Genome-Wide Association Mapping for Kernel and Malting Quality Traits Using Historical European Barley Records

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.     

Analysis of the Genetic Structure of a Barley Collection Using DNA Diversity Array Technology (DArT)

Analysis of the extent of genetic variation within genetic resources is important for diversity preservation and also for breeders who exploit it. We investigated the recently introduced molecular marker technique of DNA diversity array technology (DArT), with the objective of characterising diversity in the likely relatively narrow genetic background of Czech malting barley cultivars. A total of 94 obsolete or registered barley cultivars and some hulless barley lines primarily of Czech origin were characterised by DArT analysis. A total of 271 polymorphic marker alleles were revealed across the analysed set of accessions, 37 of which were identified as being overrepresented; the other 234 markers were used for further analysis. The average dissimilarity value within the analysed set of accessions was 0.692. To assess how well DArT is suited for individual barley characteristic evaluation, available agronomical data from three yield field trials were used. Out of 94 barley genotypes used in the field trials that were assessed by DArTs, 41 have been grown over time as malting cultivars in the region. Similarity matrices based on Gower’s coefficient for mixed data and simple matching coefficient were used to compare DaRT and agronomical results. We demonstrate that a DArT-based similarity matrix and an agronomical data-based similarity matrix correlated well. To assess the genetic structure of the entire collection, K-means and simple matching coefficient clustering were used. Statistical analysis confirmed the power of the DArT system, in fact they efficiently grouped old genetic resources and modern cultivars in the expected way. Our results show that the level of genetic diversity has not changed substantially over time, but significant shifts in allelic frequency have occurred. In addition, a DArT-based dendrogram and principal component analysis (PCA) plots clearly demonstrated the impact of breeding practices on the diversity of Czech spring malting barley cultivars over time.     

Molecular marker-assisted selection for enhanced yield in malting barley

Brewers are reluctant to change malting barley (Hordeum vulgare ssp. vulgare L.) cultivars due to concerns of altered flavor and brewing procedures. The U.S. Pacific Northwest is capable of producing high yielding, high quality malting barley but lacks adapted cultivars with desirable malting characteristics. Our goal was to develop high yielding near isogenic lines that maintain traditional malting quality characteristics by transferring quantitative trait loci (QTL) associated with yield, via molecular marker-assisted backcrossing, from the high yielding cv. Baronesse to the North American two-row malting barley industry standard cv. Harrington. For transfer, we targeted Baronesse chromosome 2HL and 3HL fragments presumed to contain QTL that affect yield. Analysis of genotype and yield data suggests that QTL reside at two regions, one on 2HL (ABG461C-MWG699) and one on 3HL (MWG571A-MWG961). Genotype and yield data indicate that additional Baronesse genome regions are probably involved, but need to be more precisely defined. Based on yield trials conducted over 22 environments and malting analyses from 6 environments, we selected one isogenic line (00-170) that has consistently produced yields equal to Baronesse while maintaining a Harrington-like malting quality profile. We conclude there is sufficient data to warrant experiments testing whether the 2HL and 3HL Baronesse QTL would be effective in increasing the yield of other low yielding barley cultivars.     

Genetic diversity among cultivars of spring barley revealed by random amplified polymorphic DNA (RAPD)

RAPD (random amplified polymorphic DNA) polymorphism was studied in 23 malting and non-malting spring barley cultivars included in the official list of Polish cultivated varieties. Twenty-four 10-mer primers were tested in each cultivar, giving altogether 149 amplification products, 45% of which were polymorphic. The number of polymorphic bands revealed by one primer ranged from 1 to 6, with an average of 2.8. Genetic distance for all pairs of compared varieties was estimated and a dendrogram was constructed using unweighted pair group method of arithmetic means. The genetic distance between cultivars ranged from 0.11 for cvs. Apex and Bryl to 0.62 for cvs. Orthega and Madonna. Of the seven malting cultivars only two (Brenda and Stratus) formed one group at D = 0.25. The genetic distance between cvs. Brenda and Scarlett, especially recommended for brewery, was equal to 0.34. The detected polymorphism appeared to be sufficient for assessing genetic distances between cultivars, but on the basis of this polymorphism groups of malting and non-malting cultivars were not clearly distinguished.     

QTL mapping reveals genetic architectures of malting quality between Australian and Canadian malting barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.)

