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Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through divergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.

Using genomic structural equation modelling, this research demonstrates an efficient way to identify genetically correlating traits and provides an effective proxy for multi-trait selection to consider the joint genetic architecture of multiple interacting traits in crop breeding. Breeding crop cultivars with optimal value across multiple traits has been a challenge, as traits may negatively correlate due to pleiotropy or genetic linkage. For example, grain yield and grain protein content correlate negatively with each other in cereal crops. Future crop breeding needs to be based on practical yet accurate evaluation and effective selection of beneficial trait to retain genes with the best agronomic score for multiple traits. Here, we test the framework of whole-system-based approach using structural equation modelling (SEM) to investigate how one trait affects others to guide the optimal selection of a combination of agronomically important traits. Using ten traits and genome-wide SNP profiles from a worldwide barley panel and SEM analysis, we revealed a network of interacting traits, in which tiller number contributes positively to both grain yield and protein content; we further identified common genetic factors affecting multiple traits in the network of interaction. Our method demonstrates an efficient way to identify genetically correlating traits and underlying pleiotropic genetic factors and provides an effective proxy for multi-trait selection within a whole-system framework that considers the joint genetic architecture of multiple interacting traits in crop breeding. Our findings suggest the promise of a whole-system approach to overcome challenges such as the negative correlation of grain yield and protein content to facilitating quantitative and objective breeding decisions in future crop breeding.

Functional divergence after gene duplication plays a central role in plant evolution. Among cereals, only Hordeum vulgare (barley), Triticum aestivum (wheat) and Secale cereale (rye) accumulate delphinidin-derived (blue) anthocyanins in the aleurone layer of grains, whereas Oryza sativa (rice), Zea mays (maize) and Sorghum bicolor (sorghum) do not. The underlying genetic basis for this natural occurrence remains elusive. Here, we mapped the barley Blx1 locus involved in blue aleurone to an approximately 1.13 Mb genetic interval on chromosome 4HL, thus identifying a trigenic cluster named MbHF35 (containing HvMYB4H, HvMYC4H and HvF35H). Sequence and expression data supported the role of these genes in conferring blue-coloured (blue aleurone) grains. Synteny analyses across monocot species showed that MbHF35 has only evolved within distinct Triticeae lineages, as a result of dispersed gene duplication. Phylogeny analyses revealed a shared evolution pattern for MbHF35 in Triticeae, suggesting that these genes have co-evolved together. We also identified a Pooideae-specific flavonoid 3',5'-hydroxylase (F3'5'H) lineage, termed here Mo_F35H2, which has a higher amino acid similarity with eudicot F3'5'Hs, demonstrating a scenario of convergent evolution. Indeed, selection tests identified 13 amino acid residues in Mo_F35H2 that underwent positive selection, possibly driven by protein thermostablility selection. Furthermore, through the interrogation of barley germplasm there is evidence that HvMYB4H and HvMYC4H have undergone human selection. Collectively, our study favours blue aleurone as a recently evolved trait resulting from environmental adaptation. Our findings provide an evolutionary explanation for the absence of blue anthocyanins in other cereals and highlight the importance of gene functional divergence for plant diversity and environmental adaptation.

Using gene-set association test and epistasis analysis, this research achieved higher statistical power with potentially high accuracy, and detected significant genes and gene networks that influence flowering time in barley., Single-marker genome-wide association studies (GWAS) have successfully detected associations between single nucleotide polymorphisms (SNPs) and agronomic traits such as flowering time and grain yield in barley. However, the analysis of individual SNPs can only account for a small proportion of genetic variation, and can only provide limited knowledge on gene network interactions. Gene-based GWAS approaches provide enormous opportunity both to combine genetic information and to examine interactions among genetic variants. Here, we revisited a previously published phenotypic and genotypic data set of 895 barley varieties grown in two years at four different field locations in Australia. We employed statistical models to examine gene–phenotype associations, as well as two-way epistasis analyses to increase the capability to find novel genes that have significant roles in controlling flowering time in barley. Genetic associations were tested between flowering time and corresponding genotypes of 174 putative flowering time-related genes. Gene–phenotype association analysis detected 113 genes associated with flowering time in barley, demonstrating the unprecedented power of gene-based analysis. Subsequent two-way epistasis analysis revealed 19 pairs of gene×gene interactions involved in controlling flowering time. Our study demonstrates that gene-based association approaches can provide higher capacity for future crop improvement to increase crop performance and adaptation to different environments.

