A barley RFLP map: alignment of three barley maps and comparisons to Gramineae species

Several gene linkage maps have been produced for cultivated barley. We have produced a new linkage map for barley, based on a cross between Hordeum vulgare subsp. spontaneum and Hordeum vulgare subsp. vulgare (Hvs x Hvv), having a higher level of polymorphism than most of the previous barley crosses used for RFLP mapping. Of 133 markers mapped in the Hvs x Hvv F₂ population, 69 were previously mapped on other barley maps, and 26 were mapped in rice, maize, or wheat. Two known gene clones were mapped as well as two morphological markers. The distributions of previously mapped markers were compared with their respective barley maps to align the different maps into one consensus map. The distributions of common markers among barley, wheat, rice and maize were also compared, indicating colinear linkage groups among these species.To be considered dual first authorsPublished with the approval of the Director of the Colorado State University/Agricultural Experiment Station.     

Assessment of genetic diversity in Brazilian barley using SSR markers

Barley is a major cereal grown widely and used in several food products, beverage production and animal fodder. Genetic diversity is a key component in breeding programs. We have analyzed the genetic diversity of barley accessions using microsatellite markers. The accessions were composed of wild and domesticated barley representing genotypes from six countries and three breeding programs in Brazil. A total of 280 alleles were detected, 36 unique to Brazilian barley. The marker Bmag120 showed the greatest polymorphism information content (PIC), with the highest mean value found on chromosome three, and the lowest on chromosomes four and six. The wild accessions presented the highest diversity followed by the foreign genotypes. Genetic analysis was performed using Principal Coordinates Analysis, UPGMA clustering, and Bayesian clustering analysis implemented in Structure. All results obtained by the different methods were similar. Loss of genetic diversity has occurred in Brazilian genotypes. The number of alleles detected in genotypes released in 1980s was higher, whereas most of the cultivars released thereafter showed lower PIC and clustered in separate subgroups from the older cultivars. The use of a more diverse panel of genotypes should be considered in order to exploit novel alleles in Brazilian barley breeding programs.     

A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers

Background

Sugarcane genetic mapping has lagged behind other crops due to its complex autopolyploid genome structure. Modern sugarcane cultivars have from 110-120 chromosomes and are in general interspecific hybrids between two species with different basic chromosome numbers: Saccharum officinarum (2n = 80) with a basic chromosome number of 10 and S. spontaneum (2n = 40-128) with a basic chromosome number of 8. The first maps that were constructed utilised the single dose (SD) markers generated using RFLP, more recent maps generated using AFLP and SSRs provided at most 60% genome coverage. Diversity Array Technology (DArT) markers are high throughput allowing greater numbers of markers to be generated.

Results

Progeny from a cross between a sugarcane variety Q165 and a S. officinarum accession IJ76-514 were used to generate 2467 SD markers. A genetic map of Q165 was generated containing 2267 markers, These markers formed 160 linkage groups (LGs) of which 147 could be placed using allelic information into the eight basic homology groups (HGs) of sugarcane. The HGs contained from 13 to 23 LGs and from 204 to 475 markers with a total map length of 9774.4 cM and an average density of one marker every 4.3 cM. Each homology group contained on average 280 markers of which 43% were DArT markers 31% AFLP, 16% SSRs and 6% SNP markers. The multi-allelic SSR and SNP markers were used to place the LGs into HGs.

Conclusions

The DArT array has allowed us to generate and map a larger number of markers than ever before and consequently to map a larger portion of the sugarcane genome. This larger number of markers has enabled 92% of the LGs to be placed into the 8 HGs that represent the basic chromosome number of the ancestral species, S. spontaneum. There were two HGs (HG2 and 8) that contained larger numbers of LGs verifying the alignment of two sets of S. officinarum chromosomes with one set of S. spontaneum chromosomes and explaining the difference in basic chromosome number between the two ancestral species. There was also evidence of more complex structural differences between the two ancestral species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-152) contains supplementary material, which is available to authorized users.     

