Cavanagh et al. Genetics Selection Evolution 2010, 42:36 http://www.gsejournal.org/content/42/1/36 time to assessment is long and therefore the response to selection is slow. Therefore, the use of marker assisted selection or MAS is seen as an attractive aid to increase the efficiency of selection for these traits expensive to measure. Linkage studies indicate the presence of one or a few major genes for increased muscling and fatness in differ- ent sheep populations [8-10]. Two full and 12 partial genome scans have reported QTL for carcass composi- tion including bone density on chromosomes 1-6, 8, 18, 20, 21, and 24 in populations of Coopworth, Scottish Blackface, British Texel, Charollais, Suffolk, Texel and different cross-breed sheep populations [8,11-18]. At present two DNA tests (LoinMax and MyoMax; http:// www.pfizeranimalgenetics.com.au/sites/PAG/aus/Pages/ sheep.aspx[19]) are commercially available, which test for genetic variants in the Carwell and Myostatin genes [8,10,16,17,20-25]. This study uses CT imaging to accurately determine body composition in vivo in relation to body weight at two different stages of maturity. For the first time, a full genome scan was conducted to identify genomic regions associated with CT-derived parameters in an ovine backcross resource population. Methods Resource population A resource population from crosses between fat-tail Awassi (A) and small-framed Merino (M) sheep was established. Further details of the development of the resource population can be found in Raadsma et al. [26,27]. In the QTL study reported here, only phenoty- pic and genotypic information from the second genera- tion male backcross (AMM) progeny from one of four F1 sires was analysed in full. Carcass traits The backcross progeny were weighed approximately bi- monthly until 83 weeks of age. Weights were recorded as non-fasted body weights immediately off pasture on the same day. At 83 weeks of age, male animals were randomly allocated to two management cohorts. Cohort 1 (n = 86) was lot fed for 90 days after which time all animals were CT scanned prior to slaughter at two years of age. Cohort 2 (n = 79) were grazed under pad- dock conditions for a further 18 months and then lot fed for 90 days followed by CT scanning and slaughter at 3.5 years of age. Both cohorts were fed ad libitum on a grain and lucerne pelleted ratio with a metabolisable energy content of 12.1 MJ/kg during the feedlot period. The two cohorts were created to capture the differences in fat deposition due to changes in maturity. At the end of the ad libitum phase and three days prior slaughter, CT scanning was used to estimate lean, Page 2 of 14 fat and bone quantities for individual sheep. Animals were fasted overnight, body weights were recorded and animals were scanned using a Hitachi CT-W400 scanner located in the Meat Science Group at the University of New England, Armidale. Animals were restrained in the supine position using three adjustable belts over the abdomen, chest and neck during the scans at 120 kV tube voltages and 150 mA current. Cross-section images were collected every 40 mm starting proximal to the articulatio genus (rear knee joint) and finishing at the first cervical vertebra. Between 24 and 28 images were collected from each animal depending on their length. The carcass weight was estimated from the CT images. Three sets of data (images) were derived from each image by cropping restraining equipment, internal organs and hooves, distal portion of leg, internal fat and kidney, using AUTOCAT [28]. These images provided an estimate of total body composition including hooves, internal organs and abdominal fat (first set), internal fat - comprising kidney, pelvic, mesenteric and heart fat (second set minus third set) and typical carcass compo- nents including total lean, carcass lean and total amount of bone (third set). Furthermore AUTOCAT was used to calculate the area, mean pixel value and variance of each tissue group for each animal from the three sets of images. Subcutaneous fat depth was measured over the eye muscle at the first lumbar two thirds ventral to the vertebrae. The area of fat surrounding the eye muscle (M. longissimus dorsi) was termed the subcutaneous fat area. The eye muscle area was estimated by averaging the area of muscle at the closest image to the first lum- bar and the next caudal image. Percentages of lean, fat and bone were calculated as a percentage of the carcass weight estimated by CT (i.e. the sum of individual com- ponents estimated by CT). A list of all traits used in this study is provided in Table 1. A linear model was fitted using SAS (version 9.2) to adjust the scanning results for final body weight and cohort. For some of the traits, a scatter plot of the trait versus final body weight revealed a linear association for the first cohort but a nonlinear association for the sec- ond cohort. To allow for this nonlinearity, a quadratic term was included for the second cohort only. The full model allowing for this takes the form Trait = 0 + 1Cohort2 +  2FBW + 3Cohort2 × FBW +  4Cohort2 × FBW 2 +  where Trait is the measurement to be adjusted for, Cohort2 is a 0-1 indicator variable taking the value 1 for the second cohort, FBW is the final body weight of the sheep, and ε is the random error. Non-significant terms from the above model were dropped, with quadratic terms retained for all traits except dressing percentage, carcass bone, percentage fat in carcass, percentage lean in carcass.