Summary Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here, we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target‐capture method was used to detect genome‐wide polymorphisms in a panel of 174 flowering time‐related genes, chosen based on prior knowledge from barley, rice and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas.

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.

Using genomic structural equation modelling, this research demonstrates an efficient way to identify genetically correlating traits and provides an effective proxy for multi-trait selection to consider the joint genetic architecture of multiple interacting traits in crop breeding. Breeding crop cultivars with optimal value across multiple traits has been a challenge, as traits may negatively correlate due to pleiotropy or genetic linkage. For example, grain yield and grain protein content correlate negatively with each other in cereal crops. Future crop breeding needs to be based on practical yet accurate evaluation and effective selection of beneficial trait to retain genes with the best agronomic score for multiple traits. Here, we test the framework of whole-system-based approach using structural equation modelling (SEM) to investigate how one trait affects others to guide the optimal selection of a combination of agronomically important traits. Using ten traits and genome-wide SNP profiles from a worldwide barley panel and SEM analysis, we revealed a network of interacting traits, in which tiller number contributes positively to both grain yield and protein content; we further identified common genetic factors affecting multiple traits in the network of interaction. Our method demonstrates an efficient way to identify genetically correlating traits and underlying pleiotropic genetic factors and provides an effective proxy for multi-trait selection within a whole-system framework that considers the joint genetic architecture of multiple interacting traits in crop breeding. Our findings suggest the promise of a whole-system approach to overcome challenges such as the negative correlation of grain yield and protein content to facilitating quantitative and objective breeding decisions in future crop breeding.

The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. 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 breeding had on the genetic diversity of 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 dataset and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.Author summaryToday’s gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Genetic diversity is vital for crop species to be able to adapt to changing environments. There is concern that recent breeding efforts have eroded the genetic diversity of many domesticated crops including barley. The present study assembled a global panel of barley genotypes with a focus on historical and modern Australian varieties.Genome-wide data was used to detect genes that are thought to have been under selection during crop breeding in Australian barley. The results demonstrate that despite being more extensively bred, modern Australian barley varieties exhibit higher genetic diversity than historical cultivars, countering the common perception that intensive breeding leads to genetic erosion of adaptive diversity in modern cultivars. In addition, some loci (particularly those related to phenology) were subject to selection during the introduction of other barley varieties to Australia – these genes might continue to be important targets in breeding efforts in the face of changing climatic conditions.

An effective and stable quantitative resistance locus, QSc.VR4, was fine mapped, characterized and physically anchored to the short arm of 4H, conferring adult plant resistance to the fungus Rhynchosporium commune in barley. Scald caused by Rhynchosporium commune is one of the most destructive barley diseases worldwide. Accumulation of adult plant resistance (APR) governed by multiple resistance alleles is predicted to be effective and long-lasting against a broad spectrum of pathotypes. However, the molecular mechanisms that control APR remain poorly understood. Here, quantitative trait loci (QTL) analysis of APR and fine mapping were performed on five barley populations derived from a common parent Vlamingh, which expresses APR to scald. Two QTLs, designated QSc.VR4 and QSc.BR7, were detected from a cross between Vlamingh and Buloke. Our data confirmed that QSc.VR4 is an effective and stable APR locus, residing on the short arm of chromosome 4H, and QSc.BR7 derived from Buloke may be an allele of reported Rrs2. High-resolution fine mapping revealed that QSc.VR4 is located in a 0.38 Mb genomic region between InDel markers 4H2282169 and 4H2665106. The gene annotation analysis and sequence comparison suggested that a gene cluster containing two adjacent multigene families encoding leucine-rich repeat receptor kinase-like proteins (LRR-RLKs) and germin-like proteins (GLPs), respectively, is likely contributing to scald resistance. Adult plant resistance (APR) governed by QSc.VR4 may confer partial levels of resistance to the fungus Rhynchosporium commune and, furthermore, be an important resource for gene pyramiding that may contribute broad-based and more durable resistance.

