Intra-chromosomal estimates of inbreeding and coancestry in the Spanish Holstein cattle population

• Coancestry can be estimated for particular regions of the genome.
• Holstein genomic data have been used to calculate intra-chromosomal coancestry.
• Differential intra-chromosomal patterns of coancestry have been detected.
• These patterns provide a more detailed picture of the genetic diversity.

In recent years, inbreeding and coancestry are being estimated from genome-wide molecular information using a large number of SNPs. Molecular inbreeding and coancestry can be calculated for the whole genome or for particular regions of the genome. In this study, genome-based inbreeding and coancestry were estimated per chromosome and at intra-chromosomal level in a group of Holstein animals genotyped with the Illumina BovineSNP50 BeadChip. After applying filtering criteria, the genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Genome-based inbreeding and coancestry at intra-chromosomal level were calculated using sliding windows of approximately 5 Mb. The results showed differential patterns of inbreeding and coancestry on specific chromosome regions. These patterns provide a more detailed picture of genetic diversity that could be used, for example, for the detection of regions with low levels of genetic diversity that require a specific genetic management in conservation programmes.