier Sánchez-Martín
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Helen Zbinden
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Miroslava Karafiátová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Julien Gronnier
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Manuel Poretti
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Gaétan Glauser
- Neuchâtel Platform of Analytical Chemistry, Université de Neuchâtel, Avenue de Bellevaux 51, 2000, Neuchâtel, Switzerland
| | - Wangsheng Zhu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
- College of Plant Protection, China Agricultural University, 100193, Beijing, China
| | - Philipp Köster
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Cyril Zipfel
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Thomas Wicker
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Simon G Krattinger
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Beat Keller
- University of Zurich, Department of Plant and Microbial Biology, Zollikerstrasse 107, 8008, Zurich, Switzerland.
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12
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Zwyrtková J, Šimková H, Doležel J. Chromosome genomics uncovers plant genome organization and function. Biotechnol Adv 2020; 46:107659. [PMID: 33259907 DOI: 10.1016/j.biotechadv.2020.107659] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/10/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023]
Abstract
The identification of causal genomic loci and their interactions underlying various traits in plants has been greatly aided by progress in understanding the organization of the nuclear genome. This provides clues to the responses of plants to environmental stimuli at the molecular level. Apart from other uses, these insights are needed to fully explore the potential of new breeding techniques that rely on genome editing. However, genome analysis and sequencing is not straightforward in the many agricultural crops and their wild relatives that possess large and complex genomes. Chromosome genomics streamlines this task by dissecting the genome to single chromosomes whose DNA is then used instead of nuclear DNA. This results in a massive and lossless reduction in DNA sample complexity, reduces the time and cost of the experiment, and simplifies data interpretation. Flow cytometric sorting of condensed mitotic chromosomes makes it possible to purify single chromosomes in large quantities, and as the DNA remains intact this process can be coupled successfully with many techniques in molecular biology and genomics. Since the first experiments with flow cytometric sorting in the late 1980s, numerous applications have been developed, and chromosome genomics has been having a significant impact in many areas of research, including the sequencing of complex genomes of important crops and gene cloning. This review discusses these applications, describes their contribution to advancements in plant genome analysis and gene cloning, and outlines future directions.
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Affiliation(s)
- Jana Zwyrtková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic.
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic.
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic.
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13
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Orman-Ligeza B, Borrill P, Chia T, Chirico M, Doležel J, Drea S, Karafiátová M, Schatlowski N, Solomon CU, Steuernagel B, Wulff BBH, Uauy C, Trafford K. LYS3 encodes a prolamin-box-binding transcription factor that controls embryo growth in barley and wheat. J Cereal Sci 2020; 93:102965. [PMID: 32508376 PMCID: PMC7263734 DOI: 10.1016/j.jcs.2020.102965] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mutations at the LYS3 locus in barley have multiple effects on grain development, including an increase in embryo size and a decrease in endosperm starch content. The gene underlying LYS3 was identified by genetic mapping and mutations in this gene were identified in all four barley lys3 alleles. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF). Its role in controlling embryo size was confirmed using wheat TILLING mutants. To understand how PBF controls embryo development, we studied its spatial and temporal patterns of expression in developing grains. The PBF gene is expressed in both the endosperm and the embryos, but the timing of expression in these organs differs. PBF expression in wild-type embryos precedes the onset of embryo enlargement in lys3 mutants, suggesting that PBF suppresses embryo growth. We predicted the down-stream target genes of PBF in wheat and found them to be involved in a wide range of biological processes, including organ development and starch metabolism. Our work suggests that PBF may influence embryo size and endosperm starch synthesis via separate gene control networks. LYS3 encodes a transcription factor called Prolamin Binding Factor (PBF) that is expressed in grains only. Wheat and barley LYS3/PBF mutants have enlarged embryos suggesting that this gene suppresses embryo growth. The predicted targets of wheat PBF are involved in a wide range of biological processes, including organ development.
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Affiliation(s)
| | - Philippa Borrill
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Tansy Chia
- NIAB, Genetics and Breeding, Huntington Road, Cambridge, CB3 0LE, UK
| | - Marcella Chirico
- NIAB, Genetics and Breeding, Huntington Road, Cambridge, CB3 0LE, UK
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Sinead Drea
- Department of Genetics, University of Leicester, Adrian Building University Road, Leicester, LE1 7RH, UK
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Charles U Solomon
- Department of Genetics, University of Leicester, Adrian Building University Road, Leicester, LE1 7RH, UK.,Department of Plant Science and Biotechnology, Abia State University, PMB 2000, Uturu, Nigeria
| | | | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kay Trafford
- NIAB, Genetics and Breeding, Huntington Road, Cambridge, CB3 0LE, UK
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14
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Hiebert CW, Moscou MJ, Hewitt T, Steuernagel B, Hernández-Pinzón I, Green P, Pujol V, Zhang P, Rouse MN, Jin Y, McIntosh RA, Upadhyaya N, Zhang J, Bhavani S, Vrána J, Karafiátová M, Huang L, Fetch T, Doležel J, Wulff BBH, Lagudah E, Spielmeyer W. Stem rust resistance in wheat is suppressed by a subunit of the mediator complex. Nat Commun 2020; 11:1123. [PMID: 32111840 PMCID: PMC7048732 DOI: 10.1038/s41467-020-14937-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/11/2020] [Indexed: 11/18/2022] Open
Abstract
Stem rust is an important disease of wheat that can be controlled using resistance genes. The gene SuSr-D1 identified in cultivar ‘Canthatch’ suppresses stem rust resistance. SuSr-D1 mutants are resistant to several races of stem rust that are virulent on wild-type plants. Here we identify SuSr-D1 by sequencing flow-sorted chromosomes, mutagenesis, and map-based cloning. The gene encodes Med15, a subunit of the Mediator Complex, a conserved protein complex in eukaryotes that regulates expression of protein-coding genes. Nonsense mutations in Med15b.D result in expression of stem rust resistance. Time-course RNAseq analysis show a significant reduction or complete loss of differential gene expression at 24 h post inoculation in med15b.D mutants, suggesting that transcriptional reprogramming at this time point is not required for immunity to stem rust. Suppression is a common phenomenon and this study provides novel insight into suppression of rust resistance in wheat. Stem rust is an important disease of wheat and resistance present in some cultivars can be suppressed by the SuSr-D1 locus. Here the authors show that SuSr-D1 encodes a subunit of the Mediator Complex and that nonsense mutations are sufficient to abolish suppression and confer stem rust resistance.
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Affiliation(s)
- Colin W Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK.
| | - Tim Hewitt
- Plant Breeding Institute Cobbitty, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia.,CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Inma Hernández-Pinzón
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK
| | - Phon Green
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UK, UK
| | - Vincent Pujol
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Peng Zhang
- Plant Breeding Institute Cobbitty, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - Matthew N Rouse
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA
| | - Yue Jin
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA
| | - Robert A McIntosh
- Plant Breeding Institute Cobbitty, University of Sydney, Private Bag 4011, Narellan, NSW, 2567, Australia
| | | | - Jianping Zhang
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Sridhar Bhavani
- CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market, Nairobi, 00621, Kenya
| | - Jan Vrána
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Li Huang
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Tom Fetch
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Jaroslav Doležel
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | | | - Evans Lagudah
- CSIRO Agriculture & Food, GPO Box 1700, Canberra, ACT, 2601, Australia.
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15
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Dhar MK, Kour J, Kaul S. Origin, Behaviour, and Transmission of B Chromosome with Special Reference to Plantago lagopus. Genes (Basel) 2019; 10:E152. [PMID: 30781667 PMCID: PMC6410184 DOI: 10.3390/genes10020152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 11/30/2022] Open
Abstract
B chromosomes have been reported in many eukaryotic organisms. These chromosomes occur in addition to the standard complement of a species. Bs do not pair with any of the A chromosomes and they have generally been considered to be non-essential and genetically inert. However, due to tremendous advancements in the technologies, the molecular composition of B chromosomes has been determined. The sequencing data has revealed that B chromosomes have originated from A chromosomes and they are rich in repetitive elements. In our laboratory, a novel B chromosome was discovered in Plantago lagopus. Using molecular cytogenetic techniques, the B chromosome was found to be composed of ribosomal DNA sequences. However, further characterization of the chromosome using next generation sequencing (NGS) etc. revealed that the B chromosome is a mosaic of sequences derived from A chromosomes, 5S ribosomal DNA (rDNA), 45S rDNA, and various types of repetitive elements. The transmission of B chromosome through the female sex track did not follow the Mendelian principles. The chromosome was found to have drive due to which it was perpetuating in populations. The present paper attempts to summarize the information on nature, transmission, and origin of B chromosomes, particularly the current status of our knowledge in P. lagopus.
