Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and Breeding Selection.

Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation. Domestication and crop breeding often target the scaling traits in the opposite directions. The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored. Here, we revisited a diverse barley (Hordeum vulgare L.) panel with genome-wide single-nucleotide polymorphisms (SNPs) profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling. Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit. Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network. We discovered seventeen novel SNPs (quantitative trait locus) conferring pleiotropic effect on plant height and seed weight, involving genes with function in diverse traits related to plant growth and development. Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome. We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley. Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.

Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley.

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.

Molecular Pathways of WRKY Genes in Regulating Plant Salinity Tolerance.

Salinity is a natural and anthropogenic process that plants overcome using various responses. Salinity imposes a two-phase effect, simplified into the initial osmotic challenges and subsequent salinity-specific ion toxicities from continual exposure to sodium and chloride ions. Plant responses to salinity encompass a complex gene network involving osmotic balance, ion transport, antioxidant response, and hormone signaling pathways typically mediated by transcription factors. One particular transcription factor mega family, WRKY, is a principal regulator of salinity responses. Here, we categorize a collection of known salinity-responding WRKYs and summarize their molecular pathways. WRKYs collectively play a part in regulating osmotic balance, ion transport response, antioxidant response, and hormone signaling pathways in plants. Particular attention is given to the hormone signaling pathway to illuminate the relationship between WRKYs and abscisic acid signaling. Observed trends among WRKYs are highlighted, including group II WRKYs as major regulators of the salinity response. We recommend renaming existing WRKYs and adopting a naming system to a standardized format based on protein structure.

Multi-locus genome-wide association studies reveal novel alleles for flowering time under vernalisation and extended photoperiod in a barley MAGIC population.

KEY MESSAGE: Key genes controlling flowering and interactions of different photoperiod alleles with various environments were identified in a barley MAGIC population. A new candidate gene for vernalisation requirements was also detected. Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley (Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhancing yield potential. Although bi-parental populations were used intensively to map genes controlling flowering, their lack of genetic diversity requires additional work to obtain desired gene combinations in the selected lines, especially when the two parental cultivars did not carry the genes. Multi-parent mapping populations, which use a combination of four or eight parental cultivars, have higher genetic and phenotypic diversity and can provide novel genetic combinations that cannot be achieved using bi-parental populations. This study uses a Multi-parent advanced generation intercross (MAGIC) population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq), and Kompetitive allele-specific polymerase chain reaction (KASP) genetic markers were developed. Phenotypic data were collected from fifteen different field trials for three consecutive years. Planting was conducted at various sowing times, and plants were grown with/without additional vernalisation and extended photoperiod treatments. This study detected fourteen stable regions associated with flowering time across multiple environments. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. As the founder lines of the multi-parental population are elite germplasm, the favourable alleles identified in this study are directly relevant to breeding, increasing the efficiency of subsequent breeding strategies and offering better grain yield and adaptation to growing conditions.

Grain-Filling Rate Improves Physical Grain Quality in Barley Under Heat Stress Conditions During the Grain-Filling Period.

Heat stress is a primary constraint to Australia's barley production. In addition to impacting grain yield, it adversely affects physical grain quality (weight and plumpness) and market value. The incidence of heat stress during grain filling is rising with global warming. However, breeding for new superior heat-tolerant genotypes has been challenging due to the narrow window of sensitivity, the unpredictable nature of heat stress, and its frequent co-occurrence with drought stress. Greater scientific knowledge regarding traits and mechanisms associated with heat tolerance would help develop more efficient selection methods. Our objective was to assess 157 barley varieties of contrasting genetic backgrounds for various developmental, agro-morphological, and physiological traits to examine the effects of heat stress on physical grain quality. Delayed sowing (i.e., July and August) increased the likelihood of daytime temperatures above 30°C during grain-filling. Supplementary irrigation of field trials ensured a reduced impact of drought stress. Heat tolerance appeared to be the primary factor determining grain plumpness. A wide variation was observed for heat tolerance, particularly among the Australian varieties. Genotypic variation was also observed for grain weight, plumpness, grain growth components, stay-green and stem water-soluble carbohydrates (WSC) content, and mobilisation under normal and delayed sown conditions. Compared to normal sowing, delayed sowing reduced duration of developmental phases, plant height, leaf size, head length, head weight, grain number, plumpness, grain width and thickness, stem WSC content, green leaf area retention, and harvest index (HI), and increased screenings, grain length, grain-filling rate (GFR), WSC mobilisation efficiency (WSCME), and grain protein content. Overall, genotypes with heavier and plumper grains under high temperatures had higher GFR, longer grain-filling duration, longer green leaf area retention, higher WSCME, taller stature, smaller leaf size, greater HI, higher grain weight/plumpness potentials, and earlier flowering. GFR played a significant role in determining barley grain weight and plumpness under heat-stress conditions. Enhancing GFR may provide a new avenue for improving heat tolerance in barley.

