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.

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    Epigenetic Basis of Morphological Variation and Phenotypic Plasticity in Arabidopsis thaliana
    Kooke, R. ; Johannes, F. ; Wardenaar, R. ; Becker, F.F.M. ; Etcheverry, M. ; Colot, V. ; Vreugdenhil, D. ; Keurentjes, J.J.B. - \ 2015
    The Plant Cell 27 (2015)2. - ISSN 1040-4651 - p. 337 - 348.
    quantitative trait loci - dna methylation - transcription factor - qtl analysis - population - plant - inheritance - stability - evolution - performance
    Epigenetics is receiving growing attention in the plant science community. Epigenetic modifications are thought to play a particularly important role in fluctuating environments. It is hypothesized that epigenetics contributes to plant phenotypic plasticity because epigenetic modifications, in contrast to DNA sequence variation, are more likely to be reversible. The population of decrease in DNA methylation 1-2 (ddm1-2)-derived epigenetic recombinant inbred lines (epiRILs) in Arabidopsis thaliana is well suited for studying this hypothesis, as DNA methylation differences are maximized and DNA sequence variation is minimized. Here, we report on the extensive heritable epigenetic variation in plant growth and morphology in neutral and saline conditions detected among the epiRILs. Plant performance, in terms of branching and leaf area, was both reduced and enhanced by different quantitative trait loci (QTLs) in the ddm1-2 inherited epigenotypes. The variation in plasticity associated significantly with certain genomic regions in which the ddm1-2 inherited epigenotypes caused an increased sensitivity to environmental changes, probably due to impaired genetic regulation in the epiRILs. Many of the QTLs for morphology and plasticity overlapped, suggesting major pleiotropic effects. These findings indicate that epigenetics contributes substantially to variation in plant growth, morphology, and plasticity, especially under stress conditions
    Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought
    El-Soda, M. ; Kruijer, Willem ; Malosetti, M. ; Koornneef, M. ; Aarts, M.G.M. - \ 2015
    Plant, Cell & Environment 38 (2015)3. - ISSN 0140-7791 - p. 585 - 599.
    genome-wide association - natural variation - abiotic stress - inbred lines - qtl analysis - growth - reveals - protein - genetics - adaptation
    Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short-day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis accessions using genome-wide association (GWA) mapping, and conventional linkage analysis of a recombinant inbred line (RIL) population. Results showed significant genotype by environment interaction (G×E) for all traits in response to different watering regimes. For the RIL population, the observed G×E was reflected in 17 QTL by environment interactions (Q×E), while 17 additional QTLs were mapped not showing Q×E. GWA mapping identified 58 single nucleotide polymorphism (SNPs) associated with loci displaying Q×E and an additional 16 SNPs associated with loci not showing Q×E. Many candidate genes potentially underlying these loci were suggested. The genes for RPS3C and YLS7 were found to contain conserved amino acid differences when comparing Arabidopsis accessions with strongly contrasting drought response phenotypes, further supporting their candidacy. One of these candidate genes co-located with a QTL mapped in the RIL population
    A Genome-Wide Association Study Reveals Dominance Effects on Number of Teats in Pigs
    Lopes, M.S. ; Bastiaansen, J.W.M. ; Harlizius, B. ; Knol, E.F. ; Bovenhuis, H. - \ 2014
    PLoS ONE 9 (2014)8. - ISSN 1932-6203 - 8 p.
    quantitative trait loci - milk fatty-acids - resource population - affecting reproduction - carcass composition - genetic-basis - dairy-cattle - meat quality - qtl analysis - meishan
    Dominance has been suggested as one of the genetic mechanisms explaining heterosis. However, using traditional quantitative genetic methods it is difficult to obtain accurate estimates of dominance effects. With the availability of dense SNP (Single Nucleotide Polymorphism) panels, we now have new opportunities for the detection and use of dominance at individual loci. Thus, the aim of this study was to detect additive and dominance effects on number of teats (NT), specifically to investigate the importance of dominance in a Landrace-based population of pigs. In total, 1,550 animals, genotyped for 32,911 SNPs, were used in single SNP analysis. SNPs with a significant genetic effect were tested for their mode of gene action being additive, dominant or a combination. In total, 21 SNPs were associated with NT, located in three regions with additive (SSC6, 7 and 12) and one region with dominant effects (SSC4). Estimates of additive effects ranged from 0.24 to 0.29 teats. The dominance effect of the QTL located on SSC4 was negative (-0.26 teats). The additive variance of the four QTLs together explained 7.37% of the total phenotypic variance. The dominance variance of the four QTLs together explained 1.82% of the total phenotypic variance, which corresponds to one-fourth of the variance explained by additive effects. The results suggest that dominance effects play a relevant role in the genetic architecture of NT. The QTL region on SSC7 contains the most promising candidate gene: VRTN. This gene has been suggested to be related to the number of vertebrae, a trait correlated with NT.