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Affiliation(s)
- Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu-180006, India.
| | - Jasmeet Kour
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu-180006, India.
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu-180006, India.
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16
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Svačina R, Karafiátová M, Malurová M, Serra H, Vítek D, Endo TR, Sourdille P, Bartoš J. Development of Deletion Lines for Chromosome 3D of Bread Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:1756. [PMID: 32047508 PMCID: PMC6997527 DOI: 10.3389/fpls.2019.01756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/16/2019] [Indexed: 05/20/2023]
Abstract
The identification of genes of agronomic interest in bread wheat (Triticum aestivum L.) is hampered by its allopolyploid nature (2n = 6x = 42; AABBDD) and its very large genome, which is largely covered by transposable elements. However, owing to this complex structure, aneuploid stocks can be developed in which fragments or entire chromosomes are missing, sometimes resulting in visible phenotypes that help in the cloning of affected genes. In this study, the 2C gametocidal chromosome from Aegilops cylindrica was used to develop a set of 113 deletion lines for chromosome 3D in the reference cultivar Chinese Spring. Eighty-four markers were used to show that the deletions evenly covered chromosome 3D and ranged from 6.5 to 357 Mb. Cytogenetic analyses confirmed that the physical size of the deletions correlated well with the known molecular size deduced from the reference sequence. This new genetic stock will be useful for positional cloning of genes on chromosome 3D, especially for Ph2 affecting homoeologous pairing in bread wheat.
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Affiliation(s)
- Radim Svačina
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Magdaléna Malurová
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Heïdi Serra
- INRA, Génétique, Diversité, Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Dominik Vítek
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
| | | | - Pierre Sourdille
- INRA, Génétique, Diversité, Ecophysiologie des Céréales, Clermont-Ferrand, France
| | - Jan Bartoš
- Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czechia
- *Correspondence: Jan Bartoš,
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17
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Moreno R, Castro P, Vrána J, Kubaláková M, Cápal P, García V, Gil J, Millán T, Doležel J. Integration of Genetic and Cytogenetic Maps and Identification of Sex Chromosome in Garden Asparagus ( Asparagus officinalis L.). FRONTIERS IN PLANT SCIENCE 2018; 9:1068. [PMID: 30108600 PMCID: PMC6079222 DOI: 10.3389/fpls.2018.01068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/02/2018] [Indexed: 05/30/2023]
Abstract
A genetic linkage map of dioecious garden asparagus (Asparagus officinalis L., 2n = 2x = 20) was constructed using F1 population, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. In total, 1376 SNPs and 27 SSRs were used for genetic mapping. Two resulting parental maps contained 907 and 678 markers spanning 1947 and 1814 cM, for female and male parent, respectively, over ten linkage groups representing ten haploid chromosomes of the species. With the aim to anchor the ten genetic linkage groups to individual chromosomes and develop a tool to facilitate genome analysis and gene cloning, we have optimized a protocol for flow cytometric chromosome analysis and sorting in asparagus. The analysis of DAPI-stained suspensions of intact mitotic chromosomes by flow cytometry resulted in histograms of relative fluorescence intensity (flow karyotypes) comprising eight major peaks. The analysis of chromosome morphology and localization of 5S and 45S rDNA by FISH on flow-sorted chromosomes, revealed that four chromosomes (IV, V, VI, VIII) could be discriminated and sorted. Seventy-two SSR markers were used to characterize chromosome content of individual peaks on the flow karyotype. Out of them, 27 were included in the genetic linkage map and anchored genetic linkage groups to chromosomes. The sex determining locus was located on LG5, which was associated with peak V representing a chromosome with 5S rDNA locus. The results obtained in this study will support asparagus improvement by facilitating targeted marker development and gene isolation using flow-sorted chromosomes.
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Affiliation(s)
- Roberto Moreno
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Patricia Castro
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Petr Cápal
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Verónica García
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Juan Gil
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Teresa Millán
- Department of Genetics-ETSIAM, University of Córdoba, Córdoba, Spain
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
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18
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Sun H, Song J, Lei J, Song X, Dai K, Xiao J, Yuan C, An S, Wang H, Wang X. Construction and application of oligo-based FISH karyotype of Haynaldia villosa. J Genet Genomics 2018; 45:463-466. [PMID: 30170984 DOI: 10.1016/j.jgg.2018.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 05/30/2018] [Accepted: 06/19/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Jingjing Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Jia Lei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Xinying Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Keli Dai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Chunxia Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Shengmin An
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China.
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China.
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Xiao J, Dai K, Fu L, Vrána J, Kubaláková M, Wan W, Sun H, Zhao J, Yu C, Wu Y, Abrouk M, Wang H, Doležel J, Wang X. Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order. BMC Genomics 2017; 18:791. [PMID: 29037165 PMCID: PMC5644170 DOI: 10.1186/s12864-017-4211-7] [Citation(s) in RCA: 6] [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: 01/22/2017] [Accepted: 10/12/2017] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Haynaldia villosa (H. villosa) has been recognized as a species potentially useful for wheat improvement. The availability of its genomic sequences will boost its research and application. RESULTS In this work, the short arm of H. villosa chromosome 4V (4VS) was sorted by flow cytometry and sequenced using Illumina platform. About 170.6 Mb assembled sequences were obtained. Further analysis showed that repetitive elements accounted for about 64.6% of 4VS, while the coding fraction, which is corresponding to 1977 annotated genes, represented 1.5% of the arm. The syntenic regions of the 4VS were searched and identified on wheat group 4 chromosomes 4AL, 4BS, 4DS, Brachypodium chromosomes 1 and 4, rice chromosomes 3 and 11, and sorghum chromosomes 1, 5 and 8. Based on genome-zipper analysis, a virtual gene order comprising 735 gene loci on 4VS genome was built by referring to the Brachypodium genome, which was relatively consistent with the scaffold order determined for Ae. tauschii chromosome 4D. The homologous alleles of several cloned genes on wheat group 4 chromosomes including Rht-1 gene were identified. CONCLUSIONS The sequences provided valuable information for mapping and positional-cloning genes located on 4VS, such as the wheat yellow mosaic virus resistance gene Wss1. The work on 4VS provided detailed insights into the genome of H. villosa, and may also serve as a model for sequencing the remaining parts of H. villosa genome.
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Affiliation(s)
- Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Keli Dai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Lian Fu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671 Olomouc, Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671 Olomouc, Czech Republic
| | - Wentao Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Jing Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Chunyan Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671 Olomouc, Czech Republic
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Haná Region for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-783671 Olomouc, Czech Republic
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095 China
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20
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Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly. Nat Biotechnol 2017; 35:793-796. [PMID: 28504667 DOI: 10.1038/nbt.3877] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/11/2017] [Indexed: 11/08/2022]
Abstract
Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago long-range linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.
