Genome-wide association mapping for kernel and malting quality traits using hostorical European barley records
Matthies, I.E. ; Malosetti, M. ; Roder, M.S. ; Eeuwijk, F.A. van - \ 2014
PLoS ONE 9 (2014)11. - ISSN 1932-6203 - 15 p.
marker-assisted selection - grain protein-content - hordeum-vulgare l. - doubled-haploid population - different germplasm groups - backcross-qtl analysis - linkage disequilibrium - spring barley - yield components - 2-row barley
Malting quality is an important trait in breeding barley (Hordeum vulgare L.). It requires elaborate, expensive phenotyping, which involves micro-malting experiments. Although there is abundant historical information available for different cultivars in different years and trials, that historical information is not often used in genetic analyses. This study aimed to exploit historical records to assist in identifying genomic regions that affect malting and kernel quality traits in barley. This genome-wide association study utilized information on grain yield and 18 quality traits accumulated over 25 years on 174 European spring and winter barley cultivars combined with diversity array technology markers. Marker-trait associations were tested with a mixed linear model. This model took into account the genetic relatedness between cultivars based on principal components scores obtained from marker information. We detected 140 marker-trait associations. Some of these associations confirmed previously known quantitative trait loci for malting quality (on chromosomes 1H, 2H, and 5H). Other associations were reported for the first time in this study. The genetic correlations between traits are discussed in relation to the chromosomal regions associated with the different traits. This approach is expected to be particularly useful when designing strategies for multiple trait improvements.
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.
Greenhouse gas mitigation effects of integrating biomass production into European agriculture
Wit, M.P. de; Lesschen, J.P. ; Londo, M. ; Faaij, A.P.C. - \ 2014
Biofuels Bioproducts and Biorefining 8 (2014)3. - ISSN 1932-104X - p. 374 - 390.
biofuel production potentials - nitrous-oxide emissions - cultivated land - sustainable use - spring barley - n2o emissions - carbon - tillage - management - soil
As energy crop production on European croplands expands, driven by accelerating consumption of bioenergy, there is a pressing need to evaluate the environmental impacts associated with this production. The present study considers on-going yield increases as a means of boosting agricultural output which results in a limited need to convert nature areas and grasslands to additional cropland. For nine land-use variants, the study evaluates cumulative greenhouse gas emissions, net organic carbon fluxes from the soil, and abated emissions achieved by replacing fossil fuels for transport with biofuels. The main finding is that, in European agriculture, it is possible to combine large-scale biomass production with food production sustained at current levels, with limited direct or indirect land-use changes and while accomplishing significant net greenhouse gas mitigation. Maintaining the current (business as usual) agricultural system results in 4.9 GtCO2-eq. of cumulative emissions by 2030. Intensifi ed food production and energy crop production on freed cropland combined with mitigation measure implementation signifi cantly reduces cumulative emissions for the annual crop groups of oil, starch and sugarbeet to 1.9, 1.5 and 2.1 GtCO2-eq., respectively. By 2030, perennial energy crop production can mitigate cumulative emissions to a large extent, reaching negative emissions (i.e. net sequestration) for grass and wood crops of –3.3 and –4.5 GtCO2-eq., respectively. For the variants compared to the baseline, nitrous oxide emissions will increase modestly due to higher fertilizer-application rates, though at improved effi ciencies per unit crop quantity produced. Emission mitigation results partly from the temporary increase in SOC sequestration though mainly from replacement of fossil resources by biomass resources. The results indicate that research and policy efforts aimed at further increasing productivity can raise the output from existing European croplands while being able to reduce or mitigate emissions significantly.
