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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A model-based approach to analyse genetic variation in potato using standard cultivars and a segregating population. II. Tuber bulking and resource use efficiency
Khan, Muhammad Sohail ; Yin, Xinyou ; Putten, Peter E.L. van der; Jansen, Hans J. ; Eck, Herman J. van; Eeuwijk, Fred A. van; Struik, Paul C. - \ 2019
Field Crops Research 242 (2019). - ISSN 0378-4290
Genotype-by-environment interaction - Heritability - Maturity type - Path coefficient analysis - QTL mapping

Quantitative differences in tuber bulking of 100 genotypes in a segregating F1 population, their parents (SH, RH) and five contrasting cultivars of potato (Solanum tuberosum) grown in six environments were analysed using a piece-wise expolinear function. Tuber bulking was characterised by three parameters: cm, ED and wmax, where cm and ED were growth rate and effective duration, respectively, of the linear phase of tuber bulking, and wmax was the final tuber dry weight at the end of the linear phase (tE). We also analysed radiation (RUET) and nitrogen use efficiency (NUET), and their relationships with the model parameters. Values of cm and RUET were highest for early-maturing genotypes. Late-maturing genotypes had largest ED and NUET. As a result, wmax was higher in late genotypes than in early genotypes. Most traits exhibited high heritability and high genetic correlations with wmax. Path analysis showed that RUET, cm and a previously quantified parameter for total canopy cover Asum, had a major influence on wmax. Sixteen QTLs were detected for all traits explaining the phenotypic variance by up to 66%. One particular QTL on paternal linkage group V was detected for all traits with a major additive effect and maximum total phenotypic variance. Additional QTLs mostly associated with RH (cm, tE and ED) or both SH-RH linkage groups (NUET, wmax). Our study demonstrates that there are opportunities for improving tuber dry matter yield by selecting an optimal combination of important physiological traits.

A model-based approach to analyse genetic variation in potato using standard cultivars and a segregating population. I. Canopy cover dynamics
Khan, Muhammad Sohail ; Struik, Paul C. ; Putten, Peter E.L. van der; Jansen, Hans J. ; Eck, Herman J. van; Eeuwijk, Fred A. van; Yin, Xinyou - \ 2019
Field Crops Research 242 (2019). - ISSN 0378-4290
Genotype-by-environment interaction - Haulm growth - Heritability - Maturity type - QTL mapping

We designed a model to quantify the canopy cover dynamics in potato (Solanum tuberosum L.). It describes the dynamics during the build-up phase, maximum cover phase, and decline phase of canopy development through five parameters defining timing of three phases and maximum canopy cover (vmax). These five parameters were estimated for 100 individuals of an F1 population, their parents, and five standard cultivars, using data from six field experiments, and used to estimate secondary traits, related to duration and area under the canopy cover curve for the three phases. The duration of the canopy build-up phase (DP1) was rather conserved, but the duration of maximum canopy cover (DP2) and the decline phase (DP3) varied greatly, with late maturing genotypes having longer DP2 and DP3 and thus a higher area under the canopy cover curve (Asum). High genetic variability coupled with high heritability was recorded for end of canopy senescence (te), DP2 and Asum. Strong positive phenotypic and genetic correlations were observed between DP2 and te, vmax or Asum indicating that genotypes with longer DP2 could be indirectly obtained by selecting for these traits. Several quantitative trait loci (QTLs) were detected for model traits explaining the variance by up to 74%. Clustering of many QTLs were found on position 18.2 cM on paternal linkage group V with major additive effects. Many additional QTLs with minor effects were mostly associated with maternal linkage groups. Our model approach could be used to exploit available genetic variability in canopy cover dynamics of potato.

Host/nonhost status and genetics of resistance in barley against three pathotypes of Magnaporthe blast fungi
Aghnoum, R. ; Bvindi, C. ; Menet, G. ; D’hoop, B. ; Maciel, J.L.N. ; Niks, R.E. - \ 2019
Euphytica 215 (2019)7. - ISSN 0014-2336
Association mapping - Barley - Blast disease - GWAS - Magnaporthe oryzae - mlo - QTL mapping

