Genetic and morphological diversity of okra (Abelmoschus esculentus [L.] Moench.) genotypes and their possible relationships, with particular reference to Greek landraces
Kyriakopoulou, O.G. ; Arens, P.F.P. ; Pelgrom, K.T.B. ; Karapanos, I. ; Bebeli, P. ; Passam, H.C. - \ 2014
Scientia Horticulturae 171 (2014). - ISSN 0304-4238 - p. 58 - 70.
numerical-analysis - germplasm - aflp - collection - cultivars - stability - patterns - distance - markers - plants
Despite its high economic value in many countries (especially in developing regions of the tropics and sub-tropics), okra has received little attention with respect to its source of origin and genetic diversity, particularly at the molecular level. Phenotypic description (morphology, pod characteristics and seed germination) and AFLP (amplified fragment length polymorphism) analysis were performed on Greek and international genotypes. Whereas morphological descriptors did not separate the accessions according to their geographical origin, AFLP analysis revealed a low level (12%) of polymorphism and distinct geographical groupings. Greek germplasm separated into three distinct groups with no overlap between them on the basis of molecular markers. A higher degree of genetic heterogeneity was found (UPGMA analysis) among the accessions of the Boyiatiou group than in the Pylaias group, whereas the occurrence of some common phylogenetic characteristics made separation on the basis of morphology alone difficult. The results from AFLP markers indicate that Greek germplasm constitutes a significant pool of variation with respect to morphological parameters, pod characteristics and seed germinability. Moreover, differences in seed germination among phenotypes may relate to their geographical origin (mainland or islands).
High level of molecular and phenotypic biodiversity in Jatropha curcas from Central America compared to Africa, Asia and South America
Montes Osorio, L.R. ; Torres Salvador, A.F. ; Jongschaap, R.E.E. ; Azurdia, C. ; Berduo, J. ; Trindade, L.M. ; Visser, R.G.F. ; Loo, E.N. van - \ 2014
BMC Plant Biology 14 (2014). - ISSN 1471-2229
net assimilation rate - relative growth-rate - genetic diversity - leaf-area - germplasm collection - biofuel plant - l. accessions - markers - aflp - variability
Background The main bottleneck to elevate jatropha (Jatropha curcas L.) from a wild species to a profitable biodiesel crop is the low genetic and phenotypic variation found in different regions of the world, hampering efficient plant breeding for productivity traits. In this study, 182 accessions from Asia (91), Africa (35), South America (9) and Central America (47) were evaluated at genetic and phenotypic level to find genetic variation and important traits for oilseed production. Results Genetic variation was assessed with SSR (Simple Sequence Repeat), TRAP (Target Region Amplification Polymorphism) and AFLP (Amplified fragment length polymorphism) techniques. Phenotypic variation included seed morphological characteristics, seed oil content and fatty acid composition and early growth traits. Jaccard’s similarity and cluster analysis by UPGM (Unweighted Paired Group Method) with arithmetic mean and PCA (Principle Component Analysis) indicated higher variability in Central American accessions compared to Asian, African and South American accessions. Polymorphism Information Content (PIC) values ranged from 0 to 0.65. In the set of Central American accessions. PIC values were higher than in other regions. Accessions from the Central American population contain alleles that were not found in the accessions from other populations. Analysis of Molecular Variance (AMOVA; P¿
The diploid origins of allopolyploid rose species studied using single nucleotide polymorphism haplotypes flanking a microsatellite repeat
Zhang, J. ; Esselink, G. ; Che, D. ; Fougère-Danezan, M. ; Arens, P. ; Smulders, M.J.M. - \ 2013
Journal of Horticultural Science and Biotechnology 88 (2013)1. - ISSN 1462-0316 - p. 85 - 92.