    Normal adult survival but reduced Bemisia tabaci oviposition rate on tomato lines carrying an introgression from S. habrochaites
    Lucatti, A.F. ; Meijer-Dekens, R.G. ; Mumm, R. ; Visser, R.G.F. ; Vosman, B.J. ; Heusden, A.W. van - \ 2014
    BMC Genetics 15 (2014). - ISSN 1471-2156 - 23 p.
    nematode-resistance gene - hirsutum-f-glabratum - whitefly trialeurodes-vaporariorum - mediated insect resistance - wild tomato - lycopersicon-pennellii - glandular trichomes - feeding-behavior - potato aphid - qtl analysis
    Background Host plant resistance has been proposed as one of the most promising approaches in whitefly management. Already in 1995 two quantitative trait loci (Tv-1 and Tv-2) originating from S. habrochaites CGN1.1561 were identified that reduced the oviposition rate of the greenhouse whitefly (Trialeurodes vaporariorum). After this first study, several others identified QTLs affecting whitefly biology as well. Generally, the QTLs affecting oviposition were highly correlated with a reduction in whitefly survival and the presence of high densities of glandular trichomes type IV. The aim of our study was to further characterize Tv-1 and Tv-2, and to determine their role in resistance against Bemisia tabaci. Results We selected F2 plants homozygous for the Tv-1 and Tv-2 QTL regions and did three successive backcrosses without phenotypic selection. Twenty-three F2BC3 plants were phenotyped for whitefly resistance and differences were found in oviposition rate of B. tabaci. The F2BC3 plants with the lowest oviposition rate had an introgression on Chromosome 5 in common. Further F2BC4, F2BC4S1 and F2BC4S2 families were developed, genotyped and phenotyped for adult survival, oviposition rate and trichome type and density. It was possible to confirm that an introgression on top of Chr. 5 (OR-5), between the markers rs-2009 and rs-7551, was responsible for reducing whitefly oviposition rate. Conclusion We found a region of 3.06 Mbp at the top of Chr. 5 (OR-5) associated with a reduction in the oviposition rate of B. tabaci. This reduction was independent of the presence of the QTLs Tv- 1 and Tv-2 as well as of the presence of trichomes type IV. The OR-5 locus will provide new opportunities for resistance breeding against whiteflies, which is especially relevant in greenhouse cultivation.
    Linking ecophysiological modelling with quantitative genetics to support marker-assisted crop design for improved yields of rice (Oryza sativa) under drought stress
    Gu Junfei, Junfei ; Yin, X. ; Zhang, C. ; Wang, H. ; Struik, P.C. - \ 2014
    Annals of Botany 114 (2014)3. - ISSN 0305-7364 - p. 499 - 511.
