Barley Chromosome Research Articles

Significant induction by drought of HvPKDM7-1, a gene encoding a jumonji-like histone demethylase homologue in barley (H. vulgare)

Reversible histone methylations of the fourth lysine on histone 3 (H3K4) are key epigenetic marks, involved in establishing and maintaining epigenetic transcriptional states of genes during normal development and in response to environmental stresses like drought. Their dynamic regulation is modulated by a complex mechanism employing specific epigenetic factors such as histone lysine methyltransferases and the counteracting histone demethylases. The identification and characterization of such drought-responsive epigenetic factors involved in H3K4 methylation in temperate cereal crops would provide a major advantage in their breeding for higher yield. For better understanding these mechanisms and their implication in drought stress tolerance in the annual cereal crop barley (Hordeum vulgare L.), we have isolated, cloned and characterized a drought-induced PKDM7 subfamily-like H3K4 demethylase homologue, designated HvPKDM7-1. The complete cDNA clone obtained using the RCA-RACE (Rolling Circle Amplification-RACE) method, contained a 3,861 bp ORF encoding the 1,287 a.a. putative protein, which includes conserved residues compatible with the demethylation activity. Comparative genomic analysis enabled us to locate the gene on locus 3260 on the long arm of the barley chromosome 1H. Constant transcript accumulation in early barley seed development was followed by almost complete silencing, coinciding with the stage of active storage of proteins. Transcript induction by drought stress was observed in two barley cultivars and was considerably higher in the drought-tolerant cultivar, indicating that HvPKDM7-1 may be actively involved in drought tolerance control, an agronomically very important trait.

Development and identification of wheat–barley 2H chromosome translocation lines carrying the Isa gene

With 4 figures and 2 tablesAbstractThe bifunctional α‐amylase/subtilisin inhibitor (BASI) encoded by the Isa gene on barley chromosome 2HL could inhibit wheat α‐amylase activity, thereby reducing sprouting and improving the quality of wheat. Regenerated plants were derived from immature embryo culture of hybrids of common wheat varieties ‘Zhengmai 9023’, ‘CB037’ and ‘Zhongmai 16’ with the wheat–barley 2H alien substitution lines 2H(2A) and 2H(2B) after callus induction, subculture and differentiation. The presence of barley 2H chromatin was detected in regenerated plants (SC1) and their selfed progeny (SC2–5) using homoeologous group 2 SSR markers from barley and further identified in selected SC4 and SC5 lines using genomic in situ hybridization with barley genomic DNA as probe and CS genomic DNA for blocking. The Isa gene from the identified SC4 and SC5 lines was also amplified using Isa‐specific primers. We identified wheat–barley 2H chromosome translocation lines carring the Isa gene.

Molecular mapping of powdery mildew resistance gene Eg-3 in cultivated oat (Avena sativa L. cv. Rollo)

Powdery mildew is a prevalent fungal disease affecting oat (Avena sativa L.) production in Europe. Common oat cultivar Rollo was previously shown to carry the powdery mildew resistance gene Eg-3 in common with cultivar Mostyn. The resistance gene was mapped with restriction fragment length polymorphism (RFLP) markers from Triticeae group-1 chromosomes using a population of F(3) lines from a cross between A. byzantina cv. Kanota and A. sativa cv. Rollo. This comparative mapping approach positioned Eg-3 between cDNA-RFLP marker loci cmwg706 and cmwg733. Since both marker loci were derived from the long arm of barley chromosome 1H, the subchromosomal location of Eg-3 was assumed to be on the long arm of oat chromosome 17. Amplified fragment length polymorphism (AFLP) marker technology featured as an efficient means for obtaining markers closely linked to Eg-3.

Control of barley (Hordeum vulgare L.) development and senescence by the interaction between a chromosome six grain protein content locus, day length, and vernalization.

