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Whealbi

Wheat and barley Legacy for Breeding Improvement

Grant agreement number: FP7-613556

Collaborative Project

SEVENTH FRAMEWORK PROGRAMME

Deliverable D3.4: Detailed and quantitative information on wheat or barley resistance towards the main plant diseases, novel sources of disease resistance and new resistant loci.

Due date: 54

Actual submission date: 59

Project start date: January 1st, 2014 Duration: 60 months

Workpackage concerned: 3

Concerned workpackage leader: CREA

Dissemination level: PU

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Table of contents

TABLE OF CONTENTS ...................................................................................................................................... 2

GLOSSARY AND DEFINITIONS ...................................................................................................................... 3

SUMMARY ........................................................................................................................................................... 4

1. WHEAT AND STAGONOSPORA NODORUM (WHEAT LEAF BLOTCH) ........................................ 5

2. WHEAT AND BLUMERIA GRAMINIS F. SP. GRAMINIS (WHEAT POWDERY MILDEW) ...... 5

A. RACE-SPECIFIC RESISTANCE ............................................................................................................... 5

B. ADULT PLANT RESISTANCE .................................................................................................................. 6

3. WHEAT AND FUSARIUM HEAD BLIGHT ........................................................................................... 8

4. WHEAT AND PUCCINIA TRITICINA (WHEAT LEAF RUST) ......................................................... 11

5. WHEAT AND ZYMOSEPTORIA TRITICI (SEPTORIA LEAF BLOTCH) ....................................... 12

6. BARLEY AND BLUMERIA GRAMINIS F. SP. HORDEI (BARLEY POWDERY MILDEW) ........ 14

7. BARLEY AND PHYRENOPHORA TERES (BARLEY NET BLOCH) ............................................... 16

CONCLUSION.................................................................................................................................................... 17

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Glossary and Definitions ANOVA Analysis Of Variance AUDPC Area Under Disease Progress Curve Bgh Blumeria graminis f. sp. hordei Bgt Blumeria graminis f. sp. tritici ddpi degree days post inoculation DI disease index (PDS×DS) DLA Detached leaf assay DS Disease severity FHB Fusarium Head Blight GWAS Genome Wide Association Studies INC Incidence is the percentage of infected spikes per plot INDEL Insertion/Deletion polymorphism INDEX Disease Index = SEV x INC PDS Percentage of diseased spikelets QTL Quantitative Trait Loci r2 Percentage of phenotypic variation explained by the QTL (obtained by

ANOVA with strongest associated marker as factor) SEV Mean score per plot of disease severity on spikes SNP Single Nucleotide Polymorphism

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Summary Objectives: This deliverable aims to explore the diversity of the WHEALBI germplasm

collection for response to the main wheat and barley diseases and to identify and support the

mapping of new resistance genes/QTLs.

Rationale: The deliverable has carried out the analyses about the following diseases: i)

Stagonospora nodorum (wheat leaf blotch), ii) Blumeria graminis f.sp. tritici (wheat powdery

mildew), iii) Fusarium Head Blight in wheat, iv) Puccinia striiformis f.sp. tritici (wheat stripe

rust), v) Zymoseptoria tritici blotch (wheat septoria leaf blotch), vi) Blumeria graminis f.sp.

hordei (barley powdery mildew); vii) Phyrenophora teres (barley net bloch). Depending on

the specific disease, the inoculations have been carried out in field conditions, greenhouses

or growth chambers using selected strains. The inoculation method and the evaluation of the

disease severity were tailored on the specific disease tested. The phenotypic data have been

used for postulation analyses (wheat rust) or integrated with genotypic data (WP2) and

employed either for GWAS analysis or for allele mining (WP5).

Teams involved: INRA, IPK, CREA, UZH

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Figure 1: Reaction types of wheat accessions with Stagonospora nodorum isolate SnToxA. -: insensitive (absence of necrosis); +: sensitive (extensive necrosis); -/+: inconsistent insensitive/sensitive reaction

1. Wheat and Stagonospora nodorum (wheat leaf blotch)

Out of 512 accessions tested for the presence of the Tsn1 toxin receptor-encoding gene, 344

were insensitive to the toxin, 132 sensitive and 36 did not show a consistent

insensitive/sensitive (classified as intermediate phenotype). As the CDS of the Tsn1 gene

was not present on the exome capture array, the GWAS analysis of the 476 clearly

insensitive or sensitive accessions did not reveal the genetic region of chromosome 1BS

where the SnToxA receptor gene Tsn1 is located. However, GWAS identified a genomic

region in chromosome 5B associated with SnToxA resistance that did not overlap with known

resistance loci and hence might be a novel source of resistance. Extensive gene annotation

and haplotyping studies are ongoing to identify candidate genes conferring SnToxA

resistance.

