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.     

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.     

Trends in genetic diversity change of spring bread wheat cultivars released in Russia in 1929-2003

Using genealogy analysis, we studied genetic diversity of 340 cultivars of spring bread wheat that were released on the territory of Russia in 1929-2003. Trends in the temporal change of genetic diversity were inferred from analysis of a set of n x m matrices, where n is the number of the released cultivars and m is the number of original ancestors. The pool of original ancestors of the spring bread wheat cultivars for the total period of study included 255 landraces, of which 88 were from the former USSR and modern Russia. The original ancestors showed great differences in their presence in the cultivar sets examined and, consequently, in their importance for the gene pool of Russian spring wheats. The distributions of contributions of dominant original ancestors to cultivar diversity were significantly different in different regions, indicating that the ancestors were specific for the cultivation conditions. During the last 75 years, the genetic diversity of the spring bread wheat cultivars has been increasing owing to the wide use of foreign material in Russian breeding programs. However, our analysis showed that about 60 landraces, including the Russian ones, were lost during the studied time period. The lost part makes up 35% of the gene pool of the Russian original ancestors. It is reasonable to assume that the lost landraces carried a gene complex f or adaptation to specific Russian environments. Specificity of the contributions of the original ancestors in the sets of cultivars produced in different breeding centers was established. A comparative analysis of genetic similarity of cultivars was carried out using coefficients of parentage. Significant differences in this parameter between breeding institutes and regions of cultivation were revealed.     

Trends in Genetic Diversity Change of Spring Bread Wheat Cultivars Released in Russia in 1929–2003

Using genealogy analysis, we studied genetic diversity of 340 cultivars of spring bread wheat that were released on the territory of Russia in 1929–2003. Trends in the temporal change of genetic diversity were inferred from analysis of a set of n × m matrices, where n is the number of the released cultivars and m is the number of original ancestors. The pool of original ancestors of the spring bread wheat cultivars for the total period of study included 255 landraces, of which 88 were from the former USSR and modern Russia. The original ancestors showed great differences in their presence in the cultivar sets examined and, consequently, in their importance for the gene pool of Russian spring wheats. The distributions of contributions of dominant original ancestors to cultivar diversity were significantly different in different regions, indicating that the ancestors were specific for the cultivation conditions. During the last 75 years, the genetic diversity of the spring bread wheat cultivars has been increasing owing to the wide use of foreign material in Russian breeding programs. However, our analysis showed that about 60 landraces, including the Russian ones, were lost during the studied time period. The lost part makes up 35% of the gene pool of the Russian original ancestors. It is reasonable to assume that the lost landraces carried a gene complex f or adaptation to specific Russian environments. Specificity of the contributions of the original ancestors in the sets of cultivars produced in different breeding centers was established. A comparative analysis of genetic similarity of cultivars was carried out using coefficients of parentage. Significant differences in this parameter between breeding institutes and regions of cultivation were revealed.     

Analysis of genetic diversity of spring durum wheat (Triticum durum Desf.) cultivars released in Russia in 1929-2004

Based on genealogical analysis, the genetic diversity of 78 spring durum wheat cultivars released in Russia in 1929-2004 have been examined. The temporal trends of change in diversity were studied using series of n x m matrices (where n is the number of the cultivars and m is the number of original ancestors) and calculating coefficients of parentage in sets of cultivars released in particular years. The pool of original ancestors of spring durum wheat cultivars includes 90 landraces and old varieties, more than a half (57%) of which originate from European countries, including Russia and Ukraine (45%). The original ancestors strongly differ in the frequency of presence in the cultivar pedigrees. Landraces Beloturka, Sivouska, Kubanka (T. durum Desf.), Transbaikalian emmer, Yaroslav emmer (T. dicoccum Schuebl.), Poltavka (T. aestivum L.), and the original ancestors of cultivars Kharkov 46, Narodnaya, and Melanopus 1932 enter in the pedigrees of more than half of cultivars created within the framework of various breeding programs. At that, their distribution by cultivars from different breeding centers strongly varies. Analysis of temporal dynamics of genetic diversity, based on genetic profiles and coefficients of parentage, has shown that the genetic diversity of Russian durum wheats increased during the period examined. Nevertheless, genetic erosion of the local material-a loss of approximately 20% of the pool of Russian original ancestors-has been found. The contribution of the original ancestors to the pedigrees of different cultivars, constructed in different breeding centers and recommended for cultivation in different regions, has been estimated. The variation of the released cultivars was highest in the Lower Volga region and lowest in the Ural region. In all, the lower threshold of genetic diversity in all regions does not reach the critical level, corresponding to the similarity of half-sibs. The set of modern cultivars included in the Russian Official List 2004 has a cluster structure.     

