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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Molecular analysis of genetic diversity, population structure, and phylogeny of wild and cultivated tulips (Tulipa L.) by genic microsatellites
Pourkhaloee, Ali ; Khosh-Khui, Morteza ; Arens, Paul ; Salehi, Hassan ; Razi, Hooman ; Niazi, Ali ; Afsharifar, Alireza ; Tuyl, Jaap van - \ 2018
Horticulture Environment and Biotechnology 59 (2018)6. - ISSN 2211-3452 - p. 875 - 888.
Bulb crop - Conservation implications - EST–SSR markers - Population genetics

Tulip (Tulipa L.) is one of the most important ornamental geophytes in the world. Analysis of molecular variability of tulips is of great importance in conservation and parental lines selection in breeding programs. Of the 70 genic microsatellites, 15 highly polymorphic and reproducible markers were used to assess the genetic diversity, structure, and relationships among 280 individuals of 36 wild and cultivated tulip accessions from two countries: Iran and the Netherlands. The mean values of gene diversity and polymorphism information content were 0.69 and 0.66, respectively, which indicated the high discriminatory power of markers. The calculated genetic diversity parameters were found to be the highest in wild T. systola Stapf (Derak region). Bayesian model-based STRUCTURE analysis detected five gene pools for 36 germplasms which corresponded with morphological observations and traditional classifications. Based on analysis of molecular variance, to conserve wild genetic resources in some geographical locations, sampling should be performed from distant locations to achieve high diversity. The unweighted pair group method with arithmetic mean dendrogram and principal component analysis plot indicated that among wild tulips, T. systola and T. micheliana Hoog exhibited the closest relationships with cultivated tulips. Thus, it can be assumed that wild tulips from Iran and perhaps other Middle East countries played a role in the origin of T. gesneriana, which is likely a tulip species hybrid of unclear origin. In conclusion, due to the high genetic variability of wild tulips, they can be used in tulip breeding programs as a source of useful alleles related to resistance against stresses.

Diseases of Lily
Chastagner, G.A. ; Tuyl, J.M. van; Verbeek, M. ; Miller, William ; Westerdahl, Becky B. - \ 2017
In: Handbook of Florists' Crops Diseases, Handbook of Plant Disease Management / McGovern, R.J., Elmer, W.H., Springer International Publishing (Handbook of Plant Disease Management ) - ISBN 9783319323749 - 61 p.
Lilies (Lilium spp. and hybrids) are the second largest flower bulb crop in the Netherlands and the most important flower bulb crop in the world. They are grown for bulbs, as cut flowers, as container (potted) plants, or in gardens. Lilies are a vegetatively propagated crop and may be routinely increased by micropropagation (tissue culture) or through scaling (removal of bulb scales from which adventitious bulblets are produced). The propagules are subsequently grown in fields for 2 or 3 y to allow the bulbs to reach sufficient size (generally measured in circumference) for proper flowering and maximum horticultural quality. Although the majority of bulbs produced for worldwide distribution are grown mainly in the Netherlands, bulbs are also grown in other northern European countries, the USA, Asia, Israel, and southern hemisphere locations including Brazil, Australia, New Zealand, Tasmania, and Chile. There are a number of diseases caused by fungi, viruses, bacteria, and nematodes and physiological disorders that affect the production and quality of lily bulb and cut flower crops worldwide. Information on the distribution, epidemiology and management, of the common diseases and disorders is presented in this chapter.
Erratum to: Genetic mapping and QTL analysis of Botrytis resistance in Gerbera hybrida : (Molecular Breeding, (2017), 37, 2, (13), 10.1007/s11032-016-0617-1)
Fu, Yiqian ; Silfhout, Alex van; Shahin, Arwa ; Egberts, Ronny ; Beers, Martin ; Velde, Ans van der; Houten, Adrie van; Tuyl, Jaap M. van; Visser, Richard G.F. ; Arens, Paul - \ 2017
Molecular Breeding 37 (2017)4. - ISSN 1380-3743

Unfortunately, in the original version of this article part of Fig. 1 was deleted in the final proofing step. The missing part of Fig. 1 with linkage groups 18–24.(Figure presented.).

