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BackgroundA typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community.DescriptionUsing a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits). Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them.ConclusionBy integrating barley genotypic, phenotypic and mRNA abundance data sets directly within GeneNetwork's analytical environment we provide simple web access to the data for the research community. In this environment, a combination of correlation analysis and linkage mapping provides the potential to identify and substantiate gene targets for saturation mapping and positional cloning. By integrating datasets from an unsequenced crop plant (barley) in a database that has been designed for an animal model species (mouse) with a well established genome sequence, we prove the importance of the concept and practice of modular development and interoperability of software engineering for biological data sets.

Previous studies have shown that there is considerable population structure in cultivated barley (Hordeum vulgare Lo), with the strongest structure corresponding to differences in row number and growth habit. U.S. barley breeding programs include six-row and two-row types and winter and spring types in all combinations. To facilitate mapping of complex traits in breeding germplasm, 1816 barley lines from 10 U.S. breeding programs were scored with 1536 single nucleotide polymorphism (SNP) genotyping assays. The number of SNPs segregating within breeding programs varied from 854 to 1398. Model-based analysis of population structure showed the expected clustering by row type and growth habit; however, there was additional structure, some of which corresponded to the breeding programs. The model that fit the data best had seven populations: three two-row spring, two six-row spring, and two six-row winter. Average linkage disequilibrium (LD) within populations decayed over a distance of 20 to 30 cM, but some populations showed long-range LD suggestive of admixture. Genetic distance (allele-sharing) between populations varied from 0.11 (six-row spring vs. six-row spring) to 0.45 (two-row spring vs. six-row spring). Analyses of pairwise LD revealed that the phase of allelic associations was not well correlated between populations, particularly when their allele-sharing distance was >0.2. These results suggest that pooling divergent barley populations for purposes of association mapping may be inadvisable. doi: 10.2135/cropsci2009.04.0198

Doubled haploid (DH) plants represent valuable tools for plant breeding and genetic study. While DH plant production efficiency via anther culture has improved, genotypic effects are still considerable. The objective of this study was to investigate the inheritance of anther culture response to facilitate the application of anther culture to breeding programs. Two donor plant environment (field vs. growth chamber) were compared for anther culture performance of four barley (Hordeum vulgare L.) parents [WA10217-83 and 'Hazen' with high green plant regeneration (GPR), WA9035-84 and WA7773-83 with low GPR] and their 12 [F.sub.1] hybrids (4 X 4 complete diallel). The traits evaluated were number of embryoids, total number of plants regenerated, and number of GPR per 100 anther cultured. Genetic effects were significant while the effects of the two donor plant environments were not. There were additive and dominance effects for all three traits evaluated, and reciprocal effects for GPR. Intermediate responses generally resulted from high X low parent crosses in the [F.sub.1] for the thre traits. The performance of [F.sub.2] populations from reciprocal crosses betwee Hazen and WA9035-84, and WA9035-84 and WA7773-83, confirmed the [F.sub.1] additive and dominance effects. The reciprocal effect in [F.sub.1] from crosses between WA9035-84 and WA7773-83 for GPR per 100 anthers was probably maternal. The GPR of two selected [F.sub.3] families verified transgressive segregation observed in the [F.sub.2]. [F.sub.3] performance indicated that selection of recombinant genotypes for higher GPR ability was effective. In conclusion, specific but complex genetic effects for anther culturability were demonstrated and this information has application to barley breeding strategy.

Introduction of certain semidwarf genes into wheat (Triticum spp.) has improved N-use efficiency, particularly at high N supply. This study was conducted to determine whether yield and grain quality differ between standard height (STD) and mutant semidwarf (SD) malting barley (Hordeum vulgare L.) isotypes with varying levels of N supply. Isotype pairs (|Morex', |Hazen', |Norbert', and |Andre') and check cultivars (Steptoe, Klages) were grown vath 30, 60, 90, and 120 kg N [ha.sup.-1] in 1987 and 1989. Yield, grain characteristics, and malting quality parameters were evaluated. The STD isotypes had higher yield (6781 vs. 5642 and 5202 vs. 4504 kg [ha.sup.-1] in 1987 and 1989, respectively) and generally higher values for yield components and harvest index, as well as better grain quality than their respective SD isotypes; however, two-row SD isotypes had better malting quality than their STD isotypes. The generally superior performance of STD isotypes in part may be due to the SD isotypes being raw induced mutants that had not been improved by crossing. Malting quality parameters, such as total malt protein and malt extract, were affected negatively by N >60 kg [ha.sup.-1], when the preceding crop was pea (Pisum sativum L.; high N); however, for yield and some malt quality parameters such as diastatic power, all genotypes responded significantly and positively to N fertilization when the preceding crop was barley (low N). In general, the response to N was similar for both barley types. As SD malting barley cultivars are developed to control lodging, they may not utilize more N or yield more than STD types.

The Crop Science Society of America (CSSA), since its inception in 1955, and before that the American Society of Agronomy (ASA), recognized the importance of free exchange of information and [...]