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A selection of 147 wheat D-genome and 130 barley genomic simple sequence repeat (gSSR) markers were screened for their utility in Hordeum chilense, as an alien donor genome for cereal breeding. Fifty-eight wheat D-genome and 71 barley PCR primer pairs consistently amplified products from H. chilense. Nineteen wheat D-genome and 20 barley gSSR markers were polymorphic and allowed wide genome coverage of the H. chilense genome. Twenty-three of the wheat D-genome and 11 barley PCR primer pairs were suitable for studying the introgressions of H. chilense into wheat, amplifying H. chilense products of distinct size. In 88% of the markers tested, H. chilense products were maintained in the expected homeologous linkage group, as revealed by the analysis of wheat/ H. chilense addition lines. Twenty-nine microsatellite markers (eight gSSRs and 21 expressed sequence tags-SSRs) uniformly distributed across the genome were tested for their utility in genetic diversity analysis within the species. Three genetic clusters are reported, in accordance with previous morphological and amplified fragment length polymorphism data. These results show that it is possible to discriminate the three previously established germplasm groups with microsatellite markers. The reported markers represent a valuable resource for the genetic characterisation of H. chilense, for the analysis of its genetic variability, and as a tool for wheat introgression. This is the first intraspecific study in a collection of H. chilense germplasm using microsatellite markers. [ABSTRACT FROM AUTHOR]

Amylases play an essential role in the germination and malting process. Therefore, these genes are interesting candidates for marker development in order to improve malting quality as an important breeding aim. The intervarietal diversity of the α-amylase gene amy1 mapping to chromosome 6H was investigated. A total of six single nucleotide polymorphisms (SNPs) were detected which defined four haplotypes. Associations between SNP-markers and important malting parameters were discovered in a collection of 117 European spring and winter barley cultivars, representing the current commercial germplasm. Haplotype amy1_H2 was significantly associated with a number of malting related traits and explained 19% of the phenotypic variation of the malting quality index (MQI) for all varieties and 35% in a subset of 72 winter barleys. The diagnostic SNP3 was associated with a 45% difference in the MQI. Within the spring barleys, the average value of haplotype amy1_H1 for friability was significantly higher than that of amy1_H4. All discovered SNPs were converted into high-throughput markers for pyrosequencing and can be used for marker assisted selection. [ABSTRACT FROM AUTHOR]

A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations ‘Igri × Franka’, ‘Steptoe × Morex’, ‘OWBRec × OWBDom’, ‘Lina × Canada Park’, ‘L94 × Vada’ and ‘SusPtrit × Vada’. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HV GeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HV GeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 “bridge markers” common to two or more individual maps with the help of the computer programme JoinMap® 3.0. The final map was calculated by following a “neighbours” map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley. [ABSTRACT FROM AUTHOR]

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Advanced backcross (AB)-quantitative trait locus (QTL) analysis has been successfully applied for detecting and transferring QTLs from unadapted germplasm into elite breeding lines in various plant species. Here, we describe the application of a modified AB breeding scheme to spring barley. A BC3-doubled haploid (DH) population consisting of 181 lines derived from the German spring barley cultivar ‘Brenda’ (Hordeum vulgaresubsp.vulgare) as the recurrent parent and the wild species line ‘HS213’ (H. vulgaresubsp.spontaneum) as the donor line was evaluated for yield and its components as well as malting quality traits. A set of 60 microsatellite markers was used to genotype the population, and phenotypic data were collected at two locations in Germany in continuous years. Altogether, 25 significant QTLs were detected by single-marker regression analysis and interval mapping. Most positive QTLs originated from the recurrent parent ‘Brenda’. A QTL,Qhd2.1, on chromosome 2HS from ‘Brenda’ explained 18.3% and 20.7% of the phenotypic variation for yield and heading date, respectively. Due to the small percentage of donor-parent genome of 6.25%, the BC3-DH lines could be directly used for the extraction of near-isogenic lines (NILs) forQhd2.1. Consequently, it was possible to determine the precise location of the locushd2.1within a region of 6.5 cM, using an F2 population consisting of 234 individuals developed from a cross between an NIL containing a defined donor segment at this locus and ‘Brenda’. The location of this QTL was consistent with the presence of a major photoperiod response gene,Ppd-H1, previously reported in this region, which is associated with pleiotropic effects on yield components. In summary, the analysis of a BC3-DH population in barley provides a compromise between the analysis of QTLs by means of an AB scheme and the generation of defined substitution lines. Several lines carrying defined different donor segments for only one single chromosome or trait in the genetic background of ‘Brenda’ could be selected for further genetic studies. [ABSTRACT FROM AUTHOR]

A cleaved amplified polymorphic sequence marker was used to detect the alleles Bmy-Sd2H and Bmy-Sd3 identifying highly thermostable isoforms of the enzyme β-amylase, which improves fermentability during brewing. Among the 889 accessions of barley ( Hordeum vulgare) investigated, and two accessions of H. spontaneum a total of 166 accessions were identified carrying the superior β-amylase alleles. These thermostable alleles of β-amylase were most frequently observed in six-rowed varieties originating from Asia, especially Japan, with 61.9% of the accessions from Asia carrying the alleles of interest. Additional six-rowed barleys carrying the relevant alleles were identified among accessions from America, Africa and the Near East. In the European varieties, the percentage of accessions with the alleles of interest was 5.1% with a strong predominance in two-rowed spring barleys. A pedigree analysis identified the cross ‘Binder’ × ‘Gull’ as the main source of the thermostable β-amylase alleles in European varieties. The data suggest that an improvement of malting quality in barley could be achieved by introduction of the Bmy1-Sd2H and Bmy1-Sd3 alleles into the European breeding programmes. [ABSTRACT FROM AUTHOR]

To enhance the marker density of existing genetic maps of barley (Hordeum vulgare L.), a new set of microsatellite markers containing dinucleotide motifs was developed from genomic clones. Out of 254 primer pairs tested, a total of 167 primer pairs were classifed as functional in a panel of six barley cultivars and three H. spontaneum accessions, and of those, 127 primer pairs resulting in 133 loci were either mapped or located onto chromosomes. The polymorphism information content (PIC) ranged from 0.05 to 0.94 with an average of 0.60. The number of alleles per locus varied from 1 to 9. On average, 3.9 alleles per primer pair were observed. The RFLP frameworks of two previously published linkage maps were used to locate a total of 115 new microsatellite loci on at least one mapping population. The chromosomal assignment of 48 mapped loci was corroborated on a set of wheat-barley chromosome addition lines; 18 additional loci which were not polymorphic in the mapping populations were assigned to chromosomes by this method. The microsatellites were located on all seven linkage groups with four significant clusters in the centromeric regions of 2H, 3H, 6H and 7H. These newly developed microsatellites improve the density of existing barley microsatellite maps and can be used in genetic studies and breeding research. [ABSTRACT FROM AUTHOR]