genetic diversity - genus rosa - phylogenetic analysis - dna-sequences - matk - aflp - lycopersicon - accessions - cultivars - varieties
The taxonomy of the genus Rosa is complex, not least because of hybridisations between species.We aimed to develop a method to connect the diploid Rosa taxa to the allopolyploid taxa to which they contributed, based on the sharing of haplotypes. For this we used an SNPSTR marker, which combines a short tandem repeat (STR; microsatellite) marker with single nucleotide polymorphisms (SNPs) in the flanking sequences. In total, 53 different sequences (haplotypes) were obtained for the SNPSTR marker, Rc06, from 20 diploid and 35 polyploid accessions from various species of Rosa. Most accessions of the diploid species had only one allele, while accessions of the polyploid species each contained two-to-five different alleles.Twelve SNPs were detected in the flanking sequences, which alone formed a total of 18 different haplotypes. A maximum likelihood dendrogram revealed five groups of haplotypes. Diploid species in the same Section of the genus Rosa contained SNP haplotypes from only one haplotype group. In contrast, polyploid species contained haplotypes from different haplotype groups. Identical SNP haplotypes were shared between polyploid species and diploid species from more than one Section of the genus Rosa. There were three different polymorphic repeat regions in the STR region. The STR repeat contained eight additional SNPs, but these contributed little to the resolution of the haplotype groups. Our results support hypotheses on diploid Rosa species that contributed to polyploid taxa. Finding different sets of haplotypes in different groups of species within the Sections Synstylae and Pimpinellifoliae supports the hypothesis that these may be paraphyletic.
The mode of inheritance in tetraploid cut roses
Koning-Boucoiran, C.F.S. ; Gitonga, V.W. ; Yan, Z. ; Dolstra, O. ; Linden, C.G. van der; Schoot, J. van der; Uenk-Stunnenberg, G.E. ; Verlinden, K. ; Smulders, M.J.M. ; Krens, F.A. ; Maliepaard, C.A. - \ 2012
Theoretical and Applied Genetics 125 (2012)3. - ISSN 0040-5752 - p. 591 - 607.
genetic diversity analysis - microsatellite markers - morphological markers - diploid fragaria - linkage maps - allopolyploids - polyploids - resistance - plant - aflp
Tetraploid hybrid tea roses (Rosa hybrida) represent most of the commercial cultivars of cut roses and form the basis for breeding programmes. Due to intensive interspecific hybridizations, modern cut roses are complex tetraploids for which the mode of inheritance is not exactly known. The segregation patterns of molecular markers in a tetraploid mapping population of 184 genotypes, an F1 progeny from a cross of two heterozygous parents, were investigated for disomic and tetrasomic inheritance. The possible occurrence of double reduction was studied as well. We can exclude disomic inheritance, but while our observations are more in line with a tetrasomic inheritance, we cannot exclude that there is a mixture of both inheritance modes. Two novel parental tetraploid linkage maps were constructed using markers known from literature, combined with newly generated markers. Comparison with the integrated consensus diploid map (ICM) of Spiller et al. (Theor Appl Genet 122:489–500, 2010) allowed assigning numbers to each of the linkage groups of both maps and including small linkage groups. So far, the possibility of using marker-assisted selection in breeding of tetraploid cut roses and of other species with a tetrasomic or partly tetrasomic inheritance, is still limited due to the difficulties in establishing marker-trait associations. We used these tetraploid linkage maps to determine associations between markers, two morphological traits and powdery mildew resistance. The knowledge on inheritance and marker-trait associations in tetraploid cut roses will be of direct use to cut rose breeding.
