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High sensitivity and rapid closure of wheat stomata to environmental stimuli make it difficult and inconvenient when investigating stomatal physiology and morphology using epidermal peels. This is due to inevitable mechanical stress to stomatal guard cells when separating epidermis from mesophyll cells, which induced a vast majority of stomatal closure in wheat. Stomata are more open and active in detached leaves than in epidermal peels. Based on these observations, we proposed a simple method, which promotes stomatal opening using detached leaves rather than epidermis for physiological observations. Stomatal response to stimuli was significantly increased when using intact leaf segment. The method was used to investigate stomatal behaviours of two wheat genotypes with contrasting salt tolerance to salinity stress. The effects of salt stress and exogenous abscisic acid (ABA) treatment on stomatal behaviours were also assessed. The salt-tolerant genotype, H-135, demonstrated a greater stomatal closure rate than the salt-sensitive genotype, H-093, in response to exogenous ABA under salt stress, highlighting the potential of stomatal responsiveness as an indicator for breeding salt-resistant crops. This method not only facilitates the effective initiation of stomatal opening but also ensures the continued responsiveness of stomata to subsequent treatments in wheat. [ABSTRACT FROM AUTHOR]

Aims: Aluminum (Al) toxicity in acid soil significantly reduces plant growth, agricultural productivity and ecosystem health. The Al-tolerant barley cultivars were reported to mainly rely on the Al-activated efflux of citrate from root apices, but the key mechanisms for Al tolerance may differ for wild relatives of barley adapted to acid soil. Methods: Here, we investigated plant Al tolerance from evolutionary physiological, molecular, and ecological perspectives. Results: Phylogenetic analysis of Al tolerance-associated gene families showed that most of these genes were conserved from streptophyte algae to angiosperms, indicating land plants have evolved gradually in adaption to Al-rich acid soil during plant terrestrialization. Vacuolar phosphate transporter SPX-major facility superfamily (SPX-MFS) and inorganic phosphate transporter 1 family (PHT1s) of streptophyte algae showed high genetic similarity to land plants. PHT1s exhibited a significant expand during the evolution from streptophyte algae to liverworts and then eudicots. Al-tolerant Tibetan wild barley accession, XZ29 showed high levels of P-containing glycolytic intermediates including Glu-6-P, Fru-6-P, 3-PGA, 2-PGA and PEP under Al stress. Some primary metabolites were evolutionarily conserved in liverwort, gymnosperm and three tested angiosperms. Furthermore, we found that Al-induced Pi efflux from root elongation zone to chelate rhizosphere Al3+, and immobilization of Al with P at the inner epidermal layer of root mature zone to reduce Al accumulation in the cortical layer in barley. Conclusions: These results indicated that Tibetan wild barley has evolved unique P transport and metabolism for the adaptation to harsh conditions in eastern and southeastern Tibet where acid soils contain high P. [ABSTRACT FROM AUTHOR]

Key message: Recent developments in understanding the distribution and distinctive features of recombination hotspots are reviewed and approaches are proposed to increase recombination frequency in coldspot regions. Recombination events during meiosis provide the foundation and premise for creating new varieties of crops. The frequency of recombination in different genomic regions differs across eukaryote species, with recombination generally occurring more frequently at the ends of chromosomes. In most crop species, recombination is rare in centromeric regions. If a desired gene variant is linked in repulsion with an undesired variant of a second gene in a region with a low recombination rate, obtaining a recombinant plant combining two favorable alleles will be challenging. Traditional crop breeding involves combining desirable genes from parental plants into offspring. Therefore, understanding the mechanisms of recombination and factors affecting the occurrence of meiotic recombination is important for crop breeding. Here, we review chromosome recombination types, recombination mechanisms, genes and proteins involved in the meiotic recombination process, recombination hotspots and their regulation systems and discuss how to increase recombination frequency in recombination coldspot regions. [ABSTRACT FROM AUTHOR]

Key message: Two new major QTL were identified for powdery mildew resistance. We confirmed that the QTL on 7HS contributed mainly to the adult-plant resistance, while another one on chromosome arm 1HS made a significant contribution to the seedling resistance. Powdery mildew (PM), caused by Blumeria hordei, can occur at all post emergent stages of barley and constantly threatens crop production. To identify more genes for effective resistance to powdery mildew for use in breeding programs, 696 barley accessions collected from different regions of the world were evaluated for PM resistance at seedling and adult growth stages in three different states of Australia. These barley accessions were genotyped using DArTSeq with over 18,000 markers for a genome-wide association study (GWAS). Using the FarmCPU model, 54 markers showed significant associations with PM resistance scored at the seedling and adult-plant stages in different states of Australia. Another 40 markers showed tentative associations (LOD > 4.0) with resistance. These markers are distributed across all seven barley chromosomes. Most of them were grouped into eleven QTL regions, coinciding with the locations of most of the reported resistance genes. Two major MTAs were identified on chromosome arms 3HS and 5HL, with one on 3HS contributing to adult plant resistance and the one on 5HL to both seedling and adult plant resistance. An MTA on 7HS contributed mainly to the adult-plant resistance, while another one on chromosome arm 1HS made a significant contribution to the seedling resistance. [ABSTRACT FROM AUTHOR]

Key message: Shared changes in transcriptomes caused by Fusarium crown rot infection and drought stress were investigated based on a single pair of near-isogenic lines developed for a major locus conferring tolerance to both stresses. Fusarium crown rot (FCR) is a devastating disease in many areas of cereal production worldwide. It is well-known that drought stress enhances FCR severity but possible molecular relationship between these two stresses remains unclear. To investigate their relationships, we generated several pairs of near isogenic lines (NILs) targeting a locus conferring FCR resistance on chromosome 2D in bread wheat. One pair of these NILs showing significant differences between the two isolines for both FCR resistance and drought tolerance was used to investigate transcriptomic changes in responsive to these two stresses. Our results showed that the two isolines likely deployed different strategies in dealing with the stresses, and significant differences in expressed gene networks exist between the two time points of drought stresses evaluated in this study. Nevertheless, results from analysing Gene Ontology terms and transcription factors revealed that similar regulatory frameworks were activated in coping with these two stresses. Based on the position of the targeted locus, changes in expression following FCR infection and drought stresses, and the presence of non-synonymous variants between the two isolines, several candidate genes conferring resistance or tolerance to these two types of stresses were identified. The NILs generated, the large number of DEGs with single-nucleotide polymorphisms detected between the two isolines, and the candidate genes identified would be invaluable in fine mapping and cloning the gene(s) underlying the targeted locus. [ABSTRACT FROM AUTHOR]