Regulatory processes controlling traits such as anthesis timing and whole-plant senescence are of primary importance for reproductive success and for crop quality and yield. It has previously been demonstrated that the presence of alleles associated with high grain protein content (GPC) at a locus on barley chromosome six leads to accelerated leaf senescence, and to strong (>10-fold) up-regulation of several genes which may be involved in senescence control. One of these genes (coding for a glycine-rich RNA-binding protein termed HvGR-RBP1) exhibits a high degree of similarity to Arabidopsis glycine-rich RNA-binding protein 7 (AtGRP7), which has been demonstrated to accelerate flowering under both long-day (LD) and short-day (SD) conditions, but not after vernalization. Development of near-isogenic barley lines, differing in the allelic state of the GPC locus, was compared from the seedling stage to maturity under both SD and LD and after vernalization under LD. Intriguingly, pre-anthesis plant development [measured by leaf emergence timing and pre-anthesis (sequential) leaf senescence] was enhanced in high-GPC germplasm. Differences were more pronounced under SD than under LD, but were eliminated by vernalization, associating observed effects with floral induction pathways. By contrast, differences in post-anthesis flag leaf and whole-plant senescence between low- and high-GPC germplasm persisted under all tested conditions, indicating that the GPC locus, possibly through HvGR-RBP1, impacts on both developmental stages. Detailed molecular characterization of this experimental system may allow the dissection of cross-talk between signalling pathways controlling early plant and floral development on one side, and leaf/whole-plant senescence on the other side.

Telomere-mediated truncation of barley chromosomes

Engineered minichromosomes offer an enormous opportunity to plant biotechnology as they have the potential to simultaneously transfer and stably express multiple genes. Following a top-down approach, we truncated endogenous chromosomes in barley (Hordeum vulgare) by Agrobacterium-mediated transfer of T-DNA constructs containing telomere sequences. Blocks of Arabidopsis-like telomeric repeats were inserted into a binary vector suitable for stable transformation. After transfer of these constructs into immature embryos of diploid and tetraploid barley, chromosome truncation by T-DNA-induced de novo formation of telomeres could be confirmed by fluorescent in situ hybridisation, primer extension telomere repeat amplification and DNA gel blot analysis in regenerated plants. Telomere seeding connected to chromosome truncation was found in tetraploid plants only, indicating that genetic redundancy facilitates recovery of shortened chromosomes. Truncated chromosomes were transmissible in sexual reproduction, but were inherited at rates lower than expected according to Mendelian rules.

Karyotyping of barley chromosomes by a new fluorescence banding technique combined with scanning probe microscopy

Fluorescence banding has been used to classify chromosomes, except those of barley. Four of the seven barley chromosomes are indistinguishable by length or arm ratio. C-banding has been used for classification; however, it requires a long aging period. Here, we describe a new fluorescence banding method for barley. The chromosomes are treated with warm acetate followed by staining with a fluorescent dye, YOYO-1. Using this method, all seven barley chromosomes can be clearly distinguished. Atomic force microscopy and scanning near-field microscopy analyses revealed that the surfaces of the banded chromosomes were flat, indicating that the fluorescence intensity reflected the internal DNA density or condensation of chromatin.

The homoeologous regions on long arms of group 3 chromosomes in wheat and barley harbour major crown rot resistance loci