Dynamics of senescence-related QTLs in potato
Hurtado Lopez, P.X. ; Schnabel, S.K. ; Zaban, A. ; Vetelainen, M. ; Virtanen, E. ; Eilers, P. ; Eeuwijk, F.A. van; Visser, R.G.F. ; Maliepaard, C.A. - \ 2012
Euphytica 183 (2012)3. - ISSN 0014-2336 - p. 289 - 302.
solanum-tuberosum - model - growth - temperature - resistance - gene - chromosome-4 - markers - aflp
The study of quantitative trait’s expression over time helps to understand developmental processes which occur in the course of the growing season. Temperature and other environmental factors play an important role. The dynamics of haulm senescence was observed in a diploid potato mapping population in two consecutive years (2004 and 2005) under field conditions in Finland. The available time series data were used in a smoothed generalized linear model to characterize curves describing the senescence development in terms of its onset, mean and maximum progression rate and inflection point. These characteristics together with the individual time points were used in a Quantitative trait loci (QTL) analysis. Although QTLs occurring early in the senescence process coincided with QTLs for onset of senescence, the analysis of the time points made it difficult to study senescence as a continuous trait. Characteristics estimated from the senescence curve allowed us to study it as a developmental process and provide a meaningful biological interpretation to the results. Stable QTLs in the two experimental years were identified for progression rate and year-specific QTLs were detected for onset of senescence and inflection point. Specific interactions between loci controlling senescence development were also found. Epistatic interaction between QTLs on chromosomes 4, 5 and 7 were detected in 2004 and pleiotopic effects of QTLs on chromosomes 3 and 4 were observed in 2005.
Botanical DNA evidence in criminal cases: Knotgrass (Polygonum aviculare L.) as a model species
Koopman, W.J.M. ; Kuiper, I. ; Klein Geltink, D.J.A. ; Sabatino, G.J.H. ; Smulders, M.J.M. - \ 2012
Forensic Science International Genetics 6 (2012)3. - ISSN 1872-4973 - p. 366 - 374.
populus-nigra l. - cannabis-sativa - phenotypic plasticity - self-incompatibility - genetic diversity - mating systems - markers - plants - aflp - identification
The possibilities and strategies for using DNA characteristics to link a botanical sample to a specific source plant or location vary with its breeding system. For inbreeding species, which often form small patches of identical genotypes, knotgrass (Polygonum aviculare L.) is a suitable model species because of its (1) occurrence in a wide range of natural environments, (2) abundant presence in pieces of evidence, and (3) ease in molecular processing. The value of knotgrass for forensic casework was demonstrated using data from a homicide case. Using the DNA fingerprinting technique AFLP® we were able to identify the knotgrass population at the crime site as the most likely origin of the botanical evidence. We expect that the development of tailored marker systems for knotgrass and other frequently occurring (model) species will considerably accelerate the use of botanical DNA evidence in criminal cases
A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome
Boer, J.M. de; Borm, T.J.A. ; Jesse, T. ; Brugmans, B.W. ; Tang, X. ; Bryan, G.J. ; Bakker, J. ; Eck, H.J. van; Visser, R.G.F. - \ 2011
BMC Genomics 12 (2011). - ISSN 1471-2164 - 60 p.
quantitative trait loci - candidate genes - disease resistance - linkage map - tomato - aflp - solanum - markers - dna - construction
Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). Results First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. Conclusions The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
High-resolution amplified fragment length polymorphism typing of Lactococcus lactis strains enables identification of genetic markers for subspecies-related phenotypes
Erkus Kütahya, O. ; Starrenburg, M.J.C. ; Rademaker, J.L.W. ; Klaassen, C.H.W. ; Hylckama Vlieg, J.E.T. van; Smid, E.J. ; Kleerebezem, M. - \ 2011
Applied and Environmental Microbiology 77 (2011)15. - ISSN 0099-2240 - p. 5192 - 5198.