Australia and Canada are major exporters of malting barley (Hordeum vulgare L.), with Baudin from Australia and AC Metcalfe from Canada being the benchmark varieties for premium malting quality in the past 10 years. We used the barley doubled haploid population derived from a cross of Baudin and AC Metcalfe to map quantitative trait loci (QTLs) for malting quality. The results revealed different genetic architectures controlling malting quality for the two cultivars. Sixteen QTLs were identified and located on chromosomes 1H, 2H, 5H and 7H. The Australian barley Baudin mainly contributed to the malting quality QTL traits of high diastatic power and high β-glucanase on chromosome 1H, while Canadian barley AC Metcalfe mainly contributed to the QTL traits of high hot water extract, high free amino nitrogen, high α-amylase and low malt yield in chromosome 5HL telomere region. This study demonstrated the potential to breed new barley varieties with superior malting quality by integrating genes from Australian and Canadian malting barley varieties. This paper also provides methods to anchor traditional molecular markers without sequence information, such as amplified fragment length polymorphism markers, into the physical map of barley cv. ‘Morex’.     

Breeding progress,genotypic and environmental variation and correlation of quality traits in malting barley in German official variety trials between 1983 and 2015

Key message

Evaluation of breeding progress for spring barley varieties in Germany showed that both grain yield and malting quality were considerably improved during the last 33 years, and that genetic effects of protein concentration and malting traits were not associated.

Abstract

Based on historical data, this study aimed to investigate yield potential and malting quality of 187 varieties tested and released in German registration trials to evaluate the value for cultivation and use (VCU) during 1983–2015, and to quantify the environmental variability and the association among traits. We used mixed linear models with multiple linear regression terms to dissect genetic and non-genetic trend components. Grain yield increased by 43% (23.4 dt ha^?1) in VCU trials and 35% (14.0 dt ha^?1) on-farm relative to 1983. All yield components contributed significantly. Malting quality was also considerably improved by 2.3% for extract content up to 25.1% for friability, relative to 1983, nearly completely due to new varieties. Total variability of individual traits was very different between traits (2.4–24.4% relative to 1983). The relative influence of genotypes on total variation was low for grain yield and its components, whereas it was considerably larger for other traits. We found remarkable differences between phenotypic and genetic correlation coefficients for grain yield and protein concentration with malting traits. The observed positive phenotypic relation between grain yield and malting quality can be attributed to a shift of selection and environmental effects, but genetic correlations showed a negative association. Genetic effects of protein concentration and malting quality were not correlated indicating that both were not genetically linked. Considerable yield progress and improvement of malting quality were achieved despite of their weak to moderate negative genetic dependence.

     

The consequences, for malting quality, of Hordeum laevigatum as a source of mildew resistance in barley breeding

Barley cultivars which include Hordeum laevigatum in their pedigree, have harder endosperms, higher β-glucan and lower α-amylase levels than do other cultivars of poor malting quality. Good malting cultivars are characterised by high hot water extracts, soft endosperms, low β-glucan and high α-amylase levels. Introgressions of exotic genes for mildew resistance, into breeding populations, may be accompanied by factors adversely affecting malting quality.     

Genetic diversity among barley cultivars assessed by sequence-specific amplification polymorphism

We analyzed the genetic structure and relationships among barley cultivars (Hordeum vulgare L.) with sequence-specific amplification polymorphisms (S-SAPs). Polymorphisms were identified in 824 individual barley plants representing 103 cultivars (eight plants per cultivar) widely grown in Canada and the United States, using PCR primers designed from the long terminal repeat of the barley retrotransposon BARE-1 and a subset of four selective MseI primers. From the 404 bands scored, 150 were polymorphic either within or between cultivars. Genetic structure assessed with analysis of molecular variance attributed the largest component of variation to the within groups of cultivars (69–86%). Within-cultivar genetic variation was estimated as average gene diversity over loci and ranged from 0 (completely homogenous) to 0.076 (most heterogeneous cultivar). Only 17 out of 103 cultivars (16%) were judged to be homogenous by this criterion. Relationships among cultivars were analyzed by cluster analysis using unweighted pair-groups using arithmetic averages and found groups similar to those determined by agriculturally significant phenotypic traits such as spike morphology (two-rowed or six-rowed), cultivar type (malting or feed), seed characteristic (hull-less or hulled), and growth habit (winter or spring), with minor overlaps. Discriminant analysis of groups determined by these phenotypic traits fully supported the different groups with minor overlaps between the malting/feed. S-SAP markers generated from retrotransposons such as BARE-1 are invaluable tools for the study of genetic diversity in organisms with a narrow genetic base such as barley. In this study, S-SAP analysis revealed significant amounts of cryptic variation in closely related cultivars including somaclonal variation, which could not be inferred by the pedigree analysis.     

