TY - JOUR
T1 - Application of genomic estimation methods of inbreeding and population structure in an Arabian Horse Herd
AU - Al Abri, Mohammed A.
AU - Von Borstel, Uta König
AU - Strecker, Veronique
AU - Brooks, Samantha A.
N1 - Publisher Copyright:
© The American Genetic Association. 2017.
PY - 2017/6
Y1 - 2017/6
N2 - Horse breeders rely heavily on pedigrees for identification of ancestry in breeding stock. Inaccurate pedigrees may erroneously assign individuals to false lineages or breed memberships resulting in wrong estimates of inbreeding and coancestry. Moreover, discrepancies in pedigree records can lead breeders seeking to limit inbreeding into making misguided breeding decisions. Genome-wide SNPs provide a quantitative tool to aid in the resolution of lineage assignments and the calculation of genomic measures of relatedness. The aim of this project was to pilot a comparison between pedigree and genomic relatedness and inbreeding measures in a herd of 36 pedigreed Egyptian Arabian horses genotyped using the Equine SNP70 platform (Geneseek, Inc.). Moreover, we sought to estimate the minimum number of markers sufficient for genomic inbreeding calculations. Pedigree inbreeding values were moderately correlated with genomic inbreeding values (r = 0.406), whereas genomic relationships and pedigree relationships have a high correlation (r = 0.77). Although first degree relationships were successfully reconstructed, more distant relationships were difficult to resolve. Multi-dimensional scaling and clustering analysis agreed with within-herd pedigree information. In comparing the herd to a reference sample of United States, Polish, and Egyptian Arabian horses, the herd's historically recorded Egyptian lineage was successfully recovered. We conclude that genomic estimates of inbreeding and relationships are superior to their pedigree counterparts. They can be thus utilized in conservation of valuable lines of livestock, and in breeds at risk for loss of genomic diversity. We also postulate a minimum of 2000 markers in linkage equilibrium to be used for inbreeding estimation.
AB - Horse breeders rely heavily on pedigrees for identification of ancestry in breeding stock. Inaccurate pedigrees may erroneously assign individuals to false lineages or breed memberships resulting in wrong estimates of inbreeding and coancestry. Moreover, discrepancies in pedigree records can lead breeders seeking to limit inbreeding into making misguided breeding decisions. Genome-wide SNPs provide a quantitative tool to aid in the resolution of lineage assignments and the calculation of genomic measures of relatedness. The aim of this project was to pilot a comparison between pedigree and genomic relatedness and inbreeding measures in a herd of 36 pedigreed Egyptian Arabian horses genotyped using the Equine SNP70 platform (Geneseek, Inc.). Moreover, we sought to estimate the minimum number of markers sufficient for genomic inbreeding calculations. Pedigree inbreeding values were moderately correlated with genomic inbreeding values (r = 0.406), whereas genomic relationships and pedigree relationships have a high correlation (r = 0.77). Although first degree relationships were successfully reconstructed, more distant relationships were difficult to resolve. Multi-dimensional scaling and clustering analysis agreed with within-herd pedigree information. In comparing the herd to a reference sample of United States, Polish, and Egyptian Arabian horses, the herd's historically recorded Egyptian lineage was successfully recovered. We conclude that genomic estimates of inbreeding and relationships are superior to their pedigree counterparts. They can be thus utilized in conservation of valuable lines of livestock, and in breeds at risk for loss of genomic diversity. We also postulate a minimum of 2000 markers in linkage equilibrium to be used for inbreeding estimation.
KW - ancestry
KW - genetic structure
KW - genomic inbreeding
KW - genomic relationships
KW - pedigree completeness index
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U2 - 10.1093/jhered/esx025
DO - 10.1093/jhered/esx025
M3 - Article
C2 - 28444202
AN - SCOPUS:85020189633
SN - 0022-1503
VL - 108
SP - 361
EP - 368
JO - Journal of Heredity
JF - Journal of Heredity
IS - 4
ER -