Whole-genome sequence data uncover loss of genetic diversity due to selection

Sonia E. Eynard*, Jack J. Windig, Sipke J. Hiemstra, Mario P.L. Calus

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

28 Citations (Scopus)


Background: Whole-genome sequence (WGS) data give access to more complete structural genetic information of individuals, including rare variants, not fully covered by single nucleotide polymorphism chips. We used WGS to investigate the amount of genetic diversity remaining after selection using optimal contribution (OC), considering different methods to estimate the relationships used in OC. OC was applied to minimise average relatedness of the selection candidates and thus miminise the loss of genetic diversity in a conservation strategy, e.g. for establishment of gene bank collections. Furthermore, OC was used to maximise average genetic merit of the selection candidates at a given level of relatedness, similar to a genetic improvement strategy. In this study, we used data from 277 bulls from the 1000 bull genomes project. We measured genetic diversity as the number of variants still segregating after selection using WGS data, and compared strategies that targeted conservation of rare (minor allele frequency

Original languageEnglish
Article number210
JournalGenetics, Selection, Evolution
Issue number1
Publication statusPublished - 2016


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