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21
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Development of intron targeting (IT) markers specific for chromosome arm 4VS of Haynaldia villosa by chromosome sorting and next-generation sequencing. BMC Genomics 2017; 18:167. [PMID: 28202009 PMCID: PMC5310052 DOI: 10.1186/s12864-017-3567-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 02/07/2017] [Indexed: 12/31/2022] Open
Abstract
Background Haynaldia villosa (L.) Schur (syn. Dasypyrum villosum L. Candargy, 2n = 14, genome VV) is the tertiary gene pool of wheat, and thus a potential resource of genes for wheat improvement. Among other, wheat yellow mosaic (WYM) resistance gene Wss1 and a take-all resistance gene were identified on the short arm of chromosome 4 V (4VS) of H. villosa. We had obtained introgressions on 4VS chromosome arm, with the objective of utilizing the target genes. However, monitoring these introgressions has been a daunting task because of inadequate knowledge as to H.villosa genome, as reflected by the lack of specific markers. Results This study aims to develop 4VS-specific markers by combination of chromosome sorting and next-generation sequencing. The short arm of chromosome 4VS of H.villosa was flow-sorted using a FACSVantage SE flow cytometer and sorter, and then sequenced by Illumina sequencing. The sequence of H. villosa 4VS was assembled by the software Hecate, and then was compared with the sequence assemblies of wheat chromosome arms 4AL, 4BS and 4DS and Ae. tauschii 4DS, with the objectives of identifying exon-exon junctions and localizing introns on chromosome 4VS of H. villosa. The intron length polymorphisms suitable for designing H. villosa primers were evaluated with criteria. Consequently, we designed a total of 359 intron targeting (IT) markers, among which 232 (64.62%) markers were specific for tracing the 4VS chromatin in the wheat background. Conclusion The combination of chromosome sorting and next-generation sequencing to develop specific IT markers for 4VS of H. villosa has high success rate and specificity, thus being applicable for the development of chromosome-specific markers for alien chromatin in wheat breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3567-z) contains supplementary material, which is available to authorized users.
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Abrouk M, Balcárková B, Šimková H, Komínkova E, Martis MM, Jakobson I, Timofejeva L, Rey E, Vrána J, Kilian A, Järve K, Doležel J, Valárik M. The in silico identification and characterization of a bread wheat/Triticum militinae introgression line. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:249-256. [PMID: 27510270 PMCID: PMC5259550 DOI: 10.1111/pbi.12610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 07/21/2016] [Accepted: 08/08/2016] [Indexed: 05/23/2023]
Abstract
The capacity of the bread wheat (Triticum aestivum) genome to tolerate introgression from related genomes can be exploited for wheat improvement. A resistance to powdery mildew expressed by a derivative of the cross-bread wheat cv. Tähti × T. militinae (Tm) is known to be due to the incorporation of a Tm segment into the long arm of chromosome 4A. Here, a newly developed in silico method termed rearrangement identification and characterization (RICh) has been applied to characterize the introgression. A virtual gene order, assembled using the GenomeZipper approach, was obtained for the native copy of chromosome 4A; it incorporated 570 4A DArTseq markers to produce a zipper comprising 2132 loci. A comparison between the native and introgressed forms of the 4AL chromosome arm showed that the introgressed region is located at the distal part of the arm. The Tm segment, derived from chromosome 7G, harbours 131 homoeologs of the 357 genes present on the corresponding region of Chinese Spring 4AL. The estimated number of Tm genes transferred along with the disease resistance gene was 169. Characterizing the introgression's position, gene content and internal gene order should not only facilitate gene isolation, but may also be informative with respect to chromatin structure and behaviour studies.
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Affiliation(s)
- Michael Abrouk
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Barbora Balcárková
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Hana Šimková
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Eva Komínkova
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Mihaela M. Martis
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems BiologyInstitute for Bioinformatics and Systems BiologyHelmholtz Center MunichNeuherbergGermany
- Division of Cell BiologyDepartment of Clinical and Experimental Medicine, Bioinformatics Infrastructure for Life SciencesLinköping UniversityLinköpingSweden
| | - Irena Jakobson
- Department of Gene TechnologyTallinn University of TechnologyTallinnEstonia
| | | | - Elodie Rey
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Jan Vrána
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | | | - Kadri Järve
- Department of Gene TechnologyTallinn University of TechnologyTallinnEstonia
| | - Jaroslav Doležel
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Miroslav Valárik
- Institute of Experimental BotanyCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
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Sánchez-Martín J, Steuernagel B, Ghosh S, Herren G, Hurni S, Adamski N, Vrána J, Kubaláková M, Krattinger SG, Wicker T, Doležel J, Keller B, Wulff BBH. Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biol 2016; 17:221. [PMID: 27795210 PMCID: PMC5087116 DOI: 10.1186/s13059-016-1082-1] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/10/2016] [Indexed: 11/18/2022] Open
Abstract
Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to parental chromosomes. We apply MutChromSeq to six mutants each of the barley Eceriferum-q gene and the wheat Pm2 genes. This approach unambiguously identified single candidate genes that were verified by Sanger sequencing of additional mutants. MutChromSeq enables reference-free forward genetics in barley and wheat, thus opening up their pan-genomes to functional genomics.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | | | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Severine Hurni
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Nikolai Adamski
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Marie Kubaláková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Simon G. Krattinger
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, CZ-78371 Czech Republic
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich, CH-8008 Switzerland
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Vrána J, Cápal P, Šimková H, Karafiátová M, Čížková J, Doležel J. Flow Analysis and Sorting of Plant Chromosomes. CURRENT PROTOCOLS IN CYTOMETRY 2016; 78:5.3.1-5.3.43. [PMID: 27723090 DOI: 10.1002/cpcy.9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Analysis and sorting of plant chromosomes (plant flow cytogenetics) is a special application of flow cytometry in plant genomics and its success depends critically on sample quality. This unit describes the methodology in a stepwise manner, starting with the induction of cell cycle synchrony and accumulation of dividing cells in mitotic metaphase, and continues with the preparation of suspensions of intact mitotic chromosomes, flow analysis and sorting of chromosomes, and finally processing of the sorted chromosomes. Each step of the protocol is described in detail as some procedures have not been used widely. Supporting histograms are presented as well as hints on dealing with plant material; the utility of sorted chromosomes for plant genomics is also discussed. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jan Vrána
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Hana Šimková
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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Kuligowska K, Lütken H, Müller R. Towards development of new ornamental plants: status and progress in wide hybridization. PLANTA 2016; 244:1-17. [PMID: 26969022 DOI: 10.1007/s00425-016-2493-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/19/2016] [Indexed: 05/21/2023]
Abstract
The present review provides insights into the key findings of the hybridization process, crucial factors affecting the adaptation of new technologies within wide hybridization of ornamental plants and presents perspectives of further development of this strategy. Wide hybridization is one of the oldest breeding techniques that contributed enormously to the development of modern plant cultivars. Within ornamental breeding, it represents the main source of genetic variation. During the long history of wide hybridization, a number of methods were implemented allowing the evolution from a conventional breeding tool into a modern methodology. Nowadays, the research on model plants and crop species increases our understanding of reproductive isolation among distant species and partly explains the background of the traditional approaches previously used for overcoming hybridization barriers. Characterization of parental plants and hybrids is performed using molecular and cytological techniques that strongly facilitate breeding processes. Molecular markers and sequencing technologies are used for the assessment of genetic relationships among plants, as the genetic distance is typically depicted as one of the most important factors influencing cross-compatibility in hybridization processes. Furthermore, molecular marker systems are frequently applied for verification of hybrid state of the progeny. The flow cytometry and genomic in situ hybridization are used in the assessment of hybridization partners and characterization of hybrid progeny in relation to genome stabilization as well as genome recombination and introgression. In the future, new research and technologies are likely to provide more detailed information about genes and pathways responsible for interspecific reproductive isolation. Ultimately, this knowledge will enable development of strategies for obtaining compatible lines for hybrid production. Recent development in sequencing technologies and availability of sequence data will also facilitate creation of new molecular markers that will advance marker-assisted selection in hybridization process.
