Whole genome sequencing technologies are rapidly developing, now still remains to infer how this type of data can be useful for selection strategy, especially in livestock diversity conservation. In this study, relationship matrices were computed for 118 Holstein bulls, key ancestors of the current population, from three different types of data: pedigree records, 50K SNP chips and whole genome sequences, considering three different scenarios (with, without or only using rare alleles). Estimates from different data were highly correlated. Rare alleles had a significant impact on relationship estimates, mostly when whole genome sequence data were used. Hence sequence data, and information from rare alleles, are potentially of use for better relationship computation. Estimation made with this type of data may result in different individual optimal contributions and influence selection strategies and conservation decisions of livestock species.

Sonia E Eynard, Jack J Windig, Gregoire Leroy, Etienne Verrier, Sipke Joost Hiemstra, Rianne van Binsbergen, Mario PL Calus

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Genetic Improvement Programs: Selection for harsh environments and management of animal genetic resources, , 047, 2014
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