A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

BACKGROUND: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. RESULTS: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. CONCLUSION: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations

A molecular genetic study of seed dormancy in aegilops tauschii and expression of sprouting resistance in common hexploid wheat

The wild wheat relative Aegilops tauschii, has been identified as a useful source of preharvest sprouting (PHS) resistance for hexaploid bread wheat. Seed dormancy, a major contributor to PHS resistance, was shown to be partly expressed in hexaploid wheat derived from direct hybridisation between Triticum aestivum and Ae. tauschii. The enhanced seed dormancy possessed by the Ae. tauschii derived direct-cross wheat lines was manifested by embryo and seedcoat related mechanisms. The embryo related mechanism could not confer full expression of dormancy without the presence of seedcoat related factors, suggesting that the two mechanisms may be independently inherited. The presence of seedcoat related dormancy however, was not associated with the red seedcoat phenotype, which has traditionally been associated with PHS resistance in wheat. Red pigmentation of the seedcoat is likely to be "involved in the extreme dormancy possessed by Ae. tauschii but does not preclude partial expression within a white seedcoat background. The ability of Ae. tauschii derived wheat lines to enhance seed dormancy may have potential economic benefit to breeding for PHS resistance in white wheat varieties. Presently, white wheat varieties grown in the sprouting susceptible regions of Australia possess inadequate protection, costing the industry up to $100M annually. Inheritance of seed dormancy in Ae. tauschii was found to be controlled by one or two major genes which were influenced by minor genes and/or environmental factors. These results are consistent with the findings of several previous reports. Inheritance was shown to be dominant at the F3 grain generation, consistent with the generally dominant nature of dormancy possessed by red seeded genotypes. However, preliminary assessment of individual F2 seeds indicated recessive control of dormancy. Because genes possessed by the maternal tissues of the seedcoat do not segregate until the F3 seed generation, the F2 recessive model may be indicative of separate genetic control for the embryo related dormancy mechanism(s). Based on the above inheritance information, a bulked segregant analysis approach was initially undertaken for the development of linked molecular markers for seed dormancy. One microsatellite marker on chromosome 1D produced polymorphism between resistant and susceptible DNA bulks. A mapping approach was subsequently undertaken, revealing two significant QTL mapping to chromosome 1D. The putative QTL for seed dormancy will relate to the embryo component of dormancy, as the trait data employed related to the F2 seed generation, which was segregating for embryo related genes. The D genome of hexaploid wheat presently possesses the fewest QTL for PHS resistance of the three contributing genomes. Within the D genome, chromosome 1D was poorly represented in the literature. As such, 4e. tauschii represents a potential to bolster numbers of QTL for sprouting resistance in hexaploid wheat. Given the homology between the D genomes of Ae. tauschii and T aestivum, the microsatellite markers identified, flanking the putative QTL, will likely be transferable to hexaploid bread wheat. Seed dormancy is strongly influenced by conditions during growth. As such, unambiguous selection through use of molecular markers will expedite the introgression of this economically important trait into elite wheat cultivars