title: The effect of rare alleles on estimated genomic relationships from whole genome sequence data.
abstract: BACKGROUND
  Relationships between individuals and inbreeding coefficients are commonly used for breeding decisions, but may be affected by the type of data used for their estimation. The proportion of variants with low Minor Allele Frequency (MAF) is larger in whole genome sequence (WGS) data compared to Single Nucleotide Polymorphism (SNP) chips. Therefore, WGS data provide true relationships between individuals and may influence breeding decisions and prioritisation for conservation of genetic diversity in livestock. This study identifies differences between relationships and inbreeding coefficients estimated using pedigree, SNP or WGS data for 118 Holstein bulls from the 1000 Bull genomes project. To determine the impact of rare alleles on the estimates we compared three scenarios of MAF restrictions: variants with a MAF higher than 5%, variants with a MAF higher than 1% and variants with a MAF between 1% and 5%.
  
  
  RESULTS
  We observed significant differences between estimated relationships and, although less significantly, inbreeding coefficients from pedigree, SNP or WGS data, and between MAF restriction scenarios. Computed correlations between pedigree and genomic relationships, within groups with similar relationships, ranged from negative to moderate for both estimated relationships and inbreeding coefficients, but were high between estimates from SNP and WGS (0.49 to 0.99). Estimated relationships from genomic information exhibited higher variation than from pedigree. Inbreeding coefficients analysis showed that more complete pedigree records lead to higher correlation between inbreeding coefficients from pedigree and genomic data. Finally, estimates and correlations between additive genetic (A) and genomic (G) relationship matrices were lower, and variances of the relationships were larger when accounting for allele frequencies than without accounting for allele frequencies.
  
  
  CONCLUSIONS
  Using pedigree data or genomic information, and including or excluding variants with a MAF below 5% showed significant differences in relationship and inbreeding coefficient estimates. Estimated relationships and inbreeding coefficients are the basis for selection decisions. Therefore, it can be expected that using WGS instead of SNP can affect selection decision. Inclusion of rare variants will give access to the variation they carry, which is of interest for conservation of genetic diversity.
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 338, Wageningen, 6700 AH, The Netherlands. sonia.eynard@wur.nl.|AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, 16 rue Claude Bernard, Paris 05, 75231, France. sonia.eynard@wur.nl.|INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, 78350, France. sonia.eynard@wur.nl.|Centre for Genetic Resources the Netherlands, Wageningen UR, P.O. Box 16, Wageningen, 6700 AA, The Netherlands. sonia.eynard@wur.nl.
authors.forename: Sonia E
authors.initials: SE
authors.lastname: Eynard
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 338, Wageningen, 6700 AH, The Netherlands. jack.windig@wur.nl.|Centre for Genetic Resources the Netherlands, Wageningen UR, P.O. Box 16, Wageningen, 6700 AA, The Netherlands. jack.windig@wur.nl.
authors.forename: Jack J
authors.initials: JJ
authors.lastname: Windig
authors.affiliation: AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, 16 rue Claude Bernard, Paris 05, 75231, France. gregoire.leroy@agroparistech.fr.|INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, 78350, France. gregoire.leroy@agroparistech.fr.
authors.forename: Grégoire
authors.initials: G
authors.lastname: Leroy
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 338, Wageningen, 6700 AH, The Netherlands. rianne.vanbinsbergen@wur.nl.|Biometris, Wageningen UR, P.O. Box 16, Wageningen, 6700 AA, The Netherlands. rianne.vanbinsbergen@wur.nl.
authors.forename: Rianne
authors.initials: R
authors.lastname: van Binsbergen
authors.affiliation: Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, P.O. Box 338, Wageningen, 6700 AH, The Netherlands. mario.calus@wur.nl.
authors.forename: Mario P L
authors.initials: MP
authors.lastname: Calus
mesh_terms: D000465:Algorithms; D000483:Alleles; D000818:Animals; D002417:Cattle; D005787:Gene Frequency; D016678:Genome; D055106:Genome-Wide Association Study; D023281:Genomics; D005838:Genotype; D007178:Inbreeding; D008957:Models, Genetic; D015233:Models, Statistical; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide