Review of \u3ci\u3eUrochloa\u3c/i\u3e Breeder’s Toolbox with the Theory of Change and Stage Gate System Approach

Livestock production in the global south is at crossroads as there is a demand to increase Animal Source Foods to address hunger and pressure to lighten the environmental footprint often associated with livestock production. To satisfy both needs, the use of technologies that improve animal performance, while reducing land use and net Greenhouse Gas emissions produced by animals is essential. One of such technologies are Urochloa forage grasses. Urochloa forage grasses are well known for their rusticity and their ability to grow in soils of low fertility and high aluminum content. These characteristics allow Urochloa to grow in areas temporally or spatially less suitable for crop production, but also have made ruminants production profitable in areas that would not be otherwise. However, productivity and sustainability of ruminant production in these areas is likely to fall within the next decade due to climate change unless action is taken. Despite these known benefits of Urochloa forage species, breeding programs have long delayed initiation due to apomixes and differences in ploidy. In the mid-1980s, the development of suitable sexual germplasm allowed crossings, and therefore favoured the emergence of breeding programs. In recent decades, several advances in biology, molecular biology, phenotyping, population genetics, genomics and transcriptomics have generated a plethora of information that ought to be integrated for its use in a single breeding toolbox. We use the Theory of Change and Stage-Gate systems approach to review these advances in research and the utility of the current and future available tools. Further, we address the remaining lack of information, thus bridging the knowledge gap and enabling us to maximize the genetic gain in the different Urochloa breeding programs. In this way, we identify breeding bottlenecks and help to pinpoint priorities for Urochloa research and development

Smart forage selection could significantly improve soil health in the tropics

The use of tropical grasslands to graze livestock is of high economic importance. Declining grassland soil health, leads to reduced sustainability of livestock systems. There are high levels of phenotypic diversity amongst tropical forage grasses. We hypothesise that this variation could lead to significant differences in soil health and that selection of forage cultivars to improve soil health could improve the sustainability of livestock production. We measured and compared key soil health metrics (soil organic carbon (SOC) concentration and sugar / alkane composition, aggregate stability, friability, litter decomposition rates, microbial community composition) under four tropical forage varieties (Brachiaria hybrid cv Mulato (BhMulato), B. humidicola cv Tully (CIAT679; Bh679), B. humidicola cv CIAT16888 (Bh16888), and Panicum maximum CIAT 6962 (Pmax)) and a bare soil control, there was a significant difference in soil aggregate stability, friability and SOC concentration between the forage varieties with soil under Bh679 and Bh16888 tending to have greater aggregate stability, friability and SOC concentrations compared to the soil under BhMulato and Pmax. We identified significant spatial variation in soils under BhMulato and Pmax due to their tussock forming growth habit; when compared to soil from adjacent to the tussocks, soil from the gaps between tussocks had significantly reduced aggregate stability under both species, significantly reduced friability under Pmax and significantly reduced SOC under BhMulato. We found limited impact of forage variety on soil microbial community composition, litter decomposition rates or soil alkane and sugar concentrations

Genotype-by-Environment Interaction in Interspecific \u3cem\u3eUrochloa\u3c/em\u3e Hybrids Using Factor Analytic Models

Environmental factors can influence plant phenotypes shaping the expression of pastures. The ability to test genotypes in multiple environments is critical in a breeding program because important traits are heavily influenced by the environment. Nutritional quality is critical in forage breeding because it affects the rate of live weight gain in livestock as well as the quality of end products such as milk and meat. However, there is not much information on the environmental effect on agronomic and nutritional quality traits in tropical forages. For this reason, the objective of the present study was to investigate the genotype-by-environment interaction in a breeding population of interspecific Urochloa hybrids evaluated for agronomic and nutritional quality traits across four locations in Colombia, using factor analytic mixed models. Phenotypic correlations among traits ranged from 0.26 (plant area vs dry weight) to 0.93 (fresh weight vs dry weight), indicating a strong interaction in some traits. Genetic correlations among environments showed different ranges depending on the variable evaluated. For example, plant height genetic correlations among environments ranged from 0.16 to 0.9, indicating high genotype-byenvironment interaction. The factor analytic analysis revealed that two factors explained more than 60% of the genetic variance in all traits evaluated and that 80% of the environments were clustered in the first factor. Factor analytic biplot indicates that Llanos location differed strongly from other locations evaluated. Based on the results obtained, the factor analytic analysis is a useful tool to stratify environments and identify Urochloa cultivars adapted to different ecological niches

