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She CW, Jiang XH, He CP. Comparative karyotype analysis of eight Cucurbitaceae crops using fluorochrome banding and 45S rDNA-FISH. COMPARATIVE CYTOGENETICS 2023; 17:31-58. [PMID: 37305810 PMCID: PMC10252140 DOI: 10.3897/compcytogen.v17.i1.99236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 01/23/2023] [Indexed: 06/13/2023]
Abstract
To have an insight into the karyotype variation of eight Cucurbitaceae crops including Cucumissativus Linnaeus, 1753, Cucumismelo Linnaeus, 1753, Citrulluslanatus (Thunberg, 1794) Matsumura et Nakai, 1916, Benincasahispida (Thunberg, 1784) Cogniaux, 1881, Momordicacharantia Linnaeus, 1753, Luffacylindrica (Linnaeus, 1753) Roemer, 1846, Lagenariasicerariavar.hispida (Thunberg, 1783) Hara, 1948 and Cucurbitamoschata Duchesne ex Poiret, 1819, well morphologically differentiated mitotic metaphase chromosomes were prepared using the enzymatic maceration and flame-drying method, and the chromosomal distribution of heterochromatin and 18S-5.8S-26S rRNA genes (45S rDNA) was investigated using sequential combined PI and DAPI (CPD) staining and fluorescence in situ hybridization (FISH) with 45S rDNA probe. Detailed karyotypes were established using the dataset of chromosome measurements, fluorochrome bands and rDNA FISH signals. Four karyotype asymmetry indices, CVCI, CVCL, MCA and Stebbins' category, were measured to elucidate the karyological relationships among species. All the species studied had symmetrical karyotypes composed of metacentric and submetacentric or only metacentric chromosomes, but their karyotype structure can be discriminated by the scatter plot of MCA vs. CVCL. The karyological relationships among these species revealed by PCoA based on x, 2n, TCL, MCA, CVCL and CVCI was basically in agreement with the phylogenetic relationships revealed by DNA sequences. CPD staining revealed all 45S rDNA sites in all species, (peri)centromeric GC-rich heterochromatin in C.sativus, C.melo, C.lanatus, M.charantia and L.cylindrica, terminal GC-rich heterochromatin in C.sativus. DAPI counterstaining after FISH revealed pericentromeric DAPI+ heterochromatin in C.moschata. rDNA FISH detected two 45S loci in five species and five 45S loci in three species. Among these 45S loci, most were located at the terminals of chromosome arms, and a few in the proximal regions. In C.sativus, individual chromosomes can be precisely distinguished by the CPD band and 45S rDNA signal patterns, providing an easy method for chromosome identification of cucumber. The genome differentiation among these species was discussed in terms of genome size, heterochromatin, 45S rDNA site, and karyotype asymmetry based on the data of this study and previous reports.
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Affiliation(s)
- Chao-Wen She
- Key Laboratory of Research and Utilization of
Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan,
418008, ChinaHuaihua UniversityHuaihuaChina
- College of Life Sciences and Chemistry, Hunan University
of Technology, Zhuzhou, Hunan, 412007, ChinaHunan University of TechnologyZhuzhouChina
| | - Xiang-Hui Jiang
- Key Laboratory of Research and Utilization of
Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan,
418008, ChinaHuaihua UniversityHuaihuaChina
| | - Chun-Ping He
- College of Life Sciences and Chemistry, Hunan University
of Technology, Zhuzhou, Hunan, 412007, ChinaHunan University of TechnologyZhuzhouChina
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Cytomorphological evaluation of wild and cultivated cucumber (Cucumis sativus L.). THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00390-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Bhowmick BK, Jha S. A critical review on cytogenetics of Cucurbitaceae with updates on Indian taxa. COMPARATIVE CYTOGENETICS 2022; 16:93-125. [PMID: 36761811 PMCID: PMC9849056 DOI: 10.3897/compcytogen.v16.i2.79033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/16/2022] [Indexed: 06/13/2023]
Abstract
The cytogenetic relationships in the species of Cucurbitaceae are becoming immensely important to answer questions pertaining to genome evolution. Here, a simplified and updated data resource on cytogenetics of Cucurbitaceae is presented on the basis of foundational parameters (basic, zygotic and gametic chromosome numbers, ploidy, genome size, karyotype) and molecular cytogenetics. We have revised and collated our own findings on seven agriculturally important Indian cucurbit species in a comparative account with the globally published reports. Chromosome count (of around 19% species) shows nearly three-fold differences while genome size (of nearly 5% species) shows 5.84-fold differences across the species. There is no significant correlation between chromosome numbers and nuclear genome sizes. The possible trend of evolution is discussed here based on molecular cytogenetics data, especially the types and distribution of nucleolus organizer regions (NORs). The review supersedes the scopes of general chromosome databases and invites scopes for continuous updates. The offline resource serves as an exclusive toolkit for research and breeding communities across the globe and also opens scope for future establishment of web-database on Cucurbitaceae cytogenetics.
