Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Epigenetic changes and transposon reactivation in Thai rice hybrids. Molecular Breeding
Kantama, L. ; Junbuathong, S. ; Sakulkoo, J. ; Jong, J.H.S.G.M. de; Apisitwanich, S. - \ 2013
Molecular Breeding 31 (2013)4. - ISSN 1380-3743 - p. 815 - 827.
cytosine methylation - dna methylation - elements mites - genome - retrotransposons - hybridization - markers - inheritance - activation - expression
Inter- or intraspecific hybridization is the first step in transferring exogenous traits to the germplasm of a recipient crop. One of the complicating factors is the occurrence of epigenetic modifications of the hybrids, which in turn can change their gene expression and phenotype. In this study we present an analysis of epigenome changes in rice hybrids that were obtained by crossing rice cultivars, most of them of indica type and Thai origin. Comparing amplified fragment length polymorphism (AFLP) fingerprints of twenty-four cultivars, we calculated Nei’s indexes for measuring genetic relationships. Epigenetic changes in their hybrids were established using methylation-sensitive AFLP fingerprinting and transposon display of the rice transposable elements (TEs) Stowaway Os-1 and Mashu, leading to the question whether the relationship between parental genomes is a predictor of epigenome changes, TE reactivation and changes in TE methylation. Our study now reveals that the genetic relationship between the parents and DNA methylation changes in their hybrids is not significantly correlated. Moreover, genetic distance correlates only weakly with Mashu reactivation, whereas it does not correlate with Stowaway Os-1 reactivation. Our observations also suggest that epigenome changes in the hybrids are localized events affecting specific chromosomal regions and transposons rather than affecting the genomic methylation landscape as a whole. The weak correlation between genetic distance and Mashu methylation and reactivation points at only limited influence of genetic background on the epigenetic status of the transposon. Our study further demonstrates that hybridizations between and among specific japonica and indica cultivars induce both genomic DNA methylation and reactivation/methylation change in the Stowaway Os-1 and Mashu transposons. The observed epigenetic changes seem to affect the transposons in a clear manner, partly driven by stochastic processes, which may account for a broader phenotypic plasticity of the hybrids. A better understanding of the epigenome changes leading to such transposon activation can lead to the development of novel tools for more variability in future rice breeding
Diploid apomicts of the Boechera holboelli complex display large scale chromosome substitutions and aberrant chromosomes
Kantama, L. ; Sharbel, T.F. ; Schranz, M.E. ; Mitchell-Olds, T. ; Vries, S.C. de; Jong, J.H.S.G.M. de - \ 2007
Proceedings of the National Academy of Sciences of the United States of America 104 (2007). - ISSN 0027-8424 - p. 14026 - 14031.
in-situ hybridization - gene-expression - pennisetum-squamulatum - cenchrus-ciliaris - arabis-drummondii - b-chromosome - brassicaceae - evolution - arabidopsis - apomixis
We conducted a cytogenetic study of sexual lines of Boechera stricta and Boechera holboellii (2n = 14) and seven diploid apomictic accessions of their interspecific hybrid Boechera divaricarpa and B. holboellii (2n = 14 or 15). By studying chromosome morphology, rDNA repeats, genome painting, male meiosis, pollen morphology, and flow-cytometry seed screens, we revealed an unexpected plethora of chromosome forms, pairing behavior, and hybrid composition in all apomictic lines. Genome painting demonstrated that the apomicts are alloploid with variable numbers of B. stricta and B. holboellii-like chromosomes. We assume that large-scale homeologous chromosome substitutions took place in the apomictic hybrids that resulted from recurrent diploid-polyploid transitions through restitutional meiosis and polyploicly-diploid transitions through reductional meiosis. A second peculiarity was the presence of a largely heterochromatic chromosome (Het) in all apomictic accessions (2n = 14 and 15) and an additional smaller chromosome (Den in the aneuploids (2n = 15). Both chromosomes share repetitive pericentromere repeats with those from the sexual B. stricta, suggesting that they originated from this species. Pairing and behavior at meiosis I of the Het share features with both Y and B chromosomes and suggest that the Del arose from a translocation event or homeologous recombination between a B. holboellii (or related taxon) and a B. stricta chromosome. Based on its presence exclusively in apomictic accessions, we propose that the Het chromosome plays a role in the genetic control of apomixis.