Genomic structural equation modelling provides a whole-system approach for the future crop breeding.

KEY MESSAGE: 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.

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

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

Using chlorate as an analogue to nitrate to identify candidate genes for nitrogen use efficiency in barley.

Nitrogen (N) is one of the most important macronutrients for crop growth and development. Large amounts of N fertilizers are applied exogenously to improve grain yield and quality, which has led to environmental pollution and high cost of production. Therefore, improvement of N use efficiency (NUE) is a very important aspect for sustainable agriculture. Here, a pilot experiment was firstly conducted with a set of barley genotypes with confirmed NUE to validate the fast NUE screening, using chlorate as an analogue to nitrate. High NUE genotypes were susceptible to chlorate-induced toxicity whereas the low NUE genotypes were tolerant. A total of 180 barley RILs derived from four parents (Compass, GrangeR, Lockyer and La Trobe) were further screened for NUE. Leaf chlorosis induced by chlorate toxicity was the key parameter observed which was later related to low-N tolerance of the RILs. There was a distinct variation in chlorate susceptibility of the RILs with leaf chlorosis in the oldest leaf ranging from 10 to 80%. A genome-wide association study (GWAS) identified 9 significant marker-trait associations (MTAs) conferring high chlorate sensitivity on chromosomes 2H (2), 3H (1), 4H (4), 5H (1) and Un (1). Genes flanking with these markers were retrieved as potential targets for genetic improvement of NUE. Genes encoding Ferredoxin 3, leucine-rich receptor-like protein kinase family protein and receptor kinase are responsive to N stress. MTA4H5468 which exhibits concordance with high NUE phenotype can further be explored under different genetic backgrounds and successfully applied in marker-assisted selection. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01239-8.

The barley pan-genome reveals the hidden legacy of mutation breeding.

Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the 'pan-genome'1). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley-comprising landraces, cultivars and a wild barley-that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.

Genome-Wide Association Study and Identification of Candidate Genes for Nitrogen Use Efficiency in Barley (Hordeum vulgare L.).

Nitrogen (N) fertilizer is largely responsible for barley grain yield potential and quality, yet excessive application leads to environmental pollution and high production costs. Therefore, efficient use of N is fundamental for sustainable agriculture. In the present study, we investigated the performance of 282 barley accessions through hydroponic screening using optimal and low NH4NO3 treatments. Low-N treatment led to an average shoot dry weight reduction of 50%, but there were significant genotypic differences among the accessions. Approximately 20% of the genotypes showed high (>75%) relative shoot dry weight under low-N treatment and were classified as low-N tolerant, whereas 20% were low-N sensitive (≤55%). Low-N tolerant accessions exhibited well-developed root systems with an average increase of 60% in relative root dry weight to facilitate more N absorption. A genome-wide association study (GWAS) identified 66 significant marker trait associations (MTAs) conferring high nitrogen use efficiency, four of which were stable across experiments. These four MTAs were located on chromosomes 1H(1), 3H(1), and 7H(2) and were associated with relative shoot length, relative shoot and root dry weight. Genes corresponding to the significant MTAs were retrieved as candidate genes, including members of the asparagine synthetase gene family, several transcription factor families, protein kinases, and nitrate transporters. Most importantly, the high-affinity nitrate transporter 2.7 (HvNRT2.7) was identified as a promising candidate on 7H for root and shoot dry weight. The identified candidate genes provide new insights into our understanding of the molecular mechanisms driving nitrogen use efficiency in barley and represent potential targets for genetic improvement.

Salinity tolerance in barley during germination- homologs and potential genes.

Salinity affects more than 6% of the world's total land area, causing massive losses in crop yield. Salinity inhibits plant growth and development through osmotic and ionic stresses; however, some plants exhibit adaptations through osmotic regulation, exclusion, and translocation of accumulated Na+ or Cl-. Currently, there are no practical, economically viable methods for managing salinity, so the best practice is to grow crops with improved tolerance. Germination is the stage in a plant's life cycle most adversely affected by salinity. Barley, the fourth most important cereal crop in the world, has outstanding salinity tolerance, relative to other cereal crops. Here, we review the genetics of salinity tolerance in barley during germination by summarizing reported quantitative trait loci (QTLs) and functional genes. The homologs of candidate genes for salinity tolerance in Arabidopsis, soybean, maize, wheat, and rice have been blasted and mapped on the barley reference genome. The genetic diversity of three reported functional gene families for salt tolerance during barley germination, namely dehydration-responsive element-binding (DREB) protein, somatic embryogenesis receptor-like kinase and aquaporin genes, is discussed. While all three gene families show great diversity in most plant species, the DREB gene family is more diverse in barley than in wheat and rice. Further to this review, a convenient method for screening for salinity tolerance at germination is needed, and the mechanisms of action of the genes involved in salt tolerance need to be identified, validated, and transferred to commercial cultivars for field production in saline soil.