    recombinant inbred lines - trait locus analysis - qtl analysis - physiological traits - flowering phenology - introgression lines - simulation-models - brassica-oleracea - systems biology - quality traits
    * Background and Aims: Genetic markers can be used in combination with ecophysiological crop models to predict the performance of genotypes. Crop models can estimate the contribution of individual markers to crop performance in given environments. The objectives of this study were to explore the use of crop models to design markers and virtual ideotypes for improving yields of rice (Oryza sativa) under drought stress. * Methods: Using the model GECROS, crop yield was dissected into seven easily measured parameters. Loci for these parameters were identified for a rice population of 94 introgression lines (ILs) derived from two parents differing in drought tolerance. Marker-based values of ILs for each of these parameterswere estimated fromadditive allele effects of the loci, and were fed to the model in order to simulate yields of the ILs grown under well-watered and drought conditions and in order to design virtual ideotypes for those conditions. * Key Results: To account for genotypic yield differences, itwas necessary to parameterize the model for differences in an additional trait ‘total crop nitrogen uptake’ (Nmax) among the ILs. Genetic variation in Nmax had the most significant effect on yield; five other parameters also significantly influenced yield, but seed weight and leaf photosynthesis did not. Using the marker-based parameter values, GECROS also simulated yield variation among 251 recombinant inbred lines of the same parents. The model-based dissection approach detected more markers than the analysis using only yield per se. Model-based sensitivity analysis ranked all markers for their importance in determining yield differences among the ILs. Virtual ideotypes based on markers identified by modelling had 10–36% more yield than those based on markers for yield per se. * Conclusions: This study outlines a genotype-to-phenotype approach that exploits the potential value of markerbased crop modelling in developing new plant types with high yields. The approach can provide more markers for selection programmes for specific environments whilst also allowing for prioritization. Crop modelling is thus a powerful tool for marker design for improved rice yields and for ideotyping under contrasting conditions.
    Genotype-environment interactions affecting preflowering physiological and morphological traits of Brassica rapa grown in two watering regimes
    El-Soda, M. ; Boer, M.P. ; Bagheri, H. ; Hanhart, C.J. ; Koornneef, M. ; Aarts, M.G.M. - \ 2014
    Journal of Experimental Botany 65 (2014)2. - ISSN 0022-0957 - p. 697 - 708.
    by-environment interactions - root-system architecture - phenotypic plasticity - genetic architecture - drought tolerance - qtl analysis - plant - loci - arabidopsis - evolution
    Plant growth and productivity are greatly affected by drought, which is likely to become more threatening with the predicted global temperature increase. Understanding the genetic architecture of complex quantitative traits and their interaction with water availability may lead to improved crop adaptation to a wide range of environments. Here, the genetic basis of 20 physiological and morphological traits is explored by describing plant performance and growth in a Brassica rapa recombinant inbred line (RIL) population grown on a sandy substrate supplemented with nutrient solution, under control and drought conditions. Altogether, 54 quantitative trait loci (QTL) were identified, of which many colocated in 11 QTL clusters. Seventeen QTL showed significant QTL–environment interaction (Q×E), indicating genetic variation for phenotypic plasticity. Of the measured traits, only hypocotyl length did not show significant genotype–environment interaction (G×E) in both environments in all experiments. Correlation analysis showed that, in the control environment, stomatal conductance was positively correlated with total leaf dry weight (DW) and aboveground DW, whereas in the drought environment, stomatal conductance showed a significant negative correlation with total leaf DW and aboveground DW. This correlation was explained by antagonistic fitness effects in the drought environment, controlled by a QTL cluster on chromosome A7. These results demonstrate that Q×E is an important component of the genetic variance and can play a great role in improving drought tolerance in future breeding programmes
    Identification of candidate genes required for susceptibility to powdery or downy mildew in cucumber
    Schouten, H.J. ; Krauskopf, J. ; Visser, R.G.F. ; Bai, Y. - \ 2014
    Euphytica 200 (2014)3. - ISSN 0014-2336 - p. 475 - 486.
    quantitative trait loci - sativus l. - disease resistance - mlo-gene - qtl analysis - cell-death - arabidopsis - defense - protein - barley
    Powdery mildew (PM, caused by Podosphaera fusca) and downy mildew (DM, caused by Pseudoperonospora cubensis) are important diseases of cucumber (Cucumis sativus). Breeding for resistance has been undertaken since the 1940s, but underlying resistance genes have not been functionally analysed yet. The published genome sequence of cucumber catalyses the search for such genes. Genetic studies have indicated that resistances to PM and DM in cucumber are often inherited recessively, which indicates the presence of susceptibility genes (S-genes). Therefore we analyzed the cucumber genome for homologs of functionally proven S-genes known from other plant species. We identified 13 MLO-like genes in cucumber, three of which cluster in Clade V, the clade that contains all known MLO-like susceptibility genes to powdery mildews in other dicots. The expression of one of these three genes, CsaMLO1, located on chromosome 1, was upregulated after PM inoculation. It co-localizes with a QTL for PM resistance previously identified. Also homologs of the susceptibility genes PMR4 and PMR5 are located at this QTL. The second MLO-like gene from Clade V (CsaMLO8) resides in a recessively inherited major QTL for PM resistance at the bottom of chromosome 5, together with a PMR6-like gene. Two major QTL for DM recessive resistance at the top of chromosome 5 co-localize with CsaDMR6-2, which is homologous to the DMR6 susceptibility gene in Arabidopsis. This study has identified several candidate genes for susceptibility to PM and DM in cucumber that may explain QTL for recessively inherited resistance, reported earlier.