Key Message: A major QTL (qS7.1) for salinity damage score and Na+ exclusion was identified on chromosome 7H from a barley population derived from a cross between a cultivated variety and a wild accession. qS7.1 was fine-mapped to a 2.46 Mb physical interval and HvNCX encoding a sodium/calcium exchanger is most likely the candidate gene. Soil salinity is one of the major abiotic stresses affecting crop yield. Developing salinity-tolerant varieties is critical for minimizing economic penalties caused by salinity and providing solutions for global food security. Many genes/QTL for salt tolerance have been reported in barley, but only a few of them have been cloned. In this study, a total of 163 doubled haploid lines from a cross between a cultivated barley variety Franklin and a wild barley accession TAM407227 were used to map QTL for salinity tolerance. Four significant QTL were identified for salinity damage scores. One (qS2.1) was located on 2H, determining 7.5% of the phenotypic variation. Two (qS5.1 and qS5.2) were located on 5H, determining 5.3–11.7% of the phenotypic variation. The most significant QTL was found on 7H, explaining 27.8% of the phenotypic variation. Two QTL for Na+ content in leaves under salinity stress were detected on chromosomes 1H (qNa1.1) and 7H(qNa7.1). qS7.1 was fine-mapped to a 2.46 Mb physical interval using F4 recombinant inbred lines. This region contains 23 high-confidence genes, with HvNCX which encodes a sodium/calcium exchanger being most likely the candidate gene. HvNCX was highly induced by salinity stress and showed a greater expression level in the sensitive parent. Multiple nucleotide substitutions and deletions/insertions in the promoter sequence of HvNCX were found between the two parents. cDNA sequencing of the HvNCX revealed that the difference between the two parents is conferred by a single Ala77/Pro77 amino acid substitution, which is located on the transmembrane domain. These findings open new prospects for improving salinity tolerance in barley by targeting a previously unexplored trait. [ABSTRACT FROM AUTHOR]

Cropping of rice and wheat (Triticum aestivum L.) in rotation contiguously in the same field is a fundamental pillar of double-cropping systems in southern China. Yields of such cropping systems are increasingly challenged as climate change (CC) drives increases in autumnal rainfall, delaying rice harvesting and subsequent sowing of wheat. Here, our purpose was to identify prospective traits of wheat crops enabling adaptation to later sowing and successively truncated growing seasons caused by CC. To identify traits that maintained or improved yields, we constructed 4,096 hypothetical genotypes underpinned by step-wise variations in parameters regulating phenology, growth and yield components. We then assimilated biophysical response surfaces through genotype (G) by environment (E) by management (M) analyses (G×E×M) using six locations spread across the breadth of southern China. We showed that later sowing reduced cumulative radiation interception, cumulative thermal time and crop capture of growing season rainfall. The culmination of these factors shortened crop duration and decreased biomass accumulation and retranslocation after anthesis, reducing grain number and penalising yields. Genotypes that had greater radiation use efficiency, longer juvenile phases and greater grain filling rates were more effective in alleviating yield losses with delayed sowing. However, not even the highest yielding genotype × management combination could entirely alleviate yield losses with delayed sowing. Our results suggest that CC and increasingly frequent extreme climatic events may reduce wheat yields in such cropping systems in the absence of other adaptation. [ABSTRACT FROM AUTHOR]

Soil salinity is a major threat to crop productivity and quality worldwide. In order to reduce the negative effects of salinity stress, it is important to understand the genetic basis of salinity tolerance. Identifying new salinity tolerance QTL or genes is crucial for breeders to pyramid different tolerance mechanisms to improve crop adaptability to salinity. Being one of the major cereal crops, wheat is known as a salt-sensitive glycophyte and subject to substantial yield losses when grown in the presence of salt. In this study, both pot and tank experiments were conducted to investigate the genotypic variation present in 328 wheat varieties in their salinity tolerance at the vegetative stage. A Genome-Wide Association Studies (GWAS) were carried out to identify QTL conferring salinity tolerance through a mixed linear model. Six, five and eight significant marker-trait associations (MTAs) were identified from pot experiments, tank experiments and average damage scores, respectively. These markers are located on the wheat chromosomes 1B, 2B, 2D, 3A, 4B, and 5A. These tolerance alleles were additive in their effects and, when combined, increased tolerance to salinity. Candidate genes identified in these QTL regions encoded a diverse class of proteins involved in salinity tolerance in plants. A Na+/H+ exchanger and a potassium transporter on chromosome 5A (IWB30519) will be of a potential value for improvement of salt tolerance of wheat cultivars using marker assisted selection programs. Some useful genotypes, which showed consistent tolerance in different trials, can also be effectively used in breeding programs. [ABSTRACT FROM AUTHOR]