Blast disease, caused by the Magnaporthe oryzae/grisea species complex, occurs in a wide range of wild and cultivated gramineous plant species including rice, wheat and barley. We inoculated a collection of cultivated (Hordeum vulgare ssp. vulgare L.) and wild (ssp. spontaneum) barley accessions with M. oryzae Oryza pathotype (MoO), Triticum pathotype (MoT) and Pennisetum pathotype (MsP) to quantify the host status of barley, and to identify sources of blast resistance. Unlike wheat, the barley gene pool is rich with sources of complete and partial resistance against Magnaporthe. Cultivated barley appeared a nonhost to MsP, whereas wild barley showed some degree of susceptibility. All 153 tested rice accessions were resistant to the MoT isolate, suggesting that rice is nonhost to this pathotype. Inoculation of L94/Vada and Vada/SusPtrit RIL mapping populations with MoO and/or MoT isolates of M. oryzae indicated one large effect QTL, designated as Rmoq1, on the short arm of chromosome 7H against the MoT isolate PY 67.1 in both populations. Resistance in L94 to the MoO isolate was due to a different QTL, located at 5H. An association mapping panel of West European barley cultivars also suggested that most QTLs were pathotype specific. Six blast resistance genes found in the biparental and association mapping studies coincided with map positions of powdery mildew resistance genes viz. Mlt, Mla6, Mlg, mlo, Mlj, and Mlhb genes. Our QTL and association mapping analyses do not support the association of the mlo resistance gene with enhanced susceptibility to M. oryzae as reported in literature.

Trichome Independent Resistance against Western Flower Thrips in Tomato
Bac-Molenaar, Johanna A. ; Mol, Selena ; Verlaan, Maarten G. ; Elven, Joke van; Kim, Hye Kyong ; Klinkhamer, Peter G.L. ; Leiss, Kirsten A. ; Vrieling, Klaas - \ 2019
Plant and Cell Physiology 60 (2019)5. - ISSN 0032-0781 - p. 1011 - 1024.
Insect resistance - Metabolite profiles - QTL mapping - Tomato - Trichome-derived volatiles - α-Tomatine

Western flower thrips (WFT) are a major pest on many crops, including tomato. Thrips cause yield losses, not only through feeding damage, but also by the transmission of viruses of which the Tomato Spotted Wilt Virus is the most important one. In cultivated tomato, genetic diversity is extremely low, and all commercial lines are susceptible to WFT. Several wild relatives are WFT resistant and these resistances are based on glandular trichome-derived traits. Introgression of these traits in cultivated lines did not lead to WFT resistant commercial varieties so far. In this study, we investigated WFT resistance in cultivated tomato using a F2 population derived from a cross between a WFT susceptible and a WFT resistant cultivated tomato line. We discovered that this WFT resistance is independent of glandular trichome density or trichome-derived volatile profiles and is associated with three QTLs on chromosomes 4, 5 and 10. Foliar metabolic profiles of F3 families with low and high WFT feeding damage were clearly different. We identified α-tomatine and a phenolic compound as potential defensive compounds. Their causality and interaction need further investigation. Because this study is based on cultivated tomato lines, our findings can directly be used in nowadays breeding programs.

Genetic dissection of flowering time in Brassica rapa responses to temperature and photoperiod
Xiao, Dong ; Shen, Hao Ran ; Zhao, Jian Jun ; Wei, Yan Ping ; Liu, Dong Rang ; Hou, Xi Lin ; Bonnema, Guusje - \ 2019
Plant Science 280 (2019). - ISSN 0168-9452 - p. 110 - 119.
Brassica rapa - FLOWERING LOCUS C (FLC) - Flowering time - Photoperiod - QTL mapping - Temperature

The Brassica rapa (B. rapa) species displays enormous phenotypic diversity, with leafy vegetables, storage root vegetables and oil crops. These different crops all have different flowering time, which determine their growing season and cultivation area. Little is known about the effects of diverse temperature and day-lengths on flowering time QTL associated with FLC paralogues. We phenotyped the flowering time of a doubled haploid population, established from a cross between Yellow sarson and Pak choi under diverse environmental conditions. We identified flowering-time QTL (fQTL) in different photoperiod and temperature regimes in the greenhouse, and studied their colocation with known flowering time genes. As several fQTL colocalized with FLC paralogues, we studied the expression patterns of four FLC paralogues during the course of vernalization in parental lines. Under all environmental conditions tested the major fQTL that mapped to the BrFLC2_A02 locus was detected, however its effect decreased when plants were grown at low temperatures. Another fQTL that mapped to the FLC paralogue, BrFLC5_A03 was also identified under all tested environments, while no fQTL colocated with BrFLC1_A10 or BrFLC3_A03. Furthermore, the vernalization treatment decreased expression of all BrFLC paralogues in the parental lines, and showed the lowest transcript level after 28 days of vernalization. Transcript abundance stayed low after returning the plants for seven days to normal growth temperature. Interestingly, transcript abundance of BrFLC3_A03 and BrFLC5_A03 was repressed much stronger and already reached lowest levels after 14d in the early-flowering type YS-143. This study improves understanding of the effects of daylength and vernalization on flowering time in B. rapa and the role of the different BrFLC paralogues therein.