Using Genetic Diversity in Deep Root Systems of Perennial Forage Grasses and Rice to Capture Carbon in Tropical Soils

Agricultural soils have the potential not only to be sinks of carbon dioxide (CO2) but also to mitigate the emissions of this gas to the atmosphere, thus, alleviating global warming. Perennial tropical grasses and rice upland and lowland varieties exhibit a large untapped genetic diversity in their root systems (e.g., deep rooting ability, exudation rates and chemical composition) that, if unlocked, could contribute to increased food production in crop-livestock systems while enhancing soil organic carbon (SOC) in tropical regions. Naturebased solutions that improve crop adaptation and SOC storage in tropical soils could help to remove CO2 from the atmosphere and thereby benefit the global climate system. With the launch of Future Seeds, one of the world’s largest repositories of tropical crop varieties, the Bezos Earth Fund (BEF) granted a major project within the Program of Future of Food. The focus of this BEF funded project is to: (i) develop novel high-throughput phenotyping methods to evaluate genetic diversity of root systems of tropical grasses and rice; (ii) unravel the potential of root systems in crop-livestock systems to replenish soil organic carbon (SOC) in human-intervened areas in tropical soils; (iii) identify and target hotspots/agroecological niches for SOC storage in tropical soils; and (iv) build capacity in conducting research on root systems and SOC storage towards carbon farming in tropical regions. Implementation of land-based SOC storage practices/projects (through carbon markets) based on deep rooting ability of perennial tropical forage grasses and rice cultivars in crop-pasture rotational systems could significantly reduce net emissions from tropical soils

Peabody Picture Vocabulary Test-III: Normative data for Spanish-speaking pediatric population

OBJECTIVE: To generate normative data for the Peabody Picture Vocabulary Test-III (PPVT-III) in Spanish-speaking pediatric populations. METHOD: The sample consisted of 4,373 healthy children from nine countries in Latin America (Chile, Cuba, Ecuador, Honduras, Guatemala, Mexico, Paraguay, Peru, and Puerto Rico) and Spain. Each participant was administered the PPVT-III as part of a larger neuropsychological battery. PPVT-III scores were normed using multiple linear regressions and standard deviations of residual values. Age, age2, sex, and mean level of parental education (MLPE) were included as predictors in the analyses. RESULTS: The final multiple linear regression models showed main effects for age in all countries, such that scores increased linearly as a function of age. In addition, age2 had a significant effect in all countries, except Guatemala and Paraguay. Models showed that children whose parent(s) had a MLPE >12 years obtained higher scores compared to children whose parent(s) had a MLPE ≤12 years in all countries, except for Cuba, Peru, and Puerto Rico. Sex affected scores for Chile, Ecuador, Guatemala, Mexico, and Spain. CONCLUSIONS: This is the largest Spanish-speaking pediatric normative study in the world, and it will allow neuropsychologists from these countries to have a more accurate interpretation of the PPVT-III when used in pediatric populations

Consensus Pathways Implicated in Prognosis of Colorectal Cancer Identified Through Systematic Enrichment Analysis of Gene Expression Profiling Studies