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Affiliation(s)
- Katarzyna Kuligowska
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 9-13, 2630, Tåstrup, Denmark.
| | - Henrik Lütken
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 9-13, 2630, Tåstrup, Denmark
| | - Renate Müller
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 9-13, 2630, Tåstrup, Denmark
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Jang T, Parker JS, Weiss‐Schneeweiss H. Structural polymorphisms and distinct genomic composition suggest recurrent origin and ongoing evolution of B chromosomes in the Prospero autumnale complex (Hyacinthaceae). THE NEW PHYTOLOGIST 2016; 210:669-79. [PMID: 26643365 PMCID: PMC4949986 DOI: 10.1111/nph.13778] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/28/2015] [Indexed: 05/29/2023]
Abstract
Supernumerary B chromosomes (Bs) are genomic parasitic components, originating from the A complement via chromosomal rearrangements, which follow their own evolutionary trajectories. They often contain repetitive DNAs, some shared with regular chromosomes and some newly evolved. Genomic composition, origin and evolution of Bs have been analysed in the chromosomally variable Prospero autumnale complex. Two rDNAs and a satellite DNA (PaB6) from regular chromosomes were mapped to Bs of 26 plants from three diploid cytotypes, their hybrids and polyploid derivatives. In homoploid diploid hybrids, genomic in situ hybridization (GISH) allowed B painting with the parental DNAs. Bs were structurally variable and highly enriched in 5S rDNA and satDNA PaB6, and rarely in 35S rDNA. Eleven combinations of rDNA and PaB6 localization were observed. The quantities of PaB6 in Bs and regular chromosomes were not correlated, suggesting amplification mechanisms other than recombination. PaB6 and 5S rDNA amounts increased with increasing ploidy level. GISH revealed two independent origins of Bs. The structural variation, repeat content, repeat-type fluctuations and differing genomic affinities of Bs in different cytotypes suggest that they represent young proto-B chromosomes. Bs in P. autumnale probably form recurrently as by-products of the extensive genome restructuring within this chromosomally variable species complex.
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Affiliation(s)
- Tae‐Soo Jang
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
| | | | - Hanna Weiss‐Schneeweiss
- Department of Botany and Biodiversity ResearchUniversity of ViennaRennweg 14A‐1030ViennaAustria
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27
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Abstract
Nuclear genomes of many important plant species are tremendously complicated to map and sequence. The ability to isolate single chromosomes, which represent small units of nuclear genome, is priceless in many areas of plant research including cytogenetics, genomics, and proteomics. Flow cytometry is the only technique which can provide large quantities of pure chromosome fractions suitable for downstream applications including physical mapping, preparation of chromosome-specific BAC libraries, sequencing, and optical mapping. Here, we describe step-by-step procedure of preparation of liquid suspensions of intact mitotic metaphase chromosomes and their flow cytometric analysis and sorting.
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Affiliation(s)
- Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic.
| | - Petr Cápal
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jarmila Číhalíková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
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28
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Molnár I, Vrána J, Farkas A, Kubaláková M, Cseh A, Molnár-Láng M, Doležel J. Flow sorting of C-genome chromosomes from wild relatives of wheat Aegilops markgrafii, Ae. triuncialis and Ae. cylindrica, and their molecular organization. ANNALS OF BOTANY 2015; 116:189-200. [PMID: 26043745 PMCID: PMC4512188 DOI: 10.1093/aob/mcv073] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/27/2015] [Accepted: 04/15/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Aegilops markgrafii (CC) and its natural hybrids Ae. triuncialis (U(t)U(t)C(t)C(t)) and Ae. cylindrica (D(c)D(c)C(c)C(c)) represent a rich reservoir of useful genes for improvement of bread wheat (Triticum aestivum), but the limited information available on their genome structure and the shortage of molecular (cyto-) genetic tools hamper the utilization of the extant genetic diversity. This study provides the complete karyotypes in the three species obtained after fluorescent in situ hybridization (FISH) with repetitive DNA probes, and evaluates the potential of flow cytometric chromosome sorting. METHODS The flow karyotypes obtained after the analysis of 4',6-diamidino-2-phenylindole (DAPI)-stained chromosomes were characterized and the chromosome content of the peaks on the flow karyotypes was determined by FISH. Twenty-nine conserved orthologous set (COS) markers covering all seven wheat homoeologous chromosome groups were used for PCR with DNA amplified from flow-sorted chromosomes and genomic DNA. KEY RESULTS FISH with repetitive DNA probes revealed that chromosomes 4C, 5C, 7C(t), T6U(t)S.6U(t)L-5C(t)L, 1C(c) and 5D(c) could be sorted with purities ranging from 66 to 91 %, while the remaining chromosomes could be sorted in groups of 2-5. This identified a partial wheat-C-genome homology for group 4 and 5 chromosomes. In addition, 1C chromosomes were homologous with group 1 of wheat; a small segment from group 2 indicated 1C-2C rearrangement. An extensively rearranged structure of chromosome 7C relative to wheat was also detected. CONCLUSIONS The possibility of purifying Aegilops chromosomes provides an attractive opportunity to investigate the structure and evolution of the Aegilops C genome and to develop molecular tools to facilitate the identification of alien chromatin and support alien introgression breeding in bread wheat.
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Affiliation(s)
- István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462 Martonvásár, Hungary and
| | - Jan Vrána
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462 Martonvásár, Hungary and
| | - Marie Kubaláková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
| | - András Cseh
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462 Martonvásár, Hungary and
| | - Márta Molnár-Láng
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462 Martonvásár, Hungary and
| | - Jaroslav Doležel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic
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29
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Staňková H, Valárik M, Lapitan NLV, Berkman PJ, Batley J, Edwards D, Luo MC, Tulpová Z, Kubaláková M, Stein N, Doležel J, Šimková H. Chromosomal genomics facilitates fine mapping of a Russian wheat aphid resistance gene. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1373-1383. [PMID: 25862680 DOI: 10.1007/s00122-015-2512-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/27/2015] [Indexed: 06/04/2023]
Abstract
Making use of wheat chromosomal resources, we developed 11 gene-associated markers for the region of interest, which allowed reducing gene interval and spanning it by four BAC clones. Positional gene cloning and targeted marker development in bread wheat are hampered by high complexity and polyploidy of its nuclear genome. Aiming to clone a Russian wheat aphid resistance gene Dn2401 located on wheat chromosome arm 7DS, we have developed a strategy overcoming problems due to polyploidy and enabling efficient development of gene-associated markers from the region of interest. We employed information gathered by GenomeZipper, a synteny-based tool combining sequence data of rice, Brachypodium, sorghum and barley, and took advantage of a high-density linkage map of Aegilops tauschii. To ensure genome- and locus-specificity of markers, we made use of survey sequence assemblies of isolated wheat chromosomes 7A, 7B and 7D. Despite the low level of polymorphism of the wheat D subgenome, our approach allowed us to add in an efficient and cost-effective manner 11 new gene-associated markers in the Dn2401 region and narrow down the target interval to 0.83 cM. Screening 7DS-specific BAC library with the flanking markers revealed a contig of four BAC clones that span the Dn2401 region in wheat cultivar 'Chinese Spring'. With the availability of sequence assemblies and GenomeZippers for each of the wheat chromosome arms, the proposed strategy can be applied for focused marker development in any region of the wheat genome.
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Affiliation(s)
- Helena Staňková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, 783 71, Olomouc, Czech Republic
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Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides. Sci Rep 2015; 5:10763. [PMID: 26084265 PMCID: PMC4471722 DOI: 10.1038/srep10763] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/28/2015] [Indexed: 12/13/2022] Open
Abstract
Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world.
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Akpinar BA, Magni F, Yuce M, Lucas SJ, Šimková H, Šafář J, Vautrin S, Bergès H, Cattonaro F, Doležel J, Budak H. The physical map of wheat chromosome 5DS revealed gene duplications and small rearrangements. BMC Genomics 2015; 16:453. [PMID: 26070810 PMCID: PMC4465308 DOI: 10.1186/s12864-015-1641-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/19/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The substantially large bread wheat genome, organized into highly similar three sub-genomes, renders genomic research challenging. The construction of BAC-based physical maps of individual chromosomes reduces the complexity of this allohexaploid genome, enables elucidation of gene space and evolutionary relationships, provides tools for map-based cloning, and serves as a framework for reference sequencing efforts. In this study, we constructed the first comprehensive physical map of wheat chromosome arm 5DS, thereby exploring its gene space organization and evolution. RESULTS The physical map of 5DS was comprised of 164 contigs, of which 45 were organized into 21 supercontigs, covering 176 Mb with an N50 value of 2,173 kb. Fifty-eight of the contigs were larger than 1 Mb, with the largest contig spanning 6,649 kb. A total of 1,864 molecular markers were assigned to the map at a density of 10.5 markers/Mb, anchoring 100 of the 120 contigs (>5 clones) that constitute ~95 % of the cumulative length of the map. Ordering of 80 contigs along the deletion bins of chromosome arm 5DS revealed small-scale breaks in syntenic blocks. Analysis of the gene space of 5DS suggested an increasing gradient of genes organized in islands towards the telomere, with the highest gene density of 5.17 genes/Mb in the 0.67-0.78 deletion bin, 1.4 to 1.6 times that of all other bins. CONCLUSIONS Here, we provide a chromosome-specific view into the organization and evolution of the D genome of bread wheat, in comparison to one of its ancestors, revealing recent genome rearrangements. The high-quality physical map constructed in this study paves the way for the assembly of a reference sequence, from which breeding efforts will greatly benefit.