Background and aims: Zinc (Zn) deficiency in humans is of worldwide concern and is primarily associated with a plant-based diet of crops grown in Zn-deficient soils. This work explores the effects of both soil factors and genotype on Zn accumulation in aboveground tissues in barley (Hordeum vulgare L.). Methods: A meta-analysis was performed on collected articles data published between 1945-2020 describing Zn concentrations in barley shoots and grains in plants grown at different levels of Zn availability. Results: Higher Zn levels in the growth substrate resulted in increased Zn concentrations in barley shoots and grains. Of note is that Zn concentrations were found to be highly cultivar specific, with a 3.5-fold (shoots) to 4.5-fold (grains) difference reported between high and low Zn accumulating cultivars under the same conditions. Additionally, the Zn translocation and remobilisation rate from shoots to grains were also 2-fold greater in Zn-efficient cultivars than others. Conclusions: This meta-analysis is the first to collect all available data regarding Zn concentrations in barley. The findings demonstrate that Zn concentrations in aboveground parts of barley are highly cultivar-specific and change with substrate Zn. Target Zn concentrations in barley could be achieved through selective breeding and optimal Zn fertilisation. Further investigations revealing the major quantitative trait locus (QTLs) and candidate genes associated with desirable Zn phenotypes would allow better understanding of Zn use mechanisms in barley. [ABSTRACT FROM AUTHOR]

Key message: We identified 1.844 million barley pan-genome sequence anchors from 12,306 genotypes using genetic mapping and machine learning. There is increasing evidence that genes from a given crop genotype are far to cover all genes in that species; thus, building more comprehensive pan-genomes is of great importance in genetic research and breeding. Obtaining a thousand-genotype scale pan-genome using deep-sequencing data is currently impractical for species like barley which has a huge and highly repetitive genome. To this end, we attempted to identify barley pan-genome sequence anchors from a large quantity of genotype-by-sequencing (GBS) datasets by combining genetic mapping and machine learning algorithms. Based on the GBS sequences from 11,166 domesticated and 1140 wild barley genotypes, we identified 1.844 million pan-genome sequence anchors. Of them, 532,253 were identified as presence/absence variation (PAV) tags. Through aligning these PAV tags to the genome of hulless barley genotype Zangqing320, our analysis resulted in a validation of 83.6% of them from the domesticated genotypes and 88.6% from the wild barley genotypes. Association analyses against flowering time, plant height and kernel size showed that the relative importance of the PAV and non-PAV tags varied for different traits. The pan-genome sequence anchors based on GBS tags can facilitate the construction of a comprehensive pan-genome and greatly assist various genetic studies including identification of structural variation, genetic mapping and breeding in barley. [ABSTRACT FROM AUTHOR]

Main conclusion: To compensate for the lack of capacity for external salt storage in the epidermal bladder cells, quinoa plants employ tissue-tolerance traits, to confer salinity stress tolerance. Our previous studies indicated that sequestration of toxic Na+ and Cl− ions into epidermal bladder cells (EBCs) is an efficient mechanism conferring salinity tolerance in quinoa. However, some halophytes do not develop EBCs but still possess superior salinity tolerance. To elucidate the possible compensation mechanism(s) underlying superior salinity tolerance in the absence of the external salt storage capacity, we have selected four quinoa accessions with contrasting patterns of EBC development. Whole-plant physiological and electrophysiological characteristics were assessed after 2 days and 3 weeks of 400 mM NaCl stress. Both accessions with low EBC volume utilised Na+ exclusion at the root level and could maintain low Na+ concentration in leaves to compensate for the inability to sequester Na+ load in EBC. These conclusions were further confirmed by electrophysiological experiments showing higher Na+ efflux from roots of these varieties (measured by a non-invasive microelectrode MIFE technique) as compared to accessions with high EBC volume. Furthermore, accessions with low EBC volume had significantly higher K+ concentration in their leaves upon long-term salinity exposures compared to plants with high EBC sequestration ability, suggesting that the ability to maintain high K+ content in the leaf mesophyll was as another important compensation mechanism. [ABSTRACT FROM AUTHOR]

Blumeria graminis f. sp. tritici, the causal agent of wheat powdery mildew disease, can occur at all stages of the crop and constantly threatens wheat production. To identify candidate resistance genes for powdery mildew, we performed GWAS (genome-wide association studies) on a total set of 329 wheat varieties obtained from different origins. These wheat materials were genotyped using wheat 90K SNP array and evaluated for their resistance in either field or glasshouse condition from 2016 to 2018. Using a mixed linear model, 33 SNP markers of which 14 QTL (quantitative trait loci) were later defined were observed to associate with powdery mildew resistance. Among these, QTL on chromosome 3A, 3B, 6D and 7D were concluded as potentially new QTL. Exploration of candidate genes for new QTL suggested roles of these genes involved in encoding disease resistance and defence-related proteins, and regulating early immune response to the pathogen. Overall, the results reveal that GWAS can be an effective means of identifying marker-trait associations, though further functional validation and fine-mapping of gene candidates are required before creating opportunities for developing new resistant genotypes. [ABSTRACT FROM AUTHOR]

The disease scald of barley is caused by the pathogen Rhynchosporium commune and can cause up to 30–40% yield loss in susceptible cultivars. In this study, the Australian barley cultivar ‘Yerong’ was demonstrated to have resistance that differed from Turk (Rrs1 (Rh3 type)) based on seedling tests with 11 R. commune isolates. A doubled haploid population with 177 lines derived from a cross between ‘Yerong’ and the susceptible Australian cultivar ‘Franklin’ was used to identify quantitative trait loci (QTL) for scald resistance. A QTL on chromosome 3H was identified with large effect, consistent with a major gene conferring scald resistance at the seedling stage. Under field conditions, a bivariate analysis was used to model scald percentage of infected leaf area and relative maturity, the residuals from the regression were used as our phenotype for QTL analysis. This analysis identified one major QTL on chromosome 3H, which mapped to the same position as the QTL at seedling stage. The identified QTL on 3H is proposed to be different from the Rrs1 on the basis of seedling resistance against different R. commune isolates and physical map position. This study increases the current understanding of scald resistance and identifies genetic material possessing QTLs useful for the marker-assisted selection of scald resistance in barley breeding programs. [ABSTRACT FROM AUTHOR]

