Whole genome fine mapping of quantitative trait loci for ultrasound and carcass merit traits in beef cattle
Nalaila, S.M., Stothard, P., Moore, S.S., Wang, Z., Li, C. (2011). Whole genome fine mapping of quantitative trait loci for ultrasound and carcass merit traits in beef cattle, 91(1), 61-73. http://dx.doi.org/10.4141/CJAS10007
Quantitative trait loci (QTL) mapped to large chromosomal regions have limited utility as DNA markers for marker-assisted selection (MAS) and are less informative as a reference for the identification of the underlying causative quantitative trait nucleotides (QTN). The objective of this study was to conduct a whole genome fine mapping of QTL for ultrasound and carcass merit traits in beef cattle using a greater density of single nucleotide polymorphism (SNP) markers, and to identify SNP markers within the QTL regions that are associated with the traits. A total of 418 steers from 28 sires were used in this study with nine ultrasound and seven carcass merit traits that were collected as part of a feedlot trial conducted from 2003 to 2005 at the University of Alberta Kinsella ranch. Sires and their progeny were genotyped for a total of 4592 SNP markers distributed across all 29 bovine autosomes (BTA). Across-family analyses detected 12 QTL for five ultrasound traits on nine chromosomes and 18 QTL for six carcass merit traits on 10 chromosomes (P <0.05). Within-family analyses identified 78 significant QTL for nine ultrasound and seven carcass merit traits (P <0.01). The use of a denser panel of SNP markers allowed fine mapping of QTL to smaller chromosomal regions ranging from 0.6 to 11 cM compared with relatively larger QTL regions of 4 to 24 cM reported in previous studies. Furthermore, single SNP marker association analyses identified 22 SNPs that were significantly associated with three ultrasound and four carcass merit traits under 12 QTL regions (PB0.05). These identified SNP markers significantly associated with the traits under the fine mapped QTL regions provide genomic tools for potential application of MAS and a reference to assist with the identification of QTN causing variations in ultrasound and carcass merit traits in beef cattle.
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