Genetic mapping and QTL analysis of Botrytis resistance in Gerbera hybrida
Fu, Yiqian ; Silfhout, Alex van; Shahin, Arwa ; Egberts, Ronny ; Beers, Martin ; Velde, Ans van der; Houten, Adrie van; Tuyl, Jaap M. van; Visser, Richard G.F. ; Arens, Paul - \ 2017
Molecular Breeding 37 (2017)2. - ISSN 1380-3743
Gerbera grey mould - Linkage group - QTL mapping - SNP
Gerbera hybrida is an economically important cut flower. In the production and transportation of gerbera with unavoidable periods of high relative humidity, grey mould occurs and results in losses in quality and quantity of flowers. Considering the limitations of chemical use in greenhouses and the impossibility to use these chemicals in auction or after sale, breeding for resistant gerbera cultivars is considered as the best practical approach. In this study, we developed two segregating F1 populations (called S and F). Four parental linkage maps were constructed using common and parental specific SNP markers developed from expressed sequence tag sequencing. Parental genetic maps, containing 30, 29, 27 and 28 linkage groups and a consensus map covering 24 of the 25 expected chromosomes, could be constructed. After evaluation of Botrytis disease severity using three different tests, whole inflorescence, bottom (of disc florets) and ray floret, quantitative trait locus (QTL) mapping was performed using the four individual parental maps. A total of 20 QTLs (including one identical QTL for whole inflorescence and bottom tests) were identified in the parental maps of the two populations. The number of QTLs found and the explained variance of most QTLs detected reflect the complex mechanism of Botrytis disease response.
The Role of Polyploidization and Interspecific Hybridization in the Breeding of Ornamental Crops
Marasek-Ciolakowska, A. ; Arens, P.F.P. ; Tuyl, J.M. van - \ 2016
In: Polyploidy and Hybridization for Crop Improvement / Mason, Annaliese, CRC Press - ISBN 9781498740661 - p. 159 - 181.
Polyploidy and hybridisation are critical processes in plant evolution and speciation. Many current agricultural crops are either natural or agricultural hybrids or polyploids, including potato, sugarcane, wheat, strawberries, and banana. There is a great deal of potential to utilise these natural evolutionary processes for targeted crop improvement; for example, through introgression of desired traits from wild species into crops, production of seedless fruits, or even creation of entirely new crop types. This book provides a comprehensive summary of how the processes of polyploidy and hybridisation have shaped the foods we eat and how these processes can be used for crop improvement. Contents: Interspecific Hybridization For Upland Cotton Improvement. Allopolyploidy and Interspecific Hybridization for Wheat Improvement. Potato Breeding through Ploidy Manipulations. Polyploid Induction Techniques and Breeding Strategies in Poplar. Musa Interspecific Hybridization and Polyploidy for Breeding Banana and Plantain (Musaceae). Strawberry (Plants in the Genus Fragaria). The role of polyploidization and interspecific hybridization in the breeding of ornamental crops. Polyploidy in maize: The impact of homozygosity and hybridity on phenotype. Broadening the genetic basis for crop improvement: Interspecific hybridization within and between ploidy levels in Helianthus. Crop Improvement of Phaseolus spp through Interspecific and Intraspecific Hybridization. Triticale. Polyploidy and Interspecific Hybridization in Cynodon, Paspalum, Pennisetum, and Zoysia. Interploid and Interspecific Hybridization for Kiwifruit Improvement. Oat Improvement and Innovation Using Wild Genetic Resources (Poaceae, Avena spp.): Elevating "Oats" to a New Level and Stature. Interspecific hybridization of chestnut. Use of Polyploids, Interspecific, and Intergeneric Wide Hybrids in Sugar Beet Improvement. Polyploidy in Watermelon. Optimization of recombination in interspecific hybrids to introduce new genetic diversity into oilseed rape (Brassica napus L.). Interspecific Hybridization for Chickpea (Cicer arietinum L.) Improvement.
Biotechnological advances in Lilium
Bakhshaie, Mehdi ; Khosravi, Solmaz ; Azadi, Pejman ; Bagheri, Hedayat ; Tuyl, Jaap M. van - \ 2016
Plant Cell Reports 35 (2016)9. - ISSN 0721-7714 - p. 1799 - 1826.
Culture medium - Genetic transformation - In vitro pollination - Lilium - Molecular markers - Polyploidization