In barley and other cereal crops, phenological diversity drives adaptation to different cultivation areas. Improvement of barley yield and quality traits requires adaptation to specific production areas with introgression of favorable alleles dependent upon precise identification of the underlying genes. Combining targeted sequence capture systems with next-generation sequencing provides an efficient approach to explore target genetic regions at high resolution, and allows rapid discovery of thousands of genetic polymorphisms. Here, we apply a versatile target-capture method to detect genome-wide polymorphisms in 174 flowering time-related genes, chosen based on prior knowledge from barley, rice, and Arabidopsis thaliana. Sequences were generated across a phenologically diverse panel of 895 barley varieties, resulting a high mean depth coverage of ~25x allowing reliable discovery and calling of insertion-deletion (InDel) and single nucleotide polymorphisms (SNPs). Sequences of InDel and SNPs from the targeted enrichment were utilized to develop 67 Kompetitive Allele Specific PCR (KASP) markers for validation. This work provides researchers and breeders a comprehensive molecular toolkit for the selection of phenology-related traits in barley., Design Type(s)genetic polymorphism analysis objective • strain comparison designMeasurement Type(s)genetic variationTechnology Type(s)DNA sequencingFactor Type(s)cultivarSample Characteristic(s)Hordeum vulgare subsp. vulgare • leaf Machine-accessible metadata file describing the reported data (ISA-Tab format)

Molecular marker-assisted backcrossing (MABC) is widely recommended for transferring favorable alleles from a donor to an elite variety. The question remains whether MABC is an effective approach to developing a competitive commercial variety. Here, we illustrate the transfer of a thermostable β-amylase allele Sd3 from wild barley into a commercial barley variety Gairdner. The elite lines were chosen for the Regional Crop Variety Test that followed a standard conventional breeding process. The results demonstrated that the Sd3 allele not only increased enzyme thermostability but dramatically enhanced diastatic power, an important malting quality trait. The BC1F1 individuals had a fundamental impact on the comprehensive agronomic and quality traits of the final progenies, demonstrating the importance of screening at the early stage of backcrossing in MABC. There was sufficient genetic variation in the BC3F3 families to select other malting quality and agronomic traits. Ten individual breeding lines with improved β-amylase thermostability also had improved yields and grain plumpness. Three elite lines with improved malting quality and agronomic traits were selected to provide a parental line to incorporate the wild barley allele for breeding a commercial variety. A new strategy should be considered that uses marker-assisted selection and backcrossing to transfer a favorable allele from a wild parent.

The association between high malting quality and pre-harvest sprouting (PHS) susceptibility is a key challenge when developing new malting barley varieties. A new malting barley variety Baudin has successfully combined high malting quality and PHS tolerance. A doubled haploid population was developed for mapping PHS tolerance and seed dormancy from a cross of Baudin × AC Metcalfe using 233 molecular markers. Three QTLs were mapped for seed dormancy based on the standard germination test at 24, 48 and 72 h. One major QTL was mapped to the long arm of chromosome 5H controlling seed dormancy and PHS tolerance from Baudin. Two other minor QTLs were identified from Baudin on chromosomes 3 and 7H. QTL/QTL interaction was detected for seed dormancy between chromosomes 3 and 5H. The PHS tolerance allele of the 5H QTL from Baudin contributes to higher malt yield without significant impact on diastatic power, beta-glucan content and wort viscosity. QTL from Baudin provide new sources to integrate PHS tolerance and high malting quality.

Net type net blotch (NTNB) is an important barley disease in Australia and elsewhere, inducing significant yield reduction. 'WPG8412' was resistant against Australian NTNB isolates 97NB1 and NB73, whereas 'Pompadour' and 'Stirling' showed differential responses to these isolates. Using these lines, three F(1)-derived double haploid populations that comprised 194 double haploid lines (DHLs) of 'WPG8412' x 'Stirling', 116 DHLs of 'WPG8412' x 'Pompadour' and 206 DHLs of 'Pompadour' x 'Stirling' were tested against these two isolates. Bimodal segregation indicated a major gene for resistance was operative: in 'WPG8412' x 'Stirling' against 97NB1; in 'WPG8412' x 'Pompadour' against NB73; and in 'Pompadour' x 'Stirling' against either of the isolate. This major gene was mapped using simple sequence repeat (SSR) markers on chromosome 6H in the centromeric region in all three populations. This work demonstrated that 6H region controlling NTNB is a complex locus, where at least three alleles or closely linked genes are possible in these parents against these isolates. This is a first report of 6H complexity for NTNB resistance against Australian isolates.