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Affiliation(s)
- Bala Ani Akpinar
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
| | - Federica Magni
- Instituto di Genomica Applicata, Via J.Linussio 51, Udine, 33100, Italy.
| | - Meral Yuce
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
| | - Stuart J Lucas
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic.
| | - Jan Šafář
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic.
| | - Sonia Vautrin
- Centre Nationales Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326, Castanet-Tolosan, France.
| | - Hélène Bergès
- Centre Nationales Ressources Génomiques Végétales, INRA UPR 1258, 24 Chemin de Borde Rouge - Auzeville 31326, Castanet-Tolosan, France.
| | - Federica Cattonaro
- Instituto di Genomica Applicata, Via J.Linussio 51, Udine, 33100, Italy.
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic.
| | - Hikmet Budak
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, Universite Cad. Orta Mah. No: 27, Tuzla, 34956, Istanbul, Turkey.
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, 34956, Istanbul, Turkey.
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Garbus I, Romero JR, Valarik M, Vanžurová H, Karafiátová M, Cáccamo M, Doležel J, Tranquilli G, Helguera M, Echenique V. Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes. BMC Genomics 2015; 16:375. [PMID: 25962417 PMCID: PMC4440537 DOI: 10.1186/s12864-015-1579-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/24/2015] [Indexed: 12/04/2022] Open
Abstract
Background The number and complexity of repetitive elements varies between species, being in general most represented in those with larger genomes. Combining the flow-sorted chromosome arms approach to genome analysis with second generation DNA sequencing technologies provides a unique opportunity to study the repetitive portion of each chromosome, enabling comparisons among them. Additionally, different sequencing approaches may produce different depth of insight to repeatome content and structure. In this work we analyze and characterize the repetitive sequences of Triticum aestivum cv. Chinese Spring homeologous group 4 chromosome arms, obtained through Roche 454 and Illumina sequencing technologies, hereinafter marked by subscripts 454 and I, respectively. Repetitive sequences were identified with the RepeatMasker software using the interspersed repeat database mips-REdat_v9.0p. The input sequences consisted of our 4DS454 and 4DL454 scaffolds and 4ASI, 4ALI, 4BSI, 4BLI, 4DSI and 4DLI contigs, downloaded from the International Wheat Genome Sequencing Consortium (IWGSC). Results Repetitive sequences content varied from 55% to 63% for all chromosome arm assemblies except for 4DLI, in which the repeat content was 38%. Transposable elements, small RNA, satellites, simple repeats and low complexity sequences were analyzed. SSR frequency was found one per 24 to 27 kb for all chromosome assemblies except 4DLI, where it was three times higher. Dinucleotides and trinucleotides were the most abundant SSR repeat units. (GA)n/(TC)n was the most abundant SSR except for 4DLI where the most frequently identified SSR was (CCG/CGG)n. Retrotransposons followed by DNA transposons were the most highly represented sequence repeats, mainly composed of CACTA/En-Spm and Gypsy superfamilies, respectively. This whole chromosome sequence analysis allowed identification of three new LTR retrotransposon families belonging to the Copia superfamily, one belonging to the Gypsy superfamily and two TRIM retrotransposon families. Their physical distribution in wheat genome was analyzed by fluorescent in situ hybridization (FISH) and one of them, the Carmen retrotransposon, was found specific for centromeric regions of all wheat chromosomes. Conclusion The presented work is the first deep report of wheat repetitive sequences analyzed at the chromosome arm level, revealing the first insight into the repeatome of T. aestivum chromosomes of homeologous group 4. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1579-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ingrid Garbus
- CERZOS (CCT - CONICET Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Argentina.
| | - José R Romero
- CERZOS (CCT - CONICET Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Argentina.
| | - Miroslav Valarik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Hana Vanžurová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Miroslava Karafiátová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Mario Cáccamo
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371, Olomouc, Czech Republic.
| | - Gabriela Tranquilli
- Instituto Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina.
| | - Marcelo Helguera
- Estación Experimental Agropecuaria Marcos Juárez, Instituto Nacional de Tecnología Agropecuaria (INTA), Marcos Juárez, Córdoba, Argentina.
| | - Viviana Echenique
- CERZOS (CCT - CONICET Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Argentina.
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Cell synchronization and isolation of chromosomes from Chinese fir root tips for flow cytometric analysis. Biotechnol Lett 2015; 37:1309-14. [DOI: 10.1007/s10529-015-1800-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/17/2015] [Indexed: 10/23/2022]
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Helguera M, Rivarola M, Clavijo B, Martis MM, Vanzetti LS, González S, Garbus I, Leroy P, Šimková H, Valárik M, Caccamo M, Doležel J, Mayer KFX, Feuillet C, Tranquilli G, Paniego N, Echenique V. New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 233:200-212. [PMID: 25711827 PMCID: PMC4352925 DOI: 10.1016/j.plantsci.2014.12.004] [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: 09/01/2014] [Revised: 11/21/2014] [Accepted: 12/02/2014] [Indexed: 05/20/2023]
Abstract
Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223Mb) and scaffolds (65Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information.
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Affiliation(s)
- Marcelo Helguera
- Estación Experimental Agropecuaria Marcos Juárez, Instituto Nacional de Tecnología Agropecuaria (INTA), Marcos Juárez, Córdoba, Argentina.
| | - Máximo Rivarola
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Bernardo Clavijo
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK.
| | - Mihaela M Martis
- MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
| | - Leonardo S Vanzetti
- Estación Experimental Agropecuaria Marcos Juárez, Instituto Nacional de Tecnología Agropecuaria (INTA), Marcos Juárez, Córdoba, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Sergio González
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Ingrid Garbus
- CERZOS (Centro de Recursos Naturales Renovables de la Zona Semiárida), (CCT-CONICET-Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Buenos Aires, Argentina.
| | - Phillippe Leroy
- INRA-UMR 1095, Genetics, Diversity and Ecophysiology of Cereals, Institut National de la Recherche Agronomique-Université Blaise Pascal, Clermont-Ferrand, France.
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic.
| | - Miroslav Valárik
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic.
| | - Mario Caccamo
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK.
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovska 6, CZ-77200 Olomouc, Czech Republic.
| | - Klaus F X Mayer
- MIPS/IBIS, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
| | | | - Gabriela Tranquilli
- Instituto de Recursos Biológicos, CIRN, INTA, Hurlingham, Buenos Aires, Argentina.
| | - Norma Paniego
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
| | - Viviana Echenique
- CERZOS (Centro de Recursos Naturales Renovables de la Zona Semiárida), (CCT-CONICET-Bahía Blanca) and Universidad Nacional del Sur, Bahía Blanca, Buenos Aires, Argentina.
