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

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Abstract

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.

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Riley, D. G., Gill, C. A., Herring, A. D., Riggs, P. K., Sawyer, J. E., & Sanders, J. O. (2014). Alternative parameterizations of relatedness in whole genome association analysis of pre-weaning traits of Nelore-Angus calves. Genetics and Molecular Biology, 37(3), 518–525. https://doi.org/10.1590/S1415-47572014000400007

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