The effect of rare alleles on estimated genomic relationships from whole genome sequence data

摘要: Relationships between individuals and inbreeding coefficients are commonly used for breeding decisions, but may be affected by the type of data their estimation. The proportion variants with low Minor Allele Frequency (MAF) is larger in whole genome sequence (WGS) compared to Single Nucleotide Polymorphism (SNP) chips. Therefore, WGS provide true relationships influence decisions prioritisation conservation genetic diversity livestock. This study identifies differences estimated using pedigree, SNP or 118 Holstein bulls from 1000 Bull genomes project. To determine impact rare alleles on estimates we three scenarios MAF restrictions: a higher than 5%, 1% 5%. We observed significant and, although less significantly, data, restriction scenarios. Computed correlations pedigree genomic relationships, within groups similar ranged negative moderate both coefficients, were high (0.49 0.99). Estimated information exhibited variation pedigree. Inbreeding analysis showed that more complete records lead correlation data. Finally, additive (A) (G) relationship matrices lower, variances when accounting allele frequencies without frequencies. Using information, including excluding below 5% coefficient estimates. basis selection decisions. it can expected instead affect decision. Inclusion will give access they carry, which interest diversity.