Key message: This study demonstrates the feasibility of developing co-segregating markers and identifying candidate genes for Fusarium crown rot resistance in barley based on the generation and exploitation of a near-isogenic line-derived large population.Abstract: Fusarium crown rot (FCR) is a chronic and severe disease in cereals in semi-arid regions worldwide. Previous studies showed that FCR assessment could be affected by many factors including plant height, growth rate as well as drought stress. Thus, accurate assessment, which is essential for detailed mapping of any locus conferring FCR resistance, is difficult. Targeting one of the resistance loci reported earlier, we developed a near-isogenic line-derived population consisting of 1820 F9 lines. By analysing this population, the Qcrs.cpi-4H locus was mapped to an interval of 0.09 cM covering a physical distance of about 637 kb and 13 markers co-segregating with the targeted locus were developed. Candidate genes underlying the resistance locus were identified by analysing the expression and sequence variation of genes in the targeted interval. The accurate localization and the development of co-segregating markers should facilitate the incorporation of this large-effect QTL into breeding programmes as well as the cloning of gene(s) underlying the locus. [ABSTRACT FROM AUTHOR]

Key message: This study demonstrates how identification of genes underpinning disease-resistance QTL based on differential expression and SNPs can be improved by performing transcriptomic analysis on multiple near isogenic lines.Abstract: Transcriptomic analysis has been widely used to understand the genetic basis of a trait of interest by comparing genotypes with contrasting phenotypes. However, these approaches identify such large sets of differentially expressed genes that it proves difficult to isolate which genes underpin the phenotype of interest. This study tests whether using multiple near isogenic lines (NILs) can improve the resolution of RNA-seq-based approaches to identify genes underpinning disease-resistance QTL. A set of NILs for a major effect Fusarium crown rot-resistance QTL in barley on the 4HL chromosome arm were analysed under Fusarium crown rot using RNA-seq. Differential gene expression and single nucleotide polymorphism detection analyses reduced the number of putative candidates from thousands within individual NIL pairs to only one hundred and two genes, which were differentially expressed or contained SNPs in common across NIL pairs and occurred on 4HL. Our findings support the value of performing RNA-seq analysis using multiple NILs to remove genetic background effects. The enrichment analyses indicated conserved differences in the response to infection between resistant and sensitive isolines suggesting that sensitive isolines are impaired in systemic defence response to Fusarium pseudograminearum. [ABSTRACT FROM AUTHOR]

Fusarium crown rot (FCR) has become one of the most damaging cereal diseases in semi-arid regions worldwide. Targeting three large-effect QTL (located on the chromosome arm 3BL, 5DS and 2DL, respectively), we investigated the feasibility of enhancing FCR resistance by gene pyramiding. Significant effects were detected for each of the three QTL in both populations assessed. Lines with any combination of two resistant alleles gave significantly better resistance than those with a single resistant allele only and those without any allele, and lines possessing all three resistant alleles showed the best resistance. These results demonstrated that gene pyramiding can be an effective approach in improving FCR resistance. Those lines with resistant alleles from all three QTL could be valuable genetic stocks for breeding programs. [ABSTRACT FROM AUTHOR]

Key message: We report the first study on the unique allele from wild barley that can improve waterlogging tolerance in cultivated barley with a substantially higher contribution to aerenchyma formation. Abstract: Waterlogging is one of the major abiotic stresses that dramatically reduce barley crop yield. Direct selection on waterlogging tolerance in the field is less effective due to its viability to environment. The most effective way of selection is to choose traits that make significant contributions to the overall tolerance and are easy to score. Aerenchyma formation under waterlogging stress is one of the most effective mechanisms to provide adequate oxygen supply and overcome stress-induced hypoxia imposed on plants. In this study, a new allele for aerenchyma formation was identified from a wild barley accession TAM407227 on chromosome 4H. Compared to that identified in cultivated barley, this allele not only produced a greater proportion of aerenchyma but made a greater contribution to the overall waterlogging tolerance. The QTL explained 76.8% of phenotypic variance in aerenchyma formation with a LOD value of 51.4. Markers co-segregating with the trait were identified and can be effectively used in marker assisted selection. [ABSTRACT FROM AUTHOR]

Main conclusion : We projected meta-QTL (MQTL) for drought, salinity, and waterlogging tolerance to the physical map of barley through meta-analysis. The positions of these MQTL were refined and candidate genes were identified. Drought, salinity and waterlogging are three major abiotic stresses limiting barley yield worldwide. Breeding for abiotic stress-tolerant crops has drawn increased attention, and a large number of quantitative trait loci (QTL) for drought, salinity, and waterlogging tolerance in barley have been detected. However, very few QTL have been successfully used in marker-assisted selection (MAS) in breeding. In this study, we summarized 632 QTL for drought, salinity and waterlogging tolerance in barley. Among all these QTL, only 195 major QTL were used to conduct meta-analysis to refine QTL positions for MAS. Meta-analysis was used to map the summarized major QTL for drought, salinity, and waterlogging tolerance from different mapping populations on the barley physical map. The positions of identified meta-QTL (MQTL) were used to search for candidate genes for drought, salinity, and waterlogging tolerance in barley. Both MQTL3H.4 and MQTL6H.2 control drought tolerance in barley. Fine-mapped QTL for salinity tolerance, HvNax4 and HvNax3, were validated on MQTL1H.4 and MQTL7H.2, respectively. MQTL2H.1 and MQTL5H.3 were also the target regions for improving salinity tolerance in barley. MQTL4H.4 is the main region controlling waterlogging tolerance in barley with fine-mapped QTL for aerenchyma formation under waterlogging conditions. Detected and refined MQTL and candidate genes are crucial for future successful MAS in barley breeding. [ABSTRACT FROM AUTHOR]

Ten pairs of near-isogenic lines (NILs) were developed for a major quantitative trait locus conferring Fusarium crown rot (FCR) resistance in barley. The locus locates on the long arm of chromosome 4H and the presence of the resistance allele reduced FCR severity by between 32.8 and 63.4 % with an average of 43.9 % across these NILs. Histological and quantitative PCR analyses all confirmed that the rates of Fusarium infection and disease development were much slower in the resistant isolines compared with those in the susceptible isolines. The contrasting phenotypes in FCR severity between the isolines for each of these NIL pairs would facilitate efforts in cloning and functional analyses of genes conferring resistance to this disease. [ABSTRACT FROM AUTHOR]

