Diverged subpopulations in tropical Urochloa (Brachiaria) forage species indicate a role for facultative apomixis and varying ploidy in their population structure and evolution

Abstract Background Urochloa (syn. Brachiaria) is a genus of tropical grasses sown as forage feedstock, particularly in marginal soils. Here we aimed to clarify the genetic diversity and population structure in Urochloa species to understand better how population evolution relates to ploidy level and occurrence of apomictic reproduction. Methods We explored the genetic diversity of 111 accessions from the five Urochloa species used to develop commercial cultivars. These accessions were conserved from wild materials collected at their centre of origin in Africa, and they tentatively represent the complete Urochloa gene pool used in breeding programmes. We used RNA-sequencing to generate 1.1 million single nucleotide polymorphism loci. We employed genetic admixture, principal component and phylogenetic analyses to define subpopulations. Results We observed three highly differentiated subpopulations in U. brizantha, which were unrelated to ploidy: one intermixed with U. decumbens, and two diverged from the former and the other species in the complex. We also observed two subpopulations in U. humidicola, unrelated to ploidy; one subpopulation had fewer accessions but included the only characterized sexual accession in the species. Our results also supported a division of U. decumbens between diploids and polyploids, and no subpopulations within U. ruziziensis and U. maxima. Conclusions Polyploid U. decumbens are more closely related to polyploid U. brizantha than to diploid U. decumbens, which supports the divergence of both polyploid groups from a common tetraploid ancestor and provides evidence for the hybridization barrier of ploidy. The three differentiated subpopulations of apomictic polyploid U. brizantha accessions constitute diverged ecotypes, which can probably be utilized in hybrid breeding. Subpopulations were not observed in non-apomictic U. ruziziensis. Sexual Urochloa polyploids were not found (U. brizantha, U. decumbens) or were limited to small subpopulations (U. humidicola). The subpopulation structure observed in the Urochloa sexual–apomictic multiploidy complexes supports geographical parthenogenesis, where the polyploid genotypes exploit the evolutionary advantage of apomixis, i.e. uniparental reproduction and clonality, to occupy extensive geographical areas

Arroz más nutritivo contra la desnutrición en América Latina

More nutritive rice against malnutrition in Latin America Three topics are addressed briefly: (1) information available on the Fe and Zn contents of the grain of 11 rice cultivars; (2) factors affecting its contents; and (3) a plant breeding strategy proposed to increase the nutritional value of rice in Latin America. The data obtained are backed up by results obtained by the International Rice Research Institute (IRRI) and reveal significant differences among cultivars regarding rice grain Fe and Zn contents in both rough and polished rice. Acceptable Fe and Zn contents were also observed in several commercial varieties; these, however, were never selected to improve this aspect of nutritional quality. Recent scientific data indicate that plant breeding is an effective and reliable tool of reasonable cost to develop improved germplasm with a better nutritional value than current varieties. Research conducted by IRRI, within the framework of the HarvestPlus project, and by CIAT, through the AgroSalud project, indicates that genetic variability does exist in rice regarding grain Fe and Zn contents. In conclusion, it is considered feasible to improve the nutritional quality of rice in Latin America, and advances have been made in several areas.Se tratan brevemente tres temas: 1) la información disponible sobre el contenido de hierro (Fe) y zinc (Zn) del grano en 11 cultivares de arroz; 2) los factores que afectan ese contenido; y 3) una estrategia de fitomejoramiento que se propone para incrementar el valor nutricional del arroz en América Latina. Los datos obtenidos, que son sustentados por los resultados del Instituto Internacional de Investigaciones sobre el Arroz (IRRI), indican diferencias significativas entre los cultivares respecto al contenido de Fe y de Zn del grano, tanto en el arroz integral como en el arroz pulido. Se observó además un contenido aceptable de Fe y de Zn en algunas variedades comerciales; éstas, sin embargo, nunca fueron seleccionadas para mejorar este aspecto de su calidad nutricional. Datos científicos recientes indican que el fitomejoramiento es una herramienta eficaz, confiable y de costo razonable para desarrollar germoplasma mejorado, cuyo valor nutricional sea mayor que el de las variedades corrientes. Las investigaciones realizadas por el IRRI, en el marco del proyecto HarvestPlus, y por el CIAT, a través del proyecto AgroSalud, indican que hay variabilidad genética en el arroz respecto al contenido de Fe y de Zn de su grano. En conclusión, se considera que es factible mejorar la calidad nutricional del arroz en América Latina, tarea en la que se ha logrado avanzar en diversas direcciones

Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species

Background and Aims Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C-4 tropical forage grasses originating from Africa are important for food security and the environment, often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species. Methods Some 362 forage grass accessions from international germplasm collections were studied, and ploidy was determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima. Key Results Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs. In situ hybridization with a combination of repetitive DNA and genomic DNA probes identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids. Conclusions We suggest a new coherent nomenclature for the genomes present. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for Urochloa brizantha, U. decumbens and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and assist in measuring and conserving biodiversity in grasslands

Spatial modeling for low pathogenicity avian influenza virus at the interface of wild birds and backyard poultry

Low pathogenicity avian influenza virus (LPAIV) is endemic in wild birds and poultry in Argentina, and active surveillance has been in place to prevent any eventual virus mutation into a highly pathogenic avian influenza virus (HPAIV), which is exotic in this country. Risk mapping can contribute effectively to disease surveillance and control systems, but it has proven a very challenging task in the absence of disease data. We used a combination of expert opinion elicitation, multicriteria decision analysis (MCDA), and ecological niche modeling (ENM) to identify the most suitable areas for the occurrence of LPAIV at the interface between backyard domestic poultry and wild birds in Argentina. This was achieved by calculating a spatially‐explicit risk index. As evidenced by the validation and sensitivity analyses, our model was successful in identifying high‐risk areas for LPAIV occurrence. Also, we show that the risk for virus occurrence is significantly higher in areas closer to commercial poultry farms. Although the active surveillance systems have been successful in detecting LPAIV‐positive backyard farms and wild birds in Argentina, our predictions suggest that surveillance efforts in those compartments could be improved by including high‐risk areas identified by our model. Our research provides a tool to guide surveillance activities in the future, and presents a mixed methodological approach which could be implemented in areas where the disease is exotic or rare and a knowledge‐driven modeling method is necessary

A DOCK8-WIP-WASp complex links T cell receptors to the actin cytoskeleton

Wiskott-Aldrich syndrome (WAS) is associated with mutations in the WAS protein (WASp), which plays a critical role in the initiation of T cell receptor-driven (TCR-driven) actin polymerization. The clinical phenotype of WAS includes susceptibility to infection, allergy, autoimmunity, and malignancy and overlaps with the symptoms of dedicator of cytokinesis 8 (DOCK8) deficiency, suggesting that the 2 syndromes share common pathogenic mechanisms. Here, we demonstrated that the WASpinteracting protein (WIP) bridges DOCK8 to WASp and actin in T cells. We determined that the guanine nucleotide exchange factor activity of DOCK8 is essential for the integrity of the subcortical actin cytoskeleton as well as for TCR-driven WASp activation, F-actin assembly, immune synapse formation, actin foci formation, mechanotransduction, T cell transendothelial migration, and homing to lymph nodes, all of which also depend on WASp. These results indicate that DOCK8 and WASp are in the same signaling pathway that links TCRs to the actin cytoskeleton in TCR-driven actin assembly. Further, they provide an explanation for similarities in the clinical phenotypes of WAS and DOCK8 deficiency