Crown rot (CR), caused by various Fusarium species, has become an important cereal disease worldwide and growing resistant varieties is an essential strategy to reduce the $A80 mil annual loss from CR in Australia. To facilitate the breeding of resistant varieties, we have screened 2514 wheat and 1059 barley genotypes and identified several lines with high levels of CR resistance in each crop. Initially focused on two wheat and one barley resistance sources, we have identified major QTL with unprecedented magnitudes. Two wheat QTL explain between 35% (LOD 7.6) and 49% (LOD 10.8) and the barley QTL explains up to 63% (LOD 14.8) of the phenotypic variance. One of the wheat QTL has been further assessed in four validation populations, and the presence of this QTL alone reduces CR severity by 33% on average. Surprisingly, all of the three major CR QTL are located in similar regions on the long arms of the homoeologous group 3 chromosomes, the two wheat QTL on 3BL and the barley QTL on 3HL. The possible homoeologous relationship between the 3BL wheat QTL and the 3HL barley QTL warrants further investigation. Relative rearrangements between 3H and 3B chromosomes are unknown, although the relative distances between the different QTL and the centromeres seem to be different. Compared with the barley QTL, the 3BL wheat QTL seems to be more distally located. However genetic distance can be affected by many factors including the use of different populations, thus the differences in genetic distances between the two different genera may have only limited value. The physical map of wheat chromosome 3B, which was recently made available as the first such resources for wheat, would make such a study much easier. Results will be presented on the detection, genetic analysis and mapping of these new sources of CR resistance.

A New Insight into Application for Barley Chromosome Addition Lines of Common Wheat: Achievement of Stigmasterol Accumulation

Barley (Hordeum vulgare) has a much higher content of bioactive substances than wheat (Triticum aestivum). In order to investigate additive and/or synergistic effect(s) on the phytosterol content of barley chromosomes, we used a series of barley chromosome addition lines of common wheat that were produced by normal crossing. In determining the plant sterol levels in 2-week-old seedlings and dry seeds, we found that the level of stigmasterol in the barley chromosome 3 addition (3H) line in the seedlings was 1.5-fold higher than that in the original wheat line and in the other barley chromosome addition lines, but not in the seeds. Simultaneously, we determined the overall expression pattern of genes related to plant sterol biosynthesis in the seedlings of wheat and each addition line to assess the relative expression of each gene in the sterol pathway. Since we elucidated the CYP710A8 (cytochrome P450 subfamily)-encoding sterol C-22 desaturase as a key characteristic for the higher level of stigmasterol, full-length cDNAs of wheat and barley CYP710A8 genes were isolated. These CYP710A8 genes were mapped on chromosome 3 in barley (3H) and wheat (3A, 3B, and 3D), and the expression of CYP710A8 genes increased in the 3H addition line, indicating that it is responsible for stigmasterol accumulation. Overexpression of the CYP710A8 genes in Arabidopsis increased the stigmasterol content but did not alter the total sterol level. Our results provide new insight into the accumulation of bioactive compounds in common wheat and a new approach for assessing plant metabolism profiles.

Effect of barley chromosome addition on the susceptibility of wheat to feeding by a gall-inducing leafhopper

The maize orange leafhopper Cicadulina bipunctata is distributed widely in tropical and subtropical regions of the Old World and feeds on various Poaceae. The leafhopper is recognized as an important pest of maize in several countries. Adults as well as nymphs of C. bipunctata induce growth stunting and galls characterized by the severe swelling of leaf veins on many cereal crops including wheat, rice, and maize, but do not on barley. To clarify the mechanism of growth stunting and gall induction by C. bipunctata, we used six barley chromosome disomic addition lines of wheat (2H-7H) and investigated the effect of barley (cv. Betzes) chromosome addition on the susceptibility of wheat (cv. Chinese Spring) to feeding by the leafhopper. Feeding by C. bipunctata significantly stunted the growth in 2H, 3H, 4H, and 5H, but did not in 6H and 7H. The degree of gall induction was significantly weaker and severer in 3H and 5H than in Chinese Spring, respectively. These results suggest that barley genes resistant to growth stunting and gall induction exist in 6H and 7H, and 3H, respectively. 5H is considered to be useful for future assays investigating the mechanism of gall induction by this leafhopper because of the high susceptibility to the feeding by C. bipunctata. Significant correlation between the degrees of growth stunting and gall induction was not detected in the six chromosome addition lines and Chinese spring. This implies that these two symptoms are independent phenomena although both are initiated by the feeding of C. bipunctata.