    Quantitative trait locus analysis of nitrogen use efficiency in barley (Hordeum vulgare L.)
    Kindu, G.A. ; Tang, J. ; Yin, X. ; Struik, P.C. - \ 2014
    Euphytica 199 (2014)1-2. - ISSN 0014-2336 - p. 207 - 221.
    recombinant inbred lines - controlling flowering time - triticum-aestivum l. - spring barley - qtl analysis - experimental populations - genetic architecture - crop production - linkage maps - major genes
    Quantitative trait locus (QTL) analysis of nitrogen use efficiency (NUE) of barley (Hordeum vulgare L.) was conducted on data generated from two pot experiments carried out in 2005 (using four nitrogen rates) and 2008 (with three rates) with AFLP markers and 94 recombinant inbred lines (RILs) of the Prisma 9 Apex mapping population. In total 41 QTLs were detected on 6 chromosomes and for 18 traits in both trials. About 95 % of the detected QTLs were with major additive effects. The percentage of variance accounted for by individual QTLs in the multiple QTL mapping model ranged from 8.4 to 54.4 %across all mapped traits in both years. Fifteen QTLs were related to NUE and its components; most of these QTLs were detected at lower nitrogen rates and none at the highest rate in both trials. These QTLs were found on Chromosomes 3(3H) and 7(5H) in 2005 and Chromosome 2(2H) in 2008. Except for the QTLs of plant height and NUE based on grain yield, none of the QTLs which were detected for a given trait in 2005, expressed themselves in 2008 irrespective of the nitrogen levels. QTLs controlling some traits were colocated in each year, and QTLs for many traits were detected on the same chromosome and close to the denso locus. Further research is needed to investigate the possibility to reduce nitrogen fertilizer requirements through breeding while maintaining high yield of barley.
    The statistical analysis of multi-environment data: Modeling genotype-by-environment interaction and its genetic basis
    Malosetti, M. ; Ribaut, J.M. ; Eeuwijk, F.A. van - \ 2013
    Frontiers in Physiology 4 (2013). - ISSN 1664-042X - 17 p.
    quantitative trait loci - wheat-variety database - ecophysiological analyses - drought conditions - evaluation trials - flanking markers - tropical maize - mixed models - qtl analysis - variance
    Genotype-by-environment interaction (GEI) is an important phenomenon in plant breeding. This paper presents a series of models for describing, exploring, understanding, and predicting GEI. All models depart from a two-way table of genotype by environment means. First, a series of descriptive and explorative models/approaches are presented: Finlay Wilkinson model, AMMI model, GGE biplot. All of these approaches have in common that they merely try to group genotypes and environments and do not use other information than the two-way table of means. Next, factorial regression is introduced as an approach to explicitly introduce genotypic and environmental covariates for describing and explaining GEL Finally, OIL modeling is presented as a natural extension of factorial regression, where marker information is translated into genetic predictors. Tests for regression coefficients corresponding to these genetic predictors are tests for main effect OIL expression and OIL by environment interaction (QED. OIL models for which QEI depends on environmental covariables form an interesting model class for predicting GEI for new genotypes and new environments. For realistic modeling of genotypic differences across multiple environments, sophisticated mixed models are necessary to allow for heterogeneity of genetic variances and correlations across environments. The use and interpretation of all models is illustrated by an example data set from the CIMMYT maize breeding program, containing environments differing in drought and nitrogen stress. To help readers to carry out the statistical analyses, GenStat (R) programs, 15th Edition and Discovery (R) version, are presented as "Appendix"
    Exploring the Natural Variation for Seedling Traits and Their link with Seed Dimensions in Tomato
    Khan, N. ; Kazmi, R.H. ; Willems, L.A.J. ; Heusden, A.W. van; Ligterink, W. ; Hilhorst, H.W.M. - \ 2012
    PLoS ONE 7 (2012)8. - ISSN 1932-6203 - 14 p.
