Primary genome scan to identify putative QTL for feedlot growth rate, feed intake, and feed efficiency of beef cattle

¹ Igenity Livestock Production Business Unit, Merial Ltd.; Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
² Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
³ Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada; Agriculture and Agri-Food Canada Research Centre, Lethbridge, Alberta, T1J 4B1 Canada
⁴ Agriculture and Agri-Food Canada Research Centre, Lethbridge, Alberta, T1J 4B1 Canada
⁵ Alberta Agriculture, Food and Rural Development, Lacombe Research Centre, 6000 C&E Trail, Lacombe, AB, Canada, T4L 1W1

^* To whom correspondence should be addressed. E-mail: stephen.moore{at}ualberta.ca.

	Abstract

Feed intake and feed efficiency of beef cattle are economically relevant traits. The study was conducted to identify QTL for feed intake and feed efficiency of beef cattle using genotype information from 100 microsatellite markers and 355 single nucleotide polymorphisms genotyped across 400 progeny of 20 Angus, Charolais, or Alberta Hybrid bulls. Traits analyzed include feedlot ADG, daily DMI, feed-to-gain ratio (F:G), and residual feed intake (RFI). A mixed model with sire as random and QTL effects as fixed was used to generate an F-statistic profile across- and within-families for each trait along each chromosome followed by empirical permutation tests to determine significance thresholds for QTL detection. Putative QTL for ADG (chromosome-wise P < 0.05) were detected across-families on chromosomes 5 (130 cM), 6 (42 cM), 7 (84 cM), 11 (20 cM), 14 (74 cM), 16 (22 cM), 17 (9 cM), 18 (46 cM), 19 (53 cM), and 28 (23 cM). For DMI, putative QTL that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 1 (93 cM), 3 (123 cM), 15 (31 cM), 17 (81 cM), 18 (49 cM), 20 (56 cM), and 26 (69 cM) in the across-family analyses. Putative across-family QTL influencing F:G that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 3 (62 cM), 5 (129 cM), 7 (27 cM), 11 (16 cM), 16 (30 cM), 17 (81 cM), 22 (72 cM), 24 (55 cM), and 28 (24 cM). Putative QTL influencing RFI that exceeded the chromosome-wise P < 0.05 threshold were detected on chromosomes 1 (90 cM), 5 (129 cM), 7 (22 cM), 8 (80 cM), 12 (89 cM), 16 (41 cM), 17 (19 cM), and 26 (48 cM) in the across-family analyses. In addition, a total of 4, 6, 1, and 8 chromosomes showed suggestive evidence (chromosome-wise P < 0.10) for putative ADG, DMI, F:G, and RFI QTL, respectively. Most of the QTL detected across families were also detected within-families, though the locations across-families were not necessarily the locations within-families, which is likely due to differences among families in marker informativeness for the different linkage groups. The locations and direction of some of the QTL effects reported in this study suggest potentially favorable pleiotropic effects for the underlying genes. Further studies will be required to confirm these QTL in other populations so that they can be fine-mapped for potential applications in marker-assisted selection and management of beef cattle.

Key Words: beef cattle, feed intake, feed efficiency, quantitative trait loci