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Sattler MC, de Oliveira SC, Mendonça MAC, Clarindo WR. Coffea cytogenetics: from the first karyotypes to the meeting with genomics. PLANTA 2022; 255:112. [PMID: 35501619 DOI: 10.1007/s00425-022-03898-z] [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: 09/23/2021] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Coffea karyotype organization and evolution has been uncovered by classical cytogenetics and cytogenomics. We revisit these discoveries and present new karyotype data. Coffea possesses ~ 124 species, including C. arabica and C. canephora responsible for commercial coffee production. We reviewed the Coffea cytogenetics, from the first chromosome counting, encompassing the karyotype characterization, chromosome DNA content, and mapping of chromosome portions and DNA sequences, until the integration with genomics. We also showed new data about Coffea karyotype. The 2n chromosome number evidenced the diploidy of almost all Coffea, and the C. arabica tetraploidy, as well as the polyploidy of other hybrids. Since then, other genomic similarities and divergences among the Coffea have been shown by karyotype morphology, nuclear and chromosomal C-value, AT and GC rich chromosome portions, and repetitive sequence and gene mapping. These cytogenomic data allowed us to know and understand the phylogenetic relations in Coffea, as well as their ploidy level and genomic origin, highlighting the relatively recent allopolyploidy. In addition to the euploidy, the role of the mobile elements in Coffea diversification is increasingly more evident, and the comparative analysis of their structure and distribution on the genome of different species is in the spotlight for future research. An integrative look at all these data is fundamental for a deeper understanding of Coffea karyotype evolution, including the key role of polyploidy in C. arabica origin. The 'Híbrido de Timor', a recent natural allotriploid, is also in the spotlight for its potential as a source of resistance genes and model for plant polyploidy research. Considering this, we also present some unprecedented results about the exciting evolutionary history of these polyploid Coffea.
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Affiliation(s)
- Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, ZIP 36.570-900, Brazil.
| | - Stéfanie Cristina de Oliveira
- Laboratório de Citogenética e Cultura de Tecidos Vegetais, Campus de Alegre, Universidade Federal Do Espírito Santo, Alegre, ES, ZIP 29.500-000, Brazil
| | | | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, ZIP 36.570-900, Brazil
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Agrawal N, Gupta M, Atri C, Akhatar J, Kumar S, Heslop-Harrison PJS, Banga SS. Anchoring alien chromosome segment substitutions bearing gene(s) for resistance to mustard aphid in Brassica juncea-B. fruticulosa introgression lines and their possible disruption through gamma irradiation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3209-3224. [PMID: 34160642 DOI: 10.1007/s00122-021-03886-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 06/08/2021] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE Heavy doses of gamma irradiation can reduce linkage drag by disrupting large sized alien translocations and promoting exchanges between crop and wild genomes. Resistance to mustard aphid (Lipaphis erysimi) infestation was significantly improved in Brassica juncea through B. juncea-B. fruticulosa introgression. However, linkage drag caused by introgressed chromatin fragments has so far prevented the deployment of this resistance source in commercial cultivars. We investigated the patterns of donor chromatin segment substitutions in the introgression lines (ILs) through genomic in situ hybridization (GISH) coupled with B. juncea chromosome-specific oligonucleotide probes. These allowed identification of large chromosome translocations from B. fruticulosa in the terminal regions of chromosomes A05, B02, B03 and B04 in three founder ILs (AD-64, 101 and 104). Only AD-101 carried an additional translocation at the sub-terminal to intercalary position in both homologues of chromosome A01. We validated these translocations with a reciprocal blast hit analysis using shotgun sequencing of three ILs and species-specific contigs/scaffolds (kb sized) from a de novo assembly of B. fruticulosa. Alien segment substitution on chromosome A05 could not be validated. Current studies also endeavoured to break linkage drag by exposing seeds to a heavy dose (200kR) of gamma radiation. Reduction in the size of introgressed chromatin fragments was observed in many M3 plants. There was a complete loss of the alien chromosome fragment in one instance. A few M3 plants with novel patterns of chromosome segment substitutions displayed improved agronomic performance coupled with resistance to mustard aphid. SNPs in such genomic spaces should aid the development of markers to track introgressed DNA and allow application in plant breeding.
