56 research outputs found
Living in fragments: Genetic variation in spatially structured populations
No full textIn de Achterhoek gaat het met de boomkikker weer wat beter dankzij beschermingsmaatregelen. Men heeft geprobeerd de lokale populaties in vijf clusters te verstevigen door in de directe omgeving nieuwe poelen te graven, het landhabitat te verbeteren en verbindingen te maken tussen lokale poelen. Toch ligt het gevaar van uitsterving ook hier nog steeds op de loer omdat de leefgebieden relatief klein en geïsoleerd zijn. Dit maakt de eveneens relatief kleine populaties kwetsbaar, bijvoorbeeld voor inteelt, omdat de genetische variatie in de populaties laag is. Inteelt, op zijn beurt, maakt populaties extra gevoelig voor toevallige omstandigheden als droogte of andere extreme (weers)omstandigheden. Paul Arens constateerde dat er tussen de clusters weinig genetische uitwisseling is, terwijl de genetische variatie binnen het hele gebied nu al gevaarlijk laag is. Recent is de belangrijkste populatie in een van de clusters bijvoorbeeld uitgestorven. Volgens Arens moeten er daarom met spoed natuurlijke verbindingen, zogenaamde corridors, tussen de clusters worden aangelegd. Dit geldt ook voor de leefgebieden van de heikikker, hoewel de genetische variatie binnen deze soort tot nu toe minder te lijden lijkt te hebben gehad van landschapsversnippering dan de boomkikker. Het leefgebied van planten en dieren in Nederland is in de laatste honderd jaar dramatisch kleiner geworden en versnipperd. Paul Arens onderzocht de consequenties voor de genetische variatie van deze natuurverarming niet alleen bij de boom- en de heikikker maar ook bij de zwarte populier, de boszegge en het dalkruid. Hij vond bij alle vijf de soorten schadelijke effecten van de versnippering van het leefgebied en/of ander menselijk handelen. Voor de drie plantensoorten lijkt vooral het ontbreken van voldoende dynamiek, die condities voor bloei en/of zaadkieming creëren, de belangrijkste oorzaak voor de achteruitgang van lokale populaties
Disentangling hexaploid genetics : towards DNA-informed breeding for postharvest performance in chrysanthemum
No full textDNA-informed selection can strongly improve the process of plant breeding. It requires the detection of DNA polymorphisms, calculation of genetic linkage, access to reliable phenotypes and methods to detect genetic loci associated with phenotypic traits of interest. Cultivated chrysanthemum is an outcrossing hexaploid with an unknown mode of inheritance. This complicates the development of resources and methods that enable the detection of trait loci. Postharvest performance is an essential trait in chrysanthemum, but is difficult to measure. This makes it an interesting but challenging trait to phenotype and detect associated genetic loci. In this thesis I describe the development of resources and methods to enable phenotyping for postharvest performance, genetic linkage map construction and detection of quantitative trait loci in hexaploid chrysanthemum. Postharvest performance is a complicated trait because it is related to many different disorders that reduce quality. One of these disorders in chrysanthemum is disk floret degreening, which occurs after long storage. In chapter 2, we show that degreening can be prevented by feeding the flower heads with sucrose, suggesting carbohydrate starvation plays a role in the degreening process. To investigate the response to carbohydrate starvation of genotypes with different sensitivity to disk floret degreening, we investigated the metabolome of sugar-fed and carbohydrate-starved disk florets by 1H-NMR and HPAEC. We show that the metabolome is severely altered at carbohydrate starvation. In general, starvation results in an upregulation of amino acid and secondary metabolism. Underlying causes of genotypic differences explaining variation in disk floret degreening in the three investigated genotypes remained to be elucidated, but roles of regulation of respiration rate and camphor metabolism were posed as possible candidates. In chapter 3, disk floret degreening was found to be the most important postharvest disorder after 3 weeks of storage among 44 white chrysanthemum cultivars. To investigate the inheritance of disk floret degreening, we crossed two genotypes with opposite phenotypic values of both disk floret degreening and carbohydrate content to obtain a population segregating for disk floret degreening. To phenotype the cultivar panel and the bi-parental population precisely and in a high throughput manner, we developed a method that quantified colour of detached capitula over time. This method was validated with visual observations of disk floret degreening during vase life tests. In a subset of the bi-parental population we measured carbohydrate content of the disk florets at harvest. The amount of total carbohydrates co-segregated with sensitivity to degreening, which shows that the difference in disk floret degreening sensitivity between the parents could be explained by their difference in carbohydrate content. However, the correlation was rather weak, indicating carbohydrate content is not the only factor playing a role. In order to develop resources for DNA-informed breeding, one needs to be able to characterize DNA polymorphisms. In chapter 4, we describe the development of a genotyping array containing 183,000 single nucleotide polymorphisms (SNPs). These SNPs were acquired by sequencing the transcriptome of 13 chrysanthemum cultivars. By comparing the genomic dosage based on the SNP assay and the dosage as estimated by the read depth from the transcriptome sequencing data, we show that alleles are expressed conform the genomic dosage, which contradicts to what is often found in disomic polyploids. In line with this finding, we conclusively show that cultivated chrysanthemum exhibits genome-wide hexasomic inheritance, based on the segregation