complete genome sequence - acid bacteria - streptococcus-lactis - genus lactococcus - cremoris - aflp - diversity - dairy - nov
A high-resolution amplified fragment length polymorphism (AFLP) methodology was developed to achieve the delineation of closely related Lactococcus lactis strains. The differentiation depth of 24 enzyme-primer-nucleotide combinations was experimentally evaluated to maximize the number of polymorphisms. The resolution depth was confirmed by performing diversity analysis on 82 L. lactis strains, including both closely and distantly related strains with dairy and nondairy origins. Strains clustered into two main genomic lineages of L. lactis subsp. lactis and L. lactis subsp. cremoris type-strain-like genotypes and a third novel genomic lineage rooted from the L. lactis subsp. lactis genomic lineage. Cluster differentiation was highly correlated with small-subunit rRNA homology and multilocus sequence analysis (MLSA) studies. Additionally, the selected enzyme-primer combination generated L. lactis subsp. cremoris phenotype-specific fragments irrespective of the genotype. These phenotype-specific markers allowed the differentiation of L. lactis subsp. lactis phenotype from L. lactis subsp. cremoris phenotype strains within the same L. lactis subsp. cremoris type-strain-like genomic lineage, illustrating the potential of AFLP for the generation of phenotype-linked genetic markers.
Authenticity of old cultivars in genebank collections: a case study on lettuce
Wouw, M.J. van de; Treuren, R. van; Hintum, T.J.L. van - \ 2011
Crop Science 51 (2011)2. - ISSN 0011-183X - p. 736 - 746.
genenbanken - slasoorten - aflp - oude plantenrassen - ex-situ conservering - cultivarauthenticiteit - lactuca sativa - rassen (planten) - cultivars - gene banks - lettuces - amplified fragment length polymorphism - old varieties - ex situ conservation - cultivar authenticity - lactuca sativa - varieties - cultivars - genetic diversity - maintenance - accessions - longevity - level - l.
Ex situ collections in genebanks conserve many old cultivars that had disappeared from mainstream agriculture before modern genebanks were established. The collections incorporated cultivars from many sources, such as botanical gardens and working collections, sometimes with little further information on their origin. Many old cultivars with identical or synonymous names are maintained in multiple collections and often more than once within collections. This research investigates the authenticity of old cultivars in genebanks using a large lettuce (Lactuca sativa L.) collection as a case study. Accessions presumed to be identical, based on the cultivar names accompanying the accessions, were compared for their DNA marker profiles, based on amplified fragment length polymorphisms (AFLPs). Using the genetic similarity of these accessions, the probability of authenticity of the old cultivars maintained in the collection was estimated. Separate analyses were done for different classes of cultivars, on the basis of the year of release or the donor history of the cultivar. The two largest cultivar groups within the collection, Sans Rivale à Graine Blanche and Maikönig, were analyzed in detail. Nonauthenticity of the investigated cultivars appeared to be high. This was especially true for the oldest cultivars, but even for the cultivars released from the 1960s to 1990 it was estimated that approximately 10% was not authentic. Recommendations to improve authenticity of cultivars in ex situ collections were presented
Microbiota of cocoa powder with particular reference to aerobic thermoresistant spore-formers
Líma, L.J.R. ; Kamphuis, H.J. ; Nout, M.J.R. ; Zwietering, M.H. - \ 2011
Food Microbiology 28 (2011)3. - ISSN 0740-0020 - p. 573 - 582.
bacillus-subtilis - heat-resistance - sp-nov - aflp - heterogeneity - bacteria - sequence - strains - milk - rna
The microbiological criteria of commercial cocoa powder are defined in guidelines instituted by the cocoa industry. Twenty-five commercial samples were collected with the aim of assessing the compliance with the microbiological quality guidelines and investigating the occurrence and properties of aerobic Thermoresistant Spores (ThrS). Seventeen samples complied with the guidelines, but one was positive for Salmonella, five for Enterobacteriaceae and two had mould levels just exceeding the maximum admissible level. The treatment of the cocoa powder suspensions from 100 °C to 170 °C for 10 min, revealed the presence of ThrS in 36% of the samples. In total 61 ThrS strains were isolated, of which the majority belonged to the Bacillus subtilis complex (65.6%). Strains resporulation and spore crops inactivation at 110 °C for 5 min showed a wide diversity of heat-resistance capacities. Amplified fragment length polymorphism analysis revealed not only a large intraspecies diversity, but also different clusters of heat-resistant spore-forming strains. The heat-resistance of spores of six B. subtilis complex strains was further examined by determination of their D and z-values. We concluded that B. subtilis complex spores, in particular those from strain M112, were the most heat-resistant and these may survive subsequent preservation treatments, being potentially problematic in food products, such as chocolate milk
Diversity between and within farmers’ varieties of tomato from Eritrea
Asgedom, S. ; Vosman, B. ; Esselink, D. ; Struik, P.C. - \ 2011
African journal of biotechnology 10 (2011)12. - ISSN 1684-5315 - p. 2193 - 2200.
