Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 544678
Title Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations
Author(s) Bosse, M.; Megens, H.J.W.C.; Madsen, O.; Crooijmans, R.P.M.A.; Ryder, O.A.; Austerlitz, F.; Groenen, M.; Cara, M.A.R. de
Department(s) Animal Breeding and Genomics
Publication type Dataset
Publication year 2015
Keyword(s) PRJEB9326 - ERP010412 - Sus scrofa - Sus cebifrons
Abstract Conservation and breeding programmes aim at maintaining most diversity, therefore avoiding deleterious effects of inbreeding while maintaining enough variation from which traits of interest can be selected. Theoretically, most diversity is maintained using optimal contributions based on many markers to calculate coancestries, but this can decrease fitness by maintaining linked deleterious variants. The heterogeneous patterns of coancestry displayed in pigs make them an excellent model to test these predictions. We propose methods to measure coancestry and fitness from resequence data, and use them in population management. We analysed resequencing data of Sus cebifrons, a highly endangered porcine species from the Philippines, and genotype data from the Pietrain domestic breed. By analysing the demographic history of Sus cebifrons we inferred two past bottlenecks that resulted in some inbreeding load. In Pietrain, we analysed signatures of selection possibly associated with commercial traits. We also simulated the management of each population to assess the performance of different optimal contribution methods to maintain diversity, fitness and selection signatures. Maximum genetic diversity was maintained using marker-by-marker coancestry, and least using genealogical coancestry. Using a measure of coancestry based on shared segments of the genome achieved best results in terms of diversity and fitness. However, this segment-based management eliminated signatures of selection. We demonstrate that maintaining both diversity and fitness depends on the genomic distribution of deleterious variants, which is shaped by demographic and selection histories. Our findings show the importance of genomic and next-generation sequencing information in the optimal design of breeding or conservation programmes.
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