Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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QTLs for barley yield adaptation to Mediterranean environments in the ‘Nure’ × ‘Tremois’ biparental population
Tondelli, A. ; Francia, E. ; Visioni, A. ; Comadran, J. ; Mastrangelo, A.M. ; Akar, T. ; Al-Yassina, A. ; Ceccarelli, S. ; Grando, S. ; Eeuwijk, F.A. van; Thomas, W.T.B. ; Stanca, A.M. ; Romagosa, I. ; Pecchioni, N. - \ 2014
Euphytica 197 (2014)1. - ISSN 0014-2336 - p. 73 - 86.
quantitative trait loci - hordeum-vulgare - drought tolerance - agronomic traits - flowering time - abiotic stress - grain-yield - major genes - linkage map - wheat
Multi-environment trials represent a highly valuable tool for the identification of the genetic bases of crop yield potential and stress adaptation. A Diversity Array Technology®-based barley map has been developed in the ‘Nure’ × ‘Tremois’ biparental Doubled Haploid population, harbouring the genomic position of a gene set with a putative role in the regulation of flowering time and abiotic stress response in barley. The population has been evaluated in eighteen location-by-year combinations across the Mediterranean basin. QTL mapping identified several genomic regions responsible for barley adaptation to Mediterranean conditions in terms of phenology, grain yield and yield component traits. The most frequently detected yield QTL had the early flowering HvCEN_EPS2 locus (chromosome 2H) as peak marker, showing a positive effect from the early winter parent ‘Nure’ in eight field trials, and explaining up to 45.8 % of the observed variance for grain yield. The HvBM5A_VRN-H1 locus on chromosome 5H and the genomic region possibly corresponding to PPD-H2 on chromosome 1H were significantly associated to grain yield in five and three locations, respectively. Environment-specific QTLs for grain yield, and clusters of yield component QTLs not related to phenology and or developmental genes (e.g. on chromosome 4H, BIN_09) were observed as well. The results of this work provide a valuable source of knowledge and tools for both explaining the genetic bases of barley yield adaptation across the Mediterranean basin, and using QTL-associated markers for MAS pre-breeding and breeding programmes.
Determinants of barley grain yield in drought-prone Mediterranean environments
Francia, E. ; Tondelli, A. ; Rizza, F. ; Badeck, F.W. ; Thomas, W.T.B. ; Eeuwijk, F. van; Romagosa, I. ; Stanca, A.M. ; Pecchioni, N. - \ 2013
Italian Journal of Agronomy 8 (2013)1. - ISSN 1125-4718 - p. 1 - 8.
The determinants of barley grain yield in drought-prone Mediterranean environments have been studied in the Nure x Tremois (NT) population. A large set of yield and other morpho-physiological data were recorded in 118 doubled-haploid lines of the population, in multi-environment field trials (18 site-year combination). Agrometeorological variables have been recorded and calculated at each site too. Four main periods of barley development were considered, vegetative, reproductive early and late grain filling phases, to dissect the effect on yield traits of the growth phases. Relationships between agrometeorological variables, grain yield (GY) and its main components (GN and GW) were also investigated by correlation. Results firstly gave a clear indication of the involvement of water consumption in determining GY and GW (r2=0.616, P=0.007 and r2=0.703, P=0.005, respectively) calculated from sowing to the early grain filling period, while GN showed its highest correlation with the total photothermal quotient (PQ) calculated for the same period (r2=0.646, P=0.013). With the only exception of total PQ calculated during the vegetative period, all significant correlations with GY were associated to water-dependent agrometeorological parameters. As a second result, the NT segregating population allowed us to weight the amount of interaction due to genotypes over environments or to environments in relation to genotypes by a GGE analysis; 47.67% of G+GE sum of squares was explained by the first two principal components. Then, the introduction of genomic information at major barley genes regulating the length of growth cycle allowed us to explain patterns of adaptation of different groups of NT lines according to the variants (alleles) harbored at venalization (Vrn-H1) in combination with earliness (Eam6) genes. The superiority of the lines carrying the Nure allele at Eam6 was confirmed by factorial ANOVA testing the four possible haplotypes obtained combining alternative alleles at Eam6 and Vrn-H1. Maximum yield potential and differentials among the NT genotypes was finally explored through Finlay-Wilkinson model to interpret grain yield of NT genotypes together with yield adaptability (Ya), as the regression coefficient bi; Ya ranged from 0.71 for NT77 to 1.20 for NT19. Lines simply harboring the Nure variants at the two genes behaved as highest yielding (3.04 t ha-1), and showed the highest yield adaptability (bi=1.05). The present study constitutes a starting point towards the introduction of genomic variables in agronomic models for barley grain yield in Mediterranean environments
Determinants of barley grain yield in a wide range of Mediterranean environments
Francia, E. ; Tondelli, A. ; Rizza, F. ; Badeck, F.W. ; Li Destri Nicosia, O. ; Akar, T. ; Grando, S. ; Al-Yassin, A. ; Benkelkacim, A. ; Thomas, W.T.B. ; Eeuwijk, F.A. van; Romagosa, I. ; Stanca, A.M. ; Pechionni, N. - \ 2011
Field Crops Research 120 (2011)1. - ISSN 0378-4290 - p. 169 - 178.