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Affiliation(s)
- Biplab Kumar Bhowmick
- Department of Botany, Scottish Church College, 1&3, Urquhart Square, Kolkata-700006, West Bengal, IndiaScottish Church CollegeKolkataIndia
| | - Sumita Jha
- Plant Cytogenetics and Biotechnology Laboratory, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, IndiaUniversity of CalcuttaKolkataIndia
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Bhowmick BK, Jha S. Dynamics of sex expression and chromosome diversity in Cucurbitaceae: a story in the making. J Genet 2016; 94:793-808. [PMID: 26690537 DOI: 10.1007/s12041-015-0562-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The family Cucurbitaceae showcases a wide range of sexual phenotypes being variedly regulated by biological and environmental factors. In the present context, we have tried to assemble reports of cytogenetic investigations carried out in cucurbits accompanied by information on sex expression diversities and chromosomal or molecular basis of sex determination in dioecious (or other sexual types, if reported) taxa known so far. Most of the Cucurbitaceae tribes have mixed sexual phenotypes with varying range of chromosome numbers and hence, ancestral conditions become difficult to probe. Occurrence of polyploidy is rare in the family and has no influence on sexual traits. The sex determination mechanisms have been elucidated in some well-studied taxa like Bryonia,Coccinia and Cucumis showing interplay of genic, biochemical, developmental and sometimes chromosomal determinants. Substantial knowledge about genic and molecular sex differentiation has been obtained for genera like Momordica, Cucurbita and Trichosanthes. The detailed information on sex determination schemes, genomic sequences and molecular phylogenetic relationships facilitate further comprehensive investigations in the tribe Bryonieae. The discovery of organ identity genes and sex-specific sequences regulating sexual behaviour in Coccinia,Cucumis and Cucurbita opens up opportunities of relevant investigations to answer yet unaddressed questions pertaining to floral unisexuality, dioecy and chromosome evolution in the family. The present discussion brings the genera in light, previously recognized under subfamily Nhandiroboideae, where the study of chromosome cytology and sex determination mechanisms can simplify our understanding of sex expression pathways and its phylogenetic impacts.
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Affiliation(s)
- Biplab Kumar Bhowmick
- Centre of Advanced Study, Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700 019, India.
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Application of a modified drop method for high-resolution pachytene chromosome spreads in two Phalaenopsis species. Mol Cytogenet 2016; 9:44. [PMID: 27275186 PMCID: PMC4893830 DOI: 10.1186/s13039-016-0254-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Preparation of good chromosome spreads without cytoplasmic contamination is the crucial step in cytogenetic mapping. To date, cytogenetic research in the Orchidaceae family has been carried out solely on mitotic metaphase chromosomes. Well-spread meiotic pachytene chromosomes can provide higher resolution and fine detail for analysis of chromosomal structure and are also beneficial for chromosomal FISH (fluorescence in situ hybridization) mapping. However, an adequate method for the preparation of meiotic pachytene chromosomes in orchid species has not yet been reported. RESULTS Two Taiwanese native Phalaenopsis species were selected to test the modified drop method for preparation of meiotic pachytene chromosomes from pollinia. In this modified method, pollinia were ground and treated with an enzyme mixture to completely remove cell walls. Protoplasts were resuspended in ethanol/glacial acetic acid and dropped onto a wet inclined slide of 30° from a height of 0.5 m. The sample was then flowed down the inclined plane to spread the chromosomes. Hundreds of pachytene chromosomes with little to no cytoplasmic contamination were well spread on each slide. We also showed that the resolution of 45S rDNA-containing chromosomes at the pachytene stage was up to 20 times higher than that at metaphase. Slides prepared following this modified drop method were amenable to FISH mapping of both 45S and 5S rDNA on pachytene chromosomes and, after FISH, the chromosomal structure remained intact for further analysis. CONCLUSION This modified drop method is suitable for pachytene spreads from pollinia of Phalaenopsis orchids. The large number and high-resolution pachytene spreads, with little or no cytoplasmic contamination, prepared by the modified drop method could be used for FISH mapping of DNA fragments to accelerate the integration of cytogenetic and molecular research in Phalaenopsis orchids.