Markers polymorphic among malting barley ( Hordeum vulgare L.) cultivars of a narrow gene pool associated with key QTLs

Barley used for malting is a fine-tuned organism, and it requires breeding within narrow gene pools for realistic cultivar enhancement. Significant phenotypic advance within such narrow gene pools has been achieved and the necessary genetic variability for breeding progress has been documented, but it was not well understood. This study was conducted to further characterize detectable genetic variability present within a select set of four closely related malting barley cultivars using three types of molecular markers: RFLP, PCR-RAPD and AFLP. The markers that identified polymorphism among the select malting cultivars tended to link with each other and to map in chromosomal regions associated with quantitative trait loci (QTLs) for agronomic and malting quality traits that differed among the four cultivars. Although RFLPs identified the least amount of polymorphism, the differences detected by the RFLPs best fit the chronology of the cultivars. These results indicate that a large amount of the genetic variability necessary for cultivar improvement may have originally been present in the breeding gene pool, but does not rule out de novo variation. Study of the populations from crosses within this narrow germplasm is needed to further elucidate the basis of the phenotypic variability found among these select barley cultivars.     

Integration of the barley genetic and seed proteome maps for chromosome 1H, 2H, 3H, 5H and 7H

Two-dimensional gel electrophoresis was used to screen spring barley cultivars for differences in seed protein profiles. In parallel, 72 microsatellite (simple sequence repeat (SSR)) markers and 11 malting quality parameters were analysed for each cultivar. Over 60 protein spots displayed cultivar variation, including peroxidases, serpins and proteins with unknown functions. Cultivars were clustered based on the spot variation matrix. Cultivars with superior malting quality grouped together, indicating malting quality to be more closely correlated with seed proteomes than with SSR profiles. Mass spectrometry showed that some spot variations were caused by amino acid differences encoded by single nucleotide polymorphisms (SNPs). Coding SNPs were validated by mass spectrometry, expressed sequence tag and 2D gel data. Coding SNPs can alter function of affected proteins and may thus represent a link between cultivar traits, proteome and genome. Proteome analysis of doubled haploid lines derived from a cross between a malting (Scarlett) and a feed cultivar (Meltan) enabled genetic localisation of protein phenotypes represented by 48 spot variations, involving e.g. peroxidases, serpins, α-amylase/trypsin inhibitors, peroxiredoxin and a small heat shock protein, in relation to markers on the chromosome map. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Sources of resistance and susceptibility to Septoria tritici blotch of wheat

An association genetics analysis was conducted to investigate the genetics of resistance to Septoria tritici blotch, caused by the fungus Zymoseptoria tritici (alternatively Mycosphaerella graminicola), in cultivars and breeding lines of wheat (Triticum aestivum) used in the UK between 1860 and 2000. The population was tested with Diversity Array Technology (DArT) and simple‐sequence repeat (SSR or microsatellite) markers. The lines formed a single population with no evidence for subdivision, because there were several common ancestors of large parts of the pedigree. Quantitative trait loci (QTLs) controlling Septoria resistance were postulated on 11 chromosomes, but 38% of variation was not explained by the identified QTLs. Calculation of best linear unbiased predictions (BLUPs) identified lineages of spring and winter wheat carrying different alleles for resistance and susceptibility. Abundant variation in Septoria resistance may be exploited by crossing well‐adapted cultivars in different lineages to achieve transgressive segregation and thus breed for potentially durable quantitative resistance, whereas phenotypic selection for polygenic quantitative resistance should be effective in breeding cultivars with increased resistance. The most potent allele reducing susceptibility to Septoria, on chromosome arm 6AL, was associated with reduced leaf size. Genes which increase susceptibility to Septoria may have been introduced inadvertently into UK wheat breeding programmes from cultivars used to increase yield, rust resistance and eyespot resistance between the 1950s and 1980s. This indicates the need to consider trade‐offs in plant breeding when numerous traits are important and to be cautious about the use of non‐adapted germplasm.     

