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Cytological characterization of three closely related pines - Pinus mugo, P. uliginosa and P. × rhaetica from the Pinus mugo complex (Pinaceae). Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00201-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AbstractThe Pinus mugo complex comprises closely related pines in different taxonomic ranks, which commonly occur in major European mountain chains. This large and polymorphic complex has been, and still is, a considerable challenge for taxonomists due to highly variable phenotypical characteristics within particular taxa, ongoing hybridization in sympatric populations, lack of distinct morphological species-specific determinants, and the absence of distinct genetic differentiation among them. Moreover, cytogenetic data on pines from this complex are very scarce. Therefore, in this study, we used C-banding methods and flow cytometric analysis in order to provide new data on karyotypical features and DNA content of three closely-related pines from the Pinus mugo complex, i.e., Pinus mugo (Turra), Pinus uliginosa (Neumann), and Pinus × rhaetica (Brügger) and to gain more insight into the taxonomic relationships between these pines. Our results confirmed that the basic number of chromosome is the same amongst the analyzed taxa (2n = 2x = 24), and that the karyotypes have a similar morphology. The number of secondary constrictions (SCs) and C-banding patterns differed slightly between P. mugo, P. uliginosa and P. × rhaetica. The nuclear DNA content (2C/pg) among analyzed taxa is from 46.41 pg for P. mugo and P. × rhaetica to 46.48 pg for P. uliginosa. For each of these pines, certain taxa-specific cytogenetic determinants were identified. Our results indicate that they may represent two different taxa, and so their names should not be used interchangeably in scientific literature.
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Koelewijn HP, Koski V, Savolainen O. MAGNITUDE AND TIMING OF INBREEDING DEPRESSION IN SCOTS PINE (PINUS SYLVESTRISL.). Evolution 2017; 53:758-768. [DOI: 10.1111/j.1558-5646.1999.tb05370.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/1998] [Accepted: 02/04/1999] [Indexed: 11/28/2022]
Affiliation(s)
| | - Veikko Koski
- Department of Forest Ecology; Finnish Forest Institute; P.O. Box 18 SF-01301 Vantaa Finland
| | - Outi Savolainen
- Department of Biology; University of Oulu; SF-90570 Oulu Finland
- Department of Forest Ecology; Finnish Forest Institute; P.O. Box 18 SF-01301 Vantaa Finland
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Donnelly K, Cottrell J, Ennos RA, Vendramin GG, A'Hara S, King S, Perry A, Wachowiak W, Cavers S. Reconstructing the plant mitochondrial genome for marker discovery: a case study using Pinus. Mol Ecol Resour 2017; 17:943-954. [DOI: 10.1111/1755-0998.12646] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/25/2016] [Accepted: 12/14/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Donnelly
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
- Institute of Evolutionary Biology; School of Biological Sciences; Ashworth Laboratories; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Joan Cottrell
- Forest Research, Northern Research Station; Roslin Midlothian EH25 9SY UK
| | - Richard A. Ennos
- Institute of Evolutionary Biology; School of Biological Sciences; Ashworth Laboratories; University of Edinburgh; Edinburgh EH9 3JT UK
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and BioResources; Division of Florence; National Research Council; Via Madonna del Piano, 10 50019 Sesto Fiorentino (Firenze) Italy
| | - Stuart A'Hara
- Forest Research, Northern Research Station; Roslin Midlothian EH25 9SY UK
| | - Sarah King
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
| | - Annika Perry
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
| | - Witold Wachowiak
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
- Institute of Dendrology; Polish Academy of Sciences; Parkowa 5 62-035 Kórnik Poland
| | - Stephen Cavers
- NERC Centre for Ecology and Hydrology, Edinburgh; Bush Estate Penicuik Midlothian EH26 0QB UK
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Jackson SA, Iwata A, Lee SH, Schmutz J, Shoemaker R. Sequencing crop genomes: approaches and applications. THE NEW PHYTOLOGIST 2011; 191:915-925. [PMID: 21707621 DOI: 10.1111/j.1469-8137.2011.03804.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many challenges face plant scientists, in particular those working on crop production, such as a projected increase in population, decrease in water and arable land, changes in weather patterns and predictability. Advances in genome sequencing and resequencing can and should play a role in our response to meeting these challenges. However, several barriers prevent rapid and effective deployment of these tools to a wide variety of crops. Because of the complexity of crop genomes, de novo sequencing with next-generation sequencing technologies is a process fraught with difficulties that then create roadblocks to the utilization of these genome sequences for crop improvement. Collecting rapid and accurate phenotypes in crop plants is a hindrance to integrating genomics with crop improvement, and advances in informatics are needed to put these tools in the hands of the scientists on the ground.
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Affiliation(s)
- Scott A Jackson
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia,111 Riverbend Rd, Athens, GA 30602, USA
| | - Aiko Iwata
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia,111 Riverbend Rd, Athens, GA 30602, USA
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, Huntsville, AL 35806, USA
| | - Randy Shoemaker
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA
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Wang X, Zhang T, Wen Z, Xiao H, Yang Z, Chen G, Zhao X. The chromosome number, karyotype and genome size of the desert plant diploid Reaumuria soongorica (Pall.) Maxim. PLANT CELL REPORTS 2011; 30:955-64. [PMID: 21327391 DOI: 10.1007/s00299-011-1020-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 12/27/2010] [Accepted: 01/19/2011] [Indexed: 05/08/2023]
Abstract
Extreme drought and salt resistant plant Reaumuria soongorica is of great potential for revealing genetic bases unique to naturally stress-tolerant plants. A preliminary genome survey, including chromosome number, karyotype, chromosomal localization of 45S rDNA loci and genome size was conducted with R. soongorica collected from Lanzhou, China. Chromosome counting showed that R. soongorica is diploid with chromosome number of 22. Karyotypical analysis illustrated that the chromosomes size ranges from 3.38 to 5.51 μm, and the chromosomal formula is 2n = 2x = 22 = 4 m + 14sm + 4st. Fluorescence in situ hybridization revealed that four pairs of 45SrDNA signals were detected at the end of R. soongorica chromosomes. The flow cytometry analysis indicated that the mean C value of R. soongorica is 0.806 pg with predicted genome size of about 778 Mb. The results indicate that the extreme drought and salt resistance of R. soongorica was not attributed to a big and complicate genome and also offer some clues in resolving the problems of taxonomy and evolution in Tamaricaceae.