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Pawełkowicz M, Zieliński K, Zielińska D, Pląder W, Yagi K, Wojcieszek M, Siedlecka E, Bartoszewski G, Skarzyńska A, Przybecki Z. Next generation sequencing and omics in cucumber (Cucumis sativus L.) breeding directed research. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:77-88. [PMID: 26566826 DOI: 10.1016/j.plantsci.2015.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/29/2015] [Accepted: 07/28/2015] [Indexed: 05/10/2023]
Abstract
In the post-genomic era the availability of genomic tools and resources is leading us to novel generation methods in plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. In this study we have mainly concentrated on the Cucumis sativus and (but much less) Cucurbitaceae family several important vegetable crops. There are many reports on research conducted in Cucurbitaceae plant breeding programs on the ripening process, phloem transport, disease resistance, cold tolerance and fruit quality traits. This paper presents the role played by new omic technologies in the creation of knowledge on the mechanisms of the formation of the breeding features. The analysis of NGS (NGS-next generation sequencing) data allows the discovery of new genes and regulatory sequences, their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Firstly a high density map should be created for the reference genome, then each re-sequencing data could be mapped and new markers brought out into breeding populations. The paper also presents methods that could be used in the future for the creation of variability and genomic modification of the species in question. It has been shown also the state and usefulness in breeding the chloroplastomic and mitochondriomic study.
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Affiliation(s)
- Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Konrad Zieliński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Dorota Zielińska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Kouhei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Michał Wojcieszek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
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Zhang Y, Cheng C, Li J, Yang S, Wang Y, Li Z, Chen J, Lou Q. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping. BMC Genomics 2015; 16:730. [PMID: 26407707 PMCID: PMC4583154 DOI: 10.1186/s12864-015-1877-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/24/2015] [Indexed: 12/23/2022] Open
Abstract
Background Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Results Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in Cucumis species. Besides, the significant correlation was found between gene density along chromosome and GISH band intensity in C. sativus and C. melo. Conclusions In summary, comparative cytogenetic mapping of major satellites and GISH revealed the distinct differentiation of chromosome structure during species formation. The evolution of repetitive sequences was the main force for the divergence of Cucumis species from common ancestor. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1877-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxia Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Shuqiong Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yunzhu Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ziang Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Lou Q, Zhang Y, He Y, Li J, Jia L, Cheng C, Guan W, Yang S, Chen J. Single-copy gene-based chromosome painting in cucumber and its application for chromosome rearrangement analysis in Cucumis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:169-79. [PMID: 24635663 DOI: 10.1111/tpj.12453] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 01/13/2014] [Accepted: 01/20/2014] [Indexed: 05/04/2023]
Abstract
Chromosome painting based on fluorescence in situ hybridization (FISH) has played an important role in chromosome identification and research into chromosome rearrangements, diagnosis of chromosome abnormalities and evolution in human and animal species. However, it has not been applied widely in plants due to the large amounts of dispersed repetitive sequences in chromosomes. In the present work, a chromosome painting method for single-copy gene pools in Cucumis sativus was successfully developed. Gene probes with sizes above 2 kb were detected consistently. A cucumber karyotype was constructed based on FISH using a cocktail containing chromosome-specific gene probes. This single-copy gene-based chromosome painting (ScgCP) technique was performed by PCR amplification, purification, pooling, labeling and hybridization onto chromosome spreads. Gene pools containing sequential genes with an interval less than 300 kb yielded painting patterns on pachytene chromosomes. Seven gene pools corresponding to individual chromosomes unambiguously painted each chromosome pair of C. sativus. Three mis-aligned regions on chromosome 4 were identified by the painting patterns. A probe pool comprising 133 genes covering the 8 Mb distal end of chromosome 4 was used to evaluate the potential utility of the ScgCP technique for chromosome rearrangement research through cross-species FISH in the Cucumis genus. Distinct painting patterns of this region were observed in C. sativus, C. melo and C. metuliferus species. A comparative chromosome map of this region was constructed between cucumber and melon. With increasing sequence resources, this ScgCP technique may be applied on any other sequenced species for chromosome painting research.