A consensus linkage map of barley

A consensus linkage map of the barley genome was constructed. The map is based on six doubled haploid and one F₂ population. The mapping data for three of the doubled haploid populations was obtained via the GrainGenes database. To allow merger of the maps, only RFLP markers that produce a single scorable band were included. Although this reduced the available markers by about half, the resultant map contains a total of 587 markers including 87 of known function. As expected, gene order was highly conserved between maps and all but two discrepancies were found in closely linked markers and are likely to result from the small population sizes used for some maps. The consensus map allows the rapid localisation of markers between published maps and should facilitate the selection of markers for high-density mapping in defined regions.     

Development of simple sequence repeat DNA markers and their integration into a barley linkage map

Simple sequence repeats (SSRs), or microsatellites, are a new class of PCR-based DNA markers for genetic mapping. The objectives of the present study were to develop SSR markers for barley and to integrate them into an existing barley linkage map. DNA sequences containing SSRs were isolated from a barley genomic library and from public databases. It is estimated that the barley genome contains one (GA)_n repeat every 330 kb and one (CA)_n repeat every 620 kb. A total of 45 SSRs were identified and mapped to seven barley chromosomes using doubled-haploid lines and/or wheat-barley addition-line assays. Segregation analysis for 39 of these SSRs identified 40 loci. These 40 markers were placed on a barley linkage map with respect to 160 restriction fragment length polymorphism (RFLP) and other markers. The results of this study demonstrate the value of SSRs as markers in genetic studies and breeding research in barley.     

Development and genetic mapping of 127 new microsatellite markers in barley

To enhance the marker density of existing genetic maps of barley (Hordeum vulgare L.), a new set of microsatellite markers containing dinucleotide motifs was developed from genomic clones. Out of 254 primer pairs tested, a total of 167 primer pairs were classifed as functional in a panel of six barley cultivars and three H. spontaneum accessions, and of those, 127 primer pairs resulting in 133 loci were either mapped or located onto chromosomes. The polymorphism information content (PIC) ranged from 0.05 to 0.94 with an average of 0.60. The number of alleles per locus varied from 1 to 9. On average, 3.9 alleles per primer pair were observed. The RFLP frameworks of two previously published linkage maps were used to locate a total of 115 new microsatellite loci on at least one mapping population. The chromosomal assignment of 48 mapped loci was corroborated on a set of wheat-barley chromosome addition lines; 18 additional loci which were not polymorphic in the mapping populations were assigned to chromosomes by this method. The microsatellites were located on all seven linkage groups with four significant clusters in the centromeric regions of 2H, 3H, 6H and 7H. These newly developed microsatellites improve the density of existing barley microsatellite maps and can be used in genetic studies and breeding research.Communicated by G. Wenzel     

Genetic relationships among South-East Turkey wild barley populations and sampling strategies of Hordeum spontaneum

To assess the genetic diversity and the genetic structure of Turkish wild barley (Hordeum spontaneum Tell.) populations, 76 genotypes from ten ecologically and geographically different locations were analyzed by means of amplified fragment length polymorphism (AFLP) markers. Five primer combinations produced 187 scorable bands, of which 117 (62.6%) were polymorphic. Several population-specific and genotype-specific bands were identified, which differentiate populations or genotypes. Genetic distance, determined by Nei’s distance coefficient, varied from 0.07 to 0.21 with an average of 0.13. In the UPGMA dendrogram based on Nei genetic distances, the Hordeum spontaneum populations were separated into two major clusters. Genetic diversity was larger among (68%) than within (32%) populations. Eight AFLP bands were strongly correlated to the altitude of the collecting site, while no clear trend was detected between geographical origin and genetic diversity. Our results strongly suggest the need for a change in Hordeum spontaneum sampling strategy: more populations, rather then more individuals within population, should be sampled to appraise and safeguard genetic diversity in the wild barley gene pool.     