    root-system architecture - lycopersicon-pimpinellifolium - interspecific cross - quantitative traits - salt tolerance - water-stress - qtl analysis - size - germination - growth
    The success of germination, growth and final yield of every crop depends to a large extent on the quality of the seeds used to grow the crop. Seed quality is defined as the viability and vigor attribute of a seed that enables the emergence and establishment of normal seedlings under a wide range of environments. We attempt to dissect the mechanisms involved in the acquisition of seed quality, through a combined approach of physiology and genetics. To achieve this goal we explored the genetic variation found in a RIL population of Solanum lycopersicum (cv. Moneymaker) x Solanum pimpinellifolium through extensive phenotyping of seed and seedling traits under both normal and nutrient stress conditions and root system architecture (RSA) traits under optimal conditions. We have identified 62 major QTLs on 21 different positions for seed, seedling and RSA traits in this population. We identified QTLs that were common across both conditions, as well as specific to stress conditions. Most of the QTLs identified for seedling traits co-located with seed size and seed weight QTLs and the positive alleles were mostly contributed by the S. lycopersicum parent. Co-location of QTLs for different traits might suggest that the same locus has pleiotropic effects on multiple traits due to a common mechanistic basis. We show that seed weight has a strong effect on seedling vigor and these results are of great importance for the isolation of the corresponding genes and elucidation of the underlying mechanisms.
    Genome-wide association studies for Agronomical Traits in a world wide Spring Barley Collection
    Pasam, R.K. ; Sharma, R. ; Malosetti, M. ; Eeuwijk, F.A. van; Haseneyer, G. ; Kilian, B. ; Graner, A. - \ 2012
    BMC Plant Biology 12 (2012). - ISSN 1471-2229
    multilocus genotype data - hordeum-vulgare l. - linkage disequilibrium - population-structure - complex traits - flowering time - qtl analysis - missing heritability - haplotype structure - genetic diversity
    Background Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS. Results Population structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions. Conclusions Our results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity
    Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations
    Uwimana, B. ; Smulders, M.J.M. ; Hooftman, D.A.P. ; Hartman, Y. ; Tienderen, P.H. van; Jansen, J. ; McHale, L.K. ; Michelmore, R. ; Visser, R.G.F. ; Wiel, C.C.M. van de - \ 2012
    BMC Plant Biology 12 (2012). - ISSN 1471-2229
    quantitative trait loci - genetically-engineered organisms - gene flow - qtl analysis - lycopersicon-esculentum - domestication traits - helianthus-paradoxus - sunflower hybrids - field conditions - mixed models
    After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop contributed QTLs with either a positive or a negative effect on plant vigour, we hypothesize that genomic regions exist where transgenes could preferentially be located in order to mitigate their persistence in natural populations through genetic hitchhiking.
    Quantitative trait loci for rooting pattern traits of common beans grown under drought stress versus non-stress conditions
    Asfaw, A. ; Blair, M.W. - \ 2012
    Molecular Breeding 30 (2012)2. - ISSN 1380-3743 - p. 681 - 695.