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Affiliation(s)
- Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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Yang L, Koo DH, Li Y, Zhang X, Luan F, Havey MJ, Jiang J, Weng Y. Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:895-906. [PMID: 22487099 DOI: 10.1111/j.1365-313x.2012.05017.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cucumber, Cucumis sativus L. is the only taxon with 2n = 2x = 14 chromosomes in the genus Cucumis. It consists of two cross-compatible botanical varieties: the cultivated C. sativus var. sativus and the wild C. sativus var. hardwickii. There is no consensus on the evolutionary relationship between the two taxa. Whole-genome sequencing of the cucumber genome provides a new opportunity to advance our understanding of chromosome evolution and the domestication history of cucumber. In this study, a high-density genetic map for cultivated cucumber was developed that contained 735 marker loci in seven linkage groups spanning 707.8 cM. Integration of genetic and physical maps resulted in a chromosome-level draft genome assembly comprising 193 Mbp, or 53% of the 367 Mbp cucumber genome. Strategically selected markers from the genetic map and draft genome assembly were employed to screen for fosmid clones for use as probes in comparative fluorescence in situ hybridization analysis of pachytene chromosomes to investigate genetic differentiation between wild and cultivated cucumbers. Significant differences in the amount and distribution of heterochromatins, as well as chromosomal rearrangements, were uncovered between the two taxa. In particular, six inversions, five paracentric and one pericentric, were revealed in chromosomes 4, 5 and 7. Comparison of the order of fosmid loci on chromosome 7 of cultivated and wild cucumbers, and the syntenic melon chromosome I suggested that the paracentric inversion in this chromosome occurred during domestication of cucumber. The results support the sub-species status of these two cucumber taxa, and suggest that C. sativus var. hardwickii is the progenitor of cultivated cucumber.
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Affiliation(s)
- Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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Nowicka A, Grzebelus E, Grzebelus D. Fluorescent in situ hybridization with arbitrarily amplified DNA fragments differentiates carrot (Daucus carota L.) chromosomes. Genome 2012; 55:205-13. [PMID: 22360760 DOI: 10.1139/g2012-003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Carrot (Daucus carota L.) chromosomes are small and poorly differentiated in size and morphology. Here we demonstrate that fluorescent in situ hybridization (FISH) signals derived from arbitrary PCR probes can be used for chromosome identification in carrot. To prepare probes, we searched for nonpolymorphic products abundantly amplified with arbitrary decamer primers in a group of accessions representing carrot genetic diversity. As a result, 13 fragments ranging in size from 517 to 1758 bp were selected, sequenced, and used as probes for fluorescent in situ hybridization. Four of these probes produced clear and reproducible hybridization signals. The sequences showed similarity to a number of carrot BAC-end sequences, indicating their repetitive character. Three of them were similar to internal portions of gypsy and copia LTR retrotransposons previously identified in plants. Hybridization signals for the four probes were observed as dotted tracks on chromosomes, differing in distribution and intensity. Generally, they were present in pericentromeric and (or) interstitial localizations on chromosome arms. The use of the four probes allowed discrimination of chromosome pairs and construction of more detailed karyotypes and idiograms of carrot.
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Affiliation(s)
- Anna Nowicka
- Department of Genetics, Plant Breeding and Seed Science, Faculty of Horticulture, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland
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Li Y, Yang L, Pathak M, Li D, He X, Weng Y. Fine genetic mapping of cp: a recessive gene for compact (dwarf) plant architecture in cucumber, Cucumis sativus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:973-83. [PMID: 21735235 DOI: 10.1007/s00122-011-1640-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Accepted: 06/13/2011] [Indexed: 05/04/2023]
Abstract
The compact (dwarf) plant architecture is an important trait in cucumber (Cucumis sativus L.) breeding that has the potential to be used in once-over mechanical harvest of cucumber production. Compact growth habit is controlled by a simply inherited recessive gene cp. With 150 F(2:3) families derived from two inbred cucumber lines, PI 308915 (compact vining) and PI 249561 (regular vining), we conducted genome-wide molecular mapping with microsatellite (simple sequence repeat, SSR) markers. A framework genetic map was constructed consisting of 187 SSR loci in seven linkage groups (chromosomes) covering 527.5 cM. Linkage analysis placed cp at the distal half of the long arm of cucumber Chromosome 4. Molecular markers cosegregating with the cp locus were identified through whole genome scaffold-based chromosome walking. Fine genetic mapping with 1,269 F(2) plants delimited the cp locus to a 220 kb genomic DNA region. Annotation and function prediction of genes in this region identified a homolog of the cytokinin oxidase (CKX) gene, which may be a potential candidate of compact gene. Alignment of the CKX gene homologs from both parental lines revealed a 3-bp deletion in the first exon of PI 308915, which can serve as a marker for marker-assisted selection of the compact phenotype. This work also provides a solid foundation for map-based cloning of the compact gene and understanding the molecular mechanisms of the dwarfing in cucumber.
