A consensus map of barley combining simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) markers has been developed by combining 5 Australian barley linkage maps, Galleon × Haruna Nijo, Chebec × Harrington, Clipper × Sahara, Alexis × Sloop, and Amaji Nijo × WI2585, using the software package JOINMAP 2.0. The new consensus map consists of 700 markers, with 136 being SSRs, and has a total genetic distance of 933 cM. The consensus map order appears to be in good agreement with the Australian barley linkage maps, with the exception of a small inversion located close to the centromere of chromosome 5H. Similarly, the SSR map orders are in good agreement with SSR markers integrated into the doubled haploid linkage map of Lina × Hordeum spontaneum, Canada Park. The new consensus map provides a framework to cross examine and align partial and complete barley linkage maps using markers common to many barley maps. This map will allow researchers to rapidly and accurately select SSR markers for chromosome regions of interest for barley genetic and plant breeding studies.

A consensus map of barley integrating SSR, RFLP, and AFLP markers

Spring radiation frost is a major abiotic stress in southern Australia, reducing yield potential and grain quality of barley by damaging sensitive reproductive organs in the latter stages of development. Field-based screening methods were developed, and genetic variation for reproductive frost tolerance was identified. Mapping populations that were segregating for reproductive frost tolerance were screened and significant QTL identified. QTL on chromosome 2HL were identified for frost-induced floret sterility in two different populations at the same genomic location. This QTL was not associated with previously reported developmental or stress-response loci. QTL on chromosome 5HL were identified for frost-induced floret sterility and frost-induced grain damage in all three of the populations studied. The locations of QTL were coincident with previously reported vegetative frost tolerance loci close to the vrn-H1 locus. This locus on chromosome 5HL has now been associated with response to cold stress at both vegetative and reproductive developmental stages in barley. This study will allow reproductive frost tolerance to be seriously pursued as a breeding objective by facilitating a change from difficult phenotypic selection to high-throughput genotypic selection.

QTL mapping of chromosomal regions conferring reproductive frost tolerance in barley ( Hordeum vulgare L.).

Using an established genetic map, a single gene conditioning covered smut resistance, Ruh.7H, was mapped to the telomere region of chromosome 7HS in an Alexis/Sloop doubled haploid barley population. The closest marker to Ruh.7H, abg704 was 7.5 cM away. Thirteen loci on the distal end of 7HS with potential to contain single nucleotide polymorphisms (SNPs) were identified by applying a comparative genomics approach using rice sequence data. Of these, one locus produced polymorphic co-dominant bands of different size while two further loci contained SNPs that were identified using the recently developed high resolution melting (HRM) technique. Two of these markers flanked Ruh.7H with the proximal marker located 3.8 cM and the distal marker 2.7 cM away. This is the first report on the application of the HRM technique to SNP detection and to rapid scoring of known cleaved amplified polymorphic sequence (CAPS) markers in plants. This simple, precise post-PCR technique should find widespread use in the fine-mapping of genetic regions of interest in complex cereal and other plant genomes.

/pdf/the-use-of-high-resolution-melting-hrm-to-map-single-3a3syuy9l1.pdf

The use of high resolution melting (HRM) to map single nucleotide polymorphism markers linked to a covered smut resistance gene in barley