Integration of Murine and Human Studies for Mapping Periodontitis Susceptibility
Nashef, A. ; Qabaja, R. ; Salaymeh, Y. ; Botzman, M. ; Munz, M. ; Dommisch, H. ; Krone, B. ; Hoffmann, P. ; Wellmann, J. ; Laudes, M. ; Berger, K. ; Kocher, T. ; Loos, B. ; Velde, N. van der; Uitterlinden, A.G. ; Groot, L.C.P.G.M. de; Franke, A. ; Offenbacher, S. ; Lieb, W. ; Divaris, K. ; Mott, R. ; Gat-Viks, I. ; Wiess, E. ; Schaefer, A. ; Iraqi, F.A. ; Haddad, Y.H. - \ 2018
Journal of Dental Research 97 (2018)5. - ISSN 0022-0345 - p. 537 - 546.
alveolar bone loss - animal model - Collaborative Cross - genetic - GWAS - QTL mapping

Periodontitis is one of the most common inflammatory human diseases with a strong genetic component. Due to the limited sample size of available periodontitis cohorts and the underlying trait heterogeneity, genome-wide association studies (GWASs) of chronic periodontitis (CP) have largely been unsuccessful in identifying common susceptibility factors. A combination of quantitative trait loci (QTL) mapping in mice with association studies in humans has the potential to discover novel risk loci. To this end, we assessed alveolar bone loss in response to experimental periodontal infection in 25 lines (286 mice) from the Collaborative Cross (CC) mouse population using micro–computed tomography (µCT) analysis. The orthologous human chromosomal regions of the significant QTL were analyzed for association using imputed genotype data (OmniExpress BeadChip arrays) derived from case-control samples of aggressive periodontitis (AgP; 896 cases, 7,104 controls) and chronic periodontitis (CP; 2,746 cases, 1,864 controls) of northwest European and European American descent, respectively. In the mouse genome, QTL mapping revealed 2 significant loci (–log P = 5.3; false discovery rate = 0.06) on chromosomes 1 (Perio3) and 14 (Perio4). The mapping resolution ranged from ~1.5 to 3 Mb. Perio3 overlaps with a previously reported QTL associated with residual bone volume in F2 cross and includes the murine gene Ccdc121. Its human orthologue showed previously a nominal significant association with CP in humans. Use of variation data from the genomes of the CC founder strains further refined the QTL and suggested 7 candidate genes (CAPN8, DUSP23, PCDH17, SNORA17, PCDH9, LECT1, and LECT2). We found no evidence of association of these candidates with the human orthologues. In conclusion, the CC populations enabled mapping of confined QTL that confer susceptibility to alveolar bone loss in mice and larger human phenotype-genotype samples and additional expression data from gingival tissues are likely required to identify true positive signals.

Identification of a large-effect QTL associated with kernel discoloration in barley
Romero, Cynara C.T. ; Vels, Anton ; Niks, Rients E. - \ 2018
Journal of Cereal Science 84 (2018). - ISSN 0733-5210 - p. 62 - 70.
Black point - Grain skinning - Kernel discoloration - QTL mapping - Seed quality

Three barley mapping populations sharing the parental line SusPtrit suffered from an unknown condition affecting grain quality and germination. Grains showed dark blotches or even whole-grain discoloration and shrivelling. Symptoms were similar to kernel discoloration as reported in wheat and barley. Some covered-seed lines affected by this quality condition produced grains that were either not covered at all or in which partial hull loss was observed, a phenotype that resembles that of grain skinning. No fungal or bacterial agent was identified as causal organism, and we demonstrate that the poor quality phenotype is not transmitted to the next generation – therefore unlikely due to a seed borne pathogen. A major effect QTL on chromosome 6H was mapped independently in all three populations, with the poor quality allele contributed by SusPtrit. A second, minor effect QTL, was mapped on chromosome 2H in the SusPtrit x Golden Promise population, with Golden Promise as the parent donor of the allele conferring poor quality. The grain quality disorder is not linked to the nud gene on chromosome 7H for the naked/covered seed trait.