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Affiliation(s)
- Yuhong Li
- Horticulture College, Northwest Agriculture & Forestry University, Yangling 712100, China
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Li D, Cuevas HE, Yang L, Li Y, Garcia-Mas J, Zalapa J, Staub JE, Luan F, Reddy U, He X, Gong Z, Weng Y. Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping. BMC Genomics 2011; 12:396. [PMID: 21816110 PMCID: PMC3199783 DOI: 10.1186/1471-2164-12-396] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/05/2011] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes. RESULTS Using two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F(2)- and RIL-based genetic maps, respectively. A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome. Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I. Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber. CONCLUSIONS Comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years since its divergence from melon. Meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. Further characterization of the genomic nature of Cucumis species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber.
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Affiliation(s)
- Dawei Li
- Horticulture College, Northwest A & F University, Yangling 712100, China
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Hugo E Cuevas
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA ARS Tropical Agriculture Research Station, Mayaguez, P.R. 00680, Puerto Rico
| | - Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Yuhong Li
- Horticulture College, Northwest A & F University, Yangling 712100, China
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB, Campus UAB, Edifici CRAG, 08193 Bellaterra (Barcelona), Spain
| | - Juan Zalapa
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Jack E Staub
- USDA-ARS, Forage & Range Research Laboratory, Utah State University, Logan, UT 84322 USA
| | - Feishi Luan
- Horticulture College, Northeast Agricultural University, Harbin, 150030, China
| | - Umesh Reddy
- Department of Biology, West Virginia State University Institute, WV 25112, USA
| | - Xiaoming He
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Zhenhui Gong
- Horticulture College, Northwest A & F University, Yangling 712100, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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15
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Comparative FISH mapping of Daucus species (Apiaceae family). Chromosome Res 2011; 19:493-506. [DOI: 10.1007/s10577-011-9202-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 03/10/2011] [Accepted: 03/13/2011] [Indexed: 10/18/2022]
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16
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Han Y, Zhang Z, Huang S, Jin W. An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2. BMC Genet 2011; 12:18. [PMID: 21272311 PMCID: PMC3039625 DOI: 10.1186/1471-2156-12-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Accepted: 01/27/2011] [Indexed: 12/16/2022] Open
Abstract
Background Integration of molecular, genetic and cytological maps is still a challenge for most plant species. Recent progress in molecular and cytogenetic studies created a basis for developing integrated maps in cucumber (Cucumis sativus L.). Results In this study, eleven fosmid clones and three plasmids containing 45S rDNA, the centromeric satellite repeat Type III and the pericentriomeric repeat CsRP1 sequences respectively were hybridized to cucumber metaphase chromosomes to assign their cytological location on chromosome 2. Moreover, an integrated molecular cytogenetic map of cucumber chromosomes 2 was constructed by fluorescence in situ hybridization (FISH) mapping of 11 fosmid clones together with the cucumber centromere-specific Type III sequence on meiotic pachytene chromosomes. The cytogenetic map was fully integrated with genetic linkage map since each fosmid clone was anchored by a genetically mapped simple sequence repeat marker (SSR). The relationship between the genetic and physical distances along chromosome was analyzed. Conclusions Recombination was not evenly distributed along the physical length of chromosome 2. Suppression of recombination was found in centromeric and pericentromeric regions. Our results also indicated that the molecular markers composing the linkage map for chromosome 2 provided excellent coverage of the chromosome.
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Affiliation(s)
- Yonghua Han
- National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100094, PR China.