Evolution characteristics related to photosynthesis,growth and yield in some old and new cotton cultivars

Changes in photosynthetic attributes related to genetic improvement of cotton yield were studied in seven Chinese cotton cultivars widely grown in Xinjiang during the past 30 years. Our results showed that a chlorophyll (Chl) content and net photosynthetic rate (P _N) of the 1980s cultivar was the highest among all after 60 days from planting (DAP). However, after 75 DAP, the Chl content, P _N, and actual photochemical efficiency of PSII of the old cultivars declined gradually, whereas those of the new cultivars remained relatively high. Compared to the old cultivars, leaves of the new cultivars endured a longer period and their senescence was slower, shoot and boll dry mass was higher, but the root to shoot ratio was lower. The lint yield of the 2000s cultivars was 14.7 and 21.4% higher than that of 1990s and 1980s cultivars, respectively. The high yield of the new cultivars was attributed to a greater number of bolls per unit of area with high lint percentage. We suggested that the improved photosynthetic capacity and the increased ability to deliver photosynthates to reproductive sites during the peak boll-setting stage to boll-opening stage were the key physiological basis in the evolution process of cotton cultivars from 1980s to 2000s for the cotton yield improvement within a short growing period.     

The effect of powdery mildew (Erysiphe graminis f.sp. avenae) on yield, yield components and grain quality of spring oats

Yield components and grain quality were investigated on eight cultivars of spring oats with known differences in adult plant resistance to mildew and with different fungicide treatments. Losses in grain yield caused by mildew could be accounted for mainly by reductions in numbers of fertile panicles and thousand grain weights. The proportion of grain yield to total biomass, (harvest index) was also reduced. There were no effects of treatment on the concentration of fatty acids in the grain, the proportions of the component fatty acids, the percentage content of grain protein or the specific weights. However, correlation analysis of the data revealed that percentage protein contents and specific weights were negatively correlated with levels of mildew. There were significant genetic differences between cultivars in all of the yield and quality characteristics but no fungicide treatment/cultivar interactions.     

Genealogical analysis of the diversity of spring barley cultivars released in former Czechoslovakia and modern Czech Republic

Genealogical analysis was employed in studying the time course of changes in genetic diversity of spring barley cultivars released in former Czechoslovakia and the modern Czech Republic. Cultivars from different regions proved to significantly differ in the distribution of dominant ancestor contributions, suggesting a specificity of original ancestors to different cultivation conditions. A comparison of cultivar groups differing in end use showed that the genetic diversity of malting cultivars was significantly lower than that of feed cultivars, although modern malting and feed cultivars of Czechia and Slovakia have virtually the same genetic basis. Temporal analysis showed that diversity tended to increase through decades. While new original ancestors were introduced in pedigrees, especially in the past 30 years, the number of local landraces and old cultivars gradually decreased. The losses accounted for about two-thirds of the local germplasm. Thus, a substantial increase in genetic diversity was accompanied by genetic erosion of the local spring barley gene pool of former Czechoslovakia. A cluster structure was observed for the set of spring barley cultivars released in the postwar period. The coefficient of parentage averaged over all possible pairs of cultivars introduced in the Czech National List was estimated at 0.11. It was concluded that the genetic diversity of modern spring barley cultivars in the Czech Republic is at an acceptable level.     

Genealogical analysis of the diversity of spring barley cultivars released in former Czechoslovakia and modern Czechia

Genealogical analysis was employed in studying the time course of changes in genetic diversity of spring barley cultivars released in former Czechoslovakia and the modem Czech Republic. Cultivars from different regions proved to significantly differ in the distribution of dominant ancestor contributions, suggesting a specificity of original ancestors to different cultivation conditions. A comparison of cultivar groups differing in end use showed that the genetic diversity of malting cultivars was significantly lower than that of feed cultivars, although modern malting and feed cultivars of Czechia and Slovakia have virtually the same genetic basis. Temporal analysis showed that diversity tended to increase through decades. While new original ancestors were introduced in pedigrees, especially in the past 30 years, the number of local landraces and old cultivars gradually decreased. The losses accounted for about two-thirds of the local germplasm. Thus, a substantial increase in genetic diversity was accompanied by genetic erosion of the local spring barley gene pool of former Czechoslovakia. A cluster structure was observed for the set of spring barley cultivars released in the postwar period. The coefficient of parentage averaged overall possible pairs of cultivars introduced in the Czech National List was estimated at 0.11. It was concluded that the genetic diversity of modern spring barley cultivars in the Czech Republic is at an acceptable level.     