The adoption of reduced height ( Rht) genes has dramatically enhanced yield potential of cereal crops. The semi-dwarfing gene uzu in barley is widely used in East Asia. Its value as an Rht gene in the warm and dry environments in Australia was evaluated in this study. In addition to plant height, this gene showed significant effects on a wide range of characteristics. It reduced the overall plant height by an average of 33.7 % with the most significant reduction occurred on the internode below the peduncle. The gene reduces spike length by 31.6 % and grain weight by 18.8 %. It increases grain number per spike by 5.6 % and grain density by 51.8 %. Seedling assays suggested that the effects of this gene became more significant with increased temperature. It reduced coleoptile and seedling length by 19.4 % and 15.1 %, respectively at 7 °C. The reduction increased to 61 % and 46.7 %, respectively, at 25 °C. These results indicated that the uzu gene could have limited values in some high temperature and drought prone environments. [ABSTRACT FROM AUTHOR]

Key message: Aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilized approach for the selection of waterlogging tolerant barley genotypes. One major QTL for aerenchyma formation after 7 days of waterlogging treatment was identified and the newly developed markers explained 44 % of the phenotypic variance. This QTL can now be effectively used in barley breeding programs. Abstract: Waterlogging is one of the important limiting conditions for crop yield and productivity. The main feature of waterlogged soils is oxygen deprivation, due to slow gas diffusion in water. Decreased oxygen content in waterlogged soils leads to the oxygen deficiency in plant tissues, resulting in reduced energy availability for plants. Rapidly induced aerenchyma formation is critical to maintaining adequate oxygen supply and overall waterlogging tolerance in barley. In this study, we have proved that quantifying aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilised approach for the selection of waterlogging tolerant barley genotypes, which is supported by measurements of redox potential (an indicator of anaerobic conditions). This protocol was also used to identify quantitative trait loci (QTL) in a doubled haploid population of barley from the cross between Yerong (tolerant) and Franklin (sensitive) genotypes. The QTL for aerenchyma formation and root porosity were at the same location as the waterlogging tolerance QTL. Seven new markers were developed and added onto this region on chromosome 4H. One major QTL for aerenchyma formation after 7 days waterlogging treatment explained 44.0 % of the phenotypic variance. This successful QTL for aerenchyma formation can be effectively used in the marker assisted selection to improve waterlogging tolerance in barley. [ABSTRACT FROM AUTHOR]

Main conclusion: Leaf tissue tolerance was strongly and positively correlated with overall salt tolerance in barley, but not in wheat where the inability of sensitive varieties to exclude Na is compensated by their better ability to handle Na accumulated in the shoot via tissue tolerance mechanisms. A new high-throughput assay was developed to use the excised leaves to eliminate the confounding contribution of sodium exclusion mechanisms and evaluate genetic variability in salinity tissue tolerance in a large number of wheat ( Triticum aestivum and Triticum turgidum ssp . durum) and barley ( Hordeum vulgare) accessions. The changes in relative chlorophyll content (measured as chlorophyll content index, CCI) in excised leaves exposed to 50 mM NaCl for 48 h were found to be a reliable indicator of leaf tissue tolerance. In both wheat and barley, relative CCI correlated strongly with the overall plant salinity tolerance (evaluated in glasshouse experiments). To a large extent, this tissue tolerance was related to more efficient vacuolar Na sequestration in leaf mesophyll, as revealed by fluorescent Na dye imaging experiments. However, while in barley this correlation was positive, tissue tolerance in wheat correlated negatively with overall salinity tolerance. As a result, more salt-sensitive durum wheat genotypes possessed higher tissue tolerance than bread wheat plants, and this negative correlation was present within each of bread and durum wheat clusters as well. Overall, these results indicate that the lack of effective Na exclusion ability in sensitive wheat varieties is compensated by their better ability to handle Na accumulated in the shoot via tissue tolerance mechanisms. Implications of these findings for plant breeding for salinity tolerance are discussed. [ABSTRACT FROM AUTHOR]

Background and aims: Plant adaptation to waterlogged conditions requires a set of morphological and physiological/biochemical changes. The formation of aerenchyma is one of the most crucial adaptive traits for waterlogging tolerance. Enzymatic scavenging may also potentially contribute to waterlogging tolerance by providing detoxification of reactive oxygen species (ROS). Methods: Changes of root porosity (as an indicator of aerenchyma formation) and activities in leaves of four major antioxidant enzymes, γ-amino butyric acid (GABA) and lactic acid contents in roots were evaluated in six barley genotypes contrasting in waterlogging tolerance. Results: Soil waterlogging caused significant increases in adventitious root porosity in all genotypes. Waterlogging-tolerant genotypes showed not only significantly higher adventitious root porosity than sensitive genotypes but also much faster development of aerenchyma. The greatest difference in adventitious root porosity among genotypes was observed after 7 days of waterlogging treatment. At the same time, antioxidant enzyme activities in leaves, GABA and lactic acid contents in roots did not correlate with waterlogging tolerance. Conclusions: A faster formation of aerenchyma in adventitious roots is one of the key factors for waterlogging tolerance in barley. This protocol is recommended to be applied in future studies to identify molecular markers linked to this trait using appropriate mapping populations. [ABSTRACT FROM AUTHOR]

The use of a three-line breeding system based on cytoplasmic male sterility has a great potential for hybrid production in barley. Hybrid vigour, or heterosis, which is an advantage of the offspring as compared to two parental lines, is one of the major factors for the success of the use of hybrids. In this study, gene differential expression profiles between barley hybrids and their parents were analysed by cDNA-AFLP analysis using forty eight crosses. Five transcript-derived fragments (TDFs) showed significant effects on heterosis of 1,000-kernel-weight, one of the major yield components. These five TDFs were successfully validated in different crosses by eliminating crosses with lower heterosis and thus can be used in breeding programs. [ABSTRACT FROM AUTHOR]