Genetic analyses of rDNA spacer-length variation in barley

Summary The genetic mechanism controlling the inheritance of single and multiple spacer-length variant (slv) phenotypes in barley was investigated in six F₂ segregating populations. The results indicated that two independently assorting loci, each with co-dominant alleles, govern genetic variability for rDNA in barley regardless of the number of bands expressed by a given phenotype. The following chromosomal locations are proposed: sl variants 1, 4, 5, 6, and 7 on chromosome 7, and sl variants 7, 8, 9, 12, and 13 on chromosome 6; sl variant 7 is thus located on both of the chromosomes.     

Correlation between hordatine accumulation, environmental factors and genetic diversity in wild barley (Hordeum spontaneum C. Koch) accessions from the Near East Fertile Crescent

Wild barley shows a large morphological and phenotypic variation, which is associated with ecogeographical factors and correlates with genotypic differences. Diversity of defense related genes and their expression in wild barley has been recognized and has led to attempts to exploit genes from H. spontaneum in breeding programs. The aim of this study was to determine the variation in the accumulation of hordatines, which are Hordeum-specific preformed secondary metabolites with strong and broad antimicrobial activity in vitro, in 50 accessions of H. spontaneum from different habitats in Israel. Differences in the accumulation of hordatines in the seedling stage were significant between different H. spontaneum genotypes from different regional locations and micro-sites. Variation in the hordatine accumulation within genotypes was between 9% and 45%, between genotypes from the same location between 13% and 38%, and between genotypes from different locations up to 121%. Principal component analysis showed that water related factors explain 39%, temperature related factors explain 33% and edaphic factors account for 11% of the observed variation between the populations of H. spontaneum. Genetic analysis of the tested accessions with LP-PCR primers that are specific for genes involved in the biosynthetic pathway of hordatines showed tight correlations between hordatine abundance and genetic diversity of these markers. Multiple regression analyses indicated associations between genetic diversity of genes directly involved in hordatine biosynthesis, ecogeographical factors and the accumulation of hordatines.     

Ribosomal DNA polymorphisms and the Oriental-Occidental genetic differentiation in cultivated barley

Summary A total of 289 accessions of cultivated barley were assayed for ribosomal DNA (rDNA) polymorphisms. These accessions comprised four independent samples: (1) 79 entries from China, (2) 59 accessions from Ethiopia, (3) 59 entries from Tibet and (4) 92 entries representing 36 barley growing countries of the world (referred to as world sample). In all, 17 rDNA phenotypes (genotypes) were observed, which were composed 10 alleles at two rDNA loci, Rrn1 and Rrn2. The world sample contained the largest number of phenotypes and alleles and also demonstrated the highest level of diversity. Ribosomal DNA phenotypes 104, 112 and 107, 112 occurred at high frequencies worldwide. Allele 112 was the predominant allele of Rrn1 in all four samples, and 104 and 107 were the two major alleles of Rrn2 worldwide. The distributions of rDNA genotypes and alleles demonstrated a clear differentiation of two distinct barley groups: an Oriental group represented by the samples from China and Tibet, which is characterized by allele 107 at the Rrn2 locus (rDNA phenotype 107, 112); and an Occidental group, represented by Ethiopian and world samples, which is comprised mostly of allele 104 at the Rrn2 locus (rDNA phenotype 104, 112). The results also raised new questions concerning the phylogeny and evolution of cultivated barley.     