Modern powerful techniques in plant biotechnology have been developed in lilies (Lilium spp., Liliaceae) to propagate, improve and make new phenotypes. Reliable in vitro culture methods are available to multiply lilies rapidly and shorten breeding programs. Lilium is also an ideal model plant to study in vitro pollination and embryo rescue methods. Although lilies are recalcitrant to genetic manipulation, superior genotypes are developed with improved flower colour and form, disease resistance and year round forcing ability. Different DNA molecular markers have been developed for rapid indirect selection, genetic diversity evaluation, mutation detection and construction of Lilium linkage map. Some disease resistance-QTLs are already mapped on the Lilium linkage map. This review presents latest information on in vitro propagation, genetic engineering and molecular advances made in lily.

Induction of viable 2n pollen in sterile Oriental × Trumpet Lilium hybrids
Luo, J.R. ; Arens, P. ; Niu, L.X. ; Tuyl, J.M. van - \ 2016
Journal of Horticultural Science and Biotechnology 91 (2016)3. - ISSN 1462-0316 - p. 258 - 263.
Interspecific hybridization - Laughing gas - Meiosis - OThybrids - Unreduced gametes

In order to induce viable 2n pollen from highly sterile diploid Oriental × Trumpet (OT) (Lilium), N2O was used to treat flower buds of four sterile diploid OT cultivars (‘Nymph’, ‘Gluhwein’, ‘Yelloween’, and ‘Shocking’) at different stages of meiosis. There was no pollen germination in the controls. However, after N2O treatment at 600 kPa, three of the OT hybrids (‘Nymph’, ‘Gluhwein’, and ‘Yelloween’) not only exhibited fertile flower percentages (4.3-16%), but also higher rates of pollen germination (18.8-72.5%). In addition, both the fertile flower percentages and rates of pollen germination were higher following 48 h N2O treatment at 600 kPa than the 24 h treatment. Following 72 h N2O treatment at 600 kPa, most flower buds or plants were damaged and any undamaged flowers showed abnormal anthers at the time of flowering. This indicated that 48 h of N2O treatment at 600 kPa was optimal to induce viable 2n pollen in three out of four sterile hybrid OT lily cultivars. These results also showed that prophase I - metaphase I was the optimum stage of meiosis at which to induce 2n pollen by N2O treatment in lily hybrids.

Transcriptome Analysis of Gerbera hybrida Including in silico Confirmation of Defense Genes Found
Fu, Y. ; Esselink, G. ; Visser, R.G.F. ; Tuyl, J.M. van; Arens, P.F.P. - \ 2016
Frontiers in Plant Science 7 (2016). - ISSN 1664-462X
For the ornamental crop Gerbera hybrida, breeding at the moment is done using conventional methods. As this has drawbacks in breeding speed and efficiency, especially for complex traits like disease resistance, we set out to develop genomic resources. The leaf and flower bud transcriptomes of four parents, used to generate two gerbera populations, were sequenced using Illumina paired-end sequencing. In total, 36,770 contigs with an average length of 1397 bp were generated and these have been the starting point for SNP identification and annotation. The consensus contig sequences were used to map reads of individual parents, to identify genotype specific SNPs, and to assess the presence of common SNPs between genotypes. Comparison with the non-redundant protein database (nr) showed that 29,146 contigs gave BLAST hits. Of sequences with blast results, 73.3% obtained a clear gene ontology (GO) annotation. EST contigs coding for enzymes were found in Kyoto Encyclopedia of Genes and Genomes maps (KEGG). Through, these annotated data and KEGG molecular interaction network, transcripts associated with the phenylpropanoid metabolism, other secondary metabolite biosynthesis pathways, phytohormone biosynthesis and signal transduction were analyzed in more detail. Identifying genes involved in these processes could provide genetic and genomic resources for studying the mechanism of disease resistance in gerbera.
Blühende Magie: Tulpenzucht – eine «Wissenschaft» für sich
Arens, Paul ; Tuyl, Jaap van - \ 2015