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17
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Hoshi Y, Yagi K, Matsuda M, Matoba H, Tagashira N, Pląder W, Malepszy S, Nagano K, Morikawa A. A Comparative Study of the Three Cucumber Cultivars Using Fluorescent Staining and Fluorescence In Situ Hybridization. CYTOLOGIA 2011. [DOI: 10.1508/cytologia.76.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yoshikazu Hoshi
- Department of Plant Science, School of Agriculture, Tokai University
| | - Kouhei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw Agricultural University
| | - Masaki Matsuda
- Course of Agricultural Sciences, Graduate School of Agriculture, Tokai University
| | - Hideyuki Matoba
- Department of Applied Biological Science, College of Bioresource Sciences, Nihon University
| | - Norikazu Tagashira
- Department of Living Design and Information Science, Faculty of Human Life Science, Hiroshima Jogakuin University
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw Agricultural University
| | - Stefan Malepszy
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture and Landscape Architecture, Warsaw Agricultural University
| | - Katsuya Nagano
- Department of Plant Science, School of Agriculture, Tokai University
| | - Atsumi Morikawa
- Agricultural Training Station, School of Agriculture, Tokai University
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18
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Barros e Silva AE, Guerra M. The meaning of DAPI bands observed after C-banding and FISH procedures. Biotech Histochem 2010. [DOI: 10.3109/10520290903149596] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Koo DH, Nam YW, Choi D, Bang JW, de Jong H, Hur Y. Molecular cytogenetic mapping of Cucumis sativus and C. melo using highly repetitive DNA sequences. Chromosome Res 2010; 18:325-36. [PMID: 20198418 DOI: 10.1007/s10577-010-9116-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 01/28/2010] [Indexed: 01/19/2023]
Abstract
Chromosomes often serve as one of the most important molecular aspects of studying the evolution of species. Indeed, most of the crucial mutations that led to differentiation of species during the evolution have occurred at the chromosomal level. Furthermore, the analysis of pachytene chromosomes appears to be an invaluable tool for the study of evolution due to its effectiveness in chromosome identification and precise physical gene mapping. By applying fluorescence in situ hybridization of 45S rDNA and CsCent1 probes to cucumber pachytene chromosomes, here, we demonstrate that cucumber chromosomes 1 and 2 may have evolved from fusions of ancestral karyotype with chromosome number n = 12. This conclusion is further supported by the centromeric sequence similarity between cucumber and melon, which suggests that these sequences evolved from a common ancestor. It may be after or during speciation that these sequences were specifically amplified, after which they diverged and specific sequence variants were homogenized. Additionally, a structural change on the centromeric region of cucumber chromosome 4 was revealed by fiber-FISH using the mitochondrial-related repetitive sequences, BAC-E38 and CsCent1. These showed the former sequences being integrated into the latter in multiple regions. The data presented here are useful resources for comparative genomics and cytogenetics of Cucumis and, in particular, the ongoing genome sequencing project of cucumber.
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Affiliation(s)
- Dal-Hoe Koo
- School of Bioscience and Biotechnology, Chungnam National University, Daejeon, 305-764, South Korea.
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20
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Dantas LG, Guerra M. Chromatin differentiation between Theobroma cacao L. and T. grandiflorum Schum. Genet Mol Biol 2010; 33:94-8. [PMID: 21637611 PMCID: PMC3036076 DOI: 10.1590/s1415-47572009005000103] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Accepted: 07/16/2009] [Indexed: 11/29/2022] Open
Abstract
A comparative analysis of mitotic chromosomes of Theobroma cacao (cacao) and T. grandiflorum (cupuaçu) was performed aiming to identify cytological differences between the two most important species of this genus. Both species have symmetric karyotypes, with 2n = 20 metacentric chromosomes ranging in size from 2.00 to 1.19 μm (cacao) and from 2.21 to 1.15 μm (cupuaçu). The interphase nuclei of both species were of the arreticulate type, displaying up to 20 chromocentres, which were more regularly shaped in cacao than in cupuaçu. Prophase chromosomes of both species were more condensed in the proximal region, sometimes including the whole short arm. Both species exhibited only one pair of terminal heterochromatic bands, positively stained with chromomycin A 3 , which co-localized with the single 45S rDNA site. Each karyotype displayed a single 5S rDNA site in the proximal region of another chromosome pair. Heterochromatic bands were also observed on the centromeric/pericentromeric regions of all 20 chromosomes of cacao after C-banding followed by Giemsa or DAPI staining, whereas in cupuaçu they were never detected. These data suggest that the chromosomes of both species have been largely conserved and their pericentromeric chromatin is the only citologically differentiated region.
