Biomedical subjects

P Lindhout

Publications and source records attributed to P Lindhout.

15 recordsLinked to original sources

PubMed2006

QTL analysis of cadmium and zinc accumulation in the heavy metal hyperaccumulator Thlaspi caerulescens.

Thlaspi caerulescens (Tc; 2n = 14) is a natural Zn, Cd and Ni hyperaccumulator species belonging to the Brassicaceae family. It shares 88% DNA identity in the coding regions with Arabidopsis thaliana (At) (Rigola et al. 2006). Although the physiology of heavy metal (hyper)accumulation has been intensively studied, the molecular genetics are still largely unexplored. We address this topic by constructing a genetic map based on AFLP markers and expressed sequence tags (ESTs). To establish a genetic map, an F(2) population of 129 individuals was generated from a cross between a plant from a Pb/Cd/Zn-contaminated site near La Calamine, Belgium, and a plant from a comparable site near Ganges (GA), France. These two accessions show different degrees of Zn and, particularly, Cd accumulation. We analyzed 181 AFLP markers (of which 4 co-dominant) and 13 co-dominant EST sequences-based markers and mapped them to seven linkage groups (LGs), presumably corresponding to the seven chromosomes of T. caerulescens. The total length of the genetic map is 496 cM with an average density of one marker every 2.5 cM. This map was used for Quantitative Trait Locus (QTL) mapping in the F(2). For Zn as well as Cd concentration in root we mapped two QTLs. Three QTLs and one QTL were mapped for Zn and Cd concentration in shoot, respectively. These QTLs explain 23.8-60.4% of the total variance of the traits measured. We found only one common locus (LG6) for Zn and Cd (concentration in root) and one common locus for shoot and root concentrations of Zn (LG1) and of Cd (LG3). For all QTLs, the GA allele increased the trait value except for two QTLs for Zn accumulation in shoot (LG1 and LG4) and one for Zn concentration in root (LG1).

Cadmium↗

PubMed2005

Parthenocarpic fruit development in tomato.

Parthenocarpic fruit development is a very attractive trait for growers and consumers. In tomato, three main sources of facultative parthenocarpy, pat, pat-2, pat-3/pat-4, are known to have potential applications in agriculture. The parthenocarpic fruit development in these lines is triggered by a deregulation of the hormonal balance in some specific tissues. Auxins and gibberellins are considered as the key elements in parthenocarpic fruit development of those lines. An increased level of these hormones in the ovary can substitute for pollination and trigger fruit development. This has opened up genetic engineering approaches for parthenocarpy that have given promising results, both in quality and quantity of seedless fruit production.

Fruit↗

PubMed2004

The development of lettuce backcross inbred lines (BILs) for exploitation of the Lactuca saligna (wild lettuce) germplasm.

Backcross inbred lines (BILs) were developed in which chromosome segments of Lactuca saligna (wild lettuce) were introgressed into L. sativa (lettuce). These lines were developed by four to five backcrosses and one generation of selfing. The first three generations of backcrossing were random. Marker-assisted selection began in the BC(4) generation and continued until the final set of BILs was reached. A set of 28 lines was selected that together contained 96% of the L. saligna genome. Of these lines, 20 had a single homozygous introgression (BILs), four had two homozygous introgressions (doubleBILs) and four lines had a heterozygous single introgression (preBILs). Segregation ratios in backcross generations were compared to distorted segregation ratios in an F(2) population, and the results indicated that most of the distorted segregations can be explained by genetic effects on pollen- or egg-cell fitness. By means of BIL association mapping we were able to map 12 morphological traits and hundreds of additional amplified fragment length polymorphic (AFLP) markers. The total AFLP map now comprises 757 markers. This set of BILs is very useful for future genetic studies.

Chromosome Mapping↗

PubMed2004

Mapping OI-4, a gene conferring resistance to Oidium neolycopersici and originating from Lycopersicon peruvianum LA2172, requires multi-allelic, single-locus markers.

Lycopersicon peruvianum LA2172 is completely resistant to Oidium neolycopersici, the causal agent of tomato powdery mildew. Despite the large genetic distance between the cultivated tomato and L. peruvianum, fertile F1 hybrids of L. esculentum cv. Money maker x L.peruvianum LA2172 were produced, and a pseudo-F2 population was generated by mating F, half-sibs. The disease tests on the pseudo-F2 population and two BC,families showed that the resistance in LA2172 is governed by one dominant gene, designated as 01-4. In the pseudo-F2 population, distorted segregation was observed, and multi-allelic, single-locus markers were used to display different marker-allele configurations per locus. Para-meters for both distortion and linkage between genetic loci were determined by maximum likelihood estimation, and the necessity of using multi-allelic, single-locus markers was illustrated. Finally, a genetic linkage map of chromosome 6 around the 01-4 locus was constructed by using the pseudo-F2 population.

