The use of whole genome sequence data to estimate genetic relationships including rare alleles information

Whole genome sequencing technologies are rapidly developing. In some ways, the speed of this development has outstripped our capacity to use this type of data in selection strategies, 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 improving relationship computation. Estimation of relationships made with this type of data may result in different individual optimal contributions and influence selection strategies and conservation decisions of livestock species