Mildew-resistant mutants induced in North American two- and six-rowed malting barley cultivars

Mildew-resistant mutants were induced with sodium azide in three North American malting barley cultivars, two in the six-rowed Ursula (URS1 and URS2), one in the six-rowed Gertrud (GER1), and one in the two-rowed Prudentia (PRU1). Two of the mutants, URS1 and PRU1, showed complete resistance and were shown to have two new alleles at the mlo locus; these were designated, respectively, mlo31 and mlo32. Mutant URS2, showing partial resistance, was inherited as a dominant gene, but was not an allele at the Mla locus. The mean yield of each mutant was higher than that of its parental line, but yield levels varied across environments, although this was independent of the severity of the mildew attack. Other reasons, for example, the severity of the necrotic lesions in the mutants, may account for yield variations. The malting quality of the GER1 mutant proved similar to that of Gertrud, but both URS1 and URS2 showed lower malt extract than Ursula. This lower extract might be due to the smaller grain size of the mutants that could, in turn, result from necrotic lesions in the leaves, as implied by the effects on grain yield.Communicated by G. Wenzel     

AFLP analysis of genetic relationships between barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) landraces from north Shewa in Ethiopia

Local cultivars adapted to specific environmental conditions are the chief source of seed for farmers in Ethiopia and deserve research priority. The aim of this study was, therefore, to determine the genetic relationships between different barley landraces, from north Shewa in Ethiopia so as to differentiate genotypes known by different local names and facilitate their conservation and use in breeding new varieties. Five AFLP primer combinations were analyzed for 19 barley landraces and five malting varieties. The number of scoreable fragments amplified by each AFLP primer combination varied from 49 to 118 with an average of 84.5 and polymorphic fragments for each primer combination varied from 27 to 77 with an average of 58.5. The average percent polymorphism was 69.9% with values ranging from 55.1% to 75.8%. Cluster analysis placed the accessions and malting varieties into one main group while all the farmers’ cultivars, with the exception of two, were in the other main group. It was shown that sampling of germplasm at a given locality might not represent the whole array of genetic variability of locally grown famers’ cultivars. A comprehensive study of all the farmers’ barley cultivars, grown in different parts of Ethiopia, is required to maximize the efforts of germplasm conservation and utilization in national and regional breeding programs.     

Quantitative trait loci of barley malting quality trait components in the Stellar/01Ab8219 mapping population

Malting barley is of high economic and scientific importance. Determining barley grains that are suitable for malting involves measuring malting quality, which is an expensive and complex process. In order to decrease the cost of phenotyping and accelerate the process of developing superior malting barley cultivars, markers for marker-assisted breeding are needed. In this study, we identified quantitative trait loci (QTLs) for malting traits in a Stellar/01Ab8219 F6:8 recombinant inbred line population grown at Aberdeen and Tetonia, Idaho, USA in 2009 and 2010. We identified QTLs associated with malt extract (ME), wort protein, soluble/total protein (S/T), diastatic power (DP), alpha-amylase, beta-glucan (BG) and free amino nitrogen (FAN) at a logarithm of odds score ≥2.5 using a high-density genetic map produced by merging Diversity Arrays Technology markers with the current single nucleotide polymorphism map. Novel QTLs were identified for DP and FAN on chromosome 5H, S/T on 6H, and BG and ME on 7H. Dissection of the genetic regions associated with malting traits suggests the involvement of multiple molecular pathways. The resulting molecular markers may prove useful for barley improvement.     

Stomatal conductance is a key parameter to assess limitations to photosynthesis and growth potential in barley genotypes

Fourteen genotypes of barley were compared for response to salinity by monitoring the parameters gas exchange and chlorophyll fluorescence. We present relationships between stomatal conductance (gs) gas exchange chlorophyll fluorescence parameters and aboveground dry matter (AGDM). We found that genetic variability provided a continuum of data for gs across control and saline conditions. We used this continuum of gs values to test the overall relationships between gs and net photosynthesis (A), leaf internal CO2 concentration (Ci), actual quantum yield of PSII electron transport (PhiPSII), relative electron yield over net CO2 assimilation rate (ETR/A), and AGDM. The relationship between gs and A was highly significant (P < 0.0001) for both control and saline treatments, while correlations between gs and Ci, and Ci and A were significant only under control conditions. Unexpectedly, we found positive correlations between gs and PhiPSII (P < 0.0001) for both conditions. A comparison between relationships of gs and A, and gs and PhiPSII seemed to indicate a possible acclimation to salinity at the chloroplastic level. Finally, the relationships between gs and ETR/A were exceptionally strong for both growing conditions (P < 0.0001) indicating that, as gs values were negatively affected in barley by genetics and salinity as main or interactive effects, there was a progressive increase in photorespiration in barley. Overall, we found that stomatal conductance was a key parameter in the study of barley responses to limiting situations for photosynthesis. We also found a strong relationship between AGDM and gs regardless of growing conditions and genotypes. For breeding evaluations to select barley genotypes for salinity tolerance, it may be possible to replace all measurements of gas exchange and chlorophyll fluorescence by the simple use of a porometer.