Ascomycota↗

PubMed2003

A genetic linkage map of the diplosporous chromosomal region in Taraxacum officinale (common dandelion; Asteraceae).

In this study, we mapped the diplosporous chromosomal region in Taraxacum officinale, by using amplified fragment length polymorphism technology (AFLP) in 73 plants from a segregating population. Taraxacum serves as a model system to investigate the genetics, ecology, and evolution of apomixis. The genus includes sexual diploid as well as apomictic polyploid, mostly triploid, plants. Apomictic Taraxacum is diplosporous, parthenogenetic, and has autonomous endosperm formation. Previous studies have indicated that these three apomixis elements are controlled by more than one locus in Taraxacum and that diplospory inherits as a dominant, monogenic trait ( Ddd; DIP). A bulked segregant analysis provided 34 AFLP markers that were linked to DIP and were, together with two microsatellite markers, used for mapping the trait. The map length was 18.6 cM and markers were found on both sides of DIP, corresponding to 5.9 and 12.7 cM, respectively. None of the markers completely co-segregated with DIP. Eight markers were selected for PCR-based marker development, of which two were successfully converted. In contrast to all other mapping studies of apomeiosis to date, our results showed no evidence for suppression of recombination around the DIP locus in Taraxacum. No obvious evidence for sequence divergence between the DIP and non- DIP homologous loci was found, and no hemizygosity at the DIP locus was detected. These results may indicate that apomixis is relatively recent in Taraxacum.

Chromosome Mapping↗

PubMed2003

QTL mapping provides evidence for lack of association of the avoidance of leaf rust in Hordeum chilense with stomata density.

In cereals, rust fungi are among the most harmful pathogens. Breeders usually rely on short-lived hypersensitivity resistance. As an alternative, "avoidance" may be a more durable defence mechanism to protect plants to rust fungi. In Hordeum chilense avoidance is based on extensive wax covering of stomata, which interferes with the induction of appressorium formation by the rust fungi. High avoidance levels are associated with a higher stoma density on the abaxial leaf epidermis. The avoidance level was assessed as the percentage of germ tube/stoma encounters that did not result in appressorium differentiation by Puccinia hordei, the barley leaf rust fungus. One hundred F(2) individuals from the cross between two H. chilense accessions with contrasting levels of avoidance showed a continuous distribution for avoidance of the rust fungus and for stoma density, indicating quantitative inheritance of the traits. No significant correlation was found between avoidance and stoma density in the segregating F(2) population. In order to map quantitative trait loci (QTLs) for both traits, an improved molecular marker linkage map was constructed, based on the F(2) population. The resulting linkage map spanned 620 cM and featured a total of 437 AFLP markers, thirteen RFLPs, four SCARs, nine SSRs, one STS and two seed storage protein markers. It consisted of seven long and two shorter linkage groups, and was estimated to cover 81% of the H. chilense genome. Restricted multiple interval mapping identified two QTLs for avoidance and three QTLs for stoma density in the abaxial leaf surface. The QTLs for avoidance were mapped on chromosome 3 and 5; those for stoma density on chromosomes 1, 3 and 7. Only the two QTLs regions located on chromosome 3 (one for avoidance and the other for stoma density) overlapped. The wild barley H. chilense has a high crossability with other members of the Triticeae tribe. The knowledge on the location of the QTLs responsible for the avoidance trait is a prerequisite to transfer this favourable agronomic trait from H. chilense to cultivated cereal genomes.

Basidiomycota↗

PubMed2002

Genomic regions determining resistance to leaf stripe (Pyrenophora graminea) in barley.

Leaf stripe is a seed-borne disease of barley (Hordeum vulgare) caused by Pyrenophora graminea. Little is known about the genetics of resistance to this pathogen. In the present work, QTL analysis was applied on two recombinant inbred line (RIL) populations derived from two- and six-rowed barley genotypes with different levels of partial resistance to barley leaf stripe. Quantitative trait loci for partial resistance were identified using the composite interval mapping (CIM) method of PLABQTL software, using the putative QTL markers as cofactors. In the L94 x 'Vada' mapping population, one QTL for resistance was detected on chromosome 2H; the same location as the leaf-stripe resistance gene Rdg1 mapped earlier in 'Alf', where it confers complete resistance to the pathogen. An additional minor-effect QTL was identified by further analyses in this segregating population on chromosome 7H. In L94 x C123, two QTLs for resistance were mapped, one each on chromosomes 7H and 2H.

Analysis of Variance↗

PubMed2000

Dispersion of the Cf-4 disease resistance gene in Lycopersicon germplasm.

