2010-Bierman_et_al - Fine-mapping quantitative trait loci...

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C. D. Bierman, E. Kim, K. Weigel, P. J. Berger and B. W. Kirkpatrick North American Holsteins chromosome 14 in Bos taurus Fine-mapping quantitative trait loci for twinning rate on doi: 10.2527/jas.2010-2808 originally published online March 26, 2010 2010, 88:2556-2564. J ANIM SCI http://jas.fass.org/content/88/8/2556 the World Wide Web at: The online version of this article, along with updated information and services, is located on www.asas.org by guest on August 22, 2011 jas.fass.org Downloaded from
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ABSTRACT: A previous genome-wide search with a moderate-density 10,000-SNP set identified many mark- er associations with twinning rate on BTA14 through either single-marker analysis or combined linkage-link- age disequilibrium (LLD; haplotype) analysis. The ob- jective of the current study was to fine-map putative QTL using a more densely populated marker map and both a larger and an independent set of phenotypic data. Holstein bulls (n = 921) from 100 paternal half- sib families were genotyped for 129 SNP markers that included both original and additionally selected mark- ers for increasing marker density in the targeted 34 megabase region. Twinning rate predicted transmitting abilities were calculated using calving records from 1994 to 1998 (data I) and 1999 to 2006 (data II), and the un- derlying liability scores from threshold model analysis were used as the trait in marker association analyses. The previous analysis used 201 bulls with daughter re- cords in data I. In the current analysis, this was in- creased to 434, providing a revised estimate of effect and significance. Bulls with daughter records in data II totaled 851, and analysis of these data provided an opportunity for an independent analysis separate from data I. Single-marker association and LLD analyses were performed. Fifteen significant single-marker asso- ciations were found (minimally exceeding P < 8.74 × 10 −3 ) to concur between data sets. Three and 12 regions in data I and data II, respectively, showed positive re- sults for the presence of QTL from LLD analysis ( P < 0.001) within the respective data sets. After combining results from single-marker association, LLD analysis, and model-building strategies, 3 QTL were identified on BTA14. Based on single-marker results from data II, BTA14 harbors QTL responsible for approximately 24% of the variation in twinning rate predicted trans- mitting ability. Key words: Holstein, linkage disequilibrium, single nucleotide polymorphism, twin, twinning rate ©2010 American Society of Animal Science. All rights reserved. J. Anim. Sci. 2010. 88:2556–2564 doi:10.2527/jas.2010-2808 INTRODUCTION Twinning in cattle is a complex trait likely controlled by many genes. In dairy cattle, twinning is associated with adverse effects on current milk production and future reproduction. Negative effects from twinning in- clude increased rates of dystocia, increased incidences of retained placenta and freemartins, longer return-to- estrus intervals, increased involuntary culling, and re- duced milk production (Nielen et al., 1989; Beerepoot et al., 1992; Fricke and Wiltbank, 1999). This trans- lates into an economic loss to the dairy industry of more than $110/cow (Eddy et al., 1991). Twinning rate
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