Recursive algorithms for modeling genomic ancestral origins in a fixed pedigree
Zheng, Chaozhi ; Boer, Martin P. ; Eeuwijk, Fred A. van - \ 2018
G3 : Genes Genomes Genetics 8 (2018)10. - ISSN 2160-1836 - p. 3231 - 3245.
Ancestral inference - Collaborative cross (CC) - Identical by descent - Junction theory - Multiparent advanced generation intercross (MAGIC) - Multiparental populations mpp - QTL mapping - Recombinant inbred line (RIL) - Resolution

The study of gene flow in pedigrees is of strong interest for the development of quantitative trait loci (QTL) mapping methods in multiparental populations. We developed a Markovian framework for modeling ancestral origins along two homologous chromosomes within individuals in fixed pedigrees. A highly beneficial property of our method is that the size of state space depends linearly or quadratically on the number of pedigree founders, whereas this increases exponentially with pedigree size in alternative methods. To calculate the parameter values of the Markov process, we describe two novel recursive algorithms that differ with respect to the pedigree founders being assumed to be exchangeable or not. Our algorithms apply equally to autosomes and sex chromosomes, another desirable feature of our approach. We tested the accuracy of the algorithms by a million simulations on a pedigree. We demonstrated two applications of the recursive algorithms in multiparental populations: design a breeding scheme for maximizing the overall density of recombination breakpoints and thus the QTL mapping resolution, and incorporate pedigree information into hidden Markov models in ancestral inference from genotypic data; the conditional probabilities and the recombination breakpoint data resulting from ancestral inference can facilitate follow-up QTL mapping. The results show that the generality of the recursive algorithms can greatly increase the application range of genetic analysis such as ancestral inference in multiparental populations.

QTL epi mapping in Arabidopsis thaliana
Lauss, Kathrin ; Keurentjes, Joost J.B. - \ 2018
In: Plant Chromatin Dynamics Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493973170 - p. 373 - 394.
Epigenotyping - epiRILs - Phenotyping - QTL mapping
While DNA sequence variation is known to be a major driver of phenotypic divergence, epigenetic variation has long been disregarded. One reason for that was the lack of suitable tools. The creation of epigenetically divergent but otherwise largely isogenic Arabidopsis populations has now alleviated some of these constraints. Epigenetic recombinant inbred line (epiRIL) populations allow for examining the effects of epigenetic variation on phenotypes. In addition, epiRILs enabled the development of epigenetic quantitative trait locus (QTLepi) mapping, an approach to identify causal epigenetic factors. Here, we describe the successive steps of QTLepi mapping in a broad sense, from the creation of epigenetically divergent populations to the identification of causal genes underlying particular phenotypes in Arabidopsis.
Construction of a high-density genetic map from RNA-Seq data for an Arabidopsis bay-0 × shahdara ril population
Serin, Elise A.R. ; Snoek, L.B. ; Nijveen, Harm ; Willems, Leo A.J. ; Jiménez-Gómez, Jose M. ; Hilhorst, Henk W.M. ; Ligterink, Wilco - \ 2017
Frontiers in Genetics Livestock Genomics 8 (2017)DEC. - ISSN 1664-8021
Arabidopsis - Genetic map - Genotyping by sequencing - QTL mapping - Resolution - RIL population - RNA-seq
High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches.
Genetic mapping and QTL analysis of Botrytis resistance in Gerbera hybrida
Fu, Yiqian ; Silfhout, Alex van; Shahin, Arwa ; Egberts, Ronny ; Beers, Martin ; Velde, Ans van der; Houten, Adrie van; Tuyl, Jaap M. van; Visser, Richard G.F. ; Arens, Paul - \ 2017
Molecular Breeding 37 (2017)2. - ISSN 1380-3743
Gerbera grey mould - Linkage group - QTL mapping - SNP
Gerbera hybrida is an economically important cut flower. In the production and transportation of gerbera with unavoidable periods of high relative humidity, grey mould occurs and results in losses in quality and quantity of flowers. Considering the limitations of chemical use in greenhouses and the impossibility to use these chemicals in auction or after sale, breeding for resistant gerbera cultivars is considered as the best practical approach. In this study, we developed two segregating F1 populations (called S and F). Four parental linkage maps were constructed using common and parental specific SNP markers developed from expressed sequence tag sequencing. Parental genetic maps, containing 30, 29, 27 and 28 linkage groups and a consensus map covering 24 of the 25 expected chromosomes, could be constructed. After evaluation of Botrytis disease severity using three different tests, whole inflorescence, bottom (of disc florets) and ray floret, quantitative trait locus (QTL) mapping was performed using the four individual parental maps. A total of 20 QTLs (including one identical QTL for whole inflorescence and bottom tests) were identified in the parental maps of the two populations. The number of QTLs found and the explained variance of most QTLs detected reflect the complex mechanism of Botrytis disease response.
Back to acid soil fields : The citrate transporter sbmate is a major asset for sustainable grain yield for sorghum cultivated on acid soils
Carvalho, Geraldo ; Schaffert, Robert Eugene ; Malosetti Zunin, Marcos ; Eeuwijk, Fred van - \ 2016
G3 : Genes Genomes Genetics 6 (2016)2. - ISSN 2160-1836 - p. 475 - 484.
Al tolerance - Alt - Field trials - QTL mapping - Sorghum bicolor

