Alternative parameterizations of relatedness in whole genome association analysis of pre-weaning traits of Nelore-Angus calves

• Published in: Genetics and molecular biology 2014-09, Vol.37 (3), p.518-525
• Main Authors: Riley, David G, Gill, Clare A, Herring, Andy D, Riggs, Penny K, Sawyer, Jason E, Sanders, James O
• Format: Article
• Language: English
• Subjects: Animal Genetics; BIOCHEMISTRY & MOLECULAR BIOLOGY; birth weight; GENETICS & HEREDITY; gestation length; Nelore; weaning weight; whole genome association
• ISSN: 1415-4757; 1678-4685; 1415-4757; 1678-4685
• DOI: 10.1590/S1415-47572014000400007

Gestation length, birth weight, and weaning weight of F2 Nelore-Angus calves (n = 737) with designed extensive full-sibling and half-sibling relatedness were evaluated for association with 34,957 SNP markers. In analyses of birth weight, random relatedness was modeled three ways: 1) none, 2) random animal, pedigree-based relationship matrix, or 3) random animal, genomic relationship matrix. Detected birth weight-SNP associations were 1,200, 735, and 31 for those parameterizations respectively; each additional model refinement removed associations that apparently were a result of the built-in stratification by relatedness. Subsequent analyses of gestation length and weaning weight modeled genomic relatedness; there were 40 and 26 trait-marker associations detected for those traits, respectively. Birth weight associations were on BTA14 except for a single marker on BTA5. Gestation length associations included 37 SNP on BTA21, 2 on BTA27 and one on BTA3. Weaning weight associations were on BTA14 except for a single marker on BTA10. Twenty-one SNP markers on BTA14 were detected in both birth and weaning weight analyses.