2. Wheat and Blumeria graminis f. sp. graminis (wheat powdery mildew)

a. Race-specific resistance

To discover new sources of race-specific resistance against powdery mildew, the collection

was evaluated at seedling stage against three Swiss (Bgt94204, Bgt96224 and Bgt98230)

and an English (JIW2) wheat mildew isolate with complementing virulence spectra. Infection

tests were performed on detached segments of the first leaves of 8-10 d old seedlings.

Results are based on four biological replicates (two independent inoculation experiments)

and analysed by manual disease scoring. Three classes of host reactions were

distinguished: r = resistant (0-10% of the leaf surface covered), i = intermediate (10-25% of

the leaf surface covered) and s = susceptible (25% of the leaf surface covered). Only

hexaploid wheat lines were evaluated to circumvent misleading conclusions derived from

eventual non-host resistance mechanisms. As a result, 446 wheat lines were subjected to

infection tests. 18 accessions were resistant and 241 susceptible to the four isolates. The

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Figure 2: Virulence of the four Bgt isolates tested on 444 accessions of the Whealbi collection. Res: <10% area covered by mildew; Int: 10-25% leaf area covered by mildew; Sus: >25% leaf area covered by mildew

remaining 187 lines showed resistance to at least one of the isolates. Based on this data, it

could be inferred that, at least, 187 accessions harbour one (or more) Pm resistance gene.

42

7

397

Res Int Sus

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ac

ce

ss

ion

s

BgtJIW2

64

21

361

Res Int Sus

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119

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306

Res Int Sus

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120

18

308

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b. Adult plant resistance

To search QTLs for effective field resistance to powdery mildew, the population was

evaluated through multi-year, multi-site trials involving only hexaploid genotypes for the same

reasons cited above. On the one hand, 121 spring wheat accessions were evaluated over

the growing seasons 2015-2016, 2016-2017 and 2017-2018 at two contrasting locations in

Switzerland (Nyon and Zurich). However, due to the small population size, the GWAS

analysis did not reveal significant QTLs associated with powdery mildew resistance.

Nevertheless, genotype-environment interactions were studied using heritability-adjusted

genotype plus genotype-environment biplots analysis (HA-GGE).

HA-Biplots revealed nine accessions (WW-071, WW-314, WW-363, WW-373, WW-404,

WW-440, WW-470, WW-497 and WW-502) showing stable resistance over the environments

studied. Interestingly, these accessions have been reported not to harbour race-specific

resistance genes (data not shown). These data suggest that these nine accessions carry a

horizontal type of resistance to powdery mildew, making those accessions potential donors

of quantitative resistance mildew to be introgressed in elite wheat cultivars. On the other

hand, the remaining 325 winter accessions were evaluated over the growing seasons 2016-

2017 and 2017-2018 at the same locations. The preliminary GWAS analysis did not identify

genomic regions significantly associated with adult plant resistance, most probably due to the

high genetic relatedness between the most resistant varieties. Finally, the HA-Biplots

identified a group of accessions (WW-012, WW-015, WW-030, WW-031, WW-039, WW-040,

WW-053, WW-055, WW-159, WW-161, WW-353, WW-451) with very high and stable

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Figure 4: GGE biplot based on powdery mildew incidence on 325 winter-type accessions at three location-year environments (orange vectors): Reckenholz 2017, 2018 and Nyon 2018.

Figure 3: A) GGE biplot based on powdery mildew incidence on 121 spring-type accessions at four location-year environments (blue vectors): from 2016 to 2017 at Reckenholz and Nyon. B) Zoom-in focussing on the accessions showing more stable across the environments. Accessions coloured in red were susceptible to the four isolates in the seedling evaluation experiments.

resistance to powdery mildew across the environments, with AUDPC values lower than 15%

compared to the most susceptible wheat line.

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3. Wheat and Fusarium Head Blight

A panel of 478 wheat accessions has been phenotyped for Fusarium Head Blight (FHB)

response during year 2016 in INRA Clermont-Ferrand station. Trial followed a 3-randomized

complete block design, with 2 artificially inoculated blocks, and one non-inoculated control

block. Each plot of 3 lines per accession was individually spray-inoculated at mid-anthesis

with a 105 spores/ml inoculum of the pathogenic and mycotoxinogen FG1 Fusarium

graminearum strain.