carbon-isotope discrimination - drought tolerance - stress tolerance - number - genes - wheat - improvement - adaptation - temperature - photoperiod
Barley grain yield in rainfed Mediterranean regions can be largely influenced by terminal drought events. In this study the ecophysiological performance of the ‘Nure’ (winter) × ‘Tremois’ (spring) barley mapping population (118 Doubled Haploids, DHs) was evaluated in a multi-environment trial of eighteen site–year combinations across the Mediterranean Basin during two consecutive harvest years (2004 and 2005). Mean grain yield of sites ranged from 0.07 to 5.43 t ha-1, clearly dependent upon both the total water input (rainfall plus irrigation) and the water stress index (WSI) accumulated during the growing season. All DHs were characterized for possessing molecular marker alleles tagging four genes that regulate barley cycle, i.e. Vrn-H1, Vrn-H2, Ppd-H2 and Eam6. Grain yield differences were initially interpreted in terms of mean differences between genotypes (G), environments (E), and for each combination of genotype and environment (GE) through a “full interaction” ANOVA model. Variance components estimates clearly showed the greater importance of GE over G, although both were much lower than E. Alternative linear and bilinear models of increasing complexity were used to describe GE. A linear model fitting allelic variation at the four genes explained genotype main effect and genotype × environment interaction much better than growth habit itself. Adaptation was primarily driven by the allelic constitution at three out of the four segregating major genes, i.e. Vrn-H1, Ppd-H2 and Eam6. In fact, the three genes together explained 47.2% of G and 26.3% of GE sum of squares. Grain yield performance was more determined by the number of grains per unit area than by the grain weight (phenotypic correlation across all genotypic values: r = 0.948 and 0.559, respectively). The inter-relationships among a series of characters defining grain yield and its components were also explored as a function of the length of the different barley developmental phases, i.e. vegetative, reproductive, and grain filling stages. In most environments, the best performing (adapted) genotypes were those with faster development until early occurrence of anthesis. This confirmed the crucial role of the period defining the number of grains per unit area in grain yield determination under Mediterranean environments
Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin
Comodran, J. ; Thomas, W.T.B. ; Eeuwijk, F.A. van; Ceccarelli, S. ; Grando, S. ; Stanca, A.M. ; Pecchioni, N. ; Akar, T. ; Al-Yassin, A. ; Benbelkacem, A. ; Ouabbou, H. ; Bort, J. ; Romagosa, I. ; Hackett, C.A. ; Russel, J.R. - \ 2009
Theoretical and Applied Genetics 119 (2009)1. - ISSN 0040-5752 - p. 175 - 187.
multilocus genotype data - ssp-spontaneum - haplotype structure - powdery mildew - barley - genome - resistance - loci - polymorphism - cultivars
Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley
Statistical Analysis of Genotype by Environment Data
Romagosa, I. ; Eeuwijk, F.A. van; Thomas, W.T.B. - \ 2009
In: Handbook for Plant Breeding. Vol. 3. Cereals. Pt. 2 / Carena, M.J., Springer Science + Business Media - ISBN 9780387722979 - p. 1 - 41.
We introduce in this chapter a series of linear and bilinear models for the study of genotype by environment interaction (GE) and adaptation. These models increasingly incorporate available genetic, physiological, and environmental information for modelling genotype by environment interaction (GE). They are based on analyses of variance and regression and can be formulated in most standard statistical packages. We use the data of a series of trials for 65 barley genotypes (G) grown in 12 environments (E) for illustration and interpretation of the output of such analyses. We aim at identifying key environmental covariables to explain differential phenotypic responses as well as to estimate genotypic sensitivities to these covariables. Using genetic covariables in the form of molecular markers, we partition genotypic main effect terms and GE terms into main effects for quantitative trait loci (QTL) and QTL by environment interaction (QTL.E). The QTL.E estimates can be further regressed on environmental covariables to target differential QTL expression potentially related to environmental factors. We believe that the statistical models that describe GE in direct association to genetic, physiological, and environmental information provide insight in GE and facilitate the development and deployment of new breeding strategies
Mapping adaptation of barley to droughted environments
Comadran, J. ; Russell, J.R. ; Eeuwijk, F.A. van; Ceccarelli, S. ; Grando, S. ; Baum, M. ; Stanca, A.M. ; Pecchioni, N. ; Mastrangelo, A.M. ; Akar, T. ; Al-Yassin, A. ; Benbelkacem, A. ; Choumane, W. ; Ouabbou, H. ; Dahan, R. ; Bort, J. ; Araus, J.L. ; Pswarayi, A. ; Romagosa, I. ; Hackett, C.A. ; Thomas, W.T.B. - \ 2008
Euphytica 161 (2008)1-2. - ISSN 0014-2336 - p. 35 - 45.