Aluminum (Al) toxicity damages plant roots and limits crop production on acid soils, which comprise up to 50% of the world's arable lands. A major Al tolerance locus on chromosome 3, AltSB, controls aluminum tolerance in sorghum [Sorghum bicolor (L.) Moench] via SbMATE, an Al-activated plasma membrane transporter that mediates Al exclusion from sensitive regions in the root apex. As is the case with other known Al tolerance genes, SbMATE was cloned based on studies conducted under controlled environmental conditions, in nutrient solution. Therefore, its impact on grain yield on acid soils remains undetermined. To determine the real world impact of SbMATE, multi-trait quantitative trait loci (QTL) mapping in hydroponics, and, in the field, revealed a large-effect QTL colocalized with the Al tolerance locus AltSB, where SbMATE lies, conferring a 0.6 ton ha-1 grain yield increase on acid soils. A second QTL for Al tolerance in hydroponics, where the positive allele was also donated by the Al tolerant parent, SC283, was found on chromosome 9, indicating the presence of distinct Al tolerance genes in the sorghum genome, or genes acting in the SbMATE pathway leading to Al-activated citrate release. There was no yield penalty for AltSB, consistent with the highly localized Al regulated SbMATE expression in the root tip, and Al-dependent transport activity. A female effect of 0.5 ton ha-1 independently demonstrated the effectiveness of AltSB in hybrids. Al tolerance conferred by AltSB is thus an indispensable asset for sorghum production and food security on acid soils, many of which are located in developing countries.

Data from: Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations
Santure, Anna W. ; Poissant, Jocelyn ; Cauwer, Isabelle De; Oers, K. van; Robinson, Matthew R. ; Quinn, John L. ; Groenen, Martien ; Visser, Marcel ; Sheldon, Ben C. ; Slate, Jon - \ 2015
University of Auckland
quantitative genetics - GWAS - chromosome partitioning - genomics - Parus major - genome wide association - QTL mapping
Currently there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long-term studies across Europe, and consequently are considered an ecological 'model organism'. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long-term study populations of great tit - one in the Netherlands, and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population-specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population-specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations, and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free-living populations.
Replicated analysis of the genetic architecture of quantitative traits in two wild great tit populations
Santure, Anna W. ; Poissant, Jocelyn ; Cauwer, Isabelle De; Oers, Kees van; Robinson, Matthew R. ; Quinn, John L. ; Groenen, M.A.M. ; Visser, M.E. ; Sheldon, Ben C. ; Slate, Jon - \ 2015
Molecular Ecology 24 (2015)24. - ISSN 0962-1083 - p. 6148 - 6162.
chromosome partitioning - genome-wide association - genomics - GWAS - QTL mapping - quantitative genetics

Currently, there is much debate on the genetic architecture of quantitative traits in wild populations. Is trait variation influenced by many genes of small effect or by a few genes of major effect? Where is additive genetic variation located in the genome? Do the same loci cause similar phenotypic variation in different populations? Great tits (Parus major) have been studied extensively in long-term studies across Europe and consequently are considered an ecological 'model organism'. Recently, genomic resources have been developed for the great tit, including a custom SNP chip and genetic linkage map. In this study, we used a suite of approaches to investigate the genetic architecture of eight quantitative traits in two long-term study populations of great tits - one in the Netherlands and the other in the United Kingdom. Overall, we found little evidence for the presence of genes of large effects in either population. Instead, traits appeared to be influenced by many genes of small effect, with conservative estimates of the number of contributing loci ranging from 31 to 310. Despite concordance between population-specific heritabilities, we found no evidence for the presence of loci having similar effects in both populations. While population-specific genetic architectures are possible, an undetected shared architecture cannot be rejected because of limited power to map loci of small and moderate effects. This study is one of few examples of genetic architecture analysis in replicated wild populations and highlights some of the challenges and limitations researchers will face when attempting similar molecular quantitative genetic studies in free-living populations.

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