Prediction of haplotypes for ungenotyped animals and its effect on marker-assisted breeding value estimation

Background: In livestock populations, missing genotypes on a large proportion of animals are a major problem to implement the estimation of marker-assisted breeding values using haplotypes. The objective of this article is to develop a method to predict haplotypes of animals that are not genotyped using mixed model equations and to investigate the effect of using these predicted haplotypes on the accuracy of marker-assisted breeding value estimation. Methods: For genotyped animals, haplotypes were determined and for each animal the number of haplotype copies (nhc) was counted, i.e. 0, 1 or 2 copies. In a mixed model framework, nhc for each haplotype were predicted for ungenotyped animals as well as for genotyped animals using the additive genetic relationship matrix. The heritability of nhc was assumed to be 0.99, allowing for minor genotyping and haplotyping errors. The predicted nhc were subsequently used in marker-assisted breeding value estimation by applying random regression on these covariables. To evaluate the method, a population was simulated with one additive QTL and an additive polygenic genetic effect. The QTL was located in the middle of a haplotype based on SNP-markers. Results: The accuracy of predicted haplotype copies for ungenotyped animals ranged between 0.59 and 0.64 depending on haplotype length. Because powerful BLUP-software was used, the method was computationally very efficient. The accuracy of total EBV increased for genotyped animals when marker-assisted breeding value estimation was compared with conventional breeding value estimation, but for ungenotyped animals the increase was marginal unless the heritability was smaller than 0.1. Haplotypes based on four markers yielded the highest accuracies and when only the nearest left marker was used, it yielded the lowest accuracy. The accuracy increased with increasing marker density. Accuracy of the total EBV approached that of gene-assisted BLUP when 4-marker haplotypes were used with a distance of 0.1 cM between the markers. Conclusions: The proposed method is computationally very efficient and suitable for marker-assisted breeding value estimation in large livestock populations including effects of a number of known QTL. Marker-assisted breeding value estimation using predicted haplotypes increases accuracy especially for traits with low heritabilit

Including copy number variation in association studies to predict genotypic values

The objective of this study was to investigate, both empirically and deterministically, the ability to explain genetic variation resulting from a copy number polymorphism (CNP) by including the CNP, either by its genotype or by a continuous derivation thereof, alone or together with a nearby single nucleotide polymorphism (SNP) in the model. This continuous measure of a CNP genotype could be a raw hybridization measurement, or a predicted CNP genotype. Results from simulations showed that the linkage disequilibrium (LD) between an SNP and CNP was lower than LD between two SNPs, due to the higher mutation rate at the CNP loci. The model R2 values from analysing the simulated data were very similar to the R2 values predicted with the deterministic formulae. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including a continuous measure of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the continuous measure explained only 15% of the variation at the CNP locus

The succession effect within management decisions of family farms

The preparation of the farm transfer or farm exit is a process that starts in the consolidation stage of the farm life cycle. In this stage, the decision to transfer the farm or not is taken and the farm management is adapted to this decision. The objective of this paper is to model the succession effect on farm management. The results show that the succession effect plays a role from the age of 45. An early designation of the successor gives an incentive to invest and to improve the management.farm transfer, succussor, farm life cycle, Farm Management,

Persistence of family farming, learning from its dynamics

Traditionally, the family farm has always been seen as a cornerstone of the agricultural production system. Given social, economic and political evidence (Calus, 2009), this organisational form might still continue to shape agricultural development. However, important changes in social and economic environment (e.g. industrialisation of agriculture, increased risk level and public vision on agriculture) become threats to the traditional model. A SWOT analysis of the family farms indicates the various intrinsic characteristics that make family farms resilient to changing conditions. Even in a changing economic and social landscape these aspects provide them with building blocks for creating new organisational forms or institutional arrangements. This paper shows these building blocks, and is only, prudentially, indicative for possible new institutional arrangements. Creativity may produce numerous outcomes from building blocks. Land tenure is only one example from past and present to show how institutions can deal with a potential threat, such as the large demand for land as production factor. Similar creativity is needed to the exploding capital demand in agriculture. One of the major challenges will be to provide family farms with low-costing capital. Food security and local community viability is the social price for this low cost supply.family farm, corporate farm, peasant, SWOT, Consumer/Household Economics,

The Iasi-Ungheni pipeline: a means of achieving energy independence from Russia? Moldova's attempts at gas supply diversification. OSW Commentary No. 118, 2013-10-08

Since taking power in 2009, the Alliance for European Integration (AIE) has been trying to end Moldova’s dependence on Russian gas. Currently, natural gas accounts for about 50% of the country’s energy balance (excluding Transnistria), and Gazprom has a monopoly on the supply of gas to the republic. The key element of Chișinău’s diversification project is the construction of the Iasi-Ungheni pipeline, which is designed to link the Moldovan and Romanian gas transmission networks, and consequently make it possible for Moldova to purchase gas from countries other than Russia. Despite significant delays, construction work on the interconnector began in August 2013. The Moldovan government sees ensuring energy independence from Russia as its top priority. The significance and urgency of the project reflect Chișinău’s frustration at Moscow’s continued attempts to use its monopoly of Moldova’s energy sector to exert political pressure on the republic. Nonetheless, despite numerous declarations by Moldovan and Romanian politicians, the Iasi- -Ungheni pipeline will not end Moldova’s dependence on Russian gas before the end of the current decade. This timeframe is unrealistic for two reasons: first, because an additional gas pipeline from Ungheni to Chisinau and a compression station must be constructed, which will take at least five years and will require significant investment; and second, because of the unrelenting opposition to the project coming from Gazprom, which currently controls Moldova’s pipelines and will likely try to torpedo any energy diversification attempts. Independence from Russian gas will only be possible after the the Gazprom-controlled Moldova-GAZ, the operator of the Moldovan transmission network and the country’s importer of natural gas, is divided. The division of the company has in fact been envisaged in the EU’s Third Energy Package, which is meant to be implemented by Moldova in 2020

Power politics on the outskirts of the EU: why Transnistria matters

In September this year, Transnistria, the separatist region located in the Eastern part of Moldova, is set to celebrate the 24th anniversary of its de-facto independence. And yet there is little scope for celebrations – as only the contested states of Abkhazia, Nagorno-Karabakh and South Ossetia recognise its independence. To understand why the Transnistrian dispute has not yet been solved, and why two decades of negotiations have never brought us any closer to the solution, we have to look at the interest of the three main actors involved: Russia, Moldova and the West. Kamil Całus explains