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Affiliation(s)
- Xiaohua Wang
- Key Laboratory of Eco-hydrology and of Inland River Basin, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, 320 Donggangxilu, Lanzhou, Gansu 730000, China.
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Marum L, Loureiro J, Rodriguez E, Santos C, Oliveira MM, Miguel C. Flow cytometric and morphological analyses of Pinus pinaster somatic embryogenesis. J Biotechnol 2009; 143:288-95. [PMID: 19665503 DOI: 10.1016/j.jbiotec.2009.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 07/24/2009] [Accepted: 08/03/2009] [Indexed: 10/20/2022]
Abstract
An approach combining morphological profiling and flow cytometric analysis was used to assess genetic stability during the several steps of somatic embryogenesis in Pinus pinaster. Embryogenic cell lines of P. pinaster were established from immature zygotic embryos excised from seeds obtained from open-pollinated trees. During the maturation stage, phenotype of somatic embryos was characterized as being either normal or abnormal. Based upon the prevalent morphological traits, different types of abnormal embryos underwent further classification and quantification. Nuclear DNA content of maritime pine using the zygotic embryos was estimated to be 57.04 pg/2C, using propidium iodide flow cytometry. According to the same methodology, no significant differences (P< or =0.01) in DNA ploidy were detected among the most frequently observed abnormal phenotypes, embryogenic cell lines, zygotic and normal somatic embryos, and somatic embryogenesis-derived plantlets. Although the differences in DNA ploidy level do not exclude the occurrence of a low level of aneuploidy, the results obtained point to the absence of major changes in ploidy level during the somatic embryogenesis process of this economically important species. Therefore, our primary goal of true-to-typeness was assured at this level.
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Affiliation(s)
- Liliana Marum
- Instituto de Biologia Experimental e Tecnológica (IBET)/Instituto de Tecnologia Química e Biológica-Universidade Nova de Lisboa (ITQB-UNL), Av. República (EAN) 2784-505 Oeiras, Portugal
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Fuchs J, Jovtchev G, Schubert I. The chromosomal distribution of histone methylation marks in gymnosperms differs from that of angiosperms. Chromosome Res 2008; 16:891-8. [PMID: 18679813 DOI: 10.1007/s10577-008-1252-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/30/2008] [Accepted: 06/30/2008] [Indexed: 11/28/2022]
Abstract
The chromosomal distribution of seven histone methylation marks (H3K4me2, H3K9me1,2,3 and H3K27me1,2,3) was analysed in the gymnosperm species Pinus sylvestris and Picea abies. Similarly to the situation in other investigated eukaryotes, dimethylation of lysine 4 of histone H3 is restricted to euchromatin in gymnosperms. Surprisingly, also H3K9me1-a mark classified as heterochromatin-specific in angiosperms-labels the euchromatin in P. sylvestris and P. abies. The other investigated methylation marks are either equally distributed along the chromosomes, as H3K9me2 and H3K27me1 (in both species) and H3K9me3 (in P. abies), or enriched at specific types of heterochromatin, as H3K9me3 (in P. sylvestris) and H3K27me2 and H3K27me3 in both species. Although the methylation marks themselves are apparently conserved, their functional specificity within the frame of the 'epigenetic code' might have diverged during evolution.
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Affiliation(s)
- Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstrasse 3, 06466, Gatersleben, Germany.
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Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman AH. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci U S A 2000; 97:6603-7. [PMID: 10823912 PMCID: PMC18673 DOI: 10.1073/pnas.110587497] [Citation(s) in RCA: 333] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The replicative spread of retrotransposons in the genome creates new insertional polymorphisms, increasing retrotransposon numbers and potentially both their share of the genome and genome size. The BARE-1 retrotransposon constitutes a major, dispersed, active component of Hordeum genomes, and BARE-1 number is positively correlated with genome size. We have examined genome size and BARE-1 insertion patterns and number in wild barley, Hordeum spontaneum, in Evolution Canyon, Lower Nahal Oren, Mount Carmel, Israel, along a transect presenting sharply differing microclimates. BARE-1 has been sufficiently active for its insertional pattern to resolve individuals in a way consonant with their ecogeographical distribution in the canyon and to distinguish them from provenances outside the canyon. On both slopes, but especially on the drier south-facing slope, a simultaneous increase in the BARE-1 copy number and a decrease in the relative number lost through recombination, as measured by the abundance of solo long terminal repeats, appear to have driven the BARE-1 share of the genome upward with the height and dryness of the slope. The lower recombinational loss would favor maintenance of more full-length copies, enhancing the ability of the BARE-1 family to contribute to genome size growth. These local data are consistent with regional trends for BARE-1 in H. spontaneum across Israel and therefore may reflect adaptive selection for increasing genome size through retrotransposon activity.
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Affiliation(s)
- R Kalendar
- Institute of Biotechnology, University of Helsinki, Plant Genomics Laboratory, Viikki Biocenter, P.O. Box 56, FIN-00014 Helsinki, Finland
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