Characterization of a new 4BS.7HL wheat–barley translocation line using GISH, FISH, and SSR markers and its effect on the β-glucan content of wheat

A spontaneous interspecific Robertsonian translocation was revealed by genomic in situ hybridization (GISH) in the progenies of a monosomic 7H addition line originating from a new wheat 'Asakaze komugi' × barley 'Manas' hybrid. Fluorescence in situ hybridization (FISH) with repetitive DNA sequences (Afa family, pSc119.2, and pTa71) allowed identification of all wheat chromosomes, including wheat chromosome arm 4BS involved in the translocation. FISH using barley telomere- and centromere-specific repetitive DNA probes (HvT01 and (AGGGAG)(n)) confirmed that one of the arms of barley chromosome 7H was involved in the translocation. Simple sequence repeat (SSR) markers specific to the long (L) and short (S) arms of barley chromosome 7H identified the translocated chromosome segment as 7HL. Further analysis of the translocation chromosome clarified the physical position of genetically mapped SSRs within 7H, with a special focus on its centromeric region. The presence of the HvCslF6 gene, responsible for (1,3;1,4)-β-D-glucan production, was revealed in the centromeric region of 7HL. An increased (1,3;1,4)-β-D-glucan level was also detected in the translocation line, demonstrating that the HvCslF6 gene is of potential relevance for the manipulation of wheat (1,3;1,4)-β-D-glucan levels.

454 sequencing of pooled BAC clones on chromosome 3H of barley

BackgroundGenome sequencing of barley has been delayed due to its large genome size (ca. 5,000Mbp). Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H.ResultsWe sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1.ConclusionsWe demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.

Variation in feed quality traits for beef cattle in Steptoe × Morex barley population

Barley is a major feed source for livestock in the western regions of North America. Feed quality of beef cattle has been neglected as a selection criterion because of lack of understanding of the feed characteristics that could be responsive to selection and would improve feedlot performance. A Steptoe × Morex population was planted in irrigated and rain-fed environments, and collected data were used to evaluate the genetic variation in dry matter and starch digestibilities, acid detergent fiber, protein and starch contents, and to map quantitative trait loci controlling the variation in these traits. Transgressive genotypes indicate the wide genetic variation of these traits. High heritability estimates for these traits suggest that early selection for these traits during breeding would be achievable. A total of 32 main effect QTL and five epistatic QTL were identified which conditioned feed traits on different barley chromosomes. QTL for acid detergent fiber and starch contents overlapped on chromosome 6H at the Nar7 locus. Tight negative correlation between the two traits suggest the usability of Nar7 as anchor marker in marker-assisted selection programs to develop barley with low acid detergent fiber and high starch content.

High-density fluorescence in situ hybridization signal detection on barley (Hordeum vulgare L.) chromosomes with improved probe screening and reprobing procedures

The barley (Hordeum vulgare L.) genome was screened to identify sequences that could be used for fluorescence in situ hybridization (FISH). From 2000 transformed bacterium colonies carrying barley clones, 56 colonies were selected on the basis of the patterns that their PCR products produced when subjected to agarose gel electrophoresis. Among them, 42 (75%) exhibited fluorescent signals on barley chromosomes after in situ hybridization using the directly labeled PCR products. Sequencing revealed seven clones, pHv-365, pHv-177, pHv-1112, pHv-689, pHv-1476, pHv-1889, and pHv-1972, to be newly identified FISH-positive sequences. The remainder possess previously described sequences such as 5S, GAA microsatellite, centromere repeats, HVT01, and pHvMWG2315 (324 bp repeat). It is shown here that a combination of five probes, which produce strong signals on barley chromosomes, pHv-38 (5S), pHv-365, pHv-961 (HVT01), GAA, and TAG microsatellites, offer unequivocal recognition of each chromosome. The combination of three probes, i.e., pHv-1123 (barley 324 bp repeat), GAA, and TAG, decorated entire chromosomes with fine dotted signals and was useful for detecting the break points of aberrant chromosomes. The signals' distributions of pHv-177, pHv-1112, and TAG were highly polymorphic. An improved reprobing procedure and its usefulness are also discussed.