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Affiliation(s)
- Neha Agrawal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Mehak Gupta
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Chhaya Atri
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Javed Akhatar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Sarwan Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | - Surinder S Banga
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
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Iacia AAS, Pinto-Maglio CAF. Mapping pachytene chromosomes of coffee using a modified protocol for fluorescence in situ hybridization. AOB PLANTS 2013; 5:plt040. [PMID: 24244840 PMCID: PMC3828664 DOI: 10.1093/aobpla/plt040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
Fluorescence in situ hybridization (FISH) is the most direct method for physically mapping DNA sequences on chromosomes. Fluorescence in situ hybridization mapping of meiotic chromosomes during the pachytene stage is an important tool in plant cytogenetics, because it provides high-resolution measurements of physical distances. Fluorescence in situ hybridization mapping of coffee pachytene chromosomes offers significant advantages compared with FISH mapping of somatic chromosomes, because pachytene chromosomes are 30 times longer and provide additional cytological markers. However, the application of this technique to pachytene chromosomes has been complicated by problems in making preparations of meiotic chromosomes and by difficulties in the application of standard FISH protocols. We have been able to overcome most of these obstacles in applying the FISH technique to the pachytene chromosomes of coffee plants. Digesting the external callose layer surrounding the pollen mother cells (PMCs) in conjunction with other procedures permitted suitable pachytene chromosomes to be obtained by increasing cell permeability, which allowed the probe sequences to enter the cells. For the first time, hybridization signals were registered on coffee pachytene chromosomes using the FISH technique with a repetitive sequence as a probe. We obtained slides on which 80 % of the PMCs had hybridization signals, resulting in FISH labelling with high efficiency. The procedure does not seem to be dependent on the genotype, because hybridization signals were detected in genetically different coffee plants. These findings enhance the possibilities for high-resolution physical mapping of coffee chromosomes.
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Bobadilla Landey R, Cenci A, Georget F, Bertrand B, Camayo G, Dechamp E, Herrera JC, Santoni S, Lashermes P, Simpson J, Etienne H. High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate. PLoS One 2013; 8:e56372. [PMID: 23418563 PMCID: PMC3572038 DOI: 10.1371/journal.pone.0056372] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 01/08/2013] [Indexed: 01/30/2023] Open
Abstract
Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings) were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200,000 plant). Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0-0.003% and 0.07-0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied) and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1-3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee somatic embryogenesis. The main change in most of the rare phenotypic variants was aneuploidy, indicating that mitotic aberrations play a major role in somaclonal variation in coffee.
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Affiliation(s)
- Roberto Bobadilla Landey
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Alberto Cenci
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Frédéric Georget
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Benoît Bertrand
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | - Gloria Camayo
- Centro Nacional de Investigaciones de Café, Manizales, Colombia
| | - Eveline Dechamp
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
| | | | - Sylvain Santoni
- Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Tropicales et Méditerranéennes, Institut National de la Recherche Agronomique, Montpellier, France
| | - Philippe Lashermes
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - June Simpson
- Department of Plant Genetic Engineering, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| | - Hervé Etienne
- Unité Mixte de Recherche Résistance des Plantes aux Bioagresseurs, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France
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Yuyama PM, Pereira LFP, dos Santos TB, Sera T, Vilas-Boas LA, Lopes FR, Carareto CMA, Vanzela ALL. FISH using a gag-like fragment probe reveals a common Ty3-gypsy-like retrotransposon in genome of Coffea species. Genome 2012; 55:825-33. [PMID: 23231601 DOI: 10.1139/gen-2012-0081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The genus Coffea possesses about 100 species, and the most economically important are Coffea canephora and Coffea arabica. The latter is predominantly self-compatible with 2n = 4x = 44, while the others of the genus are diploid with 2n = 2x = 22 and mostly self-incompatible. Studies using molecular markers have been useful to detect differences between genomes in Coffea; however, molecular and cytogenetic studies have produced only limited information on the karyotypes organization. We used DOP-PCR to isolate repetitive elements from genome of Coffea arabica var. typica. The pCa06 clone, containing a fragment of 775 bp length, was characterized by sequencing and used as a probe in chromosomes of C. arabica and six other species: C. canephora, Coffea eugenioides, Coffea kapakata, Coffea liberica var. dewevrei, Coffea racemosa, and Coffea stenophylla. This insert shows similarities with a gag protein of the Ty3-gypsy-like super-family. Dot blot and FISH analyses demonstrated that pCa06 is differentially accumulated between species and chromosomes. Signals appeared scattered and clustered on the chromosomes and were also associated with heterochromatic regions. While the literature shows that there is a high karyotype similarity between Coffea species, our results point out differences in the accumulation and dispersion of this Ty3-gypsy-like retrotransposon during karyotype differentiation of Coffea.