Seit über 400 Jahren wird in den Niederlanden Tulpenzucht betrieben. Die Entwicklung neuer Sorten der beliebten Zierpflanze beschäftigt auch die Wissenschaft.

GISH analyzed progenies generated from allotriploid lilies as female parent
Xi, Mengli ; Tuyl, J.M. van; Arens, Paul - \ 2015
Scientia Horticulturae 183 (2015). - ISSN 0304-4238 - p. 130 - 135.
Aneuploid - Genome composition - Genomic in situ hybridization (GISH) - Lilium

Allotriploid lilies can produce aneuploid or euploid functional female gametes and can be used as the maternal parents in lily introgression breeding. In this study, the genome composition of 14 allopolyploid progenies, including 5 progenies which were derived from LLO×TTTT, 5 progenies which were derived from LLO×OTOT, and 4 BC2 progenies which were derived from MAD×AA/AAAA, were analyzed using genomic in situ hybridization (GISH) technique. The GISH results indicated that all of the 10 progenies which were derived from LLO×TTTT/OTOT were aneuploids, 4 BC2 progenies were euploids. Moreover, LLO always produced aneuploid functional female gametes, giving rise to aneuploid progenies, and MAD produced euploid functional female gametes including n or 2n gametes. Most interestingly, T/O recombinant chromosomes, which were caused by abnormal meiosis, were observed in 2 progenies of LLO×OTOT. Based on the analysis, we proposed that aneuploids might provide a promising approach for lily breeding.

The use of a candidate gene approach to arrive at botrytis resistance in gerbera
Fu, Yiqian ; Chen, Meng ; Tuyl, J. Van; Vißer, R.G.F. ; Arens, P. - \ 2015
Acta Horticulturae 1087 (2015). - ISSN 0567-7572 - p. 461 - 466.
2-PS - Botrytis resistance - Candidate gene approach - Gerbera

Gerbera grey mould (Botrytis cinerea) causes substantial loßes in quality and quantity during gerbera production and postharvest transportation. Developing cultivars with resistance to Botrytis is therefore an important goal for gerbera breeding. In this study, we employed a candidate-gene (CG) approach to map potential candidate genes for Botrytis resistance and screened those genes for colocalisation with quantitative trait loci (QTL) regions, which were mapped in two segregating populations. For example, the selected candidate gene 2-pyrone synthase (2-PS) codes for polyketide synthase which synthesises a putative precursor for two phytoalexins in gerbera. Using our recently developed transcriptome resource for the parents of mapping population, 2-PS gene sequence variation was found and employed as single nucleotide polymorphism (SNPs) markers. Segregation results in the population showed that the 2-PS gene may indeed be aßociated with Botrytis resistance. The SNP markers for the 2-PS gene can be used to improve Botrytis resistance in gerbera by selecting for the favourable alleles of the 2-PS gene in marker-Aßisted selection.