Dissection and cytological mapping of barley chromosome 2H in the genetic background of common wheat

We used gametocidal (Gc) chromosomes 2C and 3C(SAT) to dissect barley 2H added to common wheat. The Gc chromosome induces chromosomal breakage resulting in chromosomal aberrations in the progeny of the 2H addition line of common wheat carrying the monosomic Gc chromosome. We conducted in situ hybridization to select plants carrying structurally rearranged aberrant 2H chromosomes and characterized them by sequential C-banding and in situ hybridization. We established 66 dissection lines of common wheat carrying single aberrant 2H chromosomes. The aberrant 2H chromosomes were of either deletion or translocation or complicated structural change. Their breakpoints were distributed in the short arm (2HS), centromere (2HC) and the long arm (2HL) at a rough 2HS/2HC/2HL ratio of 2:1:2. We conducted PCR analysis of the 66 dissection lines using 115 EST markers specific to chromosome 2H. Based on the PCR result, we constructed a physical or cytological map of chromosome 2H that were divided into 34 regions separated by the breakpoints of the aberrant 2H chromosomes. Forty-seven markers were present in 2HS and 68 in 2HL. We compared the 2H cytological map with a previously reported 2H genetic map using 44 markers that were used in common to construct both maps. The order of markers in the distal region was the same on both maps but that in the proximal region was somewhat contradictory between the two maps. We found that the markers distributed rather evenly in the genetic map were actually concentrated in the distal regions of both arms as revealed by the cytological map. We also recognized an EST-marker or gene-rich region in the 2HL interstitial region slightly to the telomere.

Genetic mapping and QTL analysis of disease resistance traits in the barley population Baudin×AC Metcalfe

A genetic map of barley (Hordeum vulgare L.) with 163 amplified fragment length polymorphism and 69 simple sequence repeat (SSR) markers was constructed using a population of 178 doubled haploid lines from a cross between the varieties ‘Baudin’ and ‘AC Metcalfe’. Linkage groups were assigned to barley chromosomes using published map locations of SSR markers as reference points. The total length of the map was 1307.2 cM with an average interval length of 5.6 cM between markers. The genetic map was used to locate quantitative trait loci (QTLs) for several disease resistance traits. The population was tested for spot type net blotch, caused by Pyrenophora teres f. maculata, and net type net blotch, caused by Pyrenophora teres f. teres, in greenhouse experiments and in a range of field environments in Western Australia and Queensland. The response of the lines to leaf rust (caused by Puccinia hordei L.) at adult plant growth stages was evaluated in Western Australia. Significant marker–trait associations were found for seedling resistance and symptom severity in adult plants to these diseases. A new locus conferring resistance to P. teres f. maculata at both seedling and adult plant stages was detected on the short arm of chromosome 6H. From the seedling testing against P. teres f. teres, five highly repeatable QTLs were detected, on chromosomes 2HS, 2HL, 3HS, 4HL, and 6HS. For leaf rust, one highly significant QTL was detected on chromosome 2HL. The markers within these QTL regions present an opportunity for marker-assisted selection for these traits in barley-breeding programs.

Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources

BackgroundBecause of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B). However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B.ResultsThree dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B.ConclusionOur study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.

Mapping resistance to the bird cherry‐oat aphid (Rhopalosiphum padi) in barley

With 4 figures and 3 tables AbstractAphid resistance is a desirable trait in barley to combat the spread of the barley yellow dwarf virus and also to reduce the direct damage that aphids can inflict on cereals. A significant quantitative trait locus (QTL) on barley chromosome 3H was mapped based on a doubled‐haploid population derived from F1 of the cross ‘Lina’ × ‘5172‐28:4’ that showed segregation for resistance to bird cherry‐oat aphid. This QTL explained 9% of the variance in aphid growth and is a novel QTL for aphid resistance to bird cherry‐oat aphid. Combining this QTL on chromosome 3H with another major QTL on chromosome 2H would potentially provide a more durable and higher level of resistance. Depending on the prevalent species in the cultivated areas, pyramiding resistance to other aphid species such as the corn leaf aphid and the Russian wheat aphid will provide greater protection to the plant in the field against both aphids and barley yellow dwarf virus.