simple sequence repeat - ssr-markers - lycopersicon-esculentum - genetic-variation - polymorphic dna - identification - regions - plants - aflp - l.
Tomato yields in Eritrea are low (15 Mg/ha) compared with 19 Mg/ha in Africa and 27 Mg/ha worldwide. This is partly caused by poor quality of varieties used. This study analysed the diversity among and heterogeneity within farmers’ varieties of tomato from Eritrea and compared these varieties with other African and Italian varieties. Fifteen simple sequence repeat (SSR) markers were used for the genetic analysis. Genetic similarities among the varieties were calculated and an Unweighted Pair Group Method with Arithmetic Mean analysis was performed. Furthermore, individual plants of varieties were genotyped to evaluate uniformity within varieties. A high degree of diversity was observed among the Eritrean varieties. Thirteen out of the 15 SSRs were polymorphic, with 2 to 5 alleles per marker. The dendrogram showed two major types of varieties: San-Marzano and Marglob. Eritrean varieties were closely related to old Italian varieties in both types. Analysis of the within-variety variation showed that the Eritrean tomato genotypes were less uniform than the other varieties, probably because of deliberate mixing. A survey among farmers showed that some of them purposely mixed seeds to prolong the harvesting period, for yield stability and stress tolerance. Farmers value ‘new material’ as a source of influx
The patterns of population differentiation in a Brassica rapa core collection
Pino del Carpio, D. ; Basnet, R.K. ; Vos, R.C.H. de; Maliepaard, C.A. ; Visser, R.G.F. ; Bonnema, A.B. - \ 2011
Theoretical and Applied Genetics 122 (2011)6. - ISSN 0040-5752 - p. 1105 - 1118.
genetic diversity - morphological traits - l. - association - aflp - microsatellites - spectroscopy - metabolomics - frequencies - landraces
With the recent advances in high throughput profiling techniques the amount of genetic and phenotypic data available has increased dramatically. Although many genetic diversity studies combine morphological and genetic data, metabolite profiling has yet to be integrated into these studies. For our study we selected 168 accessions representing the different morphotypes and geographic origins of Brassica rapa. Metabolite profiling was performed on all plants of this collection in the youngest expanded leaves, 5 weeks after transplanting and the same material was used for molecular marker profiling. During the same season a year later, 26 morphological characteristics were measured on plants that had been vernalized in the seedling stage. The number of groups and composition following a hierarchical clustering with molecular markers was highly correlated to the groups based on morphological traits (r = 0.420) and metabolic profiles (r = 0.476). To reveal the admixture levels in B. rapa, comparison with the results of the programme STRUCTURE was needed to obtain information on population substructure. To analyze 5546 metabolite (LC–MS) signals the groups identified with STRUCTURE were used for random forests classification. When comparing the random forests and STRUCTURE membership probabilities 86% of the accessions were allocated into the same subgroup. Our findings indicate that if extensive phenotypic data (metabolites) are available, classification based on this type of data is very comparable to genetic classification. These multivariate types of data and methodological approaches are valuable for the selection of accessions to study the genetics of selected traits and for genetic improvement programs, and additionally provide information on the evolution of the different morphotypes in B. rapa
Development of microsatellite markers for identifying Brazilian coffee arabica varieties
Vieira, E.S.N. ; Pinho, E.V.R. Von; Carvalho, M.G.G. ; Esselink, G. ; Vosman, B. - \ 2010
Genetics and Molecular Biology 33 (2010)3. - ISSN 1415-4757 - p. 507 - 514.