Dynamics of genetic diversity in winter common wheat Triticum aestivum L. cultivars released in Russia from 1929 to 2005

Genealogical analysis was used to study the dynamics of genetic diversity in Russian cultivars of winter common wheat from 1929 to 2005. The Shannon diversity index of the total set of released cultivars remained almost unchanged, although the number of original ancestors (landraces and genetic lines) increased almost tenfold in the period under study. This was explained in terms of the dependence of the modified Shannon diversity index on two parameters, the number of original ancestors and the mean coefficient of parentage. Significant direct effects were revealed: a positive effect of the former parameter and a negative of the latter. As a result, the increase in the number of original ancestors was compensated by the increase in relatedness of cultivars. Genetic erosion of released diversity was observed, as a half of Russian landraces were lost. Although the mean coefficient of parentage did not reach its critical value $(\bar R = 0.25)$ , cultivars of some regions (Central and Volga-Vyatka) proved to be closely related. A favorable gradual decrease in the mean coefficient of parentage was observed in the past 15 years. A set of modern winter wheat cultivars, which were introduced in the Russian Official List from 2002 to 2005, displayed a cluster structure. The overwhelming majority of cultivars formed two clusters originating from Bezostaya 1 (67% of cultivars) and Mironovskaya 808 (31%).     

Analysis of Genetic Diversity of Spring Durum Wheat (<Emphasis Type="Italic">Triticum durum</Emphasis> Desf.) Cultivars Released in Russia in 1929–2004

Based on genealogical analysis, the genetic diversity of 78 spring durum wheat cultivars released in Russia in 1929–2004 have been examined. The temporal trends of change in diversity were studied using series of n × m matrices (where n is the number of the cultivars and m is the number of original ancestors) and calculating coefficients of parentage in sets of cultivars released in particular years. The pool of original ancestors of spring durum wheat cultivars includes 90 landraces and old varieties, more than a half (57%) of which originate from European countries, including Russia and Ukraine (45%). The original ancestors strongly differ in the frequency of presence in the cultivar pedigrees. Landraces Beloturka, Sivouska, Kubanka (T. durum Desf.), Transbaikalian emmer, Yaroslav emmer (T. dicoccum Schuebl.), Poltavka (T. aestivum L.), and the original ancestors of cultivars Kharkov 46, Narodnaya, and Melanopus 1932 enter in the pedigrees of more than half of cultivars created within the framework of various breeding programs. At that, their distribution by cultivars from different breeding centers strongly varies. Analysis of temporal dynamics of genetic diversity, based on genetic profiles and coefficients of parentage, has shown that the genetic diversity of Russian durum wheats increased during the period examined. Nevertheless, genetic erosion of the local material—a loss of approximately 20% of the pool of Russian original ancestors—has been found. The contribution of the original ancestors to the pedigrees of different cultivars, constructed in different breeding centers and recommended for cultivation in different regions, has been estimated. The variation of the released cultivars was highest in the Lower Volga region and lowest in the Ural region. In all, the lower threshold of genetic diversity in all regions does not reach the critical level, corresponding to the similarity of half-sibs. The set of modern cultivars included in the Russian Official List 2004 has a cluster structure.     

Dynamics of genetic diversity in winter common wheat Triticum aestivum L. cultivars released in Russia from 1929 to 2005

Genealogical analysis was used to study the dynamics of genetic diversity in Russian cultivars of winter common wheat from 1929 to 2005. The Shannon diversity index of the total set of released cultivars remained almost unchanged, although the number of original ancestors (landraces and genetic lines) increased almost tenfold in the period under study. This was explained in terms of the dependence of the modified Shannon diversity index on two parameters, the number of original ancestors and the mean coefficient of parentage. Significant direct effects were revealed: a positive effect of the former parameter and a negative of the latter. As a result, the increase in the number of original ancestors was compensated by the increase in relatedness of cultivars. Genetic erosion of realized diversity was observed, as a half of Russian landraces were lost. Although the mean coefficient of parentage did not reach its critical value (R = 0.25), cultivars of some regions (Central and Volga-Vyatka) proved to be closely related. A favorable gradual decrease in the mean coefficient of parentage was observed in the past 15 years. A set of modem winter wheat cultivars, which were introduced in the Russian State Catalog from 2002 to 2005, displayed a cluster structure. The overwhelming majority of cultivars formed two clusters originating from Bezostaya 1 (67% of cultivars) and Mironovskaya 808 (31%).     