Analysis of genetic diversity of hordein in wild close relatives of barley from Tibet

We analyzed genetic diversity in the storage protein hordein encoded at Hor-1, Hor-2 and Hor-3 loci in seeds from 211 accessions of wild close relatives of barley, Hordeum vulgare ssp. agriocrithon and H. vulgare ssp. spontaneum. Altogether 32, 27 and 13 different phenotypes were found for Hor-1, Hor-2 and Hor-3, respectively. A comparison of our results with those of previous studies indicates that Tibetan samples reflect the highest diverse level of hordein phenotypes when compared to samples from Israel and Jordan. This high degree of polymorphism supports the hypothesis that Tibet is one of the original centers of H. vulgare L.Communicated by H.F. Linskens     

Ecotypes and genetic divergence among sympatrically distributed populations of Hordeum vulgare and Hordeum spontaneum from the xeric region of Jordan

Summary The progeny of paired samples of Hordeum vulgare L. and Hordeum spontaneum C. Koch, collected from Jordan's xeric region was used in this study. Statistical analyses of seven easily measured morphometric traits were used to elucidate the relationships and distances between populations of both species, to detect any ecogeographical races, and to study the interrelationships and adjustments in the morphometric traits under study. Flag leaf area and plant height were the two most important discriminating variables which totally separated Hordeum vulgare from Hordeum spontaneum and accounted for 85.3% of total phenotypic variance in the collection. Cluster analysis indicated that the level of divergence among populations of both species was considerably different. Populations of Hordeum vulgare clustered at a maximum Euclidean distance of 2.08, while the maximum distance at which populations of Hordeum spontaneum clustered was 1.49. Three ecotypes each of Hordeum vulgare and Hordeum spontaneum were identified. These ecotypes corresponded to the environmental range of the collection sites. The interrelationships between the seven morphometric traits were adjusted in different ways as revealed by the principal components analysis. Sampling from the different clusters identified in this analysis is expected to increase the allelic diversity for selection and breeding purposes.     

A mutator nuclear gene inducing a wide spectrum of cytoplasmically inherited chlorophyll deficiences in barley

Summary Some striped plants were observed in plots of a long-grain mutant barley grown at a field nursery. All of the plants of these plots, which were naturally self pollinated, were individually harvested, and most of their progenies (92.5%) segregated seedlings carrying chlorophyll deficiencies (CD) as determined by greenhouse analysis. The majority of the mutant seedlings (84.3%) showed a pattern of longitudinal chlorophyll sectors. The spectrum of CD was wide among the solid mutant seedlings and consisted of three main types (albina, viridis and discontinuous). In association with some CD types morphological changes were frequently observed. Non-CD-associated morphological changes and diminished seed-set were scarce and, so far, none of them has proved to be inherited. Analysis of CD in reciprocal crosses and backcrosses proved that while CD were transmitted cytoplasmically their induction was controlled by a single nuclear mutator gene, active when homozygous. In addition once the CD were induced, they were expressed independently of the nuclear constitution. The results suggest that the mutator gene induces diverse mutational events on chloroplast (cp) DNA. In barley, as in other monocots, nuclear genes which are inductors of cytoplasmic genetic changes have been reported. However, all of them produced a narrower spectrum of CD and had a more rapid sorting-out of the cytoplasmic mutants than what we observed. On this basis a distinction between chloroplast and mitochondrial (mt) mutator genes is proposed. Accordingly, the chloroplast mutator here described would be the first one reported for monocots. Increased knowledge on this subject can play a fundamental role in elucidating organelle heredity and its interactions with the nuclear genome. Moreover, this material could be a valuable source of variability of the otherwise conservative genetic information encoded in the chloroplast.Paper GEN 792, Institute of Genetics, CICA, INTA, Castelar     

Extraction and genetic control of two new water-soluble proteins of mature barley seed

This paper describes the genetic control of two new water-soluble proteins in barley. Water-soluble proteins (WSPs) of mature barley seed form part of the albumin/globulin class of seed proteins. They can be extracted from hand-milled grain with water, though some WSPs are more efficiently extracted with a solution of 10 mM dithiothreitol. Polymorphisms for WSPs were detected in isoelectric focusing gels incorporating various ampholine combinations. Two new controlling genes (Wsp4 andWsp5) have been identified and located using wheat/barley chromosome addition lines and barley doubled haploids.Wsp4 is located on chromosome 2 (2H), andWsp5 was found to be tightly linked toWsp2 on the long arm of chromosome 7 (5HL). Segregation of a sixth gene (Wsp6) is also described, but this has not been mapped. The results are discussed with respect to other previously mappedWsp loci.This work was funed by the Scottish Office of Agriculture and Fisheries Department and the Agricultural and Food Research Council.     