Asexual reproduction in a close relative of Arabidopsis: a genetic investigation of apomixis in Boechera ( Brassicaceae).
Schranz, M.E. ; Kantama, L. ; Jong, J.H.S.G.M. de; Mitchell-Olds, T. - \ 2006
New Phytologist 171 (2006)2. - ISSN 0028-646X - p. 425 - 438.
holboellii brassicaceae - dandelions taraxacum - molecular markers - arabis-drummondii - poa-pratensis - apomixis - apospory - evolution - populations - inheritance
Understanding apomixis (asexual reproduction through seeds) is of great interest to both plant breeders and evolutionary biologists. The genus Boechera is an excellent system for studying apomixis because of its close relationship to Arabidopsis, the occurrence of apomixis at the diploid level, and its potentially simple inheritance by transmission of a heterochromatic (Het) chromosome. ¿ Diploid sexual Boechera stricta and diploid apomictic Boechera divaricarpa (carrying a Het chromosome) were crossed. Flow cytometry, karyotype analysis, genomic in situ hybridization, pollen staining and seed-production measurements were used to analyse the parents and resulting F1, F2 and selected F3 and test-cross (TC) generations. ¿ The F1 plant was a low-fertility triploid that produced a swarm of aneuploid and polyploid F2 progeny. Two of the F2 plants were fertile near-tetraploids, and analysis of their F3 and TC progeny revealed that they were sexual and genomically stabilized. ¿ The apomictic phenotype was not transmitted by genetic crossing as a single dominant locus on the Het chromosome, suggesting a complex genetic control of apomixis that has implications for future genetic and evolutionary analyses in this group
Use of the SSLP-based method for detection of rare apomictic events in a sexual AtSERK1 transgenic Arabidopsis population
Kantama, L. ; Lambert, J.M. ; Hu, H. ; Jong, H. de; Vries, S.C. de; Russinova, E. - \ 2006
Sexual Plant Reproduction 19 (2006)2. - ISSN 0934-0882 - p. 73 - 82.
polycomb group gene - poa-pratensis l - somatic embryogenesis - apomixis - expression - fertilization - seeds - embryos - growth - strategies
Here we present a screening method to evaluate the potential of genes to transfer aspects of apomixis into sexual crop plants. Based on the assumption that an apomictic progeny is an exact genetic replica of the mother plant we employed a set of single sequence length polymorphism (SSLP) markers to identify individuals displaying heterozygosity fixation in segregating sexual populations as an indication of rare apomictic events. Here we present the results of such a study using the Arabidopsis thaliana SOMATIC EMBRYOGENESIS RECEPTOR KINASE 1 (AtSERK1) gene expressed under the control of the AtLTP1 promoter in sexual Arabidopsis plants. In one of the three tested F2 transgenic populations expressing the AtLTP1::AtSERK1 construct we observed two plants with heterozygosity maintenance for the full set of SSLP markers indicating a possible clonal inheritance. However, as their offspring revealed a close to binomial segregation for a number of heterozygous loci, it was concluded that these two putative apomictic plants either lost their clonal ability in the next generation or resulted from incidental recombination events displaying the genotype of the parent
Chromosome studies and genetic analysis of natural and synthetic apomictic model species
Kantama, L. - \ 2005
Wageningen University. Promotor(en): Sacco de Vries, co-promotor(en): Hans de Jong; E.T. Russinova. - [S.l.] : S.n. - ISBN 9085043212 - 120
chromosoomanalyse - genetische analyse - karyotypen - apomixis - brassicaceae - chromosome analysis - genetic analysis - karyotypes - apomixis - brassicaceae
Biogeographic distribution of polyploidy and B chromosomes in the apomictic Boechera holboellii complex
Sharbel, T.F. ; Mitchell-Olds, T. ; Dobes, C. ; Kantama, L. ; Jong, J.H.S.G.M. de - \ 2005
Cytogenetic and Genome Research 109 (2005)1-3. - ISSN 1424-8581 - p. 283 - 292.