    phaseolus-vulgaris l. - rain-fed conditions - phosphorus acquisition - water-stress - qtl analysis - architecture traits - shoot genotypes - resistance - yield - cultivars
    Drought is the major abiotic constraint contributing to yield reduction in common bean (Phaseolus vulgaris L.) worldwide. An increasing scarcity of water in the future will make improving adaptation to drought stress a major objective of most crop breeding efforts. Drought avoidance by increased extraction of soil moisture from greater depth under drought conditions is an adaptive mechanism of common bean. A recombinant inbred line population of DOR364 × BAT477 was evaluated for rooting pattern traits in soil cylinder tubes under soil drying (progressive water stress) and non-stress (well-watered with 80% of field capacity) treatments in a greenhouse. One of the parents, BAT 477, is a deep-rooting genotype while the other parent, DOR 364, is a commercial cultivar in Central America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for ten rooting pattern traits as well as five shoot traits of 48-day-old plants. A mixed model quantitative trait locus (QTL) mapping analysis was carried out using a genetic map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. Genotype estimates were calculated from best design and spatial effects model for each trait. A total of 15 putative QTL were identified for seven rooting pattern traits and four shoot traits. The QTL detected were scattered over five of the 11 linkage groups. The QTL detected for all the root traits except total root length and fine root length were main effect QTL and did not interact with the level of water supply. The total root length and fine root length QTL with significant QTL × environment interaction only differed in magnitude of effect, and interaction was of a non-crossover type. Other QTL for total root length, fine roots, thick roots, root volume and root biomass were co-localized and also explained relatively more genetic variance. This suggests that the QTL affecting root traits in common beans are based on constitutive expression of genes and that drought avoidance based on deep rooting, longer root length, thicker roots, increasing root length distribution with depth, root volume and root biomass can be used in molecular breeding. The positive alleles for most of the QTL detected in this study were derived from the paternal parent BAT477. The results from the present analyses highlighted the feasibility of marker-aided selection as an alternative to conventional labor-intensive, phenotypic screening of drought avoidance root traits
    Population structure revealed by different marker types (SSR or DArT) has an impact on the results of genome-wide association mapping in European barley cultivars
    Matthies, I.E. ; Hintum, T.J.L. van; Weise, S. ; Röder, M.S. - \ 2012
    Molecular Breeding 30 (2012)2. - ISSN 1380-3743 - p. 951 - 966.
    different germplasm groups - multilocus genotype data - doubled-haploid progeny - simple sequence repeats - malting-quality - linkage disequilibrium - genetic diversity - qtl analysis - yield components - spring barley
    Diversity arrays technology (DArT) and simple sequence repeat (SSR) markers were applied to investigate population structure, extent of linkage disequilibrium and genetic diversity (kinship) on a genome-wide level in European barley (Hordeum vulgare L.) cultivars. A set of 183 varieties could be clearly distinguished into spring and winter types and was classified into five subgroups based on 253 DArT or 22 SSR markers. Despite the fact, that the same number of groups was revealed by both marker types, it could be shown that this grouping was more distinct for the SSRs than the DArTs, when assigned to a Q-matrix by STRUCTURE. This was supported by the findings from principal coordinate analysis, where the SSRs showed a better resolution according to seasonal habit and row number than the DArTs. A considerable influence on the rate of significant associations with malting and kernel quality parameters was revealed by different marker types in this genome-wide association study using general and mixed linear models considering population structure. Fewer spurious associations were observed when population structure was based on SSR rather than on DArT markers. We therefore conclude that it is advisable to use independent marker datasets for calculating population structure and for performing the association analysis.
    Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium
    Kazmi, R.H. ; Khan, N. ; Willems, L.A.J. ; Heusden, A.W. van; Ligterink, J.W. ; Hilhorst, H.W.M. - \ 2012
    Plant, Cell & Environment 35 (2012)5. - ISSN 0140-7791 - p. 929 - 951.
    quantitative trait loci - abiotic stress tolerance - abscisic-acid - arabidopsis-thaliana - qtl analysis - drought tolerance - salt tolerance - line population - low-temperature - water-stress
    Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and genetically complex. Using a recombinant inbred line population of Solanum lycopersicum × Solanum pimpinellifolium, we identified quantitative trait loci (QTLs) influencing seed quality phenotypes under non-stress, as well as salt, osmotic, cold, high-temperature and oxidative stress conditions. In total, 42 seed quality traits were analysed and 120 QTLs were identified for germination traits under different conditions. Significant phenotypic correlations were observed between germination traits under optimal conditions, as well as under different stress conditions. In conclusion, one or more QTLs were identified for each trait with some of these QTLs co-locating. Co-location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. However, several QTLs also dissected seed quality in its separate components, suggesting different physiological mechanisms and signalling pathways for different seed quality attributes.
