Carola Wagner

Intraspecific diversity and relationship between subspecies of Origanum vulgare revealed by comparative AFLP and SAMPL marker analysis

The genus Origanum is often referred to as an under-utilized taxon because of its complex taxonomy. Origanum vulgare L., the most variable species of the genus, is a spice and medicinal herb that is characterized by high morphological diversity (six subspecies). In this study, the relative efficiencies of two PCR-based marker approaches, amplified fragment length polymorphism (AFLP) and selectively amplified microsatellite polymorphic loci (SAMPL), were used for comparable genetic diversity surveys and subspecies discrimination among 42 oregano accessions. Seven assays each of AFLP and SAMPL markers were utilized. Effective multiplex ratio (EMR), average heterozygosity (Hav-p), marker index (MI), and resolving power (RP) of the primer combinations were calculated for the two marker systems. UPGMA and Structure analysis along with PCoA plots derived from the binary data matrices of the two markers depicted the genetic distinction of accessions. Our results indicate that both marker systems are suitable but SAMPL markers are slightly more efficient in differentiating accessions and subspecies than AFLPs.

Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork

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 GeneNetworks 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.

Reproductive system and molecular phylogenetic relationships of Fonio Millets (Digitaria spp., Poaceae) with some polyploid wild relatives

Fonio millets (Digitaria exilis, D. iburua) are minor but important indigenous cereals in the semiarid areas of West-Africa. Recent interest in breeding strategies for these crops requires a better understanding of their biology and genetics. Amplified Fragment Length Polymorphism (AFLP) markers were employed to assess the phylogenetic relationships among cultivated fonio species and some polyploid wild relatives and examine proposed hypotheses on fonio ancestry. The AFLP analysis was found quite suitable for identifying each species. A very strong genetic affinity (over 92% similarity) was detected between the wild D. longiflora and D. ternata and the cultivated D. exilis and D. iburua, respectively. These data provided additional molecular evidence supporting the previous view of direct domestication of fonio millets from these two wild species. High genetic divergences were expectedly found between fonio species and the other taxonomically distant Digitaria taxa investigated. The results also revealed D. ciliaris and D. sanguinalis as separate species sharing close ancestry. Selfing experiments and subsequent progeny analyses using three isozymes supplemented by AFLPs were further conducted to determine the reproductive system in fonio millets. The results revealed apomixis as absolute mode of reproduction of these crops, except D. exilis in which 2% residual sexuality was detected. Additional data documented on seed set and pollen viability suggested that apomixis in fonio would be of pseudogamous type. The data also revealed fonio crops as highly self-compatible and of allopolyploid origin. This study adds new information about the reproductive system and the evolution of fonio, contributing to the knowledge on their biology, and thus providing useful subsides for future genetic improvement of these valuable crops.