Deliverable 2 (SustainAQ)

The European Project SustainAQ (Framework 6) aims to identify the limiting factors for the sustainable production of aquatic origin food in Eastern Europe. It focuses on the possible use of Recirculation Aquaculture Systems (RAS) as sustainable method for the production of aquatic animals as mentioned in the communication of the European Commission on Aquaculture in 2009. RASs already exist mainly in western countries and proved economically feasible. RASs allow controlling the production process including effluents, biosecurity and escapes. Eastern European countries are facing challenges related to their excessive water use waste emission, and others. Therefore, these countries are potential beneficiaries of improved sustainability through RAS use. This project intends to assess the benefits of introducing and applying RAS for Eastern European aquaculture. This project involves three Western European countries (Norway, the Netherlands and France) and six East European countries (Croatia, Turkey, Romania, Hungary, Czech Republic and Poland). Ten research institutions collaborate in different tasks (coordination, data collection, data analysis, etc.), and nine small-medium enterprises (SME) participate in data mining (Table 1). The present data is therefore based on the situation in those countries during 2006 till 2008 before the report got finally compiled in 2008/2009

Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis – contribution to improved aboveground apple plant growth?

Replant disease (RD) severely affects apple production in propagation tree nurseries and in fruit orchards worldwide. This study aimed to investigate the effects of soil disinfection treatments on plant growth and health in a biotest in two different RD soil types under greenhouse conditions and to link the plant growth status with the bacterial community composition at the time of plant sampling. In the biotest performed we observed that the aboveground growth of apple rootstock M26 plants after 8 weeks was improved in the two RD soils either treated at 50°C or with gamma irradiation compared to the untreated RD soils. Total community DNA was extracted from soil loosely adhering to the roots and quantitative real-time PCR revealed no pronounced differences in 16S rRNA gene copy numbers. 16S rRNA gene-based bacterial community analysis by denaturing gradient gel electrophoresis (DGGE) and 454-pyrosequencing revealed significant differences in the bacterial community composition even after 8 weeks of plant growth. In both soils, the treatments affected different phyla but only the relative abundance of Acidobacteria was reduced by both treatments. The genera Streptomyces, Bacillus, Paenibacillus, and Sphingomonas had a higher relative abundance in both heat treated soils, whereas the relative abundance of Mucilaginibacter, Devosia, and Rhodanobacter was increased in the gamma-irradiated soils and only the genus Phenylobacterium was increased in both treatments. The increased abundance of genera with potentially beneficial bacteria, i.e., potential degraders of phenolic compounds might have contributed to the improved plant growth in both treatments.BÖLNDF

Conservation of genetic diversity : assessing genetic variation using marker estimated kinships

This dissertation focuses on assessing genetic diversity in a quantitative way through the use of Malecots coefficients of kinship. Kinships between and within populations and individuals can be estimated using microsatellite marker genes that are assumed to be selectively neutral.Genetic diversity is estimated from such Marker Estimated Kinships (MEK) by (1 - average (MEK)), where genetic diversity of a set of breeds is defined as the maximum genetic variation in a population that can be bred from this set of breeds. The concept of core sets is applied to livestock genetic diversity and a new measure of genetic diversity present in a set of breeds, based on the mean kinship within a core set, is developed. Log-linear (mixed) models can be used to simultaneously estimate kinships and the probability for alleles alike in state (AIS). Error variance of the kinship estimates may lead to populations that have incorrectly received a null-contribution. An analysis of a data set concerning African cattle populations, using the developed methods is described. Effects of conservation by breed type or regional versus continental conservation are examined, in terms of efficiency of conservation and changes of priorities of breeds.</p

Computational strategies for the preconditioned conjugate gradient method applied to ssSNPBLUP, with an application to a multivariate maternal model

Background: The single-step single nucleotide polymorphism best linear unbiased prediction (ssSNPBLUP) is one of the single-step evaluations that enable a simultaneous analysis of phenotypic and pedigree information of genotyped and non-genotyped animals with a large number of genotypes. The aim of this study was to develop and illustrate several computational strategies to efficiently solve different ssSNPBLUP systems with a large number of genotypes on current computers. Results: The different developed strategies were based on simplified computations of some terms of the preconditioner, and on splitting the coefficient matrix of the different ssSNPBLUP systems into multiple parts to perform its multiplication by a vector more efficiently. Some matrices were computed explicitly and stored in memory (e.g. the inverse of the pedigree relationship matrix), or were stored using a compressed form (e.g. the Plink 1 binary form for the genotype matrix), to permit the use of efficient parallel procedures while limiting the required amount of memory. The developed strategies were tested on a bivariate genetic evaluation for livability of calves for the Netherlands and the Flemish region in Belgium. There were 29,885,286 animals in the pedigree, 25,184,654 calf records, and 131,189 genotyped animals. The ssSNPBLUP system required around 18 GB Random Access Memory and 12 h to be solved with the most performing implementation. Conclusions: Based on our proposed approaches and results, we showed that ssSNPBLUP provides a feasible approach in terms of memory and time requirements to estimate genomic breeding values using current computers.</p