    Visualizing the genetic landscape of Arabidopsis seed performance
    Joosen, R.V.L. ; Arends, D. ; Willems, L.A.J. ; Ligterink, J.W. ; Jansen, R.C. ; Hilhorst, H.W.M. - \ 2012
    Plant Physiology 158 (2012)2. - ISSN 0032-0889 - p. 570 - 589.
    quantitative trait loci - natural allelic variation - heterogeneous inbred family - controlling root-growth - abscisic-acid - environmental covariables - line population - complex traits - qtl analysis - thaliana
    Perfect timing of germination is required to encounter optimal conditions for plant survival and is the result of a complex interaction between molecular processes, seed characteristics, and environmental cues. To detangle these processes, we made use of natural genetic variation present in an Arabidopsis (Arabidopsis thaliana) Bayreuth × Shahdara recombinant inbred line population. For a detailed analysis of the germination response, we characterized rate, uniformity, and maximum germination and discuss the added value of such precise measurements. The effects of after-ripening, stratification, and controlled deterioration as well as the effects of salt, mannitol, heat, cold, and abscisic acid (ABA) with and without cold stratification were analyzed for these germination characteristics. Seed morphology (size and length) of both dry and imbibed seeds was quantified by using image analysis. For the overwhelming amount of data produced in this study, we developed new approaches to perform and visualize high-throughput quantitative trait locus (QTL) analysis. We show correlation of trait data, (shared) QTL positions, and epistatic interactions. The detection of similar loci for different stresses indicates that, often, the molecular processes regulating environmental responses converge into similar pathways. Seven major QTL hotspots were confirmed using a heterogeneous inbred family approach. QTLs colocating with previously reported QTLs and well-characterized mutants are discussed. A new connection between dormancy, ABA, and a cripple mucilage formation due to a naturally occurring mutation in the MUCILAGE-MODIFIED2 gene is proposed, and this is an interesting lead for further research on the regulatory role of ABA in mucilage production and its multiple effects on germination parameters.
    Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions
    Gu, J. ; Yin, X. ; Struik, P.C. ; Stomph, T.J. ; Wang, J. - \ 2012
    Journal of Experimental Botany 63 (2012)1. - ISSN 0022-0957 - p. 455 - 469.
    qtl analysis - upland rice - chlorophyll fluorescence - reproductive-stage - genetic-variation - grain-yield - physiological traits - plant photosynthesis - carbon assimilation - advanced backcross
    Photosynthesis is fundamental to biomass production, but sensitive to drought. To understand the genetics of leaf photosynthesis, especially under drought, upland rice cv. Haogelao, lowland rice cv. Shennong265, and 94 of their introgression lines (ILs) were studied at flowering and grain filling under drought and well-watered field conditions. Gas exchange and chlorophyll fluorescence measurements were conducted to evaluate eight photosynthetic traits. Since these traits are very sensitive to fluctuations in microclimate during measurements under field conditions, observations were adjusted for microclimatic differences through both a statistical covariant model and a physiological approach. Both approaches identified leaf-to-air vapour pressure difference as the variable influencing the traits most. Using the simple sequence repeat (SSR) linkage map for the IL population, 1–3 quantitative trait loci (QTLs) were detected per trait–stage–treatment combination, which explained between 7.0% and 30.4% of the phenotypic variance of each trait. The clustered QTLs near marker RM410 (the interval from 57.3¿cM to 68.4¿cM on chromosome 9) were consistent over both development stages and both drought and well-watered conditions. This QTL consistency was verified by a greenhouse experiment under a controlled environment. The alleles from the upland rice at this interval had positive effects on net photosynthetic rate, stomatal conductance, transpiration rate, quantum yield of photosystem II (PSII), and the maximum efficiency of light-adapted open PSII. However, the allele of another main QTL from upland rice was associated with increased drought sensitivity of photosynthesis. These results could potentially be used in breeding programmes through marker-assisted selection to improve drought tolerance and photosynthesis simultaneously
    Identification and mapping of quantitative resistance to late blight (Phytophthora infestans) in Solanum habrochaites LA1777
    Junming Li, J. ; Liu, L. ; Bai, Y. ; Finkers, H.J. ; Visser, R.G.F. ; Heusden, A.W. van - \ 2011
    Euphytica 179 (2011)3. - ISSN 0014-2336 - p. 427 - 438.