Key message: One major QTL-controlling malt extract was identified on 2H, based on the data from four different environments and a large number of DH lines, determining 48 % of phenotypic variation. This QTL is of a high value for marker-assisted selection. Abstract: Improving malting quality traits is one of the major breeding objectives for barley breeding programmes. Among different quality traits, malt extract is one of the most important, determining the yield of beer production. The use of molecular markers linked to loci affecting the quality traits can greatly improve selection efficiency. However, the discovery of closely linked markers relies on not only the availability of the loci, but the accuracy of phenotyping. In this experiment, 188 doubled-haploid lines derived from the cross between a Japanese malting barley and a Chinese feed barley were grown in four different environments (two sites × 2 years). Different quality traits were determined and used to map QTL for these traits. Several QTLs were identified for different quality traits. One major QTL-controlling malt extract was identified on 2H and determined 48 % of phenotypic variation with the closest marker of GBM1121. This QTL was consistently expressed in all four environments and is of a high value for marker-assisted selection in malting barley breeding. [ABSTRACT FROM AUTHOR]

Key message: Resistance to Puccinia striiformis in 18 barleys was conferred by one or more genes. In two genotypes, resistance mapped to chromosomes 5HL and 7HL (seedling), and 5HS (adult plant). Abstract: Twenty barley genotypes were assessed for resistance to a variant of P. striiformis [barley grass yellow rust (BGYR)] that is adapted to wild Hordeum sp. (barley grass) and is known to be virulent on several Australian barley cultivars. With the exception of Biosaline-19, all of the genotypes tested were resistant to BGYR. Genetic analyses of 16 Australian and three exotic barley lines indicated that each carried at least a single gene for resistance. Seedling resistance genes identified in the doubled haploid population developed from a cross between Franklin and Yerong were mapped to the long arm of chromosomes 5H and 7H, respectively. These genes were given the temporary designations of Rpsp- hFranklin and Rpsp- hYerong. Three QTL were detected in the same population when tested at the adult plant stage, two of them being in a similar position to Rpsp- hFranklin and Rpsp- hYerong and the third one was mapped to 5HS. Allelism tests between genotypes that exhibited seedling infection type responses to BGYR that were similar to Franklin and Yerong revealed that resistance in most were genetically independent of Rpsp- hFranklin and Rpsp- hYerong. [ABSTRACT FROM AUTHOR]

Fusarium crown rot (FCR) is a serious disease in wheat and barley in semiarid regions worldwide. The feasibility of enhancing FCR resistance by gene pyramiding was investigated by generating and assessing two populations segregating for three large-effect QTL located on the long arms of chromosomes 1H, 3H and 4H, respectively. Significant effects were detected for each of the three QTL in both of the populations assessed. Lines with any combination of two resistant alleles from the three QTL gave, on average, significantly better resistance than those with a single resistant allele only, and lines with resistant alleles from all three of the QTL gave the least FCR symptom. However, wide variations in FCR severity were detected for lines belonging to each of the groups with different numbers of resistant alleles. Significant effects of plant height on FCR were detected in both populations, and a significant association between heading date and FCR severity was detected in one of the two populations assessed. Results from the current study also showed that the effects of a given allele of resistance decreased with the increase in the number of resistant alleles an individual group possessed. Overall, results from this study demonstrate that gene pyramiding can be an effective approach in improving FCR resistance and those lines with resistant alleles from all of the three QTL could be valuable for breeding programs. [ABSTRACT FROM AUTHOR]

Tolerance to waterlogging is an important breeding objective for barley (Hordeum vulgare L.); however, it is a complex quantitative trait. It is difficult to screen large numbers of lines in the field due to environmental variability, and it is also challenging to screen large numbers in controlled conditions if yield data are to be collected. The direct measurement of traits that contribute to waterlogging tolerance, such as aerenchyma development in roots, may offer advantages especially if molecular markers can be developed to screen breeding populations. A doubled haploid population from a cross between Franklin and YuYaoXiangTian Erleng was screened for adventitious root porosity (gas-filled volume per unit root volume) as an indicator of aerenchyma formation. A single QTL for root porosity was identified on chromosome 4H which explained 35.7 and 39.0 % of phenotypic variation in aerated and oxygen-deficient conditions, respectively. The nearest marker was EBmac0701. This QTL is located in the same chromosomal region that contributed to tolerance when the same population was screened in an earlier independent soil waterlogging experiment. Comparative mapping revealed that this QTL is syntenic with the Qaer1.02-3 QTL in maize and the Sub1A-1 gene in rice, which are associated with aerenchyma formation (maize) and submergence tolerance (rice), respectively. This is the first report of a QTL for root porosity in barley which elucidates a major mechanism of waterlogging tolerance. [ABSTRACT FROM AUTHOR]

The transition from dormancy to germination is crucial for malt barley in the malt house. Seed dormancy is a quantitative trait and the depths of dormancy controlled by environment/genetics remain unclear. Quantitative trait locus (QTL) analysis was conducted to evaluate the number, location and phenotypic variation explained by QTLs from data collected from different years, sites and germination conditions in the Stirling × Harrington population. QTLs on 4H, 5H and 6H could explain 25, 81 and 12 % of phenotypic variations, respectively. Consistent QTLs were detected on 5HL and other QTLs were subjected to growth or germination conditions. Germination tests under light detected more QTLs than in the dark. The QTL at 5HL were more important for seed dormancy under the Mediterranean environment and evidence showed at least two genes controlling seed dormancy at 5HL. [ABSTRACT FROM AUTHOR]