Plastid genome characterisation in Brassica and Brassicaceae using a new set of nine SSRs

The objective of the present study was to identify favourable exotic Quantitative Trait Locus (QTL) alleles for the improvement of agronomic traits in the BC₂DH population S42 derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). QTLs were detected as a marker main effect and/or a marker × environment interaction effect (M × E) in a three-factorial ANOVA. Using field data of up to eight environments and genotype data of 98 SSR loci, we detected 86 QTLs for nine agronomic traits. At 60 QTLs the marker main effect, at five QTLs the M × E interaction effect, and at 21 QTLs both the effects were significant. The majority of the M × E interaction effects were due to changes in magnitude and are, therefore, still valuable for marker assisted selection across environments. The exotic alleles improved performance in 31 (36.0%) of 86 QTLs detected for agronomic traits. The exotic alleles had favourable effects on all analysed quantitative traits. These favourable exotic alleles were detected, in particular on the short arm of chromosome 2H and the long arm of chromosome 4H. The exotic allele on 4HL, for example, improved yield by 7.1%. Furthermore, the presence of the exotic allele on 2HS increased the yield component traits ears per m² and thousand grain weight by 16.4% and 3.2%, respectively. The present study, hence, demonstrated that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve quantitative agronomic traits.     

AB-QTL analysis in spring barley: III. Identification of exotic alleles for the improvement of malting quality in spring barley (<Emphasis Type="Italic">H. vulgare</Emphasis> ssp. <Emphasis Type="Italic">spontaneum</Emphasis>)

Malting quality is genetically determined by the complex interaction of numerous traits which are expressed prior to and, in particular, during the malting process. Here, we applied the advanced backcross quantitative trait locus (AB-QTL) strategy (Tanksley and Nelson, Theor Appl Genet 92:191–203, 1996), to detect QTLs for malting quality traits and, in addition, to identify favourable exotic alleles for the improvement of malting quality. For this, the BC₂DH population S42 was generated from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). A QTL analysis in S42 for seven malting parameters measured in two different environments yielded 48 QTLs. The exotic genotype improved the trait performance at 18 (37.5%) of 48 QTLs. These favourable exotic alleles were detected, in particular, on the chromosome arms 3HL, 4HS, 4HL and 6HL. The exotic allele on 4HL, for example, improved α-amylase activity by 16.3%, fermentability by 0.8% and reduced raw protein by 2.4%. On chromosome 6HL, the exotic allele increased α-amylase by 16.0%, fermentability by 1.3%, friability by 7.3% and reduced viscosity by 2.9%. Favourable transgressive segregation, i.e. S42 lines exhibiting significantly better performance than the recurrent parent Scarlett, was recorded for four traits. For α-amylase, fermentability, fine-grind extract and VZ45 20, 16, 2 and 26 S42 lines, respectively, surpassed the recurrent parent Scarlett. The present study hence demonstrates that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve malting quality traits.     