Plots were shot directly in the field at two different dates, 350 and 450 degree-days post

inoculation (ddpi), using a camera device controlling light condition. Images analyses were

performed with the “Fusatech processing” algorithm (issued from DOPM GDEC INRA –

Veodis 3D collaboration) to produce two types of phenotyping traits: disease severity (DS, 1-

9 scale) and percentage of diseased spikelets (PDS). DI (disease index) = PDS×DS has not

been calculated yet but will be done. Plots were then harvested at maturity state; seeds are

stored at 4°C to permit measures of fusarium damaged kernels percentages. Phenotyping

data were analysed with R software. Statistical results showed the reliability of the trial with

development of FHB and good repeatabilities with no significant differences between

replicates. Broad-sense heritabilities were high with 0,87 and 0,84 for disease severity at 350

and 450 ddpi respectively. Heritabilities for percentage of diseased spikelets were identical to

disease severity for both dates. Correlation coefficients were up to 0.83 between disease

severity measured by an expert (SEV_450_expert) and disease severity assessed

automatically by the algorithm (SEV_350 and SEV_450).

Genotypic data were obtained by exome sequencing (provided by WP2) for 433 wheat

accessions and about 500.000 SNP or INDEL markers were used for GWAS analyses

performed on adjusted means of FHB traits using GenABEL R software package. Nineteen

QTLs involved in the determination of FHB resistance have been detected considering a

threshold of 4 for –log10(p-value) (Table 1). No co-localisation was found with heading date

or plant height. Several QTLs were associated with INDEX traits, each time with a second

FHB trait (with suitable distribution for GWAS), except on chromosomes 1B and 2A.

Strongest r2 (23%) was obtained for a QTL on chromosome 2D associated with incidence

measured by an expert at 450 ddpi, with an allelic effect of 11% of infected spikes per plot.

The second one (r2 = 20%) was obtained for disease index and disease severity at 350 ddpi

on chromosome 7D. This QTL was also the most certain QTL with a –log10(p-value) of 10.6

(above Bonferroni threshold of 6.6). The main results are reported in Figure 2.

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Figure 5. Manhattan plots of QTLs detected on chromosomes 5A (left) and 7D (right) for incidence at

450 ddpi and disease index at 350ddpi respectively.

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Table 1. Parameters of QTLs detected with GenABEL for Whealbi panel toward FHB: strongest associated Marker Name, TRAIT concerned, physical POSITION of this marker on CHROMOSOME (in base pair). R2 indicates percentage of phenotypic variation explained by this association. Allelic effect (effB), standard error (se_effB) of the minor allele (=A2), minor allele frequency (MAF) and favorable allele (Allele_FAV) to the QTL are given for this marker.

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4. Wheat and Puccinia triticina (wheat leaf rust)

Given the host specificity of Puccinia triticina, only the 454 bread wheat accessions from the

Whealbi panel were evaluated with bread wheat derived isolates at INRA BIOGER. The

objective of the evaluation was the postulation of known Lr-resistance genes in each

accession and the detection of new sources of resistance to P. triticina. The panel was

evaluated in two steps. In the first step, the 454 accessions were evaluated with 4 isolates

carrying few virulences to detect and eliminate the susceptible accessions. About half, 47%

of the accessions, were susceptible and didn’t carry any resistance gene (Table 2). In the

second step, the 240 remaining accessions were evaluated with 15 isolates differential for

their virulences and allowing the postulation of Lr-genes with the limitation that the

postulation of Lr-genes becomes complicated when an accession carries more than 3 Lr-

genes. About 47% of the accessions carried 1, 2 or 3 Lr-genes. The most common genes

were Lr13, Lr14a and Lr37, respectively (Figure 6A), often in combinations within the same

accession (Figure 6B). Other genes Lr10, Lr3, Lr26 and Lr1 were detected in more than 5%

of the accessions (Figure 6A). Finally, 39 accessions carry at least one unknown resistance

gene, and 7 accessions had a resistance effective towards all tested isolates: Sibilla, Galil,

3716-1, Daeraad, Orfield, M45/66, and M708//G25/N163. Presence/absence of the 7 most

common Lr-genes are being used as a qualitative binary phenotype to detect linked

molecular markers through GWAS analyses performed in collaboration with partner 9 at

Haifa University.

