Statistical associations between restriction fragment length polymorphisms and quantitative traits in beef cattle.
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Data on 41 traits from 677 animals produced in a five-breed diallel were matched with genotypes for five marker-loci provided by restriction fragment length polymorphisms to detect quantitative effects associated with the markers, following three different designs based on inbred lines, half-sib families, and on assumptions of the markers being quantitative trait loci (QTL). Three growth hormone-TaqI alleles, B, C, and D, in high frequencies in this sample of the Brahman breed, were associated with decreases in birth weight, as a maternal trait (P < .01), and decreases in shoulder width at birth (P < .05). Among F2 Angus-Brahman and Brahman-Hereford cows, homozygotes for the B, C, or D alleles gave birth to calves 4.0 kg lighter than cows homozygous for the A allele, an effect that amounts to the magnitude of the corresponding breed difference in the diallel, and represents one phenotypic SD. A putative cytoplasmic effect seems to interact (P = .02) with this effect on maternal birth weight. Also, at birth, F2 calves homozygous for the B, C, or D alleles were .8 cm narrower at the shoulders than those homozygous for the A allele, after adjusting for birth weight. Significant associations (P < .05) between the parathyroid hormone-MspI marker and measures of body size were detected, as well as an effect on weaning weight (P = .03) as a maternal trait, whose magnitude (17.5 kg) equals the Brahman vs Angus and Hereford breed difference, as quantified in the diallel, and represents .8 of a phenotypic SD. No significant associations were found for three other marker-loci (prolactin-MspI, osteonectin-EcoRI, and keratin VI-MspI). Restriction fragment length polymorphisms have the potential to provide new insights and useful applications to animal breeding, but, as in this work, small sample sizes, extreme susceptibility to Type I errors, and different types of possible confounding obfuscate the conclusions that can be drawn from studies of limited scope and less than ideal planning.