In the past, numerous Cf genes have been reported in tomato (Lycopersicon esculentum Mill.) that confer resistance against leaf mould (Cladosporium fulvum Cke.). We are interested in genetic variation at Cf loci. Therefore, previously uncharacterized Cf genes were further analysed. Recognition of the AVR4 elicitor, DNA gel blot analysis, PCR analysis and sequencing of part of the Cf-4 locus showed that a large proportion of the accessions tested harboured the Cf-4 resistance gene. We concluded that despite differences in nomenclature, all these accessions harbour the same Cf-4 locus, probably introgressed from the same donor. The origin of the Cf-4 locus and the reasons for discrepancies with earlier reports are discussed.

Blotting, Southern↗

PubMed2000

Characterization and mapping of resistance to Oidium lycopersicum in two Lycopersicon hirsutum accessions: evidence for close linkage of two Ol-genes on chromosome 6 of tomato.

The cultivated tomato is susceptible to powdery mildew (Oidium lycopersicum). Several accessions of wild species are resistant. In this study we describe (i) the genetics and mapping of resistance to O. lycopersicum in G1.1290, one of the resistant accessions in Lycopersicon hirsutum, (ii) fine mapping of Ol-1 originated from L. hirsutum G1.1560, another resistant accession of L. hirsutum, and (iii) tests of allelism for resistance in G1.1290 and G1.1560. Initially, it is demonstrated that the resistance in G1.1290 to O. lycopersicum is controlled by an incompletely dominant gene, designated Ol-3. By using an advanced breeding line (ABL) containing introgression fragment(s) from G1.1290, Ol-3 was found to be associated with several RFLP and SCAR markers on chromosome 6. By using these markers, Ol-3 was mapped between markers TG25/SCAF10 and H9A11 on chromosome 6. Secondly, after testing some F3 lines and their progenies from the cross between L. esculentum cv Moneymaker and L. hirsutum G1.1560, we provided more evidence for the map position of Ol-1 to lie between SCAF10 and H9A11, indicating that Ol-1 and Ol-3 are in the same chromosome region. Thirdly, although allelism tests could not discriminate between Ol-1 and Ol-3, (indirect) evidence suggested that these two genes are not identical. They might instead represent functional genes of a cluster of Ol-homologues.

Alleles↗

PubMed1999

The Cf-ECP2 gene is linked to, but not part of, the Cf-4/Cf-9 cluster on the short arm of chromosome 1 in tomato.

A gene has been identified in tomato, which confers resistance to Cladosporium fulvum through recognition of the pathogenicity factor ECP2. Segregation analysis of F2 and F3 populations showed monogenic dominant inheritance, as for previously reported Cf resistances. The gene has been designated Cf-ECP2. Using several mapping populations, Cf-ECP2 was accurately mapped on chromosome 1, 7.7 cM proximal to TG236 and 6.0 cM distal to TG184. Although Cf-ECP2 is linked to Cf-4, it is not located in the Hcr9 cluster "Milky Way". Therefore, Cf-ECP2 is the first functional Cf homologue on chromosome 1 that does not belong to this Hcr9 cluster. No recombination events between Cf-ECP2 and CT116 have been observed in three populations tested, representing 282 individuals. The low value for the physical distance per cM around CT116 reported previously and the high probability that Cf-ECP2 is also a member of a Hcr9 cluster will facilitate cloning of the locus.

Base Sequence↗

PubMed1998

Successful search for a resistance gene in tomato targeted against a virulence factor of a fungal pathogen.

The interaction between tomato and its fungal pathogen Cladosporium fulvum complies with the gene-for-gene system, in which specific recognition of fungal proteins by plant genotypes with matching resistance genes results in host resistance. Two proteins, ECP1 and ECP2, secreted by C. fulvum during infection, are required for full virulence of the fungus on tomato. We chose the most important virulence factor, ECP2, for a targeted search for hypersensitive response (HR)-based resistance among a collection of tomato genotypes. By screening with recombinant potato virus X that expresses the Ecp2 gene, we identified four lines that respond with HR toward ECP2. The capacity to recognize ECP2 and induce HR is sufficient to confer resistance in tomato against C. fulvum producing ECP2. Resistance is based on a single dominant gene, which we have designated Cf-ECP2, for resistance to C. fulvum through recognition of ECP2. Accordingly, an Ecp2-minus strain created by gene replacement is pathogenic on Cf-ECP2 plants. However, due to lack of ECP2 the mutant strain is only weakly virulent. All strains of a worldwide collection of C. fulvum strains that were tested were found to produce a HR-inducing ECP2 protein. Because the Cf-ECP2 gene operates through recognition of an important virulence factor, we expect it will confer durable resistance against C. fulvum. A similar targeted approach should allow the discovery of new valuable resistance genes in other pathosystems.