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Affiliation(s)
- Liliane G Dantas
- Laboratório de Citogenética Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Pernambuco, Recife Brazil
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21
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Lee SH, Choi HW, Sung JS, Bang JW. Inter-genomic relationships among three medicinal herbs: Cnidium officinale, Ligusticum chuanxiong and Angelica polymorpha. Genes Genomics 2010. [DOI: 10.1007/s13258-009-0871-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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22
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Centromere repositioning in cucurbit species: implication of the genomic impact from centromere activation and inactivation. Proc Natl Acad Sci U S A 2009; 106:14937-41. [PMID: 19706458 DOI: 10.1073/pnas.0904833106] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The centromere of an eukaryotic chromosome can move to a new position during evolution, which may result in a major alteration of the chromosome morphology and karyotype. This centromere repositioning phenomenon has been extensively documented in mammalian species and was implicated to play an important role in mammalian genome evolution. Here we report a centromere repositioning event in plant species. Comparative fluorescence in situ hybridization mapping using common sets of fosmid clones between two pairs of cucumber (Cucumis sativus L.) and melon (Cucumis melo L.) chromosomes revealed changes in centromere positions during evolution. Pachytene chromosome analysis revealed that the current centromeres of all four cucumber and melon chromosomes are associated with distinct pericentromeric heterochromatin. Interestingly, inactivation of a centromere in the original centromeric region was associated with a loss or erosion of its affixed pericentromeric heterochromatin. Thus, both centromere activation and inactivation in cucurbit species were associated with a gain/loss of a large amount of pericentromeric heterochromatin.
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23
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Ren Y, Zhang Z, Liu J, Staub JE, Han Y, Cheng Z, Li X, Lu J, Miao H, Kang H, Xie B, Gu X, Wang X, Du Y, Jin W, Huang S. An integrated genetic and cytogenetic map of the cucumber genome. PLoS One 2009; 4:e5795. [PMID: 19495411 PMCID: PMC2685989 DOI: 10.1371/journal.pone.0005795] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 05/04/2009] [Indexed: 12/02/2022] Open
Abstract
The Cucurbitaceae includes important crops such as cucumber, melon, watermelon, squash and pumpkin. However, few genetic and genomic resources are available for plant improvement. Some cucurbit species such as cucumber have a narrow genetic base, which impedes construction of saturated molecular linkage maps. We report herein the development of highly polymorphic simple sequence repeat (SSR) markers originated from whole genome shotgun sequencing and the subsequent construction of a high-density genetic linkage map. This map includes 995 SSRs in seven linkage groups which spans in total 573 cM, and defines approximately 680 recombination breakpoints with an average of 0.58 cM between two markers. These linkage groups were then assigned to seven corresponding chromosomes using fluorescent in situ hybridization (FISH). FISH assays also revealed a chromosomal inversion between Cucumis subspecies [C. sativus var. sativus L. and var. hardwickii (R.) Alef], which resulted in marker clustering on the genetic map. A quarter of the mapped markers showed relatively high polymorphism levels among 11 inbred lines of cucumber. Among the 995 markers, 49%, 26% and 22% were conserved in melon, watermelon and pumpkin, respectively. This map will facilitate whole genome sequencing, positional cloning, and molecular breeding in cucumber, and enable the integration of knowledge of gene and trait in cucurbits.
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Affiliation(s)
- Yi Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Zhonghua Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Jinhua Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Jack E. Staub
- USDA, ARS, Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Yonghua Han
- National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Zhouchao Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Xuefeng Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Jingyuan Lu
- National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Houxiang Kang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Yongchen Du
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
| | - Weiwei Jin
- National Maize Improvement Center of China, Key Laboratory of Crop Genetic Improvement and Genome of Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China
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24
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Ondrej V, Kitner M, Dolezalová I, Nádvorník P, Navrátilová B, Lebeda A. Chromatin structural rearrangement during dedifferentiation of protoplasts of Cucumis sativus L. Mol Cells 2009; 27:443-7. [PMID: 19390825 DOI: 10.1007/s10059-009-0057-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 02/16/2009] [Accepted: 02/17/2009] [Indexed: 12/31/2022] Open
Abstract
This paper reports on the structural rearrangement of satellite DNA type I repeats and heterochromatin during the dedifferentiation and cell cycling of mesophyll protoplasts of cucumber (Cucumis sativus). These repeats were localized in the telomeric heterochromatin of cucumber chromosomes and in the chromocenters of interphase nuclei. The dramatic reduction of heterochromatin involves decondensation of subtelomeric repeats in freshly isolated protoplasts; however, there are not a great many remarkable changes in the expression profile. In spite of that, reformation of the chromocenters, occurring 48 h after protoplast isolation, is accompanied by recondensation of satellite DNA type I; however, only partial reassembly of these repeats was revealed. In this study, FISH and a flow cytometry assay show a correlation between the partial chromocenter and the repeats reassembly, and with the reentry of cultivated protoplasts into the cell cycle and first cell division. After that, divided cells displayed a higher variability in the expression profile than did leaves' mesophyll cells and protoplasts.