The use of dwarfing genes has resulted in the most significant improvements in yield and adaptation in cereal crops. The allelic dwarfing gene sdw1/denso has been used throughout the world to develop commercial barley varieties. The sdw1 gene has never been used successfully for malting barley, but only for a large number of feed varieties. One of the gibberellin 20-oxidase genes (Hv20ox₂) was identified as the candidate gene for sdw1/denso. Semi-quantitative real-time RT-PCR revealed that Hv20ox₂ was expressed at different levels in various organs of barley. Transcriptional levels were reduced in leaf blade, sheath, stem and rachis tissue in the barley variety Baudin with the denso gene. Subsequently, the relative expression levels of Hv20ox₂ were determined by quantitative real-time RT-PCR in a doubled haploid population and mapped as a quantitative trait. A single expression quantitative trait locus (eQTL) was identified and mapped to its structural gene region on chromosome 3H. The eQTL was co-located with QTLs for yield, height, development score, hectolitre weight and grain plumpness. The expression level of Hv20ox₂ was reduced fourfold in the denso mutant, but around 60-fold in the sdw1 mutant, compared to the control variety. The reduced expression level of Hv20ox₂ enhanced grain yield by increasing the number of effective tillers, but had negative effects on grain and malting quality. The sdw1 gene can be used only in feed barley due to its severe reduction of Hv20ox₂ expression. The gene expression marker for Hv20ox₂ can be used to distinguish different alleles of sdw1/denso.

Tiller angle, an important agronomic trait, contributes to crop production and plays a vital role in breeding for plant architecture. A barley line V-V-HD, which has prostrate tillers during vegetative growth and erect tillers after booting, is considered the ideal type for repressing weed growth and increasing leaf area during early growth. Genetic analysis identified that the prostrate trait in V-V-HD is controlled by a single gene. A double haploid population with 208 lines from V-V-HD × Buloke was used to map the prostrate growth gene. Ninety-six SNP markers were used for primary mapping, and subsequently, SSR and InDel markers were used for fine mapping. The gene was fine-mapped to a 3.53 Mb region on chromosome 3HL between the markers InDelz3028 and InDelz3032 with 52 candidate genes located in this region. Gene annotation analysis of the 52 genes within the target region indicated that a gene involved in zinc-ion binding (gene ID HORVU3Hr1G090910) is likely to be the candidate gene for prostrate growth in V-V-HD, and is linked to the denso/sdw gene. Association analysis showed that prostrate plants were shorter, flowered later.

The terminal region of barley chromosome 5HL controls malt extract, diastatic power, free amino acid nitrogen, alpha-amylase activity, seed dormancy and pre-harvest sprouting. Comparative analysis of the barley and rice maps has established that the terminal region of barley chromosome 5HL is syntenic to rice chromosome 3L near the telomere end. The rice BAC (Bacterial Artificial Chromosome) sequences covering the region of chromosome 3L were used to search barley expressed sequenced tags database. Thirty-three genes were amplified by PCR (polymerase chain reaction) with the primers designed from barley ESTs (expressed sequence tag). Comparison of the sequences of the PCR generated DNA fragments revealed polymorphisms including single nucleotide polymorphism (SNP), insertions or deletions between the barley varieties. Seven new PCR based molecular markers were developed and mapped within 10 cM in three doubled haploid barley populations (Stirling × Harrington, Baudin × AC Metcalfe and Chebec × Harrington). The mapped genes maintain the micro-syntenic relationship between barley and rice. These gene specific markers provide simple and efficient tools for germplasm characterization and marker-assisted selection for barley malting quality, and ultimately lead to isolation and identification of the major gene(s) controlling multiple quality traits on barley chromosome 5HL.

Salinity is a major abiotic stress to barley (Hordum vulgare L.) growth and yield. In the current study, quantitative trait loci (QTL) for yield and physiological components at the late growth stage under salt stress and non-stress environments were determined in barley using a double haploid population derived from a cross between CM72 (salt-tolerant) and Gairdner (salt-sensitive). A total of 30 QTLs for 10 traits, including tiller numbers (TN), plant height, spikes per line (SPL), spikes per plant (SPP), dry weight per plant, grains per plant, grain yield, shoot Na+ (NA) and K+ concentraitions (K) in shoot, and Na+/K+ ratio (NAK), were detected, with 17 and 13 QTLs under non-stress and salt stress, respectively. The phenotypic variation explained by individual QTL ranged from 3.25 to 29.81%. QTL flanked by markers bPb-1278 and bPb-8437 on chromosomes 4H was associated with TN, SPL, and SPP under salt stress. This locus may be useful in the breeding program of marker-assisted selection for improving salt tolerance of barley. However, QTLs associated with NA, K, and NAK differed greatly between non-stress and salt stress environments. It may be suggested that only the QTLs detected under salt stress are really associated with salt tolerance in barley.