arabis-holboellii - molecular systematics - natural-populations - rust infection - brassicaceae - evolution - plants - arabidopsis - mechanisms - apomixis
The Boechera holboellii complex comprises B. holboellii and B. drummondii, both of which can reproduce through sex or apomixis. Sexuality is associated with diploid individuals, whereas apomictic individuals are diploid or triploid and may additionally have B chromosomes. Using flow cytometry and karyotype analysis, we have shown that B chromosomes (a) occur in both diploid and triploid apomictic B. holboellii, (b) may occur in triploid B. drummondii, and (c) are dispensable for the plant. Both diploid and triploid karyotypes are found in multiple chloroplast haplotypes of both species, suggesting that triploid forms have originated multiple times during the evolution of this complex. B chromosome carriers are found in geographically and genetically distinct popu-lations, but it is unknown whether the extra chromosomes are shared by common descent (single origin) or have originated via introgressive hybridization and repeated transitions from diploidy to triploidy. Diploid plants containing the Bs reproduce apomictically, suggesting that the supernumerary elements are associated with apomixis. Finally, our analyses of pollen size and viability suggest that irregular chromosome segregation in some triploid lineages may lead to the generation of diploid individuals which carry the B chromosomes.
Is the aneuploid chromosome in an apomictic Boechera holboellii a genuine B chromosome?
Sharbel, T.F. ; Voigt, M.L. ; Mitchell-Olds, T. ; Kantama, L. ; Jong, J.H.S.G.M. de - \ 2004
Cytogenetic and Genome Research 106 (2004)2-4. - ISSN 1424-8581 - p. 173 - 183.
arabis-holboellii - evolutionary genetics - molecular systematics - natural-populations - rust infection - brassicaceae - apomixis - arabidopsis - plants - parthenogenesis
The Boechera holboellii complex comprises B. holboellii and B. drummondii, both of which can reproduce through sex or apomixis. Sexuality is associated with diploidy, whereas apomictic individuals can either be diploid, aneuploid or triploid. Aneuploid individuals are found in geographically and genetically distinct populations and contain a single extra chromosome. It is unknown whether the supernumerary chromosomes are shared by common descent (single origin) or have originated via introgressive hybridizations associated with the repeated transition from diploidy to triploidy. Diploid plants containing the extra chromosome(s) reproduce apomictically, suggesting that the supernumerary elements are associated with apomixis. In this study we compared flow cytometry data, chromosome morphology, and DNA sequences of sexual diploid and apomictic aneuploids in order to establish whether the extra chromosome fits the classical concept of a B chromosome. Karyotype analyses revealed that the supernumerary chromosome in the metaphase complement is heterochromatic and often smaller than the A chromosomes, and differs in length between apomictic plants from different populations. DNA sequence analyses furthermore demonstrated elevated levels of non-synonymous substitutions in one of the alleles, likely that on the aneuploid chromosome. Although the extra chromosome in apomictic Boechera does not go through normal reductional meiosis, in which it may get eliminated or accumulated by a B-chromosome-specific process, its variable size and heterochromatic nature does meet the remaining criteria for a genuine B chromosome in other species. Its prevalence and conserved genetic composition nonetheless implies that this chromosome, if truly a B, may be atypical with respect to its influence on its carriers. Copyright (C) 2004 S. Karger AG, Basel.
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