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Affiliation(s)
- Priscila Mary Yuyama
- Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Caixa Postal 6001, CEP 86051-990 Londrina, PR, Brazil
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Ribas AF, Cenci A, Combes MC, Etienne H, Lashermes P. Organization and molecular evolution of a disease-resistance gene cluster in coffee trees. BMC Genomics 2011; 12:240. [PMID: 21575174 PMCID: PMC3113787 DOI: 10.1186/1471-2164-12-240] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 05/16/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most disease-resistance (R) genes in plants encode NBS-LRR proteins and belong to one of the largest and most variable gene families among plant genomes. However, the specific evolutionary routes of NBS-LRR encoding genes remain elusive. Recently in coffee tree (Coffea arabica), a region spanning the SH3 locus that confers resistance to coffee leaf rust, one of the most serious coffee diseases, was identified and characterized. Using comparative sequence analysis, the purpose of the present study was to gain insight into the genomic organization and evolution of the SH3 locus. RESULTS Sequence analysis of the SH3 region in three coffee genomes, Ea and Ca subgenomes from the allotetraploid C. arabica and Cc genome from the diploid C. canephora, revealed the presence of 5, 3 and 4 R genes in Ea, Ca, and Cc genomes, respectively. All these R-gene sequences appeared to be members of a CC-NBS-LRR (CNL) gene family that was only found at the SH3 locus in C. arabica. Furthermore, while homologs were found in several dicot species, comparative genomic analysis failed to find any CNL R-gene in the orthologous regions of other eudicot species. The orthology relationship among the SH3-CNL copies in the three analyzed genomes was determined and the duplication/deletion events that shaped the SH3 locus were traced back. Gene conversion events were detected between paralogs in all three genomes and also between the two sub-genomes of C. arabica. Significant positive selection was detected in the solvent-exposed residues of the SH3-CNL copies. CONCLUSION The ancestral SH3-CNL copy was inserted in the SH3 locus after the divergence between Solanales and Rubiales lineages. Moreover, the origin of most of the SH3-CNL copies predates the divergence between Coffea species. The SH3-CNL family appeared to evolve following the birth-and-death model, since duplications and deletions were inferred in the evolution of the SH3 locus. Gene conversion between paralog members, inter-subgenome sequence exchanges and positive selection appear to be the major forces acting on the evolution of SH3-CNL in coffee trees.
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Affiliation(s)
- Alessandra F Ribas
- IRD - Institut de Recherche pour le Développement, UMR RPB, Montpellier Cedex, France
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Cenci A, Combes MC, Lashermes P. Comparative sequence analyses indicate that Coffea (Asterids) and Vitis (Rosids) derive from the same paleo-hexaploid ancestral genome. Mol Genet Genomics 2010; 283:493-501. [PMID: 20361338 DOI: 10.1007/s00438-010-0534-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Accepted: 03/16/2010] [Indexed: 11/30/2022]
Abstract
The complete sequence of Vitis vinifera revealed that the rosid clade derives from a hexaploid ancestor. At present, no analysis of complete genome sequence is available for an asterid, the other large eudicot clade, which includes the economically important species potato, tomato and coffee. To elucidate the genomic history of asterids, we compared the sequence of an 800 kb region of diploid Coffea genome to the orthologous regions of V. vinifera, Populus trichocarpa and Arabidopsis thaliana. We found a very high level of collinearity between around 80 genes of the three rosid species and Coffea. Collinearity comparisons between orthologous and paralogous regions indicates that (1) the Coffea (and consequently all asterids) and rosids share the same hexaploid ancestor; (2) the diploidization process (loss of duplicated and redundant copies from the whole genome duplication) was very advanced in the most recent common ancestor of rosids and asterids. Finally, no additional polyploidization events were detected in the Coffea lineage. Differences in gene loss rates were detected among the three rosid species and linked to the divergence in protein sequences.
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Affiliation(s)
- Alberto Cenci
- IRD, Institut de Recherche pour le Développement, UMR RPB (CIRAD, IRD Université Montpellier II), BP 64501, 34394, Montpellier Cedex 5, France.
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Benavente E, Cifuentes M, Dusautoir JC, David J. The use of cytogenetic tools for studies in the crop-to-wild gene transfer scenario. Cytogenet Genome Res 2008; 120:384-95. [PMID: 18504367 DOI: 10.1159/000121087] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2007] [Indexed: 11/19/2022] Open
Abstract
Interspecific hybridization in plants is an important evolutionary phenomenon involved in the dynamics of speciation that receives increasing interest in the context of possible gene escapes from transgenic crop varieties. Crops are able to cross-pollinate with a number of wild related species and exchange chromosome segments through homoeologous recombination. In this paper, we review a set of cytogenetic techniques that are appropriate to document the different steps required for the stable introgression of a chromosome segment from a donor species (i.e., the crop) into a recipient species (i.e., the wild). Several examples in hybrids and derivatives are given to illustrate how these approaches may be used to evaluate the potential for gene transfer between crops and wild relatives. Different techniques, from classical chromosome staining methods to recent developments in molecular cytogenetics, can be used to differentiate genomes and identify the chromosome regions eventually involved in genetic exchanges. Some clues are also given for the study of fertility restoration in the interspecific hybrid forms.
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Affiliation(s)
- E Benavente
- Departamento de Biotecnología, ETS Ingenieros Agrónomos, Universidad Politécnica de Madrid, Spain.
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