The barley sdw1/denso gene not only controls plant height but also yield and quality. The sdw1/denso gene was mapped to the long arm of chromosome 3H. Comparative genomic analysis revealed that the sdw1/denso gene was located in the syntenic region of the rice semidwarf gene sd1 on chromosome 1. The sd1 gene encodes a gibberellic acid (GA)-20 oxidase enzyme. The gene ortholog of rice sd1 was isolated from barley using polymerase chain reaction. The barley and rice genes showed a similar gene structure consisting of three exons and two introns. Both genes share 88.3% genomic sequence similarity and 89% amino acid sequence identity. A single nucleotide polymorphism was identified in intron 2 between barley varieties Baudin and AC Metcalfe with Baudin known to contain the denso semidwarf gene. The single nucleotide polymorphism (SNP) marker was mapped to chromosome 3H in a doubled haploid population of Baudin x AC Metcalfe with 178 DH lines. Quantitative trait locus analysis revealed that plant height cosegregated with the SNP. The sdw1/denso gene in barley is the most likely ortholog of the sd1 in rice. The result will facilitate understanding of the molecular mechanism controlling semidwarf phenotype and provide a diagnostic marker for selection of semidwarf gene in barley.

Limit dextrinase (LD) is a key enzyme in determining the malting quality. A survey of 60 barley varieties showed a wide range of variation for the enzyme activity and thermostability. Galleon showed low enzyme activity and high thermostability while Maud showed high activity and low thermostability. Alignment of the LD amino acid sequences of Galleon and Maud identified seven amino acid substitutions Lys/Arg-102, Thr/Ala-233, Ser/Gly-235, Gly/Ala-298, Cys/Arg-415, Ala/Ser-885 and Gly/Cys-888. Genetic diversity of LD was investigated using single strand conformation polymorphism based on the amino acid substitutions. Only limited genetic variation was detected in the current malting barley varieties, although wide variation was observed in the wider barley germplasm. The Thr/Ala-233 and Ala/Ser-885 substitutions were associated with enzyme thermostability (P < 0.0001), but no polymorphism was associated with the enzyme activity. This result was confirmed from further sequence analysis. The results will provide a tool for understanding and selection of high LD thermostability.

Race-specific resistance genes (Rph) for leaf rust (Puccinia hordei) are often overcome by new pathotypes with matching virulence. Adult plant resistance (APR) is considered potentially more durable for controlling barley leaf rust. Previous studies established that the cultivar Pompadour carried APR to leaf rust. A doubled haploid population (DH) of 200 lines developed from a cross Pompadour/Stirling, and the parents were phenotyped for leaf rust resistance at five field experimental sites in three agricultural zones in Australia. Using a linkage map of SSR and DArT molecular markers, a major QTL associated with the leaf rust resistance was identified on the short arm of chromosome 5H. This QTL explained between 31% and 86% of the phenotypic variation for the APR at different sites. A PCR-based molecular marker was developed and mapped at 1.6 cM to the APR gene. The present study provides new genetic material and a molecular tool for breeding new varieties with adult plant leaf rust resistance using marker-assisted selection.

Low phytic acid grains can provide a solution to dietary micronutrient deficiency and environmental pollution. A low phytic acid 1-1 (lpa1-1) barley mutant was identified using forward genetics and the mutant gene was mapped to chromosome 2HL. Comparative genomic analysis revealed that the lpa1-1 gene was located in the syntenic region of the rice Os-lpa-MH86-1 gene on chromosome 4. The gene ortholog of rice Os-lpa-MH86-1 (designated as HvST) was isolated from barley using polymerase chain reaction and mapped to chromosome 2HL in a doubled haploid population of Clipper×Sahara. The results demonstrate the collinearity between the rice Os-lpa-MH86-1 gene and the barley lpa1-1 region. Sequence analysis of HvST revealed a single base pair substitution (C→T transition) in the last exon of the gene in lpa1-1 (M422), which resulted in a nonsense mutation. These results will facilitate our understanding of the molecular mechanisms controlling the low phytic acid phenotype and assist in the development of a diagnostic marker for the selection of the lpa1-1 gene in barley.