    lycopersicon-pennellii - genetic backgrounds - introgression lines - qtl analysis - trait loci - tomato - esculentum - durability - library - quality
    Late blight (Phytophthora infestans) can have devastating effects on tomato production over the whole world. Most of the commercial cultivars of tomato, Solanum lycopersicum, are susceptible. Qualitative and quantitative resistance has been described in wild relatives of tomato. In general qualitative resistance can more easily be overcome by newly evolved isolates. Screening of three S. habrochaites accessions (LA1033, LA2099 and LA1777) through a whole plant assay showed that accession LA1777 had a good level of resistance to several isolates of P. infestans. To explore the potential in this wild species, an introgression line (IL) population of S. habrochaites LA1777 was used to screen individual chromosome regions of the wild species by a detached leaf assay. Two major isolates (T1,2 and T1,2,4) were used and two parameters were measured: lesion size (LS), and disease incidence (DI). Substantial variation was observed between the individual lines. QTLs were identified for LS but not for DI. The presence of five QTLs derived from LA1777 (Rlbq4a, Rlbq4b, Rlbq7, Rlbq8 and Rlbq12) results in unambiguous higher levels of resistance. All QTLs co-localized with previously described QTLs from S. habrochaites LA2099 except QTL Rlbq4b, which is therefore a novel QTL
    Natural genetic variation in plant photosynthesis
    Flood, P.J. ; Harbinson, J. ; Aarts, M.G.M. - \ 2011
    Trends in Plant Science 16 (2011)6. - ISSN 1360-1385 - p. 327 - 335.
    quantitative trait loci - association mapping population - recurrent phenotypic selection - genome-wide association - wheat triticum-aestivum - rice oryza-sativa - chlorophyll fluorescence - qtl analysis - arabidopsis-thaliana - leaf photosynthesis
    Natural genetic variation in plant photosynthesis is a largely unexplored and as a result an underused genetic resource for crop improvement. Numerous studies show genetic variation in photosynthetic traits in both crop and wild species, and there is an increasingly detailed knowledge base concerning the interaction of photosynthetic phenotypes with their environment. The genetic factors that cause this variation remain largely unknown. Investigations into natural genetic variation in photosynthesis will provide insights into the genetic regulation of this complex trait. Such insights can be used to understand evolutionary processes that affect primary production, allow greater understanding of the genetic regulation of photosynthesis and ultimately increase the productivity of our crops
    Seedling salt tolerance in tomato
    Junming Li, J. ; Liu, L. ; Bai, Y. ; Zhang, Pujuan ; Finkers, H.J. ; Du, Y. ; Visser, R.G.F. ; Heusden, A.W. van - \ 2011
    Euphytica 178 (2011)3. - ISSN 0014-2336 - p. 403 - 414.
    quantitative trait loci - introgression line population - lycopersicon-esculentum - vegetative growth - cultivated tomato - bacterial canker - qtl analysis - fruit yield - germination - salinity
    Soils with higher concentrations of salt are becoming more and more a constraint for many crops to obtain high yields. Wild tomato species, adapted to adverse environments, are a potential reservoir for genes underlying quantitative trait loci (QTL) related to salt tolerance in tomato. In this study two introgression line (IL) libraries derived from two different wild species, Solanum pennellii LA716 and Solanum lycopersicoides LA2951, were used to identify QTLs for salt tolerance in the seedling stage. In the S. pennellii IL library, four major QTLs were identified on chromosomes 6, 7 and 11. In the S. lycopersicoides IL library, six major QTLs were discovered which are located on chromosomes 4, 6, 9 and 12. Co-localization of QTLs on chromosome 6 in the two IL libraries and previously reports hinted that this locus might be conserved in the tomato crop. Three S. pennellii ILs (IL6-2, IL7-1 and IL7-5) harboring QTLs on chromosome 6 and 7 were crossed. Semi-dominance and dominance were shown for these three QTLs, and non-additive and epistatic interactions between them were observed
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