Progress in developing a potato ontology for breeders.

The potato ontology is part of a community effort to establish a set of related crop ontologies. The advantage of an ontology is that both humans and software applications can understand a data domain. This will allow the application of numerical or data mining techniques that may help to uncover previously unknown correlations. Building on previous draft versions, here we focus on traits important to breeding: we identified so far 70 descriptors. These include: morphological (36), agronomical performance (7), resistance traits (7), biochemical (6), reaction to abiotic stresses (2), molecular (1 ) and post-harvest (9). We anticipate further refinements and cross-checks

Selección participativa de variedades de papa (SPV) usando el diseño mamá y bebé: una guía para capacitadores con perspectiva de género.

El objetivo de esta guía es orientar paso a paso la facilitación y documentación de la dinámica SPV (Seleccion participativa de variedades) usando el diseño M&B para seleccionar, y eventualmente liberar, variedades de papa preferidas por los usuarios finales, que se adapten a las diferentes necesidades de los agricultores, a los diversos agro-ecosistemas y prácticas de manejo como también a las preferencias de comerciantes y consumidores

Integrating and sharing accession-level and omics-size genotype, phenotype and environmental data: Experiences at the International Potato Center (CIP).

Plant breeding consists in the creation and selection of new genotypes. This involves not only keeping records across generations and environments but also accommodating data of increasing resolution on genotypes, phenotypes, and growth environments. Some such high-resolution characterization methods are Near-Infrared spectroscopy, metabolomics, next-generation sequencing and high resolution spatial-temporal-spectral photos. A first need is the integration and retrieval of this information. Such an integrated and complete set can be described in breeder’s terms in six dimensions: a plant phenotype (P) is the result of a genotypes (G) interaction with its environment (E) given certain field management (M) practices. In addition, data on the administrative (A) context should be kept including staff involved, objectives and, if applicable, projects and donors; as well as on data documentation standards (S) like ontologies. The latter play an important part in exchanging and aggregating information. Here we describe the adoption of the ‘Biomart’ database for this purpose. While Biomart was developed originally to accommodate gene and sequencing data at a genomic scale we describe here how it can be used for breeding program data. This is being illustrated by current data warehousing in the potato breeding program at the International Potato Center (CIP). Particularly, genotype and phenotype can be transparently combined for further analysis in the decision process for the selection of new genotypes

The influenza A virus NS1 protein binds small interfering RNAs and suppresses RNA silencing in plants

RNA silencing comprises a set of sequence-specific RNA degradation pathways that occur in a wide range of eukaryotes, including animals, fungi and plants. A hallmark of RNA silencing is the presence of small interfering RNA molecules (siRNAs). The siRNAs are generated by cleavage of larger double-stranded RNAs (dsRNAs) and provide the sequence specificity for degradation of cognate RNA molecules. In plants, RNA silencing plays a key role in developmental processes and in control of virus replication. It has been shown that many plant viruses encode proteins, denoted RNA silencing suppressors, that interfere with this antiviral response. Although RNA silencing has been shown to occur in vertebrates, no relationship with inhibition of virus replication has been demonstrated to date. Here we show that the NS1 protein of human influenza A virus has an RNA silencing suppression activity in plants, similar to established RNA silencing suppressor proteins of plant viruses. In addition, NS1 was shown to be capable of binding siRNAs. The data presented here fit with a potential role for NS1 in counteracting innate antiviral responses in vertebrates by sequestering siRNAs

Partial hexokinase II knockout results in acute ischemia-reperfusion damage in skeletal muscle of male, but not female, mice

Cellular studies have demonstrated a protective role of mitochondrial hexokinase against oxidative insults. It is unknown whether HK protective effects translate to the in vivo condition. In the present study, we hypothesize that HK affects acute ischemia–reperfusion injury in skeletal muscle of the intact animal. Male and female heterozygote knockout HKII (HK(+/-)), heterozygote overexpressed HKII (HK(tg)), and their wild-type (WT) C57Bl/6 littermates mice were examined. In anesthetized animals, the left gastrocnemius medialis (GM) muscle was connected to a force transducer and continuously stimulated (1-Hz twitches) during 60 min ischemia and 90 min reperfusion. Cell survival (%LDH) was defined by the amount of cytosolic lactate dehydrogenase (LDH) activity still present in the reperfused GM relative to the contralateral (non-ischemic) GM. Mitochondrial HK activity was 72.6 ± 7.5, 15.7 ± 1.7, and 8.8 ± 0.9 mU/mg protein in male mice, and 72.7 ± 3.7, 11.2 ± 1.4, and 5.9 ± 1.1 mU/mg in female mice for HK(tg), WT, and HK(+/-), respectively. Tetanic force recovery amounted to 33 ± 7% for male and 17 ± 4% for female mice and was similar for HK(tg), WT, and HK(+/-). However, cell survival was decreased (p = 0.014) in male HK(+/-) (82 ± 4%LDH) as compared with WT (98 ± 5%LDH) and HK(tg) (97 ± 4%LDH). No effects of HKII on cell survival was observed in female mice (92 ± 2% LDH). In conclusion, in this mild model of acute in vivo ischemia–reperfusion injury, a partial knockout of HKII was associated with increased cell death in male mice. The data suggest for the first time that HKII mediates skeletal muscle ischemia–reperfusion injury in the intact male animal

The Nutritional Contribution of Potato Varietal Diversity in Andean Food Systems: a Case Study

Potato is the backbone of agriculture and diets in high-altitude food systems of Peru, where farmers grow diverse varietal portfolios. Here we report on the role of diverse landraces and modern potato varieties in the Andean diet. The dry matter, energy, protein, iron and zinc content of 12 floury and 9 bitter landraces was determined. The contribution of varietal diversity to the dietary intake of energy, protein, iron and zinc was established during two contrasting periods of overall food availability. Results show that the potato and intraspecific diversity make an important contribution to nutrition. Most floury landraces contain higher concentrations of protein and iron compared to the reference value reported in the 2009 Peruvian food composition table for a boiled and peeled floury landrace. Traditional freeze-drying of bitter landraces doesn’t affect energy or iron concentrations, but reduces protein and zinc content considerably. Protein and iron contents in boiled chuño derived from the bitter landraces are lower compared to the mean value reported in the food composition table. The contribution of varietal diversity ideally needs to be taken into account when conducting nutrition studies in diversity hotspots like the Andes where potato is a main staple. The potato adds positively to the nutritional balance and the recommended requirements for energy, protein, iron and zinc of women and children. Floury landraces and modern varieties complement each other in light of seasonality, providing valuable nutrients during contrasting periods of the year. The potato thus contributes positively to food security. However, the overall diversity of the diet was found to be poor, resulting in micronutrient deficiencies. Options to strengthen food based approaches to attend undernutrition are discussed