sequence repeat markers - genetic diversity - molecular characterization - chloroplast dna - rapd markers - identification - cultivars - aflp - introgression - canephora
Microsatellite markers, also known as SSRs (Simple Sequence Repeats), have proved to be excellent tools for identifying variety and determining genetic relationships. A set of 127 SSR markers was used to analyze genetic similarity in twenty five Coffea arabica varieties. These were composed of nineteen commercially important Brazilians and six interspecific hybrids of Coffea arabica, Coffea canephora and Coffea liberica. The set used comprised 52 newly developed SSR markers derived from microsatellite enriched libraries, 56 designed on the basis of coffee SSR sequences available from public databases, 6 already published, and 13 universal chloroplast microsatellite markers. Only 22 were polymorphic, these detecting 2-7 alleles per marker, an average of 2.5. Based on the banding patterns generated by polymorphic SSR loci, the set of twenty-five coffee varieties were clustered into two main groups, one composed of only Brazilian varieties, and the other of interspecific hybrids, with a few Brazilians. Color mutants could not be separated. Clustering was in accordance with material genealogy thereby revealing high similarity
Distribution of genetic diversity in wild European populations of prickly lettuce (Lactuca serriola): implications for plant genetic resources management
Wiel, C.C.M. van de; Sretenovic Rajicic, T. ; Treuren, R. van; Dehmer, K.J. ; Linden, C.G. van der; Hintum, T.J.L. van - \ 2010
Plant genetic resources: characterization and utilization 8 (2010)2. - ISSN 1479-2621 - p. 171 - 181.
molecular markers - linkage map - asteraceae - evolution - netherlands - acquisition - cluster - spp. - aflp - l.
Genetic variation in Lactuca serriola, the closest wild relative of cultivated lettuce, was studied across Europe from the Czech Republic to the United Kingdom, using three molecular marker systems, simple sequence repeat (SSR, microsatellites), AFLP and nucleotide-binding site (NBS) profiling. The ‘functional’ marker system NBS profiling, targeting disease resistance genes of the NBS/LRR family, did not show marked differences in genetic diversity parameters to the other systems. The autogamy of the species resulted in low observed heterozygosity and high population differentiation. Intra-population variation ranged from complete homogeneity to nearly complete heterogeneity. The highest genetic diversity was found in central Europe. The SSR results were compared to SSR variation screened earlier in the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN). In the UK, practically only a single SSR genotype was found. This genotype together with a few other common SSR genotypes comprised a large part of the plants sampled on the continent. Among the ten most frequent SSR genotypes observed, eight were already present in the CGN collection. Overall, the CGN collection appears to already have a fair representation of genetic variation from NW Europe. The results are discussed in relation to sampling strategies for improving genebank collections of crop wild relatives.
Genetic structure of European accessions of Solanum dulcamara L. (Solanaceae)
Golas, T.M. ; Feron, R.M.C. ; Berg, R.G. van den; Weerden, G.M. van der; Mariani, C. ; Allefs, J.J.H.M. - \ 2010
Plant Systematics and Evolution 285 (2010)1-2. - ISSN 0378-2697 - p. 103 - 110.
phytophthora-infestans - aflp - populations - nigrum
Solanum dulcamara (bittersweet) is one of the few native species of Solanum present in Europe. It is a common weed that occupies a wide range of habitats and is often found in the direct vicinity of cultivated potatoes (Solanum tuberosum), where it could transmit diseases. A broad sampling of European S. dulcamara accessions was carried out to gain insight into the population structure and crossing preferences of this species. Three amplified fragment length polymorphism (AFLP®) primer combinations generating 288 polymorphic fragments were used to analyze 79 bittersweet accessions (245 individuals). Dendrograms revealed a low level of genetic polymorphism in the bittersweet populations, caused partially by the out-crossing nature of this species
Genetic diversity and genetic similarities between Iranian rose species
Samiei, L. ; Naderi, R. ; Khalighi, A. ; Shahnejat-Bushehri, A.A. ; Mozaffarian, V. ; Esselink, G.D. ; Kazempour Osaloo, S. ; Smulders, M.J.M. - \ 2010
Journal of Horticultural Science and Biotechnology 85 (2010)3. - ISSN 1462-0316 - p. 231 - 237.