Table 2. Repartition of accessions in the Whealbi panel according to their content in Lr-genes; a

including 39 accessions carrying unknown resistance genes.

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Figure 6. A: Presence of Lr- genes, and B: Occurence of combinations of Lr-genes in the Whealbi panel.

5. Wheat and Zymoseptoria tritici (septoria leaf blotch)

Given the host specificity of Zymoseptoria tritici, only the 454 bread wheat accessions from

the Whealbi panel were evaluated with bread wheat derived isolates at INRA BIOGER. The

objective of the evaluation was the identification of the most promising accessions of the

panel for the effectiveness of their resistance to a large set of Z. tritici isolates. All the

interactions were tested on seedlings under controlled conditions. The evolution of symptoms

and sporulation was quantitatively evaluated, visually, at three dates during the infectious

process. The panel was evaluated in three steps. I) the 454 accessions were inoculated with

the aggressive isolate IPO-09415 from France. II) the 112 most resistant accessions were

inoculated with 3 other French isolates carrying different virulences to known Stb- resistance

genes. III) the 30 most resistant accessions to the French isolates were inoculated with 13

world isolates carrying different virulences (Table 3). Those 30 selected accessions were

also tested in the field with isolate IPO-09415 to evaluate the effectiveness of their resistance

at the adult plant stage. This work led to the identification of only 6 accessions being

resistant to all tested septoria isolates at both developmental stages: Prince-Leopold, Blanc

Précoce, Trigo de Monte, KWS Magic, Landrace WW-472, and H93-70 (Table 3).

Quantitative data obtained with the four French isolates are being used to detect resistance

loci through GWAS analyses; performed in collaboration with partner 9 at Haifa University.

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Table 3. Mean sporulating leaf area (in %) of the 30 most resistant accessions of the Whealbi panel (and susceptible control, Taichung-29) with 17 Z. tritici isolates; 0 (green) indicates resistance and 100 (red) susceptibility.

Furthermore, new phenotyping methods were developed for septoria allowing to characterize

and quantify fungal sporulation by image and particle analyses. The image analysis method

recently published by Stewart et al. (2016: Phytopathology 106-7) was adapted to conditions

of our infection assays and used to evaluate the density of pycnidia present on inoculated

leaves. The recent acquisition of a particle analyser (Occhio Flow Cell 200) allowed

developing a protocol for the counting of pycnidiospores produced by inoculated leaves, and

to estimate the average number of pycnidiospores produced per pycnidia. These new

methods were applied to phenotype 148 progeny isolates derived from a cross between the

French isolates I05 and I07 on cultivar Renan. Previous screenings showed that I05 and I07

gave a differential reaction on cultivar Renan (Figure 7). The first results obtained showed a

significant segregation for traits pycnidia density and pycnidiospores production within the

progeny. These data will be used to map QTL implicated in the pathogenicity of Z. tritici.

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Figure 7. Classification of the selected barley Whealbi accessions based upon the development of macroscopic disease symptoms A) 460 lines of the barley Whealbi collection were inoculated with the powdery mildew isolate (D35/3) and the genotypes were grouped due to the median of the infected leaf area (%). B) 267 lines of the barley Whealbi collection were inoculated with the powdery mildew isolates D35/3 and RiIII and the genotypes were grouped due to the normalized average of the infected leaf area (%).

6. Barley and Blumeria graminis f. sp. hordei (barley powdery mildew)

The obligate biotrophic fungus Blumeria graminis f. sp. hordei (Bgh) is the causal agent of

barley powdery mildew. The project aims to identify new race-nonspecific resistance genes

or new alleles of known genes against Bgh and the basis was the precision phenotyping of

the Whealbi barley collection. The partner IPK has examined 460 barley genotypes in

response to Bgh isolate D35/3 using a phenotypic screening based on detached leaf assay

(DLA) with twelve-day old seedling leaves. The development of macroscopic disease

symptoms was visually scored after seven days. This first screen revealed that the collection

spans the complete range of susceptibility to Bgh isolate D35/3 (Figure 7A). 267 accessions

were selected after the first screening from all defined susceptibility classes and further

phenotyped as before but with two poly-virulent Bgh isolates (D35/3 and RiIII) that together

overcome more than 37 known major R-genes (Surlan-Momitovic et al., 2016 Genet Res

Crop Evol 63: 275-287). The screen revealed 21 accessions completely resistant against

both isolates (Figure 7B).