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Molnár I, Kubaláková M, Šimková H, Farkas A, Cseh A, Megyeri M, Vrána J, Molnár-Láng M, Doležel J. Flow cytometric chromosome sorting from diploid progenitors of bread wheat, T. urartu, Ae. speltoides and Ae. tauschii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1091-104. [PMID: 24553964 DOI: 10.1007/s00122-014-2282-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/03/2014] [Indexed: 05/10/2023]
Abstract
Chromosomes 5A (u) , 5S and 5D can be isolated from wild progenitors, providing a chromosome-based approach to develop tools for breeding and to study the genome evolution of wheat. The three subgenomes of hexaploid bread wheat originated from Triticum urartu (A(u)A(u)), from a species similar to Aegilops speltoides (SS) (progenitor of the B genome), and from Ae. tauschii (DD). Earlier studies indicated the potential of chromosome genomics to assist gene transfer from wild relatives of wheat and discover novel genes for wheat improvement. This study evaluates the potential of flow cytometric chromosome sorting in the diploid progenitors of bread wheat. Flow karyotypes obtained by analysing DAPI-stained chromosomes were characterized and the contents of the chromosome peaks were determined. FISH analysis with repetitive DNA probes proved that chromosomes 5A(u), 5S and 5D could be sorted with purities of 78-90 %, while the remaining chromosomes could be sorted in groups of three. Twenty-five conserved orthologous set (COS) markers covering wheat homoeologous chromosome groups 1-7 were used for PCR with DNA amplified from flow-sorted chromosomes and genomic DNA. These assays validated the cytomolecular results as follows: peak I on flow karyotypes contained chromosome groups 1, 4 and 6, peak II represented homoeologous group 5, while peak III consisted of groups 2, 3 and 7. The isolation of individual chromosomes of wild progenitors provides an attractive opportunity to investigate the structure and evolution of the polyploid genome and to deliver tools for wheat improvement.
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Affiliation(s)
- István Molnár
- Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik u. 2, H-2462, Martonvásár, Hungary,
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Tiwari VK, Wang S, Sehgal S, Vrána J, Friebe B, Kubaláková M, Chhuneja P, Doležel J, Akhunov E, Kalia B, Sabir J, Gill BS. SNP Discovery for mapping alien introgressions in wheat. BMC Genomics 2014; 15:273. [PMID: 24716476 PMCID: PMC4051138 DOI: 10.1186/1471-2164-15-273] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/31/2014] [Indexed: 11/30/2022] Open
Abstract
Background Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). Results The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. Conclusion This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and monitoring of alien segments in crop breeding programs and further enable mapping and cloning novel genes from the wild relatives of crop plants.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.
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Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Šimková H. Advances in plant chromosome genomics. Biotechnol Adv 2014; 32:122-36. [DOI: 10.1016/j.biotechadv.2013.12.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 01/09/2023]
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Kopecký D, Studer B. Emerging technologies advancing forage and turf grass genomics. Biotechnol Adv 2013; 32:190-9. [PMID: 24309540 DOI: 10.1016/j.biotechadv.2013.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
Grassland is of major importance for agricultural production and provides valuable ecosystem services. Its impact is likely to rise in changing socio-economic and climatic environments. High yielding forage grass species are major components of sustainable grassland production. Understanding the genome structure and function of grassland species provides opportunities to accelerate crop improvement and thus to mitigate the future challenges of increased feed and food demand, scarcity of natural resources such as water and nutrients, and high product qualities. In this review, we will discuss a selection of technological developments that served as main drivers to generate new insights into the structure and function of nuclear genomes. Many of these technologies were originally developed in human or animal science and are now increasingly applied in plant genomics. Our main goal is to highlight the benefits of using these technologies for forage and turf grass genome research, to discuss their potentials and limitations as well as their relevance for future applications.
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Affiliation(s)
- David Kopecký
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc-Holice, Czech Republic
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland.
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Tanaka T, Kobayashi F, Joshi GP, Onuki R, Sakai H, Kanamori H, Wu J, Simkova H, Nasuda S, Endo TR, Hayakawa K, Doležel J, Ogihara Y, Itoh T, Matsumoto T, Handa H. Next-generation survey sequencing and the molecular organization of wheat chromosome 6B. DNA Res 2013; 21:103-14. [PMID: 24086083 PMCID: PMC3989483 DOI: 10.1093/dnares/dst041] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Common wheat (Triticum aestivum L.) is one of the most important cereals in the world. To improve wheat quality and productivity, the genomic sequence of wheat must be determined. The large genome size (∼17 Gb/1 C) and the hexaploid status of wheat have hampered the genome sequencing of wheat. However, flow sorting of individual chromosomes has allowed us to purify and separately shotgun-sequence a pair of telocentric chromosomes. Here, we describe a result from the survey sequencing of wheat chromosome 6B (914 Mb/1 C) using massively parallel 454 pyrosequencing. From the 4.94 and 5.51 Gb shotgun sequence data from the two chromosome arms of 6BS and 6BL, 235 and 273 Mb sequences were assembled to cover ∼55.6 and 54.9% of the total genomic regions, respectively. Repetitive sequences composed 77 and 86% of the assembled sequences on 6BS and 6BL, respectively. Within the assembled sequences, we predicted a total of 4798 non-repetitive gene loci with the evidence of expression from the wheat transcriptome data. The numbers and chromosomal distribution patterns of the genes for tRNAs and microRNAs in wheat 6B were investigated, and the results suggested a significant involvement of DNA transposon diffusion in the evolution of these non-protein-coding RNA genes. A comparative analysis of the genomic sequences of wheat 6B and monocot plants clearly indicated the evolutionary conservation of gene contents.
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Affiliation(s)
- Tsuyoshi Tanaka
- 1Bioinformatics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
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Edwards D, Batley J, Snowdon RJ. Accessing complex crop genomes with next-generation sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1-11. [PMID: 22948437 DOI: 10.1007/s00122-012-1964-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 08/08/2012] [Indexed: 05/02/2023]
Abstract
Many important crop species have genomes originating from ancestral or recent polyploidisation events. Multiple homoeologous gene copies, chromosomal rearrangements and amplification of repetitive DNA within large and complex crop genomes can considerably complicate genome analysis and gene discovery by conventional, forward genetics approaches. On the other hand, ongoing technological advances in molecular genetics and genomics today offer unprecedented opportunities to analyse and access even more recalcitrant genomes. In this review, we describe next-generation sequencing and data analysis techniques that vastly improve our ability to dissect and mine genomes for causal genes underlying key traits and allelic variation of interest to breeders. We focus primarily on wheat and oilseed rape, two leading examples of major polyploid crop genomes whose size or complexity present different, significant challenges. In both cases, the latest DNA sequencing technologies, applied using quite different approaches, have enabled considerable progress towards unravelling the respective genomes. Our ability to discover the extent and distribution of genetic diversity in crop gene pools, and its relationship to yield and quality-related traits, is swiftly gathering momentum as DNA sequencing and the bioinformatic tools to deal with growing quantities of genomic data continue to develop. In the coming decade, genomic and transcriptomic sequencing, discovery and high-throughput screening of single nucleotide polymorphisms, presence-absence variations and other structural chromosomal variants in diverse germplasm collections will give detailed insight into the origins, domestication and available trait-relevant variation of polyploid crops, in the process facilitating novel approaches and possibilities for genomics-assisted breeding.
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Affiliation(s)
- David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia
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Jakobson I, Reis D, Tiidema A, Peusha H, Timofejeva L, Valárik M, Kladivová M, Simková H, Doležel J, Järve K. Fine mapping, phenotypic characterization and validation of non-race-specific resistance to powdery mildew in a wheat-Triticum militinae introgression line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:609-623. [PMID: 22534789 DOI: 10.1007/s00122-012-1856-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 03/21/2012] [Indexed: 05/31/2023]
Abstract
Introgression of several genomic loci from tetraploid Triticum militinae into bread wheat cv. Tähti has increased resistance of introgression line 8.1 to powdery mildew in seedlings and adult plants. In our previous work, only a major quantitative trait locus (QTL) on chromosome 4AL of the line 8.1 contributed significantly to resistance, whereas QTL on chromosomes 1A, 1B, 2A, 5A and 5B were detected merely on a suggestive level. To verify and characterize all QTLs in the line 8.1, a mapping population of double haploid lines was established. Testing for seedling resistance to 16 different races/mixtures of Blumeria graminis f. sp. tritici revealed four highly significant non-race-specific resistance QTL including the main QTL on chromosome 4AL, and a race-specific QTL on chromosome 5B. The major QTL on chromosome 4AL (QPm.tut-4A) as well as QTL on chromosome 5AL and a newly detected QTL on 7AL were highly effective at the adult stage. The QPm.tut-4A QTL accounts on average for 33-49 % of the variation in resistance in the double haploid population. Interactions between the main QTL QPm.tut-4A and the minor QTL were evaluated and discussed. A population of 98 F(2) plants from a cross of susceptible cv. Chinese Spring and the line 8.1 was created that allowed mapping the QPm.tut-4A locus to the proximal 2.5-cM region of the introgressed segment on chromosome 4AL. The results obtained in this work make it feasible to use QPm.tut-4A in resistance breeding and provide a solid basis for positional cloning of the major QTL.