Genome-Wide Association Study of Salinity Tolerance During Germination in Barley (Hordeum vulgare L.).

Barley seeds need to be able to germinate and establish seedlings in saline soils in Mediterranean-type climates. Despite being a major cereal crop, barley has few reported quantitative trait loci (QTL) and candidate genes underlying salt tolerance at the germination stage. Breeding programs targeting salinity tolerance at germination require an understanding of genetic loci and alleles in the current germplasm. In this study, we investigated seed-germination-related traits under control and salt stress conditions in 350 diverse barley accessions. A genome-wide association study, using ~24,000 genetic markers, was undertaken to detect marker-trait associations (MTA) and the underlying candidate genes for salinity tolerance during germination. We detected 19 loci containing 52 significant salt-tolerance-associated markers across all chromosomes, and 4 genes belonging to 4 family functions underlying the predicted MTAs. Our results provide new genetic resources and information to improve salt tolerance at germination in future barley varieties via genomic and marker-assisted selection and to open up avenues for further functional characterization of the identified candidate genes.

Uncovering the evolutionary origin of blue anthocyanins in cereal grains.

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.

Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection.

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.

Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley.

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.

Hybridisation-based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley.

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.

Polymorphism of floral type gene Cly1 and its association with thermal stress in barley.

Cleistogamy refers to a type of sexual breeding system with closed flowers. Cleistogamous flowers shed their pollen before flower opening, which leads to autogamy. Two SNPs in the open reading frame region of the Cly1 gene are associated with floral type. In the present study, we investigated the floral type of 436 barley accessions. Molecular markers were developed to genotype these barley accessions based on the two SNPs in the Cly1 gene region. The molecular markers explained floral type in 90% of the accessions. The Cly1 gene was sequenced in accessions with inconsistent genotype and phenotype. Thirteen SNPs were detected with ten new SNPs in the gene region. We further investigated whether floral type was associated with temperature stress tolerance in four field trials. One site experienced frost stress with a minimum temperature of -3.4°C during flowering. Grain fertility rates as low as 85% were observed at this site but ranged from 92-96% at the other three sites. The relationship between grain fertility rate and floral type under temperature stress was inconclusive. Some lines with higher grain fertility rates were identified under frost stress, and would be useful for frost stress studies in barley.

Genetic Mapping and Evolutionary Analyses of the Black Grain Trait in Barley.

Barley occupies the widest ecological area among the major cereal crops, thereby generating a high potential for adaptive genetic diversity against various environmental factors. Colored barley such as black grain barley has been suggested to result from environmental adaptation to biotic and abiotic stresses. Using one double haploid population (433 lines), plus three F5 recombinant inbred line (RIL) populations (1,009 lines), the black lemma and pericarp (Blp) gene was mapped between two Insertion/deletion (Indel) markers MC_1570156 and MC_162350 with a physical distance of 0.807 Mb, containing 21 annotated genes in the mapped interval. Whole-genome re-sequencing was performed on two Tibetan wild barley lines (X1 and W1) with black grain phenotype. The probable candidate genes for Blp were discussed based on gene functional annotation and gene sequence variation analyses. Thirteen polymorphic Indel markers covering the target genetic region were used to analyze 178 barley accessions including 49 black husk entries. Genotype-based clustering analyses showed that the black landraces of different geographical background may have evolved from a single origin. Our study represents a significant improvement on the genetic mapping of Blp and would facilitate future study on the characterization of the genetic basis underlying this interesting agronomic trait.

Early growth stages salinity stress tolerance in CM72 x Gairdner doubled haploid barley population.

A doubled haploid (DH) population of barley (Hordeum vulgare L.) generated from salinity tolerant genotype CM72 and salinity sensitive variety Gairdner was studied for salinity stress tolerance at germination, seedling emergence and first leaf full expansion growth stages. Germination study was conducted with deionized water, 150 mM and 300 mM NaCl treatments. Seedling stage salinity tolerance was conducted with three treatments: control, 150 mM NaCl added at seedling emergence and first leaf full expansion growth stages. Results from this study revealed transgressive phenotypic segregations for germination percentage and biomass at seedling stage. Twelve QTL were identified on chromosomes 2H-6H each explaining 10-25% of the phenotypic variations. A QTL located at 176.5 cM on chromosome 3H was linked with fresh weight per plant and dry weight per plant in salinity stress induced at first leaf full expansion growth stage, and dry weight per plant in salinity stress induced at seedling emergence. A stable QTL for germination at both 150 and 300 mM salinity stress was mapped on chromosome 2H but distantly located from a QTL linked with seedling stage salinity stress tolerance. QTL, associated markers and genotypes identified in this study play important roles in developing salinity stress tolerant barley varieties.