Base Sequence↗

PubMed1997

Development of AFLP markers in barley.

To investigate the application of amplified fragment length polymorphism (AFLP) markers in barley, 96 primer combinations were used to generate AFLP patterns with two barley lines, L94 and Vada. With seven primer combinations, only a few intense bands were obtained, probably derived from repeated sequences. With the majority of the remaining 89 primer combinations, on average about 120 amplification products were generated, and the polymorphism rate between the two lines was generally over 18%. Based on the number of amplified products and the polymorphism rate, the 48 best primer combinations were selected and tested on 16 barley lines, again including L94 and Vada. Using a subset of 24 primer combinations 2188 clearly visible bands within the range from 80 to 510 bp were generated; 55% of these showed some degree of polymorphism among the 16 lines. L94 versus Vada showed the highest polymorphism rate (29%) and Proctor versus Nudinka yielded the lowest (12%). The polymorphism rates per primer combination showed little dependence on the barley lines used. Hence the most efficient and informative primer combinations identified for a given pair of lines turned out to be highly efficient when applied to others. Generally, more than 100 common markers (possibly locus specific) among populations or crosses were easily identified by comparing 48 AFLP profiles of the parent lines. The existence of such a large number of markers common to populations will facilitate the merging of molecular marker data and other genetic data into one integrated genetic map of barley.

Chromosome Mapping↗

PubMed1997

Tomato chromosome 1: high resolution genetic and physical mapping of the short arm in an interspecific Lycopersicon esculentum x L. peruvianum cross.

A detailed map of part of the short arm of chromosome 1 proximal to the Cf-4/Cf-9 gene cluster was generated by using an F2 population of 314 plants obtained from the cross between the remotely related species Lycopersicon esculentum and L. peruvianum. Six markers that cosegregate in an L. esculentum x L. pennellii F2 population showed high recombination frequencies in the present interspecific population, spanning an interval of approximately 13 cM. Physical distances between RFLP markers were estimated by pulsed field gel electrophoresis of high-molecular-weight DNA and by identifying YACs that recognized more than one RFLP marker. In this region 1 cM corresponded to 55-110 kb. In comparsion with the value of 730 kb per cM averaged over the entire genome, this reflects the remarkably high recombination frequencies in this region in the hybrid L. esculentum x L. peruvianum progeny population. The present data underline the fact that recombination is not a process that occurs randomly over the entire genome, but can vary dramatically in intensity between chromosomal regions and among populations.

Chromosome Mapping↗

PubMed1995

GATA- and GACA-repeats are not evenly distributed throughout the tomato genome.

This paper describes the distribution of highly polymorphic GATA- and GACA-containing DNA regions in tomato. To study the distribution of these polymorphic regions, a mapping experiment was done. The segregation of 32 GATA- and GACA-containing loci was analyzed in a F2 population from a cross between Lycopersicon esculentum and L. pennellii. From these loci, 28 could be mapped to 8 of the 12 tomato chromosomes. Both the GATA- and GACA-containing loci seem to cluster in the same chromosomal regions. To our knowledge, this is the first report on mapping of GATA- and GACA-containing loci in plants.

Base Sequence↗

PubMed1985

Ribosomes are stalled during in vitro translation of alfalfa mosaic virus RNA 1.

In the presence of plant tRNAs the full-length translation product of alfalfa mosaic virus RNA 1 is produced in rabbit reticulocytes only at low mRNA concentration. At higher mRNA concentration translation is restricted to the 5' half of RNA 1. At high mRNA concentration the full-length product can be formed when additional plant tRNA and glutamine are supplied to the translation mixture. In contrast, in the presence of yeast or calf liver tRNA the translation pattern of alfalfa mosaic virus RNA 1 always results in the synthesis of the full-length product. Pulse-chase experiments in the presence of plant tRNAs show that the ribosomes pause at several positions in the 5' half of RNA 1. The pausing time is different at the different 'halting places'. Protein synthesis is resumed upon addition of glutamine, even when the addition is delayed for more than 3 h after the start of protein synthesis. Only one tRNA species, purified from wheat germ or tobacco, could promote full-length translation of RNA 1. This tRNA can be charged with glutamine. Analysis of the position of glutamine codons on RNA 1 shows a correlation between the positions of the CAA codons and the halting places of the ribosomes. The CAA codon (for any other codon) on its own cannot be responsible for the pausing of the ribosomes, since a variety of RNAs, known to contain all sense codons, are translated efficiently in rabbit reticulocyte lysates in the presence of plant tRNAs. Apparently other elements can restrict decoding of normal codons during protein chain elongation.

Animals↗