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Affiliation(s)
- Irena Jakobson
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia.
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42
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Doležel J, Vrána J, Safář J, Bartoš J, Kubaláková M, Simková H. Chromosomes in the flow to simplify genome analysis. Funct Integr Genomics 2012; 12:397-416. [PMID: 22895700 PMCID: PMC3431466 DOI: 10.1007/s10142-012-0293-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 07/30/2012] [Indexed: 11/25/2022]
Abstract
Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be resolved from other chromosomes in a karyotype. The analysis and sorting are carried out at rates of 10(2)-10(4) chromosomes per second, and for complex genomes such as wheat the flow sorting technology has been ground-breaking in reducing genome complexity for genome sequencing. The high sample rate provides an attractive approach for karyotype analysis (flow karyotyping) and the purification of chromosomes in large numbers. In characterizing the chromosome complement of an organism, the high number that can be studied using flow cytometry allows for a statistically accurate analysis. Chromosome sorting plays a particularly important role in the analysis of nuclear genome structure and the analysis of particular and aberrant chromosomes. Other attractive but not well-explored features include the analysis of chromosomal proteins, chromosome ultrastructure, and high-resolution mapping using FISH. Recent results demonstrate that chromosome flow sorting can be coupled seamlessly with DNA array and next-generation sequencing technologies for high-throughput analyses. The main advantages are targeting the analysis to a genome region of interest and a significant reduction in sample complexity. As flow sorters can also sort single copies of chromosomes, shotgun sequencing DNA amplified from them enables the production of haplotype-resolved genome sequences. This review explains the principles of flow cytometric chromosome analysis and sorting (flow cytogenetics), discusses the major uses of this technology in genome analysis, and outlines future directions.
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Affiliation(s)
- Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, Olomouc, Czech Republic.
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Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. Proc Natl Acad Sci U S A 2012; 109:13343-6. [PMID: 22847450 DOI: 10.1073/pnas.1204237109] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Supernumerary B chromosomes are optional additions to the basic set of A chromosomes, and occur in all eukaryotic groups. They differ from the basic complement in morphology, pairing behavior, and inheritance and are not required for normal growth and development. The current view is that B chromosomes are parasitic elements comparable to selfish DNA, like transposons. In contrast to transposons, they are autonomously inherited independent of the host genome and have their own mechanisms of mitotic or meiotic drive. Although B chromosomes were first described a century ago, little is known about their origin and molecular makeup. The widely accepted view is that they are derived from fragments of A chromosomes and/or generated in response to interspecific hybridization. Through next-generation sequencing of sorted A and B chromosomes, we show that B chromosomes of rye are rich in gene-derived sequences, allowing us to trace their origin to fragments of A chromosomes, with the largest parts corresponding to rye chromosomes 3R and 7R. Compared with A chromosomes, B chromosomes were also found to accumulate large amounts of specific repeats and insertions of organellar DNA. The origin of rye B chromosomes occurred an estimated ∼1.1-1.3 Mya, overlapping in time with the onset of the genus Secale (1.7 Mya). We propose a comprehensive model of B chromosome evolution, including its origin by recombination of several A chromosomes followed by capturing of additional A-derived and organellar sequences and amplification of B-specific repeats.
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Vrána J, Simková H, Kubaláková M, Cíhalíková J, Doležel J. Flow cytometric chromosome sorting in plants: the next generation. Methods 2012; 57:331-7. [PMID: 22440520 DOI: 10.1016/j.ymeth.2012.03.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 03/01/2012] [Accepted: 03/05/2012] [Indexed: 10/28/2022] Open
Abstract
Genome analysis in many plant species is hampered by large genome size and by sequence redundancy due to the presence of repetitive DNA and polyploidy. One solution is to reduce the sample complexity by dissecting the genomes to single chromosomes. This can be realized by flow cytometric sorting, which enables purification of chromosomes in large numbers. Coupling the chromosome sorting technology with next generation sequencing provides a targeted and cost effective way to tackle complex genomes. The methods outlined in this article describe a procedure for preparation of chromosomal DNA suitable for next-generation sequencing.
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Affiliation(s)
- Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic
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Fluch S, Kopecky D, Burg K, Šimková H, Taudien S, Petzold A, Kubaláková M, Platzer M, Berenyi M, Krainer S, Doležel J, Lelley T. Sequence composition and gene content of the short arm of rye (Secale cereale) chromosome 1. PLoS One 2012; 7:e30784. [PMID: 22328922 PMCID: PMC3273464 DOI: 10.1371/journal.pone.0030784] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 12/26/2011] [Indexed: 01/21/2023] Open
Abstract
Background The purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale) with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide. Methodology/Principal Findings Multiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3%) being the most abundant. More than four thousand simple sequence repeat (SSR) sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice. Conclusions The present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye.
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Affiliation(s)
- Silvia Fluch
- Health and Environment Department, Bioresources, Austrian Institute of Technology (AIT), Tulln, Austria
| | - Dieter Kopecky
- Health and Environment Department, Bioresources, Austrian Institute of Technology (AIT), Tulln, Austria
| | - Kornel Burg
- Health and Environment Department, Bioresources, Austrian Institute of Technology (AIT), Tulln, Austria
- * E-mail:
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Stefan Taudien
- Leibniz Institute for Age Research (Fritz Lipmann Institute), Jena, Germany
| | - Andreas Petzold
- Leibniz Institute for Age Research (Fritz Lipmann Institute), Jena, Germany
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Matthias Platzer
- Leibniz Institute for Age Research (Fritz Lipmann Institute), Jena, Germany
| | - Maria Berenyi
- Health and Environment Department, Bioresources, Austrian Institute of Technology (AIT), Tulln, Austria
| | - Siegfried Krainer
- Health and Environment Department, Bioresources, Austrian Institute of Technology (AIT), Tulln, Austria
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Tamas Lelley
- Department of Agrobiotechnology, Institute for Biotechnology in Plant Production (IFA-Tulln), University of Natural Resources and Applied Life Sciences (BOKU), Vienna, Austria
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Hernandez P, Martis M, Dorado G, Pfeifer M, Gálvez S, Schaaf S, Jouve N, Šimková H, Valárik M, Doležel J, Mayer KFX. Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 69:377-86. [PMID: 21974774 DOI: 10.1111/j.1365-313x.2011.04808.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat (Triticum aestivum) genome (approximately 17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status have impeded genome sequencing of this important crop species. Here we describe the use of mitotic chromosome flow sorting to separately purify and then shotgun-sequence a pair of telocentric chromosomes that together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A, embracing ≥85% of its total gene content, and have enabled precise localization of the various translocation and inversion breakpoints on chromosome 4A that differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of chromosome 4A, together with the emerging sequences of homoeologous wheat chromosome groups 4, 5 and 7, represent unique resources that will allow us to obtain new insights into the evolutionary dynamics between homoeologous chromosomes and syntenic chromosomal regions.
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Affiliation(s)
- Pilar Hernandez
- Instituto de Agricultura Sostenible, Alameda del Obispo s/n, 14080 Córdoba, Spain
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Molnár I, Kubaláková M, Šimková H, Cseh A, Molnár-Láng M, Doležel J. Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata. PLoS One 2011; 6:e27708. [PMID: 22132127 PMCID: PMC3223179 DOI: 10.1371/journal.pone.0027708] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Accepted: 10/22/2011] [Indexed: 01/20/2023] Open
Abstract
This study evaluates the potential of flow cytometry for chromosome sorting in two wild diploid wheats Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata. Flow karyotypes obtained after the analysis of DAPI-stained chromosomes were characterized and content of chromosome peaks was determined. Peaks of chromosome 1U could be discriminated in flow karyotypes of Ae. umbellulata and Ae. biuncialis and the chromosome could be sorted with purities exceeding 95%. The remaining chromosomes formed composite peaks and could be sorted in groups of two to four. Twenty four wheat SSR markers were tested for their position on chromosomes of Ae. umbellulata and Ae. comosa using PCR on DNA amplified from flow-sorted chromosomes and genomic DNA of wheat-Ae. geniculata addition lines, respectively. Six SSR markers were located on particular Aegilops chromosomes using sorted chromosomes, thus confirming the usefulness of this approach for physical mapping. The SSR markers are suitable for marker assisted selection of wheat-Aegilops introgression lines. The results obtained in this work provide new opportunities for dissecting genomes of wild relatives of wheat with the aim to assist in alien gene transfer and discovery of novel genes for wheat improvement.