Genetic analysis of preharvest sprouting in a six-row barley cross

Preharvest sprouting (PHS) can be a problem in barley (Hordeum vulgare L.) especially malting barley, since rapid, uniform, and complete germination are critical. Information has been gained by studying the genetics of dormancy (measured as germination percentage, GP). The objective of this study was to determine if the quantitative trait loci (QTLs) discovered in previous research on dormancy are related to PHS. PHS was measured as sprout score (SSc) based on visual sprouting in mist chamber-treated spikes and as alpha-amylase activity (AA) in kernels taken from mist chamber-treated spikes that showed little or no visible sprouting. GP was also measured. All traits were measured at 0 and 14 days after physiological maturity. Evaluation of the spring six-row cross, Steptoe (dormant)/Morex (non-dormant) doubled haploid mapping population grown in greenhouse and field environments revealed QTL regions for SSc, AA, and GP on five, four, and six of the seven barley chromosomes, respectively. In total, seven and eight regions on five and six chromosomes had effects ranging from 4 to 31% and 3 to 39% on PHS and dormancy, respectively. One chromosome 3H and three chromosome 5H QTLs had the greatest effects. All PHS QTLs coincide with known dormancy QTLs, but some QTLs appear to be more important for PHS than for dormancy. Key QTLs identified should benefit breeding of barley for a suitable balance between PHS and dormancy.     

Protein markers for anther culturability in barley

Two-dimensional electrophoresis of proteins from a recombinant population of anther culture-derived doubled haploid lines identified 4 loci or linkage groups showing a deviation from an expected 11 segregation. It was hypothesized that these markers are linked to genes involved in the process of haploid plant production and that the deviation was due to a selection for alleles conferring higher anther culture response. To check this hypothesis, the anther culturability of 50 of the doubled haploid lines and their two inbred parents was assessed. It was found that 2 of the loci which had a distortion of segregation showed a significant effect on anther culture response, the most efficient allele being the most frequent in both loci. In addition, 2 more markers associated with anther culturability were found. One of the first mentioned 2 loci and one of the latter 2 were found to be linked to genes involved in both embryoid production and subsequent green plant regeneration. The remaining two were linked to genes involved only in green plant regeneration. Of the 4 favorable alleles 3 were inherited from one parent.     

Construction of an RFLP map of barley

Summary In order to construct an RFLP map of barley, two populations were analyzed using 251 genomic and cDNA markers: one population comprised 71 F₁ antherderived double haploid (DH) individuals of an intraspecific cross (IGRI x FRANKA), and the other 135 individuals of an interspecific F₂/F₃ progeny (VADA x H. spontaneum). The distribution of nonrepetitive clones over the seven barley chromosomes revealed a maximum for chromosome 2H and a minimum for 6H. The polymorphism of the interspecific progeny (76%) clearly exceeded that of the intraspecific progeny (26%) although, based on their pedigrees, IGRI and FRANKA are only distantly related. The contribution of individual chromosomes of the DH parents to the overall polymorphism varied between 8% and 50%. A significant portion (44% versus 10% of the interspecific progeny) of the markers mapped on the DH offspring showed distorted segregation, caused mainly by the prevalence of variants originating from the parent that better responded to in vitro culture (IGRI). In contrast to the interspecific map, probes displaying skewed segregation were clustered on the DH map on discrete segments. The colinear arrangement of both maps covers a distance of 1,453 cM and identifies regions of varying map distances.     

AB-QTL analysis in spring barley. I. Detection of resistance genes against powdery mildew, leaf rust and scald introgressed from wild barley

The objective of this study was to map new resistance genes against powdery mildew (Blumeria graminis f. sp. hordei L.), leaf rust (Puccinia hordei L.) and scald [Rhynchosporium secalis (Oud.) J. Davis] in the advanced backcross doubled haploid (BC₂DH) population S42 derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). Using field data of disease severity recorded in eight environments under natural infestation and genotype data of 98 SSR loci, we detected nine QTL for powdery mildew, six QTL for leaf rust resistance and three QTL for scald resistance. The presence of the exotic QTL alleles reduced disease symptoms by a maximum of 51.5, 37.6 and 16.5% for powdery mildew, leaf rust and scald, respectively. Some of the detected QTL may correspond to previously identified qualitative (i.e. Mla) and to quantitative resistance genes. Others may be newly identified resistance genes. For the majority of resistance QTL (61.0%) the wild barley contributed the favourable allele demonstrating the usefulness of wild barley in the quest for resistant cultivars.