damascena mill. accessions - microsatellite analysis - phylogenetic-relationships - genus rosa - markers - aflp - ssr - identification - differentiation - varieties
Wild rose species were collected from different regions of Iran for a rose breeding programme. They included accessions from Rosa persica, R. foetida, R. pimpinellifolia, R. hemisphaerica, R. canina, R. iberica, R. damascena, R. beggeriana, and R. orientalis. Ten microsatellite (simple sequence repeat; SSR) markers were used to analyse the genetic variation among these rose species. The SSR markers amplified alleles in all species, even if they were from different sections within the genus. An unweighted pair group method cluster analysis (UPGMA) based on similarity values revealed five main Groups. The data showed no support for any distinction between R. canina and R. iberica, as all the accessions were placed in one Group, and accessions of these two species were more closely-related to each other within a Province than to accessions of the same species in other Provinces. Accessions of sect. Pimpinellifoliae were combined with plants from sect. Rosa and Cinnamomeae in two different Groups. Genetically, R. persica clustered distinctly from all others, with few alleles shared with the other taxa. We discuss the use of SSR markers for phylogenetic analysis when these markers are amplified in all species of a genus
On some surprising statistical properties of a DNA fingerprinting technique called AFLP
Gort, G. - \ 2010
Wageningen University. Promotor(en): A. Stein; Fred van Eeuwijk. - [S.l. : S.n. - ISBN 9789085855378 - 154
planten - statistische analyse - dna-fingerprinting - genomen - biometrie - moleculaire genetica - dna - aflp - biostatistiek - toegepaste statistiek - plants - statistical analysis - dna fingerprinting - genomes - biometry - molecular genetics - dna - amplified fragment length polymorphism - biostatistics - applied statistics
AFLP is a widely used DNA fingerprinting technique, resulting in band absence - presence profiles, like a bar code. Bands represent DNA fragments, sampled from the genome of an individual plant or other organism. The DNA fragments travel through a lane of an electrophoretic gel or microcapillary system, and are separated by length, with shorter fragments traveling further. Multiple individuals are simultaneously fingerprinted on a gel. One of the applications of AFLP is the estimation of genetic similarity between individuals, e.g. in diversity and phylogenetic studies. In that case, profiles of two individuals are compared, and the fraction of shared (comigrating) bands is calculated, e.g. using the Dice similarity coefficient. Two comigrating bands may share the same fragment, but band sharing could also be due to chance, if two equally sized, but different fragments are amplified. This is called homoplasy. Homoplasy biases similarity coefficients. Homoplasy could also occur within a lane, if two different fragments of equal length are amplified, resulting in a single band. We call this collision. The main objective of this thesis is the study of collision and homoplasy in AFLP. The length distribution of AFLP fragments plays an important role. This distribution is highly skewed with more abundant short fragments. By simulation the expected similarity for unrelated genotypes is calculated. As much as 40% of the bands may be shared by chance in case of profiles with 120 bands. The collision problem is analogous to the birthday problem, which has a surprising solution. The collision problem is even more extreme, making it even more surprising. Profiles with only 19 bands contain collision(s) with probability 1/2. These findings have consequences for practice. In some cases it is better to prevent the occurrence of collisions by decreasing the number of bands, in other cases a correction for homoplasy and collision is preferred. Modified similarity coefficients are proposed, that estimate the fraction of homologous fragments, correcting for homoplasy and collision. Partially related to homoplasy and collision, we study the codominant scoring of AFLP in association panels. Examples of AFLP in lettuce and tomato serve as illustrations.