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Affiliation(s)
- Vladan Ondrej
- Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech Republic.
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25
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26
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Hoshi Y, Mori M, Matoba H, Tagashira N, Murata T, Plader W, Malepszy S. Chromosomal Polymorphism of Two Pickling Cucumbers (Cucumis sativus L.) Revealed by Fluorescent Staining with CMA and DAPI. CYTOLOGIA 2008. [DOI: 10.1508/cytologia.73.41] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | - Hideyuki Matoba
- Department of Applied Biological Science, College of Bioresource Sciences, Nihon University
| | - Norikazu Tagashira
- Department of Living Design and Information Science, Faculty of Human Development, Hiroshima Jogakuin University
| | | | - Wojciech Plader
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw Agricultural University
| | - Stefan Malepszy
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw Agricultural University
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27
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Renner SS, Schaefer H, Kocyan A. Phylogenetics of Cucumis (Cucurbitaceae): cucumber (C. sativus) belongs in an Asian/Australian clade far from melon (C. melo). BMC Evol Biol 2007; 7:58. [PMID: 17425784 PMCID: PMC3225884 DOI: 10.1186/1471-2148-7-58] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 04/10/2007] [Indexed: 11/10/2022] Open
Abstract
Background Melon, Cucumis melo, and cucumber, C. sativus, are among the most widely cultivated crops worldwide. Cucumis, as traditionally conceived, is geographically centered in Africa, with C. sativus and C. hystrix thought to be the only Cucumis species in Asia. This taxonomy forms the basis for all ongoing Cucumis breeding and genomics efforts. We tested relationships among Cucumis and related genera based on DNA sequences from chloroplast gene, intron, and spacer regions (rbcL, matK, rpl20-rps12, trnL, and trnL-F), adding nuclear internal transcribed spacer sequences to resolve relationships within Cucumis. Results Analyses of combined chloroplast sequences (4,375 aligned nucleotides) for 123 of the 130 genera of Cucurbitaceae indicate that the genera Cucumella, Dicaelospermum, Mukia, Myrmecosicyos, and Oreosyce are embedded within Cucumis. Phylogenetic trees from nuclear sequences for these taxa are congruent, and the combined data yield a well-supported phylogeny. The nesting of the five genera in Cucumis greatly changes the natural geographic range of the genus, extending it throughout the Malesian region and into Australia. The closest relative of Cucumis is Muellerargia, with one species in Australia and Indonesia, the other in Madagascar. Cucumber and its sister species, C. hystrix, are nested among Australian, Malaysian, and Western Indian species placed in Mukia or Dicaelospermum and in one case not yet formally described. Cucumis melo is sister to this Australian/Asian clade, rather than being close to African species as previously thought. Molecular clocks indicate that the deepest divergences in Cucumis, including the split between C. melo and its Australian/Asian sister clade, go back to the mid-Eocene. Conclusion Based on congruent nuclear and chloroplast phylogenies we conclude that Cucumis comprises an old Australian/Asian component that was heretofore unsuspected. Cucumis sativus evolved within this Australian/Asian clade and is phylogenetically far more distant from C. melo than implied by the current morphological classification.
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Affiliation(s)
- Susanne S Renner
- Department of Biology, University of Munich, 80638 Munich, Germany
| | - Hanno Schaefer
- Department of Biology, University of Munich, 80638 Munich, Germany
| | - Alexander Kocyan
- Department of Biology, University of Munich, 80638 Munich, Germany
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28
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Jiang J, Gill BS. Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome 2006; 49:1057-68. [PMID: 17110986 DOI: 10.1139/g06-076] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fluorescence in situ hybridization (FISH), which allows direct mapping of DNA sequences on chromosomes, has become the most important technique in plant molecular cytogenetics research. Repetitive DNA sequence can generate unique FISH patterns on individual chromosomes for karyotyping and phylogenetic analysis. FISH on meiotic pachytene chromosomes coupled with digital imaging systems has become an efficient method to develop physical maps in plant species. FISH on extended DNA fibers provides a high-resolution mapping approach to analyze large DNA molecules and to characterize large genomic loci. FISH-based physical mapping provides a valuable complementary approach in genome sequencing and map-based cloning research. We expect that FISH will continue to play an important role in relating DNA sequence information to chromosome biology. FISH coupled with immunoassays will be increasingly used to study features of chromatin at the cytological level that control expression and regulation of genes.
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Affiliation(s)
- Jiming Jiang
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA.
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