Acid soil/aluminium toxicity is one of the major constraints on barley production around the world. Genetic improvement is the best solution and molecular-marker-assisted selection has proved to be an efficient tool for developing barley cultivars with acid soil/aluminium tolerance. In this study, barley variety Svanhals-introduced from CYMMIT (International Maize and Wheat Improvement Center)-was identified as acid soil/aluminium tolerant and the tolerance was mapped to chromosome 4H in 119 doubled haploid (DH) lines from a cross of Hamelin/Svanhals. The HvMATE gene, encoding an aluminium-activated citrate transporter, was selected as a candidate gene and gene-specific molecular markers were developed to detect acid soil/aluminium tolerance based on the polymerase chain reaction. Sequence analysis of the HvMATE gene identified a 21-bp indel (insertion-deletion) between the tolerant and sensitive cultivars. The new marker was further mapped to the QTL (quantitative trait loci) region on chromosome 4H for acid soil tolerance and accounted for 66.9 % of phenotypic variation in the DH population. Furthermore, the polymorphism was confirmed in other tolerant varieties which have been widely used as a source of acid soil tolerance in Australian barley breeding programs. The new gene-specific molecular marker provides an effective and simple molecular tool for selecting the acid soil tolerance gene from multiple tolerance sources. [ABSTRACT FROM AUTHOR]

Aims: A causal relationship between salinity and oxidative stress tolerance and a suitability of using root antioxidant activity as a biochemical marker for salinity tolerance in barley was investigated. Methods: Net ion fluxes were measured from the mature zone of excised roots of two barley varieties contrasting in their salinity tolerance using non-invasive MIFE technique in response to acute and prolonged salinity treatment. These changes were correlated with activity of major antioxidant enzymes; ascorbate peroxidase, catalase, and superoxide dismutase. Results: It was found that genotypic difference in salinity tolerance was largely independent of root integrity, and observed not only for short-term but also long-term NaCl exposures. Higher K retention ability (and, hence, salinity tolerance) positively correlated with oxidative stress tolerance. At the same time, antioxidant activities were constitutively higher in a sensitive but not tolerant variety, and no correlation was found between SOD activity and salinity tolerance index during large-scale screening. Conclusion: Although salinity tolerance in barley correlates with its oxidative stress tolerance, higher antioxidant activity at one particular time does not correlate with salinity tolerance and, as such, cannot be used as a biochemical marker in barley screening programs. [ABSTRACT FROM AUTHOR]

Limit dextrinase (LD) is a unique de-branching enzyme involved in starch mobilization of barley grains during malting, and closely related to malt quality. Genotypic variation of LD activity is controlled by genetic factors and also affected by environmental conditions. Correlation analysis between LD activity and four malt quality parameters showed that LD activity was positively correlated with diastatic power, Kolbach index and the quality of malt extract, while negatively correlated with viscosity. The structure-based association analysis demonstrated that HvLDI, a gene encoding limit dextrinase inhibitor, was a major determinant of LD activity and malt quality. The single nucleotide polymorphisms associated with LD activity could be used in early generation selection for barley breeding. [ABSTRACT FROM AUTHOR]

Salinity stress is a major limitation in barley production. Substantial genetic variation in tolerance occurs among genotypes of barley, so the development of salt-tolerant cultivars is a potentially effective approach for minimizing yield losses. The lack of economically viable methods for screening salinity tolerance in the field remains an obstacle to breeders, and molecular marker-assisted selection is a promising alternative. In this study, salinity tolerance of 172 doubled-haploid lines generated from YYXT (salinity-tolerant) and Franklin (salinity-sensitive) was assessed in glasshouse trials during the vegetative phase. A high-density genetic linkage map was constructed from 76 pairs of simple sequence repeats and 782 Diversity Arrays Technology markers which spanned a total of 1,147 cM. Five significant quantitative trait loci (QTL) for salinity tolerance were identified on chromosomes 1H, 2H, 5H, 6H and 7H, accounting for more than 50% of the phenotypic variation. The tolerant variety, YYXT, contributed the tolerance to four of these QTL and Franklin contributed the tolerance to one QTL on chromosome 1H. Some of these QTL mapped to genomic regions previously associated with salt tolerance in barley and other cereals. Markers associated with the major QTL identified in this study have potential application for marker-assisted selection in breeding for enhanced salt tolerance in barley. [ABSTRACT FROM AUTHOR]

Pasting properties are important characteristics of barley starch from a processing standpoint. A shorter time to peak viscosity and lower pasting temperature are favorable to both malting and food processing. This study was conducted to identify quantitative trait loci (QTLs) determining pasting properties of barley flour using a doubled haploid population of 177 lines from the cross between six-rowed Yerong and two-rowed Franklin. Yerong is a feed barley with a longer time to peak viscosity and a higher pasting temperature than the other parent Franklin which is a malting barley. Field trials were conducted in three different sites/years. Seven different parameters representing the pasting properties were measured using a Rapid Visco-analyser (RVA). DH lines showed significant differences in all seven parameters in most of the sites/years. For example, the pasting temperature of different DH lines ranged from 73.8 to 89.5 in 2006/2007 MTP field trial. Twenty one QTLs were associated with flour pasting properties. These QTLs were distributed on 11 chromosome regions. Genetic variance explained by these QTLs varies from 4.4 to 15.2%. The most important QTLs controlling the time to peak viscosity and pasting temperature were located on 1H, 2H, 3H and 7H. Results showed that some of the pasting properties can be effectively selected by the combination of several molecular markers. [ABSTRACT FROM AUTHOR]

Difference in isozymes and activities of peroxidase (POD) and superoxide dismutase (SOD) in two barley ( Hordeum vulgare L.) genotypes differing in salt tolerance (Gebeina, tolerant; Quzhou, sensitive) was investigated using a hydroponic experiment. The activities of both enzymes were significantly increased when the plants of the two barley genotypes were exposed to salt stress, with salt-tolerant genotype being generally higher than the sensitive one. The variation in the POD and SOD isozymes was dependent on barley genotype, salt level and exposure time. When the plants were exposed to salt stress for 10 days, two new POD isozymes were found, R m0.26 ( R m, relative mobility of enzyme to dye) in Gebeina and R m0.45 in Quzhou. Both isozymes disappeared after 20 days of salt stress, but R m0.26 appeared again 30 days after the stress. Two new SOD isozymes of R m0.19 and R m0.46 were found in Gebeina when exposed to NaCl for 10 days, but only R m0.46 in Quzhou. As the time of salt stress extended, more new SOD isozymes were detected, R m0.35 in both genotypes in all different salt treatments and R m0.48 in Gebeina under 200 mM NaCl stress. At 30 days after the stress, all the new SOD isozymes disappeared except for R m0.48 in Gebeina under 200 mM NaCl stress. The results suggest that the increased POD and SOD activities could be partly due to the formation of some new isozymes and the tolerant variety had better ability to form new isozymes to overcome salt stress. [ABSTRACT FROM AUTHOR]