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Affiliation(s)
- István Molnár
- Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - András Cseh
- Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Márta Molnár-Láng
- Agricultural Research Institute of the Hungarian Academy of Sciences, Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
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48
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Vitulo N, Albiero A, Forcato C, Campagna D, Dal Pero F, Bagnaresi P, Colaiacovo M, Faccioli P, Lamontanara A, Šimková H, Kubaláková M, Perrotta G, Facella P, Lopez L, Pietrella M, Gianese G, Doležel J, Giuliano G, Cattivelli L, Valle G, Stanca AM. First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One 2011; 6:e26421. [PMID: 22028874 PMCID: PMC3196578 DOI: 10.1371/journal.pone.0026421] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 09/26/2011] [Indexed: 01/29/2023] Open
Abstract
Wheat is one of the world's most important crops and is characterized by a large polyploid genome. One way to reduce genome complexity is to isolate single chromosomes using flow cytometry. Low coverage DNA sequencing can provide a snapshot of individual chromosomes, allowing a fast characterization of their main features and comparison with other genomes. We used massively parallel 454 pyrosequencing to obtain a 2x coverage of wheat chromosome 5A. The resulting sequence assembly was used to identify TEs, genes and miRNAs, as well as to infer a virtual gene order based on the synteny with other grass genomes. Repetitive elements account for more than 75% of the genome. Gene content was estimated considering non-redundant reads showing at least one match to ESTs or proteins. The results indicate that the coding fraction represents 1.08% and 1.3% of the short and long arm respectively, projecting the number of genes of the whole chromosome to approximately 5,000. 195 candidate miRNA precursors belonging to 16 miRNA families were identified. The 5A genes were used to search for syntenic relationships between grass genomes. The short arm is closely related to Brachypodium chromosome 4, sorghum chromosome 8 and rice chromosome 12; the long arm to regions of Brachypodium chromosomes 4 and 1, sorghum chromosomes 1 and 2 and rice chromosomes 9 and 3. From these similarities it was possible to infer the virtual gene order of 392 (5AS) and 1,480 (5AL) genes of chromosome 5A, which was compared to, and found to be largely congruent with the available physical map of this chromosome.
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Affiliation(s)
- Nicola Vitulo
- CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Alessandro Albiero
- CRIBI Biotechnology Center, University of Padova, Padova, Italy
- Bmr-genomics srl, Padova, Italy
| | - Claudio Forcato
- CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Davide Campagna
- CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | | | | | | | | | | | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | | | | | | | | | | | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc, Czech Republic
| | | | - Luigi Cattivelli
- CRA Genomics Research Centre, Fiorenzuola d'Arda, Italy
- * E-mail:
| | - Giorgio Valle
- CRIBI Biotechnology Center, University of Padova, Padova, Italy
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Zatloukalová P, Hřibová E, Kubaláková M, Suchánková P, Simková H, Adoración C, Kahl G, Millán T, Doležel J. Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes. Chromosome Res 2011; 19:729-39. [PMID: 21947955 DOI: 10.1007/s10577-011-9235-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 08/20/2011] [Accepted: 08/23/2011] [Indexed: 11/29/2022]
Abstract
Cultivated chickpea is the third most important legume after field bean and garden pea worldwide. Despite considerable breeding towards improved yield and resistance to biotic and abiotic stresses, the production of chickpea remained stagnant, but molecular tools are expected to increase the impact of current improvement programs. As a first step towards this goal, various genetic linkage maps have been established and markers linked to resistance genes been identified. However, until now, only one linkage group (LG) has been assigned to a specific chromosome. In the present work, mitotic chromosomes were sorted using flow cytometry and used as template for PCR with primers designed for genomic regions flanking microsatellites. These primers amplify sequence-tagged microsatellite site markers. This approach confirmed the assignment of LG8 to the smallest chromosome H. For the first time, LG5 was linked to the largest chromosome A, LG4 to a medium-sized chromosome E, while LG3 was anchored to the second largest chromosome B. Chromosomes C and D could not be flow-sorted separately and were jointly associated to LG6 and LG7. By the same token, chromosomes F and G were anchored to LG1 and LG2. To establish a set of preferably diagnostic cytogenetic markers, the genomic distribution of various probes was verified using FISH. Moreover, a partial genomic bacterial artificial chromosome (BAC) library was constructed and putative single/low-copy BAC clones were mapped cytogenetically. As a result, two clones were identified localizing specifically to chromosomes E and H, for which no cytogenetic markers were yet available.
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Affiliation(s)
- Pavlína Zatloukalová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Sokolovská 6, 77200 Olomouc, Czech Republic
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50
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Wicker T, Mayer KF, Gundlach H, Martis M, Steuernagel B, Scholz U, Šimková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Doležel J, Keller B, Stein N. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. THE PLANT CELL 2011; 23:1706-18. [PMID: 21622801 PMCID: PMC3123954 DOI: 10.1105/tpc.111.086629] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 04/19/2011] [Accepted: 05/16/2011] [Indexed: 05/18/2023]
Abstract
All six arms of the group 1 chromosomes of hexaploid wheat (Triticum aestivum) were sequenced with Roche/454 to 1.3- to 2.2-fold coverage and compared with similar data sets from the homoeologous chromosome 1H of barley (Hordeum vulgare). Six to ten thousand gene sequences were sampled per chromosome. These were classified into genes that have their closest homologs in the Triticeae group 1 syntenic region in Brachypodium, rice (Oryza sativa), and/or sorghum (Sorghum bicolor) and genes that have their homologs elsewhere in these model grass genomes. Although the number of syntenic genes was similar between the homologous groups, the amount of nonsyntenic genes was found to be extremely diverse between wheat and barley and even between wheat subgenomes. Besides a small core group of genes that are nonsyntenic in other grasses but conserved among Triticeae, we found thousands of genic sequences that are specific to chromosomes of one single species or subgenome. By examining in detail 50 genes from chromosome 1H for which BAC sequences were available, we found that many represent pseudogenes that resulted from transposable element activity and double-strand break repair. Thus, Triticeae seem to accumulate nonsyntenic genes frequently. Since many of them are likely to be pseudogenes, total gene numbers in Triticeae are prone to pronounced overestimates.
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Affiliation(s)
- Thomas Wicker
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Klaus F.X. Mayer
- Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Heidrun Gundlach
- Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Mihaela Martis
- Munich Information Center for Protein Sequences/Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Burkhard Steuernagel
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Hana Šimková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Marie Kubaláková
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Frédéric Choulet
- Institut National de la Recherche Agronomique University Blaise Pascal Joint Research Unit 1095, Genetics, Diversity, and Ecophysiology of Cereals, 63100 Clermont-Ferrand, France
| | - Stefan Taudien
- Leibniz Institute for Age Research–Fritz Lipmann Institute, 07745 Jena, Germany
| | - Matthias Platzer
- Leibniz Institute for Age Research–Fritz Lipmann Institute, 07745 Jena, Germany
| | - Catherine Feuillet
- Institut National de la Recherche Agronomique University Blaise Pascal Joint Research Unit 1095, Genetics, Diversity, and Ecophysiology of Cereals, 63100 Clermont-Ferrand, France
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel
| | - Hikmet Budak
- Sabanci University, Faculty of Engineering and Natural Sciences, Orhanli, Tuzla, 34956 Istanbul, Turkey
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, 77200 Olomouc, Czech Republic
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
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