ratios of large numbers of different types of markers in two different populations. Tools for genetic analysis in diploids are widely available, but these have limited use for polyploids. In chapter 5, we present a modular software package that enables genetic linkage map construction in tetraploids and hexaploids. Because of the modularity, functionality for other ploidy levels can be easily added. The software is written in the programming language R and we named it polymapR. It can generate genetic linkage maps from marker dosage scores in an F1 population, while taking the following steps: data inspection and filtering, linkage analysis, linkage group assignment and marker ordering. It is the first software package that can handle polysomic hexaploid and partial polysomic tetraploid data, and has advantages over other polyploid mapping software because of its scalability and cross-platform applicability. With the marker dosage scores of the bi-parental F1 population from the genotyping array and the developed methods to perform linkage analysis we constructed an integrated genetic linkage map for the hexaploid bi-parental population described in chapter 3 and 4. We describe this process in chapter 6. With this integrated linkage map, we reconstructed the inheritance of parental haplotypes for each individual, and expressed this as identity-by-descent (IBD) probabilities. The phenotypic data on disk floret degreening sensitivity that was acquired as described in chapter 3, was used in addition to three other traits to detect quantitative trait loci (QTL). These QTL were detected based on the IBD probabilities of 1 centiMorgan intervals of each parental homologue. This enabled us to study genetic architecture by estimating the effects of each separate allele within a QTL on the trait. We showed that for many QTL the trait was affected by more than two alleles. In chapter 7, the findings in this thesis are discussed in the context of breeding for heterogeneous traits, the implications of the mode of inheritance for breeding and the advantages and disadvantages of polyploidy in crop breeding. In conclusion, this thesis provides in general a significant step for DNA-informed breeding in polysomic hexaploids, and for postharvest performance in chrysanthemum in particular
Unraveling the genetics of Botrytis cinerea resistance in Gerbera hybrida
No full textGerbera hybrida is one of the top five cut flowers. It is well-known to people for its variation in flower color and patterning. Gerbera breeding at the moment is done using conventional methods which are based on a phenotypic selection. This has drawbacks in breeding speed and efficiency, especially for complex traits like disease resistance. Gerbera gray mold, promoted by high humidity during the production in greenhouses or by an accumulation of condensate during transportation, is a considerable threat to the gerbera production. Gerbera gray mold is caused by Botrytis cinerea and plant resistance to B. cinerea is considered to be a polygenic trait that needs the contribution of multiple loci, and on top of that is highly affected by the environment. Conventional breeding might be inefficient for improving Botrytis resistance in gerbera. In this study, the transcriptomes of four parents of two gerbera populations were sequenced using Illumina paired-end sequencing. Transcriptome data provides a resource for genetic dissection and an insight to explore gene functions for this ornamental crop. To identify the QTL regions leading to the phenotypic variation in Botrytis resistance, and establishing a relationship between marker genotype and phenotypic variation for marker assisted selection (MAS), genetic linkage maps were constructed with SNP markers in the two F1 segregating populations. A total of 20 QTLs were identified in the parental maps of the two populations. The number of QTLs found and the explained variance of most QTLs detected reflects the complex mechanism of Botrytis disease response. Narrowing down the QTL region and identifying the causal gene(s) underlying a QTL could maximize the effective use of MAS in breeding. Homologs of known functional genes involved in Botrytis resistance from other species were obtained in gerbera and SNP markers identified and mapped. Twenty-nine candidate genes were mapped and seven candidate genes could be mapped on both populations. Seven candidate genes were located in the vicinity of the QTLs detected. The co-localization of QTLs with CGs gives an indication that these candidate genes could probably be involved in resistance to Botrytis and provide a more precise possibility to use MAS in gerbera breeding in the future. A tobacco rattle virus (TRV) based gene silencing system which was used to inspect the function of two candidate genes. The two CGs are the homologs of the genes responsible for Botrytis resistance in tomato and both mapped in QTL regions related to Botrytis resistance in gerbera ray floret test. Silencing the two genes by VIGS, showed smaller lesion sizes upon Botrytis infection on gerbera ray florets compared with the controls. The entire research went from the generation of four parental transcriptome data sets to development of SNP markers (Chapter 2), construction of genetic maps and to mapping QTLs for Botrytis resistance (Chapter 3). This was further on combined with candidate gene searching in other crops, querying and mapping homologous genes (Chapter 4) and characterizing the candidate genes which co-localized with QTLs (Chapter 5). The whole process not only helped us to unravel the genetics of Botrytis resistance in gerbera and develop genetic tools for gerbera improvement, but also could serve as guidance for developing marker-assisted selection for other ornamental plants from the beginning.</p
Autosomal and sex-linked microsatellite loci in the green oak leaf roller Tortrix viridana L.