Genetic progress in Dutch crop yields
Rijk, H.C.A. ; Ittersum, M.K. van; Withagen, J.C.M. - \ 2013
plant breeding and genetics - winter wheat - spring barley - potato - sugar beet - crop yield - genetic improvement
This dataset contains the underlying data for the study: Rijk, B., Ittersum, M. van, Withagen, J. "Genetic progress in Dutch crop yields". Field Crops Research 149 (2013) 262–268, http://dx.doi.org/10.1016/j.fcr.2013.05.008
European Perspectives on the Adoption of Nonchemical Weed Management in Reduced-Tillage Systems for Arable Crops
Melander, B. ; Munier-Jolain, N.M. ; Charles, R. ; Wirth, J. ; Schwarz, J. ; Weide, R.Y. van der; Bonin, L. ; Jensen, P.K. ; Kudsk, P.K. - \ 2013
Weed Technology 27 (2013)1. - ISSN 0890-037X - p. 231 - 240.
thistle cirsium-arvense - population-dynamics - oilseed rape - no-till - alopecurus-myosuroides - herbicide performance - conservation tillage - cropping systems - stubble tillage - spring barley
Noninversion tillage with tine- or disc-based cultivations prior to crop establishment is the most common way of reducing tillage for arable cropping systems with small grain cereals, oilseed rape, and maize in Europe. However, new regulations on pesticide use might hinder further expansion of reduced-tillage systems. European agriculture is asked to become less dependent on pesticides and promote crop protection programs based on integrated pest management (IPM) principles. Conventional noninversion tillage systems rely entirely on the availability of glyphosate products, and herbicide consumption is mostly higher compared to plow-based cropping systems. Annual grass weeds and catchweed bedstraw often constitute the principal weed problems in noninversion tillage systems, and crop rotations concurrently have very high proportions of winter cereals. There is a need to redesign cropping systems to allow for more diversification of the crop rotations to combat these weed problems with less herbicide input. Cover crops, stubble management strategies, and tactics that strengthen crop growth relative to weed growth are also seen as important components in future IPM systems, but their impact in noninversion tillage systems needs validation. Direct mechanical weed control methods based on rotating weeding devices such as rotary hoes could become useful in reduced-tillage systems where more crop residues and less workable soils are more prevalent, but further development is needed for effective application. Owing to the frequent use of glyphosate in reduced-tillage systems, perennial weeds are not particularly problematic. However, results from organic cropping systems clearly reveal that desisting from glyphosate use inevitably leads to more problems with perennials, which need to be addressed in future research.
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.
Genome wide association analyses for drought tolerance related traits in barley (Hordeum vulgare L.)
Varshney, R.K. ; Paulo, M.J. ; Grando, S. ; Eeuwijk, F.A. van; Keizer, L.C.P. ; Guo, P. ; Ceccarelli, S. ; Kilian, A. ; Baum, M. ; Graner, A. - \ 2012
Field Crops Research 126 (2012). - ISSN 0378-4290 - p. 171 - 180.
multilocus genotype data - triticum-aestivum l. - ab-qtl analysis - linkage disequilibrium - population-structure - agronomic traits - spring barley - mapping population - allele frequencies - yield components
Genome wide association (GWA) analysis of yield, yield components, developmental, physiological and anatomical traits was conducted for a barley germplasm collection consisting of 185 cultivated (Hordeum vulgare L.) and 38 wild (Hordeum spontaneum L.) genotypes, originating from 30 countries of four continents. Phenotypic evaluations were performed at a dry (Breda) and wet (Tel Hadya) location in Syria. Genome wide association study was done with 816 markers comprised of 710 diversity array technology (DArT), 61 single nucleotide polymorphism (SNP) and 45 microsatellite or simple sequence repeat (SSR) markers. Diversity analysis revealed 5 groups of germplasm, related to origin (Middle East, North Africa), structural information (two-rows), and domestication (wild versus domesticated). Linkage disequilibrium (LD) decayed after 3 cM with a few exceptions at 10 and 15 cM. Although a few QTLs were identified that differed between the dry and wet site, these QTLs explained low phenotypic variation and could not unequivocally be related to drought tolerance when compared to earlier linkage mapping based QTL analysis studies. Therefore, GWA analysis seems to be not very effective for identification of major QTLs for complex traits like drought tolerance in highly structured germplasm collections
Compatible Puccinia hordei infection in barley induces basal defense to subsequent infection by Blumeria graminis
Aghnoum, R. ; Niks, R.E. - \ 2012
Physiological and Molecular Plant Pathology 77 (2012)1. - ISSN 0885-5765 - p. 17 - 22.