Barley yellow dwarf virus is a widespread disease affecting plant growth and yield in cereal crops including barley. Complete resistance to BYDV encoded by a single gene is lacking in barley. To identify novel resistance genes that can be further utilised in breeding for plant disease resistance, a doubled haploid population originated from a cultivated barley with a known resistance gene and a wild barley was constructed and assessed for barley yellow dwarf tolerance in three trials with two in Tasmania (TAS) and one in Western Australia (WA). We identified two Quantitative trait loci (QTL) in both Tasmanian trials, and four QTL in Western Australian trial. Two QTL from TAS trials were also detected from WA. The QTL on chromosome 3H corresponds to the known major resistance gene Ryd2. The other QTL, Qbyd-5H, represents a potential new resistance locus and contributed 7.0~10.4% of total phenotypic variation in the three trials. It was mapped within the interval of 125.76~139.24 cM of chromosome 5H. Two additional minor effect QTL were identified on chromosome 7H from WA trial, contributing slightly less effect on BYD tolerance. The consistently detected new gene on chromosome 5H will potentially serve as a novel source of tolerance to achieve more sustainable resistance to BYDV in barley. [ABSTRACT FROM AUTHOR]

Heading date (HD) is an important agronomic trait that influences plant adaptability to varying environment and, ultimately, grain yield. In this study, two doubled haploid (DH) populations were used to identify new QTL for HD. One of the DH populations is originated from a cross between an Australian malting barley cv. Franklin and a wild barley accession TAM407227 and the other one is from the cross between a Syrian wild barley SYR01 and an Australian malting barley cv. Gairdner. Using three times of sowing (TOS) differing in daylength and temperature, we investigated quantitative trait loci (QTL) controlling HD from both populations. Fourteen QTL were identified for HD from different populations and sowing dates. The expression of HD related genes varied with the TOS, suggesting a significant QTL × environment interaction. By comparing the positions of previously mapped HD genes and those of QTL detected in this population, we found that eleven of the fourteen QTL identified in this study were located at similar positions to those reported genes for HD. Among the three new potential QTL, one was located at 73.5 cM on chromosome 2H, explaining 19.2% and 4.6% HD of DH lines in spring and summer growing, respectively. The wild barley parent TAM407227 contributed the early maturity allele. HORVU2Hr1G088460 within the interval of QTL could be the candidate gene. The second new QTL was identified on chromosome 3H from a summer sowing trial and the third one on chromosome 4H affected HD of DH lines only under spring sowing condition. These new QTL identified will provide alternative genetic resources for plant breeders developing barley varieties with improved HD adaptability to varying environments. [ABSTRACT FROM AUTHOR]

Kernel number per spike (KNPS) is one of the key factors affecting wheat yield, which can be significantly reduced by lower fertility or sterility of the apical and basal spikelets. In this study, the spikelet number per spike (SNPS), thousand kernel weight (TKW), KNPS, total grain numbers of the top three apical spikelets (GNAS), and total grain numbers of the bottom three basal spikelets (GNBS) of 212 wheat lines were recorded from five different environmental conditions. These 212 accessions were genotyped using the 9K iSelect SNP Beadchip. A total of 3269 SNP markers were used for genome-wide association analysis (GWAS). One hundred twelve significant marker-trait associations (MTAs) were identified. Twenty-two MTAs were identified in at least two environments and two of them showed association with two or more grain setting properties. Different loci showed an additive effect with both GNAS and GNBS being much higher in the lines with more favorite alleles. Two SNP loci, wsnp_Ex_c31799_40545376 and wsnp_BF293620A_Ta_2_3, showed the largest effects on increasing KNPS through improved fertility of apical and basal spikelets, respectively. These MTAs have the potential to be used in future marker-assisted selection. [ABSTRACT FROM AUTHOR]

Species of wild rice (Oryza spp.) possess a wide range of stress tolerance traits that can be potentially utilized in breeding climate-resilient cultivated rice cultivars (Oryza sativa) thereby aiding global food security. In this study, we conducted a greenhouse trial to evaluate the salinity tolerance of six wild rice species, one cultivated rice cultivar (IR64) and one landrace (Pokkali) using a range of electrophysiological, imaging, and whole-plant physiological techniques. Three wild species (O. latifolia, O. officinalis and O. coarctata) were found to possess superior salinity stress tolerance. The underlying mechanisms, however, were strikingly different. Na + accumulation in leaves of O. latifolia, O. officinalis and O. coarctata were significantly higher than the tolerant landrace, Pokkali. Na + accumulation in mesophyll cells was only observed in O. coarctata, suggesting that O. officinalis and O. latifolia avoid Na + accumulation in mesophyll by allocating Na + to other parts of the leaf. The finding also suggests that O. coarctata might be able to employ Na + as osmolyte without affecting its growth. Further study of Na + allocation in leaves will be helpful to understand the mechanisms of Na + accumulation in these species. In addition, O. coarctata showed Proto Kranz-like leaf anatomy (enlarged bundle sheath cells and lower numbers of mesophyll cells), and higher expression of C 4 -related genes (e.g., NADPME, PPDK) and was a clear outlier with respect to salinity tolerance among the studied wild and cultivated Oryza species. The unique phylogenetic relationship of O. coarctata with C 4 grasses suggests the potential of this species for breeding rice with high photosynthetic rate under salinity stress in the future., (© 2022. The Author(s).)