'Met genetische variatie kun je heel veel doen'
Dwarswaard, A. ; Tuyl, J.M. van - \ 2015
BloembollenVisie (2015)315. - ISSN 1571-5558 - p. 24 - 25.
bloembollen - lilium - lelies - rassen (planten) - plantengenetica - plantenveredeling - landbouwkundig onderzoek - resistentie van variëteiten - ornamental bulbs - lilies - varieties - plant genetics - plant breeding - agricultural research - varietal resistance
Na ruim 42 jaar zet onderzoeker Jaap van Tuyl van PRI in Wageningen een punt achter zijn loopbaan. Menig bolgewas kreeg zijn aandacht en altijd ging het om de genetische kant ervan. Van hyacinth tot lelie, van Zantedeschia tot tulp, telkens waren het de genen die inzicht gaven. Een portret van een man die de hele wereld afreisde om vooral over lelies te vertellen.
Genetic mapping of resistance to Fusarium oxysporum f. sp. tulipae in tulip
Tang, N. ; Lee, T.A.J. van der; Shahin, A. ; Holdinga, M.R. ; Bijman, P.J.J. ; Caser, M. ; Visser, R.G.F. ; Tuyl, J.M. van; Arens, P. - \ 2015
Molecular Breeding 35 (2015). - ISSN 1380-3743 - 17 p.
Fusarium oxysporum is a major problem in the production of tulip bulbs. Breeding for resistant cultivars through a conventional approach is a slow process due to the long life cycle of tulip. Until now, marker-assisted selection (MAS) has been hampered by the large genome size and the absence of a genetic map. This study is aimed at construction of the first genetic map for tulip and at the identification of loci associated with resistance to F. oxysporum. A cross-pollinated population of 125 individuals segregating for Fusarium resistance was obtained from Tulipa gesneriana “Kees Nelis” and T. fosteriana “Cantata.” Fusarium resistance of the mapping population was evaluated through a soil infection test in two consecutive years, and a spot inoculation test in which a green fluorescent protein tagged Fusarium strain was used for inoculation. The genetic maps have been constructed for the parents separately. The genetic map of “Kees Nelis” comprised 342 markers on 27 linkage groups covering 1707 cM, while the map of “Cantata” comprised 300 markers on 21 linkage groups covering 1201 cM. Median distance between markers was 3.9 cM for “Kees Nelis” and 3.1 cM for “Cantata.” Six putative quantitative trait loci (QTLs) for Fusarium resistance were identified, derived from both parents. QTL2, QTL3, and QTL6 were significant in all disease tests. For the flanking markers of the QTLs, phenotypic means of the two allelic groups, segregating from a parent for such a marker, were significantly different. These markers will be useful for the development of MAS in tulip breeding
Snelle vermeerdering blijft wens bij tulp
Arens, Paul ; Immink, Richard ; Klerk, Geert-Jan de; Tuyl, Jaap van - \ 2014
(Molecular) Breeding of Lilium
Arens, P.F.P. ; Shahin, A. ; Tuyl, J.M. van - \ 2014
Acta Horticulturae 1027 (2014). - ISSN 0567-7572 - p. 113 - 128.
Lily 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.
GISH investigation of crossover events during meiosis of interspecific hybrids of lily
Xie, S.L. ; Ramanna, M.S. ; Arens, P.F.P. ; Tuyl, J.M. van - \ 2014
Acta Horticulturae 1027 (2014). - ISSN 0567-7572 - p. 143 - 148.
Crossover not only establishes proper segregation of omologous/homoeologous
chromosomes during meiosis I, but also promotes genetic diversity though
creating 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 translocated
Ploidy manipulation and introgression breeding in Darwin hybrid tulips
Marasek-Ciolakowska, A. ; Xie, S.L. ; Arens, P. ; Tuyl, J.M. van - \ 2014
Euphytica 198 (2014)3. - ISSN 0014-2336 - p. 389 - 400.
asiatic lilies lilium - gish analysis - sexual polyploidization - interspecific hybrids - garden tulips - genome - recombination - gesneriana - hybridization - fosteriana
