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Key message: 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. [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]

Rhynchosporium secalis can overcome a single resistance gene of barley in a relatively short period of time. Novel genes and quantitative trait locis (QTLs) are therefore vital to control scald in barley. A population of 220 double haploid lines was developed from a cross of Vlamingh and WABAR2147, where Vlamingh showed adult plant resistance (APR) and WABAR2147 showed seedling resistance to a group of isolates. The population was tested for APR to scald under natural infection in two consecutive seasons in addition to a seedling screen with three isolates. One single gene was mapped to chromosome 6H based on the seedling test, and two QTLs ( QSc.VlWa.4H and QSc.VlWa.6H) were mapped to chromosomes 4H and 6H based on APR. Epistatic interaction was observed between the two QTLs, and environment/QTL interaction was only observed for QSc.VlWa.6H which co-segregated with the seedling resistance gene and contributed to basal resistance against scald during whole growth stages. QSc.VlWa.4H explained 42.5 and 57.8 % of the phenotypic variation in the two independent trials when the effect of QSc.VlWa.6H was excluded from the analysis. We developed a high-density consensus genetic map with 7,876 molecular makers and anchored 43 QTLs and 7 genes for scald resistance from different mapping populations. No known QTLs or genes were reported in a similar position to QSc.VlWa.4H, and it was the first major QTL for APR of scald on chromosome 4HS in barley. Combination of the two QTLs achieved better and stable scald resistance across four different environments. [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]

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. [ABSTRACT FROM AUTHOR]

Photoperiod response is a key determinant for barley adaptation to diverse environments. A major quantitative trait locus (QTL) for response to long photoperiod was identified in Australia (Perth, 31°56′S) and China (Wuhan, 30°33′N) using 178 doubled haploid lines derived from a cross of an Australian barley, Baudin, and a Canadian barley, AC Metcalfe. The QTL was detected as a major QTL in the 18-h photoperiod glasshouse experiments and mapped to the Xp12m50B199- Xp13m47B399 interval on chromosome 4H with a LOD score of 57 in Australia and confirmed in China. The single QTL accounted for 77.48 and 37.81% of phenotypic variation for long photoperiod response in Australia and China, respectively. The same QTL also controlled heading date in Australia, under normal and extended photoperiod conditions, and in China, under extended photoperiod and late-sown conditions. The QTL advanced heading date by 27.8 days in Australia and 42.5 days in China under a 18-h photoperiod. In addition, QTL for heading date were identified on chromosomes 2H and 3H. The chromosome 3H QTL was associated with the denso gene and detected in all conditions, but the chromosome 2H QTL was only detected in Australia. The new photoperiod response QTL, Qhea.BM.4- 13/Qpho.BM.4- 13, on chromosome 4H and its associated markers will provide an alternative for plant breeders developing new varieties for different environments using marker-assisted selection. [ABSTRACT FROM AUTHOR]

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 ( Hv20ox) was identified as the candidate gene for sdw1/denso. Semi-quantitative real-time RT-PCR revealed that Hv20ox 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 Hv20ox 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 Hv20ox 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 Hv20ox 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 Hv20ox expression. The gene expression marker for Hv20ox can be used to distinguish different alleles of sdw1/ denso. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

A number of technologies are available to increase the abundance of DNA markers and contribute to developing high resolution genetic maps suitable for genetic analysis. The aim of this study was to expand the number of Diversity Array Technology (DArT) markers on the wheat array that can be mapped in the wheat genome, and to determine their chromosomal location with respect to simple sequence repeat (SSR) markers and their position on the cytogenetic map. A total of 749 and 512 individual DArT and SSR markers, respectively, were identified on at least one of four genetic maps derived from recombinant inbred line (RIL) or doubled haploid (DH) populations. A number of clustered DArT markers were observed in each genetic map, in which 20–34% of markers were redundant. Segregation distortion of DArT and SSR markers was also observed in each mapping population. Only 14% of markers on the Version 2.0 wheat array were assigned to chromosomal bins by deletion mapping using aneuploid lines. In this regard, methylation effects need to be considered when applying DArT marker in genetic mapping. However, deletion mapping of DArT markers provides a reference to align genetic and cytogenetic maps and estimate the coverage of DNA markers across the wheat genome. [ABSTRACT FROM AUTHOR]