Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes

AlphaImpute is a flexible and accurate genotype imputation tool that was originally designed for the imputation of genotypes on autosomal chromosomes. In some species, sex chromosomes comprise a large portion of the genome. For example, chromosome Z represents approximately 8% of the chicken genome and therefore is likely to be important in determining genetic variation in a population. When breeding programs make selection decisions based on genomic information, chromosomes that are not represented on the genotyping platform will not be subject to selection. Therefore imputation algorithms should be able to impute genotypes for all chromosomes. The objective of this research was to extend AlphaImpute so that it could impute genotypes on sex chromosomes. The accuracy of imputation was assessed using different genotyping strategies in a real commercial chicken population. The correlation between true and imputed genotypes was high in all the scenarios and was 0.96 for the most favourable scenario. Overall, the accuracy of imputation of the sex chromosome was slightly lower than that of autosomes for all scenarios considered

Agri-food supply chains and sustainability-related issues: evidence from across the Scottish agri-food economy

This paper examines the influence of agri-food supply chains on the sustainability-related activities and decisions of Scottish farmers, as well as the treatment of sustainability issues by food processors and retailers themselves. It is based on 8 whole chain case studies covering some of Scotland’s major agricultural products. The cases identify differing levels of understanding and activities related to sustainability, but widespread acknowledgement that sustainability involves the development of chains within which all parties can achieve acceptable profits. Indeed, collaborative supply chains, which seek improved economic performance, frequently assist environmental and social sustainability. The main drivers of sustainability are found to be the cost of key inputs, product markets where customers increasingly seek sustainability in products, the ethos and values of the businesses and people involved, and legislation and strategies of industry bodies. At the farm level, many farmers are seeking more sustainable production systems, particularly in economic and environmental terms, but there is a need for greater guidance and assistance. The paper presents a review of several key food supply sustainability issues, the methods and concepts used in compiling and analysing the cases, as well as the principal findings and implications for agri-food supply chain and policy development.Sustainability, Food, Supply chain, Agribusiness, Food Security and Poverty,

Promoting Mountain Quality Food Products (MQFPs) – Analysing possibilities beyond labelling policy

The new orientation of the Common Agriculture Policy encourages producers to respond to market forces. In addition, the public expect producers to contribute to a living countryside. Based on this context, the purpose of the paper is to discuss what other marketing alternatives exist for the promotion of mountain quality food products beyond labelling. This is done through the analyses of shelves and postal surveys to retailers, carried out as part of the EU project EuroMARC, which included information for Austria, France, Norway, Romania, Slovenia and UK (Scotland). The analysis concentrates on two product promotion aspects: display and store-promotion, and communication of product attributes. The results indicate that even without labelling policy there is scope to improve the promotion of mountain quality food products.Mountain food products, food promotion, local food, Food Consumption/Nutrition/Food Safety,

COMPILATION OF A UNIFIED AND HOMOGENEOUS AEROMAGNETIC MAP OF THE GREEK MAINLAND

We present a unified and homogeneous digital aeromagnetic map of the Hellenic mainland, based on the 1:50,000 map series of IGME. These maps cover the areas A1, A2, B, C1, C2, C3, D1 compiled by Hunting Geology and Geophysics Ltd. and measured at nominal ground clearances (flight altitudes) 150m AGL, 150m AGL, 300m AGL, and 2300m AMSL respectively (part of C2 with 3000m AMSL). We also include the entire area of Northern Greece, measured by ABEM AB with nominal ground clearance 275±75m AGL. The original map sheets were digitally imaged, georeferenced, digitized along contour lines and interpolated onto regular 250´250m grids. The unified aeromagnetic map was constructed by collating the mosaic of the resulting gridded data. Using upward/ downward continuation techniques various homogeneous versions of the map, were compiled by referencing of the observed mosaic total magnetic field to a unique constant ground clearance or to a unique constant elevation above mean sea level. This is the first time there is a complete and unified image of the magnetic signature of the isopic zones and rock formations comprising the Hellenic mainland, with particular reference to the ophiolite suites, which provides additional insight into the Alpine and post-alpine tectonics of the area