Net type net blotch (NTNB) is an important barley disease in Australia and elsewhere, with significant yield reduction. This trait is important in selection along with other traits of quality and agronomic value. Two-hundred doubled-haploid lines were generated through anther culture from a cross between 'Pompadour' and 'Stirling'. Quantitative trait loci (QTL) were identified against five isolates of Pyrenophora teres f. teres, which represent virulences across Australia. QTL were mapped on chromosomes 3H and 6H using simple sequence repeat (SSR) markers. The resistance locus on 6H was detected with all isolates while the 3H locus was detected with two isolates. The 6H QTL from 'Pompadour' contributed resistance to isolates 97NB1, 95NB100 and NB81, whereas 6H QTL from 'Stirling' contributed resistance to isolates NB50 and NB52B. The 3H QTL from 'Pompadour' contributed resistance to NB50 and NB52B. Significant epistatic interactions were detected between QTL on 3H and 6H. These resistance QTL are a useful resource and identifying closely linked SSR markers with allelic combinations will facilitate in marker-assisted selection to develop NTNB resistant breeding lines.

China has a large barley germplasm collection which has not been well characterized and is therefore underutilized. The Bmy1 locus encoding the β-amylase enzyme on chromosome 4H has been well characterized in the worldwide barley germplasm collections due to its importance in the malting and brewing industry. The Bmy1 locus was chosen as an indicator to understand genetic potential for improvement of malting quality in Chinese landraces and Tibetan wild barley. The genetic diversity of 91 barley accessions was assessed using allele specific Multiplex-ready molecular markers. Eight accessions were further sequenced, based on the Multiplex-ready marker diversity for Bmy1 in the germplasm. Six of the eight accessions clustered together in a unique group, and showed similarities to 'Haruna Nijo', wild barley accession PI296896 and 'Ashqelon'. Sequence comparisons with the known Bmy1 alleles identified not only the existing 13 amino acid substitutions, but also a new substitution positioned at A387T from a Chinese landrace W127, which has the highest β-amylase activity. Two new alleles/haplotypes namely Bmy1-Sd1c and Bmy1-Sd5 were designated based on different amino acid combinations. We identified new amino acid combination of C115, D165, V233, S347 and V430 in the germplasm. The broad variation in both β-amylase activity and amino acid composition provides novel alleles for the improvement of malting quality for different brewing styles, which indicates the high potential value of the Chinese landraces and Tibetan wild barley.

Heading date is a major determinant of the regional and seasonal adaptation of barley varieties. The dogma is that introduced germplasm is more likely to be adapted if it is derived from a similar latitude. However, barley germplasm introduced from similar latitudes of South-East Asia is extremely early heading in the Australian environments and vice versa. A doubled-haploid population from a cross of an Australian barley Galleon and a Japanese barley Haruna Nijo was evaluated for heading date in Australia (Perth, 31°56′S) and China (Wuhan, 30°33′N) under normal autumn sowing, late sowing in the field, and extended-light glasshouse conditions. One major QTL was identified on chromosome 5H under the three conditions in China. The single QTL accounted for up to 50% of phenotypic variation for heading date. The Australian variety contributed to late heading date. Two QTLs on chromosomes 4H and 5H were detected for controlling heading date in Australia. The QTL/QTL interaction contributed up to 35.8% of phenotypic variation for heading date in Australia, which is the major reason for the extremely early heading date of the Japanese variety in the Australian environment. The chromosome 5H QTL was detected at the same chromosomal location when the population was grown in either China or Australia. In both environments the Australian variety contributed to the late heading date. Selection against the Japanese alleles of chromosomes 4H and 5H QTLs could eliminate the extremely early genotype in Australia and selection against the Australian allele of chromosome 5H QTL could eliminate the extremely late genotype in China when Australian and Japanese germplasms are used in the breeding programs.

Background Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome. Results We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e co-segregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map. Conclusions The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3247-4) contains supplementary material, which is available to authorized users.