f-sp-hordei - systemic acquired-resistance - erysiphe-graminis - induced accessibility - powdery mildew - leaf rust - papilla formation - spring barley - cell-death - inaccessibility
Rusts and powdery mildews employ different strategies to suppress defense during penetration. We observed that a compatible interaction of barley-Puccinia hordei induced increased penetration resistance to a challenge infection by powdery mildew. This induced resistance is local and its level is not determined by the virulence spectrum of the challenger isolate. Our data suggest that the inducer effect is due to rust-stoma communication during penetration, to the presence of the rust hyphae in the apoplast, or to penetration resistance mounted by the rust attacked mesophyll cells. We hypothesized that the rust “primes” the basal defense prior to the mildew infection
Transgressive segregation for very low and high levels of basal resistance to powdery mildew in barley
Aghnoum, R. ; Niks, R.E. - \ 2011
Journal of Plant Physiology 168 (2011)1. - ISSN 0176-1617 - p. 45 - 50.
marker-assisted selection - quantitative trait loci - adult-plant resistance - erysiphe-graminis - puccinia-hordei - spring barley - host-resistance - stripe rust - lines - map
Basal resistance of barley to powdery mildew is a quantitatively inherited trait that limits the growth and sporulation of barley powdery mildew pathogen by a non-hypersensitive mechanism of defense. Two experimental barley lines were developed with a very high (ErBgh) and low (EsBgh) level of basal resistance to powdery mildew by cycles of convergent crossing and phenotypic selection between the most resistant and between the most susceptible lines, respectively, from four mapping populations of barley. Phenotypic selection in convergent crossing was highly effective in producing contrasting phenotypes for basal resistance and susceptibility. In ErBgh, almost 90% of infection units failed to form a primary haustorium in the epidermal cells in association with papilla formation, but in EsBgh only 33% of infection units failed to form a primary haustorium. The contrast between ErBgh and EsBgh for successful formation of secondary and subsequent haustoria was much less obvious (69% versus 79% successful secondary haustorium formation). In an earlier investigation, we determined seven QTLs for basal resistance in the four mapping populations. Checking the peak markers of these QTLs indicated that only four out of seven QTLs were confirmed to be present in the selected resistant lines and only four QTLs for susceptibility were confirmed to be present in the selected susceptible lines. Surprisingly, none of the expected QTLs could be detected in the resistant line ErBgh. We discuss some reasons why marker aided selection might be less efficient in raising levels of basal resistance than phenotypic selection. The very resistant and susceptible lines developed here are valuable material to be used in further experiments to characterize the molecular basis of basal resistance to powdery mildew
Genetic control of pre-heading phases and other traits related to development in a double-haploid barley (Hordeum vulgare L.) population.
Borràs-Gelonch, G. ; Slafer, G.A. ; Casas, A.M. ; Eeuwijk, F.A. van; Romagosa, I. - \ 2010
Field Crops Research 119 (2010)1. - ISSN 0378-4290 - p. 36 - 47.
controlling flowering time - photoperiod response gene - recombinant inbred lines - density consensus map - agronomic traits - mediterranean environments - stem elongation - spring barley - partial resistance - temperate cereals
Extending the phase of stem elongation (SE) has been proposed as a tool to further improve yield potential in small-grain cereals. The genetic control of pre-heading phases may also contribute to a better understanding of phenological traits conferring adaptability. Given that an optimized total time to heading is one of the most important traits in a breeding program, a prerequisite for lengthening SE would be that this and the previous phase (leaf and spikelet initiation, LS) should be under different genetic control. We studied the genetic control of these two pre-heading sub-phases (from sowing to the onset of stem elongation, LS, and from then to heading, SE) in terms of Quantitative Trait Loci (QTL) in a barley double-haploid population derived from the cross Henni × Meltan, both two-rowed spring North European barley cultivars. DH lines (118) and their parents were studied in four field trials in North-Eastern Spain. Genetic control of a number of traits related to leaf appearance and tillering dynamics, which could be important for an early crop canopy structure, were also studied. LS and SE are, at least partially, under a different genetic control in the Henni × Meltan population, mainly due to a QTL on chromosome 2HS. The QTLs responsible for a different control of LS and SE did not seem to correspond with any major gene reported in the literature. Moreover shortening LS, so as to lengthen SE without modifying heading date, would not necessarily imply a negative drawback on traits that could be important for early vigour, such as phyllochron and the onset of tillering
Basal host resistance of barley to powdery mildew: connecting quantitative trait loci and candidate genes
Aghnoum, R. ; Marcel, T.C. ; Johrde, A. ; Pecchioni, N. ; Schweizer, P. ; Niks, R.E. - \ 2010
Molecular Plant-Microbe Interactions 23 (2010)1. - ISSN 0894-0282 - p. 91 - 102.
