Geographical range and spatial structure of genetic lineages in Sophora linearifolia (Fabaceae), an endemic shrub of Central Argentina

Las sierras de Córdoba y San Luis albergan una gran riqueza de especies endémicas. Un grupo importante de ellas muestra una distribución disyunta entre ambas serranías. Hasta la actualidad no existían estudios genéticos que permitieran inferir procesos históricos asociados a este patrón. Con este propósito caracterizamos el área de distribución y el patrón filogeográfico de Sophora linearifolia, abarcando todo su rango geográfico que incluye las Sierras Chicas (SC) y las Cumbres de Gaspar (CG) en Córdoba y el suroeste de las Sierras de San Luis (SL). Contrastamos la distribución actual con la distribución predicha a partir del modelado del nicho ecológico. Analizamos el nivel de variabilidad genética, la estructuración espacial del marcador de ADN plastidial trnH-psbA y reconstruimos las relaciones genealógicas entre los haplotipos. La distribución actual y la predicha mostraron una disyunción entre Córdoba y San Luis, pero la distribución actual presentó una disyunción entre SC y CG que no fue modelada en la distribución potencial. Se obtuvieron 8 haplotipos de distribución restringida con bajos niveles de diferenciación genética agrupados en 4 filogrupos: SC, CG y dos en SL. Nuestros resultados indican que S. linearifolia presentaría baja capacidad de dispersión y que se habría diversificado recientemente, sugiriendo que se trataría de un neoendemismo.A large number of endemic species occur in the Sierras of Córdoba and San Luis. A significant group of them shows a disjunct geographic distribution between these two mountain regions. Until the present study, there were none genetic studies that allow us to infer historical processes underlying this geographical pattern. For this purpose, we characterize the distribution area and phylogeographic patterns of Sophora linearifolia, across its geographic range which includes Sierras Chicas (SC) and Cumbres de Gaspar (CG) in Córdoba and in the southwestern area of Sierras of San Luis (SL). We compared the current with the predicted species area of distribution using ecological niche modelling analysis. We also analyzed genetic variability and spatial structure of the DNA chloroplast marker trnH-psbA, and reconstructed the genealogical relationships among the retrieved haplotypes. Current and the predicted distribution agreed in showing a climatic/topographic disjunction between Sierras of Cordoba and San Luis hills, although the current distribution presents a disjunction between SC and CG in Córdoba, not shown in the potential distribution map. We obtained eight haplotypes with restricted distribution and low levels of genetic differentiation that were grouped into four phylogroups: SC, CG and two in SL. Our results indicate that S. linearifolia presents low dispersal ability and it would have recently diversified, suggesting a neoendemic taxon.Fil: Alercia, David. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Giorgis, Melisa Adriana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Funes, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; ArgentinaFil: Cosacov Martinez, Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentin

Development of GCP Ontology for Sharing Crop Information

The Generation Challenge Programme (GCP – "http://www.generationcp.org":http://www.generationcp.org) is a globally distributed crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. GCP adopted the development paradigm of a ‘model-driven architecture’ to achieve the interoperability and integration of diverse GCP data types that are available through distributed data sources and consumed by end-user data analysis tools. Its objective is to ensure semantic compatibility across the Consortium that will lead to the creation of robust global public goods from GCP research results. 

The GCP scientific domain model is an object model that encapsulates key crop science concepts and is documented using Unified Modeling Language (see GCP Models on "http://pantheon.generationcp.org/index.php":http://pantheon.generationcp.org/index.php). 

At the core of the GCP architecture is a scientific domain model, which is heavily parameterized with GCP-indexed ontology terms. The GCP-indexed ontology reuses established international standards where available, converts other publicly available controlled vocabularies into formally managed ontology, and develops novel ontology if no public vocabularies yet exist. General and crop-specific GCP ontologies are being developed by crop teams involving GCP and external scientific experts – in particular, for crop-specific ontology relating to plant anatomy, developmental stage, trait and phenotype for selected GCP crops. Crop ontologies are being developed for chickpea, maize, Musa, potato, rice, sorghum and wheat. The Bioversity crop descriptor lists already loaded into OBO format files provide the primary structure to develop the crop ontologies. Then, terms to be mapped to the ontologies are extracted from the crop databases where trait values have been stored by crop scientists. These sources allow the ontology teams to identify the most commonly used concept names and their interrelations. Experts validate the selection of keywords that will build the controlled vocabulary. 

These GCP ontologies will allow researchers and end users to query keywords related to traits, plant structure, growth stage, and molecular function, and link them to associated phenotyping and genotyping data sets including data on germplasm, crop physiology, geographic information, genes, QTL, etc. To reach that stage, the crop ontologies will be integrated into the data-entry user interface or data templates as picklists facilitating data annotation and submission of new terms. In addition, the GCP ontologies will be integrated with Plant Ontology (PO) and Gramene (Trait Ontology, TO; Environment Ontology, EO) to develop a common, internationally shared crop trait and anatomy ontology. The team will initiate collaboration with SONet (Scientific Observations Network) and OBOE (Extensible Observation Ontology), which proposed to integrate the GCP ontology as a study case.
The Open Biomedical Ontologies (OBO) edit tool has been used to develop the ontologies for rice, wheat and maize traits, which are currently available at "http://cropforge.org/projects/gcpontology/":http://cropforge.org/projects/gcpontology/ . The crop-specific work plans and ontologies related to other materials are published at "http://pantheon.generationcp.org":http://pantheon.generationcp.org. 
The development and curation of general-purpose ontologies will be continued and made available on the Pantheon and CropForge websites

Key descriptors for fodder trees

The Key descriptors for fodder trees consist of an initial minimum set of characterization and evaluation descriptors for some species of the family Fabaceae (Leguminosae). This strategic set aims at facilitating access to and utilization of these species and it does not exclude the addition of other descriptors later. This work has been done jointly with the International Livestock Research Institute (ILRI) and the FAO International Treaty on Plant Genetic Resources for Food and Agriculture. The list was based on a preliminary set of descriptors developed by ILRI. In addition, internet searches were carried out looking for the most updated information on relevant characteristics and traits. The original list was subsequently integrated with evaluation traits. Special attention was given to the inclusion of descriptors relevant to germplasm utilization and abiotic stresses of particular importance in the context of emerging adverse weather events, which are expected to intensify under current and future climate challenges. The key set of access and utilization descriptors was defined through an online survey, in which 24 experts from 14 different organizations and universities from 13 countries participated. Survey results were subsequently validated in consultation with a Core Advisory Group (see “Contributors”) led by Alice Muchugi and Jean Hanson from ILRI. The strategic set of data standards is designed to facilitate access to and utilization of plant genetic resources for food and agriculture. Together with passport information (Alercia et al. 2015, 2018), descriptors are critical to the effective sharing of characterization and evaluation data and to the efficient use of plant genetic resources for food and agriculture