Patterns of polymorphism and linkage disequilibrium in cultivated barley.

We carried out a genome-wide analysis of polymorphism (4,596 SNP loci across 190 elite cultivated accessions) chosen to represent the available genetic variation in current elite North West European and North American barley germplasm. Population sub-structure, patterns of diversity and linkage disequilibrium varied considerably across the seven barley chromosomes. Gene-rich and rarely recombining haplotype blocks that may represent up to 60% of the physical length of barley chromosomes extended across the ‘genetic centromeres’. By positioning 2,132 bi-parentally mapped SNP markers with minimum allele frequencies higher than 0.10 by association mapping, 87.3% were located to within 5 cM of their original genetic map position. We show that at this current marker density genetically diverse populations of relatively small size are sufficient to fine map simple traits, providing they are not strongly stratified within the sample, fall outside the genetic centromeres and population sub-structure is effectively controlled in the analysis. Our results have important implications for association mapping, positional cloning, physical mapping and practical plant breeding in barley and other major world cereals including wheat and rye that exhibit comparable genome and genetic features.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-010-1466-7) contains supplementary material, which is available to authorized users.

A SOS3 homologue maps to HvNax4, a barley locus controlling an environmentally sensitive Na+ exclusion trait.

Genes that enable crops to limit Na+ accumulation in shoot tissues represent potential sources of salinity tolerance for breeding. In barley, the HvNax4 locus lowered shoot Na+ content by between 12% and 59% (g−1 DW), or not at all, depending on the growth conditions in hydroponics and a range of soil types, indicating a strong influence of environment on expression. HvNax4 was fine-mapped on the long arm of barley chromosome 1H. Corresponding intervals of ∼200 kb, containing a total of 34 predicted genes, were defined in the sequenced rice and Brachypodium genomes. HvCBL4, a close barley homologue of the SOS3 salinity tolerance gene of Arabidopsis, co-segregated with HvNax4. No difference in HvCBL4 mRNA expression was detected between the mapping parents. However, genomic and cDNA sequences of the HvCBL4 alleles were obtained, revealing a single Ala111Thr amino acid substitution difference in the encoded proteins. The known crystal structure of SOS3 was used as a template to obtain molecular models of the barley proteins, resulting in structures very similar to that of SOS3. The position in SOS3 corresponding to the barley substitution does not participate directly in Ca2+ binding, post-translational modifications or interaction with the SOS2 signalling partner. However, Thr111 but not Ala111 forms a predicted hydrogen bond with a neighbouring α-helix, which has potential implications for the overall structure and function of the barley protein. HvCBL4 therefore represents a candidate for HvNax4 that warrants further investigation.

Whole-genome association mapping in elite inbred crop varietiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley ( Hordeum vulgare ) gene pool extends, on average, for <1–5 cM. Based on this information, we have developed a platform for whole genome association studies that comprises a collection of elite lines that we have characterized at 3060 genome-wide single nucleotide polymorphism (SNP) marker loci. Interrogating this data set shows that significant population substructure is present within the elite gene pool and that diversity and LD vary considerably across each of the seven barley chromosomes. However, we also show that a subpopulation comprised of only the two-rowed spring germplasm is less structured and well suited to whole genome association studies without the need for extensive statistical intervention to account for structure. At the current marker density, the two-rowed spring population is suited for fine mapping simple traits that are located outside of the genetic centromeres with a resolution that is sufficient for candidate gene identification by exploiting conservation of synteny with fully sequenced model genomes and the emerging barley physical map.