heterologous rust fungi - head blight resistance - defense-related genes - hordeum-vulgare l - pisum-sativum l. - disease-resistance - leaf rust - nonhost resistance - puccinia-hordei - spring barley
The basal resistance of barley to powdery mildew (Blumeria graminis f. sp. hordei) is a quantitatively inherited trait that is based on nonhypersensitive mechanisms of defense. A functional genomic approach indicates that many plant candidate genes are involved in the defense against formation of fungal haustoria. It is not known which of these candidate genes have allelic variation that contributes to the natural variation in powdery mildew resistance, because many of them may be highly conserved within the barley species and may act downstream of the basal resistance reaction. Twenty-two expressed sequence tag or cDNA clone sequences that are likely to play a role in the barley-Blumeria interaction based on transcriptional profiling, gene silencing, or overexpression data, as well as mlo, Ror1, and Ror2, were mapped and considered candidate genes for contribution to basal resistance. We mapped the quantitative trait loci (QTL) for powdery mildew resistance in six mapping populations of barley at seedling and adult plant stages and developed an improved high-density integrated genetic map containing 6,990 markers for comparing QTL and candidate gene positions over mapping populations. We mapped 12 QTL at seedling stage and 13 QTL at adult plant stage, of which four were in common between the two developmental stages. Six of the candidate genes showed coincidence in their map positions with the QTL identified for basal resistance to powdery mildew. This co-localization justifies giving priority to those six candidate genes to validate them as being responsible for the phenotypic effects of the QTL for basal resistance
Genetic variability in duration of pre-heading phases and relationships with leaf appearance and tillering dynamics in a barley population.
Borràs, G. ; Romagosa, I. ; Eeuwijk, F.A. van; Slafer, G.A. - \ 2009
Field Crops Research 113 (2009)2. - ISSN 0378-4290 - p. 95 - 104.
hordeum-vulgare l - harsh mediterranean environments - controlling flowering time - increasing early vigor - stem elongation - spring barley - photoperiod sensitivity - apical development - agronomic traits - fertile florets
The stem elongation phase seems critical in yield potential determination in barley (Hordeum vulgare L.). Extending its duration, without modifying total time to anthesis, has been proposed as a promising breeding tool. A prerequisite for its use is that the duration of phases before and after jointing (that including leaf and spikelet initiation, LS, and that of stem elongation, SE) should be under different genetic control. In addition, little is known about the implications of changes in the duration of LS and SE upon other developmental traits which could affect other aspects of yield generation, such as phyllochron and tillering. Thus, the objectives of the present work were to study the genetic variability in LS and SE, in traits related to leaf appearance and tillering, as well as their relationships, in a double-haploid (DH) population derived from the cross Henni × Meltan. DH lines and both parents were studied in four field trials. Despite the similarity in development between parents, there was significant genetic variability in duration of both LS and SE (i.e. considerable transgressive segregation was observed), with no major genetic correlations found between them. Although some significant genetic correlations were found between duration of phases and leaf appearance and tillering traits, it has been shown that modifying the duration of LS does not necessarily imply concomitant changes in traits that could be important for an early expansion of the crop canopy (i.e. phyllochron, onset and rate of tillering).