Malting quality is genetically determined by the complex interaction of numerous traits which are expressed prior to and, in particular, during the malting process. Here, we applied the advanced backcross quantitative trait locus (AB-QTL) strategy (Tanksley and Nelson, Theor Appl Genet 92:191–203, 1996), to detect QTLs for malting quality traits and, in addition, to identify favourable exotic alleles for the improvement of malting quality. For this, the BC2DH population S42 was generated from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp. spontaneum). A QTL analysis in S42 for seven malting parameters measured in two different environments yielded 48 QTLs. The exotic genotype improved the trait performance at 18 (37.5%) of 48 QTLs. These favourable exotic alleles were detected, in particular, on the chromosome arms 3HL, 4HS, 4HL and 6HL. The exotic allele on 4HL, for example, improved α-amylase activity by 16.3%, fermentability by 0.8% and reduced raw protein by 2.4%. On chromosome 6HL, the exotic allele increased α-amylase by 16.0%, fermentability by 1.3%, friability by 7.3% and reduced viscosity by 2.9%. Favourable transgressive segregation, i.e. S42 lines exhibiting significantly better performance than the recurrent parent Scarlett, was recorded for four traits. For α-amylase, fermentability, fine-grind extract and VZ45 20, 16, 2 and 26 S42 lines, respectively, surpassed the recurrent parent Scarlett. The present study hence demonstrates that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve malting quality traits.

/pdf/ab-qtl-analysis-in-spring-barley-iii-identification-of-zyqihs6fxk.pdf

AB-QTL analysis in spring barley: III. Identification of exotic alleles for the improvement of malting quality in spring barley ( H. vulgare ssp. spontaneum )

SSR markers closely linked to 18 loci that control 16 important barley traits were assessed for their applicability in Australian barley breeding programs A panel of 40 genotypes routinely used by the South Australian Barley Improvement Program (SABIP) was used to examine the usefulness of these SSR markers for marker assisted selection (MAS) The success of monitoring a trait locus from donor to recipient lines ranged from 10 to 98%, depending on the marker SSRs with a high polymorphic information content (PIC) value were found to be the most useful for application in MAS The assessment also indicated that SSRs derived from genomic sequences were more successful for MAS than those designed from expressed sequence tags A total of 130 SSR markers were screened among 2 panels of Australian barley genotypes to determine which markers would be the most useful for discriminating Australian germplasm PIC values generated by this screening were also compared with those generated using a panel of European barley genotypes Using ordinary correlations (parametric), rank correlations (non-parametric), and partial correlations (multi-variate), a strong association was found between the 2 Australian panels, but no or weak correlation was observed between the 2 Australian panels and the European dataset It can therefore be concluded that PIC values generated by SSR markers screened with European genotypes cannot be used to predict the usefulness of an SSR marker for discriminating Australian genotypes From PIC values generated in this study, 36 SSR markers have been selected for the discrimination of Australian genotypes These markers all show high and/or consistent PIC values among Australian and European barley genotypes

Potential of SSR markers for plant breeding and variety identification in Australian barley germplasm

A map for the barley doubled haploid population Amagi Nijo × WI2585 was constructed to examine manganese efficiency derived from Amagi Nijo. Manganese efficiency conferred by the previously identified locus Mel1 was validated. No other loci contributing to manganese efficiency were identified, possibly because of poor maker coverage in some regions. The map was additionally used to look for loci contributing to some aspects of malting quality. A locus on 2HL was found to be associated with malt extract, and 2 loci on 4HL and 5H, respectively, were found to be associated with diastatic power.

Mapping and QTL analysis of the barley population Amagi Nijo × WI2585

Two populations between the German malting variety Alexis and the Australian malting variety Sloop were constructed, mapped, phenotyped, and subjected to quantitative trait loci analysis. One population consisted of 153 F4-derived recombinant inbred lines and the other of 111 doubled haploid lines. This paper describes 18 field and laboratory experiments conducted with the populations and summarises the traits mapped and analysed. The genetic basis of 5 traits (malt extract, resistance to leaf rust, resistance to powdery mildew, early flowering, plant stature) important to Australian efforts to improve malting barley varieties was elucidated. Detailed maps for these populations are shown in this paper, while a consensus map incorporating these maps and further experiments on the populations are described elsewhere in this issue.

/pdf/mapping-and-qtl-analysis-of-the-barley-population-alexis-3gsnxtmpof.pdf

Mapping and QTL analysis of the barley population Alexis × Sloop

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Mapping and QTL analysis of the barley population Amagi Nijo × WI2585

Mapping and QTL analysis of the barley population Alexis × Sloop