Comparison of anonymous and targeted molecular markers for the estimation of genetic diversity in ex situ conserved Lactuca
Treuren, R. van; Hintum, T.J.L. van - \ 2009
Theoretical and Applied Genetics 119 (2009)7. - ISSN 0040-5752 - p. 1265 - 1279.
sativa l. - lettuce - aflp - polymorphism - genome - populations - collection - resistance - ssap - srap
The anonymous marker systems microsatellites (simple sequence repeats), amplified fragment length polymorphisms and sequence-specific amplified polymorphisms were compared with the targeted marker systems sequence-related amplified polymorphisms, target region amplification polymorphisms and nucleotide binding site profiling for their ability to describe the genetic diversity in a selected set of 80 Lactuca accessions. The accessions were also described morphologically, and all characterisation methods were evaluated against the genetic diversity assessed by a panel of three crop experts. The morphological data showed a low level of association with the molecular data, and did not display a consistently better relationship with the experts’ assessments in comparison with the molecular data. In general, the diversity described by the targeted molecular markers did not differ markedly from that of the anonymous markers, resulting in only slight differences in performance when related to the expert-based assessments. It was argued that markers targeted to specific gene sequences may still behave as anonymous markers and that the type of marker system used is irrelevant when at low taxonomic levels a clear genetic structure is absent due to intensive breeding activities
Mapping markers linked to porcine salmonellosis susceptibility
Galina-Pantoja, L. ; Siggens, K. ; Schriek, M.G.M. van; Heuven, H.C.M. - \ 2009
Animal Genetics 40 (2009)6. - ISSN 0268-9146 - p. 795 - 803.
quantitative trait loci - differential gene-expression - population-structure - natural-resistance - linkage map - aflp - choleraesuis - infection - pig - polymorphisms
The goal of this study was to identify pig chromosomal regions associated with susceptibility to salmonellosis. Genomic DNA from pig reference populations with differences in susceptibility to Salmonella enterica serovar Choleraesuis as quantified by spleen and liver bacterial colonization at day 7 post-infection (dpi; Van Diemen et al. 2002) was used. These samples belonged to the offspring of a sire thought to be heterozygous for genes involved in susceptibility to salmonellosis. Amplified fragment length polymorphism (AFLP) markers were created and used to determine associations with spleen or bacterial counts at 7 dpi. To position linked markers, two mapping populations, the Roslin and Uppsala PiGMaP pedigrees were used to create an integrated map which included the AFLP markers associated with salmonellosis. Twenty-six AFLP markers located in 14 different chromosomal regions in the porcine genome were found to be significantly associated with susceptibility (Chi-square P <0.05). More than one linked marker was found on chromosomes 1, 7, 13, 14 and 18. It is likely that these regions contain genes involved in Salmonella susceptibility. Regions on chromosomes 1, 7 and 14 were significantly associated with Salmonella counts in the liver and regions on chromosomes 11, 13 and 18 with counts in spleen. The identification of these chromosomal regions highlights specific areas to search for candidate genes that may be involved in innate or adaptive immunity. Further investigation into these chromosomal regions would be useful to improve our understanding of host responses to infection with this widespread pathogen.
Avirulentiegenen in Phytophthora infestans, de veroorzaker van de aardappelziekte
Guo, J. ; Govers, F. - \ 2009
Gewasbescherming 40 (2009)5. - ISSN 0166-6495 - p. 246 - 249.
aardappelen - phytophthora infestans - noord-china - ziekteresistentie - merken van genen - diversiteit - aflp - wetenschappelijk onderzoek - potatoes - phytophthora infestans - northern china - disease resistance - gene tagging - diversity - amplified fragment length polymorphism - scientific research
Een proefschrift van Wageningen Universiteit beschrijft het karteren en kloneren van Avr-genen in Phytophthora infestans. Ook is de fenotypische en genotypische diversiteit in P. infestans-veldisolaten in Noord China onderzocht