Grain Yield Variation in Malting Barley Cultivars in Uruguay and Its Consequences for the Design of a Trials Network
Ceretta, S.S.E. ; Eeuwijk, F.A. van - \ 2008
Crop Science 48 (2008). - ISSN 0011-183X - p. 167 - 180.
multi-environment trials - spring barley - ecophysiological analyses - high-temperature - bilinear models - short periods - wheat - genotype - selection - variety
The efficiency of cultivar trial networks is an important subject in official cultivar testing. We investigated this efficiency for malting barley (Hordeum vulgare L.) in Uruguay, using data on 213 cultivars tested across an eight-year period at six locations. The variance-components approach was used to quantify the effects of years, locations, sowing dates and replicates on the precision of cultivar mean comparisons. The relationships among testing environments and genotypic adaptation patterns were explored via biplots. Factorial regression was used to model genotype x environment interaction (GEI) directly in relation to measured environmental variables. Variance components indicated that both the number of locations and sowing dates could be reduced. Biplot analysis identified some repeatable GEI patterns. Factorial regression showed that mean daily temperature during the emergence-heading period and daily minimum temperature at heading explained 20% of GEI. Still, the majority of the GEI appeared to be highly nonrepeatable. A future network should focus on wide adaptation while enhancing the chances to exploit specific adaptation to the prevalent temperature conditions by sampling contrasting sowing dates at different locations.
Effect of partial resistance to barley leaf rust, Puccinia hordei, on the yield of three barley cultivars
Ochoa, J. ; Parlevliet, J.E. - \ 2007
Euphytica 153 (2007)3. - ISSN 0014-2336 - p. 309 - 312.
grain-yield - spring barley - brown rust - wheat - weight - leaves - mildew - race
Three barley cultivars, Shyri, Clipper and Terán, with different levels of partial resistance to barley leaf rust, caused by Puccinia hordei, were exposed to six levels of the pathogen. These levels were obtained by 5, 4, 3, 2, 1 and 0 fungicide (Propiconazol) applications respectively and occurred every 15 days starting at 66 days after sowing. No application served as the control treatment. There were three replicates. The six-row plots were surrounded by a row of a highly susceptible barley cultivar in which the barley leaf rust arrived naturally in a fairly early plant stage. The disease severity was assessed five times with 15 days intervals starting at 66 days after sowing. The yields were determined by harvesting the inner four rows of the plots. An analysis of variance was carried out on the area under the disease progress curve (AUDPC) data and on the yield data. `Shyri¿ was the least susceptible cultivar, `Terán¿ the most. The percentage yield losses varied with the six levels of pathogen from 0 to 31.5% (`Shyri¿), from 0 to 46% (`Clipper¿) and from 0 to 63.5% (`Terán¿). The yield losses correlated strongly with the AUDPC, the linear correlation coefficient being 0.97. The yield losses indicate the importance of the pathogen in Ecuador. It also means that high levels of partial resistance are needed to prevent significant yield damage.
Identification of QTLs for powdery mildew and scald resistance in barley
Shtaya, M.J.Y. ; Marcel, T.C. ; Sillero, J.C. ; Niks, R.E. ; Rubiales, D. - \ 2006
Euphytica 151 (2006)3. - ISSN 0014-2336 - p. 421 - 429.
quantitative trait loci - hordeum-vulgare l - erysiphe-graminis-hordei - rust puccinia-hordei - f-sp hordei - rhynchosporium-secalis - spring barley - ssp spontaneum - rflp markers - wild barley
A population of 103 recombinant inbred lines (RILs, F9-derived lines) developed from the two-row spring barley cross L94 × `Vada¿ was evaluated under field conditions for resistance against powdery mildew (Blumeria graminis f.sp. hordei) and scald (Rhynchosporium secalis). Apart from the major resistance gene mlo on chromosome 4 (4H), three QTLs (Rbgq1, Rbgq2 and Rbgq3) for resistance against powdery mildew were detected on chromosomes 2 (2H), 3 (3H), and 7 (5H), respectively. Rbgq1 and Rbgq2 have not been reported before, and did not map to a chromosome region where a major gene for powdery mildew had been reported. Four QTLs (Rrsq1, Rrsq2, Rrsq3 and Rrsq4) for resistance against scald were detected on chromosomes 3 (3H), 4 (4H) and 6 (6H). All four mapped to places where QTLs for scald resistance had been reported before in different populations