No full textEight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy¿Weinberg equilibrium. The other two were linked to the Z-chromosome. Values of observed heterozygosity ranged for the autosomal loci from 0.510 to 0.957. All loci will be useful to study dispersal and the autosomal loci, as well for phylogeographical studies
(Molecular) Breeding of Lilium
No full textLily breeding has become an important economic activity in the last 50 years. Within this period breeding has changed from making end-products that were mainly interspecific hybrids from the section Sinomartagon to polyploid hybrids that are derived from intersectional crosses. Especially the Longiflorum × Asiatic hybrids or LA hybrids and the Oriental × Trumpets or OT hybrids have become dominant combinations in breeding because of their superior performance over Asiatic and Oriental hybrids. Molecular breeding utilises the information of markers linked to genes of interest to develop more efficient selection strategies in what is called Marker Assisted Selection. Molecular breeding is of particular importance when desired traits are difficult to phenotype (e.g., due to environmental variation influencing the trait), when simultaneous combinations of several genes are needed (e.g., quantitative resistance genes or yield) or in a combination of the two situations. The use of markers for breed¬ing has become an integrated part of the breeding schemes in many of the world’s important food crops. Especially the development of massive parallel sequencing methods known under the collective term Next Generation Sequencing (NGS sequencing) and the availability of high throughput marker systems have revolution¬ized the possibilities for molecular breeding. In most ornamental crops, and also in lily that is a model crop for research in interspecific hybridisation and cytogenetic, molecular breeding has not been imple-mented in actual breeding yet. Nevertheless there are some promising developments in research that are presented in this paper
Natural hybridization between Populus nigra L. and P. x canadensis Moench. Hybrid offspring competes for niches along the Rhine river in the Netherlands
No full textBlack poplar (Populus nigra L.) is a major species for European riparian forests but its abundance has decreased over the decades due to human influences. For restoration of floodplain woodlands, the remaining black poplar stands may act as source population. A potential problem is that P. nigra and Populus deltoides have contributed to many interspecific hybrids, which have been planted in large numbers. As these Populus x canadensis clones have the possibility to intercross with wild P. nigra trees, their offspring could establish themselves along European rivers. In this study, we have sampled 44 poplar seedlings and young trees that occurred spontaneously along the Rhine river and its tributaries in the Netherlands. Along these rivers, only a few native P. nigra L. populations exist in combination with many planted cultivated P. x canadensis trees. By comparison to reference material from P. nigra, P. deltoides and P. x canadensis, species-specific AFLP bands and microsatellite alleles indicated that nearly half of the sampled trees were not pure P. nigra but progeny of natural hybridisation that had colonised the Rhine river banks. The posterior probability method as implemented in NewHybrids using microsatellite data was the superior method in establishing the most likely parentage. The results of this study indicate that offspring of hybrid cultivated poplars compete for the same ecological niche as native black poplars
Adders onder het gras; beschikbaarheid en bruikbaarheid van ecologische en genetische kennis over amfibieën en reptielen en de knelpunten voor beleid en beheer
No full textDit rapport beschrijft welke kennis over de ecologie en genetica van de Kamsalamander, Boomkikker, Hazelworm en Zandhagedis beschikbaar is en waar hiaten in die kennis zitten. Het rapport benadrukt de informatie die nodig is voor een juist habitatbeheer en geeft aan of die informatie bekend is bij terreinbeheerders en in welke mate de kennis wordt gebruikt om beheer van die terreinen te richten op ter plaatse voorkomende amfibieën en reptielen. Het rapport doet aanbevelingen om beheer, beleid en onderzoek beter op elkaar af te stemmen
GISH investigation of crossover events during meiosis of interspecific hybrids of lily
No full textCrossover not only establishes proper segregation of omologous/homoeologouschromosomes during meiosis I, but also promotes genetic diversity thoughcreating new recombination of maternal and paternal alleles, which is essential for introgression breeding. In this paper, crossovers between non-sister chromatids were observed during meiosis of interspecific hybrids of Lilium longiflorum × Asiatic (LA) using genomic in situ hybridization (GISH). Results showed that different types of crossing over events, viz. single, two strand double, three strand double, four strand double crossovers, occurred between non-sister chromatids during meiosis of selected interspecific lily hybrids. From an analysis of a total of 637 pairs of half-bivalents it was evident that a large majority (65%) was two strand single crossovers, 5.5% were two strands double, 3.0% three strand double, 9.3% four strand double and 17.3% were multiple crossing over events. In one specific genotype which showed the existence of a reciprocal translocation, the frequency of multiple crossovers was relatively high, which might alter the map distances of markers on the translocatedchromosomes
Isolation and characterization of highly polymorphic microsatellite markers in Hypochaeris radicata (Asteraceae)
No full textContains fulltext :
60091.pdf (Publisher’s version ) (Closed access)We developed five highly polymorphic dinucleotide microsatellite loci for the grassland species Hypochaeris radicata (Asteraceae). Polymorphism of these markers was examined in six populations in the Netherlands. All loci were polymorphic in all populations. The number of alleles per locus varied between 18 and 43. Expected heterozygosity was between 0.86 and 0.91. Cross-species amplification was tested in six Hypochaeris species and was successful for three different loci in four species. These microsatellites are a useful tool in population genetic, dispersal and metapopulation studies or in testing levels of inbreeding
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