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Table 4. Isolate test of the ten resistant genotypes with seven powdery mildew isolates The remaining ten resistant genotypes were analysed via isolate test with seven additional powdery mildew isolates. The Table includes the normalized mean values (%) of three biological replicates.

To rule out the possibility that resistance was conferred by the well-known non-race specific

locus mlo (Mildew locus O), the genotypes showing resistance to all isolates were then

tested for the mlo-11 the only natural occurring mlo allele using mlo-11 specific primers

(Piffanelli et al., 2004 Nature 430: 887-891). Eleven accessions were identified as mlo-11

carriers, therefore the ten remaining genotypes were tested with seven additional Bgh

isolates and the results have identified seven isolate-specific resistances (Table 4). One of

the three accessions showing resistance against all nine isolates, is the German cultivar

‘Barke’ carrying the mlo-9 allele. The remaining two genotypes were landraces from Syria

(WB-352) and Sudan (WB-358).

Since the phenotype of WB-352 and WB-358 resembles the typical mlo phenotype, the Mlo

gene was amplified from genomic DNA in overlapping fragments that were used for Sanger

sequencing. WB-358 displays a potential new Mlo allele with an insertion of 36 bp

interrupting the calmodulin binding motive. In contrast, the WB-352 Mlo allele displays the

exact same sequence as the reference genotype Morex. Moreover, additional WB-352

specific fragments were amplified in genomic DNA and cDNA samples. These high

molecular fragments are longer than the corresponding expected fragments. They were

purified from agarose gels and the Sanger sequencing indicates an additional Mlo-like

structure or gene consisting of repeats of at least the first eight exons of the Mlo gene. This

potential gene is expressed and the transcript is spliced.

In 2017, two field trials were performed at the IPK campus in Gatersleben and in cooperation

with KWS in Wohlde. We selected 100 barley genotypes (spring and facultative accessions),

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spanning the whole range from resistant to highly susceptible. The macroscopic disease

symptoms on adult plants were scored in seven classes. In cooperation with the ‘Quantitative

Genetics’ group of IPK a correlation analysis was performed between the calculated best

linear unbiased estimators (BLUEs) of our seedling DLA data and the adult plant data from

the fields. The Pearson correlation coefficient between the two field sets is 0.81 and the

correlation coefficient of the transformed DLA data and the combined field data is 0.45.

7. Barley and Phyrenophora teres (barley net bloch)

A panel of about 100 6-row barley landraces selected from the Wealbi panel for limited

genetic structure has been tested for the response to Phyrenophora teres. The partner

CREA has carried out the evaluation in greenhouse with an Italian isolate and a replicated

experimental design. The development of macroscopic disease symptoms was visually

scored after 14-21 days using a scale from 1 (resistant) to 10 (completely susceptible) as

described by Tekauz et al., 1985 (Can. J Plant Pathol. 7: 181-183). The results highlighted

that the collection spans a large range of susceptibility including also some accessions

completely resistant (Figure 8). The data will be used for GWAS analyses to search for novel

sources of resistance.

Figure 8. Classification of the selected barley Whealbi accessions based upon the development of macroscopic disease symptoms after inoculated with a Pyrenophopra teres isolate.

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Conclusion

The deliverable summarizes all activities carried out in the frame of Whealbi WP3 task 4.

Overall the project has considered 5 wheat and 2 barley diseases, and for each of them has

screened a large set of germplasm identifying many resistant accessions, including some of

them carrying novel sources of resistance. The phenotyping activity is only the first step

towards the identification of novel resistance genes, therefore the Whealbi project has

coupled the data generated in WP3, including those reported in this delivery, with the

genotyping information obtained in WP2 and the combination of these sets of data have

been used for GWAS as well as for allele mining in WP5. For some diseases GWAS studies

have already identified novel resistant loci, while for other diseases the activity is still

ongoing. The first publications reporting the results of this deliverable will be submitted next

year and the data will be deposited at URGI database (https://wheat-

urgi.versailles.inra.fr/Projects/Whealbi) where all genotypic and phenotypic data generated

by Whealbi are/will be publicly accessible. Nevertheless it should be noticed that the

complete exploitation of the results here reported (i.e. the understanding of the genetic bases

of accessions showing a resistance to all strains of a specific diseases, the cloning of novel

resistant genes/alleles, etc.) required additional research work. In this sense, the data

reported in D3.4 represent an important component of the legacy of Whealbi that will impact

on the future European research on wheat and barley.