Background: A large number of gene expression profiling (GEP) studies on prognosis of colorectal cancer (CRC) has been performed, but no reliable gene signature for prediction of CRC prognosis has been found. Bioinformatic enrichment tools are a powerful approach to identify biological processes in high-throughput data analysis. Principal Findings: We have for the first time collected the results from the 23 so far published independent GEP studies on CRC prognosis. In these 23 studies, 1475 unique, mapped genes were identified, from which 124 (8.4%) were reported in at least two studies, with 54 of them showing consisting direction in expression change between the single studies. Using these data, we attempted to overcome the lack of reproducibility observed in the genes reported in individual GEP studies by carrying out a pathway-based enrichment analysis. We used up to ten tools for overrepresentation analysis of Gene Ontology (GO) categories or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in each of the three gene lists (1475, 124 and 54 genes). This strategy, based on testing multiple tools, allowed us to identify the oxidative phosphorylation chain and the extracellular matrix receptor interaction categories, as well as a general category related to cell proliferation and apoptosis, as the only significantly and consistently overrepresented pathways in the three gene lists, which were reported by several enrichment tools. Conclusions: Our pathway-based enrichment analysis of 23 independent gene expression profiling studies on prognosis of CRC identified significantly and consistently overrepresented prognostic categories for CRC. These overrepresented categories have been functionally clearly related with cancer progression, and deserve further investigation

Specific genomic aberrations in primary colorectal cancer are associated with liver metastases

Background: Accurate staging of colorectal cancer (CRC) with clinicopathological parameters is important for predicting prognosis and guiding treatment but provides no information about organ site of metastases. Patterns of genomic aberrations in primary colorectal tumors may reveal a chromosomal signature for organ specific metastases. Methods: Array Comparative Genomic Hybridization (aCGH) was employed to asses DNA copy number changes in primary colorectal tumors of three distinctive patient groups. This included formalin-fixed, paraffin-embedded tissue of patients who developed liver metastases (LM; n = 36), metastases (PM; n = 37) and a group that remained metastases-free (M0; n = 25). A novel statistical method for identifying recurrent copy number changes, KC-SMART, was used to find specific locations of genomic aberrations specific for various groups. We created a classifier for organ specific metastases based on the aCGH data using Prediction Analysis for Microarrays (PAM). Results: Specifically in the tumors of primary CRC patients who subsequently developed liver metastasis, KC-SMART analysis identified genomic aberrations on chromosome 20q. LM-PAM, a shrunken centroids classifier for liver metastases occurrence, was able to distinguish the LM group from the other groups (M0&PM) with 80% accuracy (78% sensitivity and 86% specificity). The classification is predominantly based on chromosome 20q aberrations. Conclusion: Liver specific CRC metastases may be predicted with a high accuracy based on specific genomic aberrations in the primary CRC tumor. The ability to predict the site of metastases is important for improvement of personalized patient management.MediamaticsElectrical Engineering, Mathematics and Computer Scienc

Shortened Version of the Token Test: Normative data for Spanish-speaking pediatric population

OBJECTIVE: To generate normative data for the Shortened Version of the Token Test in Spanish-speaking pediatric populations. METHOD: The sample consisted of 4,373 healthy children from nine countries in Latin America (Chile, Cuba, Ecuador, Guatemala, Honduras, Mexico, Paraguay, Peru, and Puerto Rico) and Spain. Each participant was administered the Shortened Version of the Token Test as part of a larger neuropsychological battery. Shortened Version of the Token Test total scores were normed using multiple linear regressions and standard deviations of residual values. Age, age2, sex, and mean level of parental education (MLPE) were included as predictors in the analyses. RESULTS: The final multiple linear regression models showed main effects for age in all countries, such that score increased linearly as a function of age. In addition, age2 had a significant effect in all countries, except Guatemala and Puerto Rico. Models showed that children whose parent(s) had a MLPE >12 years obtained higher score compared to children whose parents had a MLPE ≤12 years in Ecuador, Guatemala, Honduras, Mexico, Paraguay, Peru, Puerto Rico, and Spain. The child’s sex did not have an effect in the Shortened Version of the Token Test total score for any of the countries. CONCLUSIONS: This is the largest Spanish-speaking pediatric normative study in the world, and it will allow neuropsychologists from these countries to have a more accurate interpretation of the Shortened Version of the Token Test when used in pediatric populations