agronomic traits - tolerance - genome - genes - associations - genotype - yield - plant - qtls
Identifying barley genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and the development of more drought tolerant cultivars. We assembled a population of 192 genotypes that represented landraces, old, and contemporary cultivars sampling key regions around the Mediterranean basin and the rest of Europe. The population was genotyped with a stratified set of 50 genomic and EST derived molecular markers, 49 of which were Simple Sequence Repeats (SSRs), which revealed an underlying population sub-structure that corresponded closely to the geographic regions in which the genotypes were grown. A more dense whole genome scan was generated by using Diversity Array Technology (DArT®) to generate 1130 biallelic markers for the population. The population was grown at two contrasting sites in each of seven Mediterranean countries for harvest 2004 and 2005 and grain yield data collected. Mean yield levels ranged from 0.3 to 6.2 t/ha, with highly significant genetic variation in low-yielding environments. Associations of yield with barley genomic regions were then detected by combining the DArT marker data with the yield data in mixed model analyses for the individual trials, followed by multiple regression of yield on markers to identify a multi-locus subset of significant markers/QTLs. QTLs exhibiting a pre-defined consistency across environments were detected in bins 4, 6, 6 and 7 on barley chromosomes 3H, 4H, 5H and 7H respectively
Barley adaptation and improvement in the Mediterranean basin
Pswarayi, A. ; Eeuwijk, F.A. van; Ceccarelli, S. ; Grando, S. ; Comadran, J. ; Russell, J.R. ; Stanca, A.M. ; Francia, E. ; Pecchioni, N. ; Akar, T. ; Al-Yassin, A. ; Benbelkacem, A. ; Choumane, W. ; Karrou, M. ; Ouabbou, H. ; Bort, J. ; Araus, J.L. ; Molina-Cano, J.L. ; Thomas, W.T.B. ; Romagosa, I. - \ 2008
Plant Breeding 127 (2008)6. - ISSN 0179-9541 - p. 554 - 560.
environment interaction - genotype - yield - selection - traits - spain
To study barley adaptation and improvement in the Mediterranean basin, a collection of 188 entries comprising landraces and old genotypes and current modern varieties from the Mediterranean basin and elsewhere was tested on moisture-contrasted environments in seven Mediterranean countries, during 2004 and 2005 harvest seasons. The experimental design consisted of an unreplicated trial for all entries, augmented by four repeated checks to which a partial replicate containing a quarter of the entries was added. Best Linear Unbiased Predictions (BLUPs) representing adjusted genotypic means were generated for individual trials using a mixed model. BLUPs were used for genotype by environment interaction analysis using main effect plus genotype by environment interaction (GGE) biplots of yield ranked data and for comparisons of landraces, old and modern genotypes using analysis of variance. Mean yields ranged from near crop failure to 6 t/ha. Local landraces were better adapted to environments yielding below 2 t/ha, thus breeding has mostly benefited environments yielding above 2 t/ha where modern genotypes out yielded landraces and old cultivars by 15%. Current barley selection is leading to specifically adapted genotypes.
Changes in allele frequencies in landraces, old and modern barley cultivars of marker loci close to QTL for grain yield under high and low input conditions
Pswarayi, A. ; Eeuwijk, F.A. van; Ceccarelli, S. ; Grando, S. ; Comadran, J. ; Russell, J.R. ; Pecchioni, N. ; Alessandro, T. ; Akar, T. ; Al-Yassin, A. ; Benbelkacem, A. ; Ouabbou, H. ; Thomas, W.T.B. ; Romagosa, I. - \ 2008
Euphytica 163 (2008)3. - ISSN 0014-2336 - p. 435 - 447.
quantitative trait loci - false discovery rate - field-grown barley - environmental covariables - stress tolerance - adaptation - genotype - genome - maize - dart
Changes in alleles frequencies of marker loci linked to yield quantitative trait loci (QTL) were studied in 188 barley entries (landraces, old and modern cultivars) grown in six trials representing low and high yielding conditions in Spain (2004) and Syria (2004, 2005). A genome wise association analysis was performed per trial, using 811 DArT® markers of known map position. At the first stage of analysis, spatially adjusted genotypic means were created per trial by fitting mixed models. At the second stage, single QTL models were fitted with correction for population substructure, using regression models. Finally, multiple QTL models were constructed by backward selection from a regression model containing all significant markers from the single QTL analyses. In addition to the association analyses per trial, genotype by environment interaction was investigated across the six trials. Landraces seemed best adapted to low yielding environments, while old and modern entries adapted better to high yielding environments. The number of QTL and the magnitude of their effects were comparable for low and high input conditions. However, none of the QTL were found within a given bin at any chromosome in more than two of the six trials. Changes in allele frequencies of marker loci close to QTL for grain yield in landraces, old and modern barley cultivars could be attributed to selection exercised in breeding, suggesting that modern breeding may have increased frequencies of marker alleles close to QTL that favour production particularly under high yield potential environments. Moreover, these results also indicate that there may be scope for improving yield under low input systems, as breeding so far has hardly changed allele frequencies at marker loci close to QTL for low yielding conditions.
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