Meiotic polyploidisation via crossing with 2n gamete producing genotypes and interploidy crosses are two of the main methods currently used to obtain polyploid tulips. In our study diploid 2n gamete producing F-1 hybrids of Darwin hybrids (Tulipa gesneriana x Tulipa fosteriana) and triploid hybrid resulting from 'Rhodos' x 'Princeps' cross were used as pollen donor and crossed with cultivars of T. gesneriana in the following combination: 2x x 2x, 3x x 2x, 2x x 3x, and 3x x 3x. The progenies resulting from crosses at diploid level were mostly diploid, whereas a few seedlings were triploid. In 3x x 2x crosses aneuploids with chromosome constitution in between triploid and tetraploid (43-45 chromosomes) were predominant, but also one tetraploid (2n = 4x = 48) and four pentaploids (2n = 5x = 60) were obtained. In 2x x 3x crosses most progenies were triploid with the exception of a few aneuploids (3x + 1 and 3x - 1), whereas in 3x x 3x cross diploid and aneuploid genotypes were recorded with chromosome number varied from 27 to 34. These results indicate that triploid parents produced aneuploid as well as euploid (x, 2x, 3x) gametes and that success in ploidy manipulation in tulip depends to a large degree on the ploidy level of the parental genotypes used for hybridization. Genome constitution of selected population of F1 and BC1 hybrids was analyzed through genomic in situ hybridization (GISH). GISH analysis of the BC1 showed a considerable amount of intergenomic recombination which is desirable for introgression breeding.
Characterization of B chromosomes in Lilium hybrids through GISH and FISH
Xie, S.L. ; Marasek-Ciolakowska, A. ; Ramanna, M.S. ; Arens, P.F.P. ; Visser, R.G.F. ; Tuyl, J.M. van - \ 2014
Plant Systematics and Evolution 300 (2014)8. - ISSN 0378-2697 - p. 1771 - 1777.
ribosomal-rna genes - in-situ hybridization - nuclear-dna amounts - plants - angiosperms - probe - recombination - isochromosome - misdivision - longiflorum
Supernumerary (B) chromosomes and small aberrant chromosomes were detected in Lilium hybrids and characterized through genomic in situ hybridization (GISH) and florescence in situ hybridization (FISH). Two small, supernumerary or B chromosomes were detected as extra chromosomes in a tetraploid plant derived from chromosome doubling of a hybrid (2n = 2x = 24) between a cultivar of the Longiflorum (L) and the Trumpet (T) group. When this tetraploid LLTT hybrid was crossed with a triploid LLO hybrid (O = Oriental), the B chromosome was transmitted to 73.4 % of the progenies. Based on GISH and FISH characterization, it was shown that the B chromosome consisted of two identical arms, with 5S rDNA hybridizing to the majority of it, which were flanked by normal telomeres, suggesting that this is an isochromosome. In another population, which is a backcross progeny between a F1 hybrid of Longiflorum x Asiatic (LA) and its Asiatic parent, the former produced functional 2n gametes which resulted in a triploid LAA progeny (2n = 3x = 36), in which three exceptional plants possessed 35 normal chromosomes and a small aberrant chromosome instead of the expected normal number of 36. In all three cases, the small aberrant chromosomes were isochromosomes which had obviously originated during the first backcross generation. These three chromosomes showed normal telomeres and mitosis. In addition, one of the new generated chromosomes possessed two 45S rDNA sites in the proximal positions. These new arisen isochromosomes were proposed to originate from centric breakage and fusion of two short arms of the missing chromosome in three genotypes, respectively, based on the comparison of arm lengths as well as rDNA loci. Their relevance to the origin of Bs is discussed.
Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
Shahin, A. ; Smulders, M.J.M. ; Tuyl, J.M. van; Arens, P.F.P. ; Bakker, F.T. - \ 2014
Frontiers in Plant Science 5 (2014). - ISSN 1664-462X
nuclear ribosomal dna - transcribed spacer region - phylogeny group classification - species trees - reticulate evolution - molecular phylogeny - flowering plants - genus lilium - apg iii - networks
Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium.
Genetic mapping of resistance to Fusarium oxysporum in tulip
Tang, N. ; Lee, T.A.J. van der; Jalink, H. ; Schoor, R. van der; Shahin, A. ; Bijman, P.J.J. ; Tuyl, J.M. van; Arens, P.F.P. - \ 2014
Gewasbescherming 45 (2014)1. - ISSN 0166-6495 - p. 12 - 12.
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