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.     

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.     

Haplotyping barley <Emphasis Type="Italic">bmy1</Emphasis> using the SNaPshot assay

The allelic status at bmy1, which encodes the enzyme β-amylase 1 in the barley grain, has an important influence over a cultivar’s malting quality. Changes in the malting process have been responsible for the need to improve the thermostability of this enzyme. We have compared a published bmy1 haplotyping assay based on TDI-FRET (template-directed dye-terminator incorporation fluorescence resonance energy transfer) with a SNaPshot protocol by jointly analysing a set of 21 cultivars of known haplotype. The two methods gave the same result, but the SNaPshot assay was easier to interpret. The SNaPshot assay was therefore used to haplotype the Czech malting barley core collection with respect to bmy1. The old Czech cultivar Kasticky was the only entry identified as carrying the high thermostability haplotype, with the remainder carrying either the intermediate or the low thermostability haplotypes. Older materials were the most variable in terms of bmy1 haplotype, but the majority carried the intermediate type. Most of the descendants of cv. Diamant carried the low thermostability haplotype. The most recently released cultivars recommended for the brewing of Czech beer tend to carry the intermediate allele.     

The use of AFLPs to examine genetic relatedness in barley

The generation of AFLPs in spring barley cultivars provided genetic information relating to the development of the crop in the UK since 1953. Principal co-ordinate (PCO) analysis of genetic similarities (gs) confirmed the marked contrast in the cultivars used in the 1970s and 1980s. The earliest cultivars, many derived from Proctor, were succeeded by tall-strawed, disease-resistant types with high yield but poor malting potential. In the 1980s they were in turn replaced by short-strawed cultivars with excellent yield and good malting quality, which originated from Triumph. A PCO plot of gs provided insight into the effects of selection for disease resistance and the antagonism between malting quality and particular resistance genes. The analysis of gs was more useful than pedigrees and estimates of kinship in revealing the genetic relationship between cultivars. Theoretical considerations for maximising the efficiency of an AFLP genotyping programme are discussed in the context of the number of primer pairs required to distinguish genotypes at varying levels of similarity.     

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.     

A global barley panel revealing genomic signatures of breeding in modern Australian cultivars

The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Today’s gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact that breeding had on the genetic diversity of Hordeum vulgare (barley) released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined data set and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.     

贵州野生大麦麦芽品质性状的SSR标记分析

采用6对啤酒大麦的麦芽浸提和糖化力紧密连锁引物对103份采自贵州的野生大麦材料进行SSR标记。结果表明,贵州野生大麦麦芽品质性状存在丰富的变异,6对SSR引物共检测出38个等位变异,每个位点平均6.33个等位变异,其中GMS001位点对贵州野生大麦基因组DNA变异检测最有效。UPGMA聚类图显示,该6对与麦芽品质紧密连锁的SSR引物对区分野生大麦在贵州不同的资源产地和棱性是有效的,表现为遵义地区野生大麦遗传多样性丰富,而来自贵州凯里地区的野生大麦资源遗传多样性狭窄。麦芽品质性状标记结果表明贵州野生六棱大麦较四棱大麦的遗传差异更显著,表明进行贵州啤酒大麦人工育种的亲本应在亲缘关系较远的六棱大麦之间选择。     

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.     

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.     

A rapid technique to predict malting quality in barley prior to harvest

Samples of grain from three spring barley cultivars of differing malting quality were collected at regular intervals during four weeks prior to harvest. The samples were dried, then assessed for relative grain hardness using the "Milling Energy" test. Ranking order of the cultivars for this character, which relates strongly to malting quality, was unaltered throughout. In a further experiment, it was demonstrated that selection for milling energy could be successfully practised on oven-dried grain collected six weeks after ear emergence.     

Genetic diversity of modern Russian durum wheat cultivars at the gliadin-coding loci

The allelic diversity at four gliadin-coding loci was studied in modern cultivars of the spring and winter durum wheat Triticum durum Desf. Comparative analysis of the allelic diversity showed that the gene pools of these two types of durum wheat, having different life styles, were considerably different. For the modern spring durum wheat cultivars, a certain reduction of the genetic diversity was observed compared to the cultivars bred in the 20th century.     

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.