second model, the two main conditions were parametrically modulated by the two categories, respectively (SOM, S5.1). The activation of the precuneus was higher for hard dominance-solvable games than for easy ones ( Fig. 4A and table S10). The activation of the insula was higher for the highly focal coordination games than for less focal ones ( Fig. 4B and table S11). Previous studies also found that precuneus activity increased when the number of planned moves increased (40, 41). The higher demand for memory-related imagery and memory retrieval may explain the greater precuneus activation in hard dominance-solvable games. In highly focal coordination games, the participants may have felt quite strongly that the pool students must notice the same salient feature. This may explain why insula activation correlates with NCI.Participants might have disagreed about which games were difficult. We built a third model to investigate whether the frontoparietal activation correlates with how hard a dominance-solvable game is and whether the activation in insula and ACC correlates with how easy a coordination game is. Here, the two main conditions were parametrically modulated by each participant's probability of obtaining a reward in each game (SOM, S2.2 and S5.2). We found a negative correlation between the activation of the precuneus and the participant's probability of obtaining a reward in dominance-solvable games ( Fig. 4C and table S12), which suggests that dominance-solvable games that yielded lower payoffs presented harder mental challenges. In a previous study on working memory, precuneus activity positively correlated with response times, a measure of mental effort (24). Both findings are consistent with the interpretation that subjective measures reflecting harder tasks (higher efforts) correlate with activation in precuneus. A positive correlation between insula activation and the participant's probability of obtaining a reward again suggests that coordination games with a highly salient feature strongly activated the "gut feeling" reported by many participants (Fig. 4D and table S13). A previous study found that the subjective rating of "chills intensity" in music correlates with activation of insula (42). Both findings are consistent with the interpretation that the subjective intensity of how salient a stimulus is correlates with activation in insula.As mentioned, choices were made significantly faster in coordination games than in dominancesolvable games. The results of the second and third models provide additional support for the idea that intuitive and deliberative mental processes have quite different properties. The "slow and effortful" process was more heavily taxed when the dominance-solvable games were harder. The "fast and effortless" process was more strongly activated when coordination was easy.

Background Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10–12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. Results We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. Conclusions We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.

. 2003. Residual feed intake and body composition in young growing cattle. Can. J. Anim. Sci. 83: 189-204. Crossbred steers (n = 176), 7-8 mo of age and from the five BeefBooster strains (M1, M2, M3, M4 and TX), were used to determine the relationships between residual feed intake (RFI) and growth rate, body composition and heat production (HP), and to quantify differences in RFI independent of differences in body composition. Animals with different RFI levels were also characterized for growth, carcass and body compositional traits. Steers from each genetic strain were selected at random and serially slaughtered on 5 pre-selected days of the finishing period. Steers grew at 1.52 (SD = 0.22) kg d -1 and had dry matter intake (DMI) of 8.5 (SD = 1.0) kg d -1 during the last 71 to 183 d before slaughter. Metabolic mid-point weight, average daily gain (ADG), gain in empty body fat and gain in empty body water accounted for 67.9, 8.6, 3.9 and 1.1%, respectively, of the variation in actual feed intake. Similarly, metabolic mid-point weight (68.5%), ADG (8.2%), gain in ultrasound backfat thickness (1.8%), gain in ultrasound marbling score (1.1%) and year (1.3%) accounted for 80.9% of the variation in actual feed intake. Residual feed intake adjusted for differences in estimated composition of gain (estimated gain in empty body fat and water; RFI II ) ranged from -2.06 kg d -1 to +1.61 kg d -1 (SD = 0.60 kg d -1 ). Residual feed intake adjusted for live animal measures of body composition (gain in ultrasound backfat thickness and marbling score; RFI III ) ranged from -2.11 kg d -1 to +1.88 kg d -1 (SD = 0.62 kg d -1 ). Low RFI III animals (efficient) had 6.0% lower metabolizable energy intake (MEI), retained 9.3% less energy and had 4.5% lower HP than medium RFI III animals (P < 0.01). Low RFI III animals also had 10.2% lower MEI, retained 12.0% less energy and produced 9.3% less heat than high RFI III animals (P < 0.01). Liver (P <0.01), small and large intestine (P = 0.09) and stomach and intestine (P < 0.01) weights were less in low and medium RFI III steers compared to high RFI III steers. There was a trend for low RFI III steers to have less dissectible carcass fat (P = 0.08), intermuscular fat (P = 0.06), body cavity fat in the butt and loin (P = 0.01), faster accretion rate of empty body water (P = 0.04) and a slower accretion rate of empty body fat (P < 0.01) than medium and high RFI III steers. A portion of the greater MEI by high RFI III steer was accounted for by differences in the chemical composition of gain. However, a greater proportion was due to a disproportionate increase in the energy required for maintenance and heat increment of feeding in high RFI III steers. An attempt should be made to adjust RFI for changes in the chemical composition of gain, possibly by the inclusion of ultrasound backfat thickness and marbling score into the equation for determining RFI. Les auteurs ont utilisé des bouvillons hybrides (n = 176) de 7 à 8 mois des cinq souches BeefBooster (M1, M2, M3, M4 et TX) pour déterminer ...

A microsatellite-based high-density genetic map facilitates for fine mapping of hereditary traits of interest, characterization of meiosis, and providing a foundation for physical map construction. Here, we developed a comprehensive genetic map on the basis of >880,000 genotypes across the USDA MARC cattle reference families with a potential genetic resolution of 0.8 cM at the 95% confidence level (∼800 kb in the bovine genome). We incorporated 2325 microsatellites into the second-generation genetic map by linkage analysis based on sex-averaged two-point LOD scores (>3.0), of which 2293 were fine-mapped by multipoint linkage analysis. The new 3160-cM map comprised of 29 sex-averaged autosomal linkage groups and a sex-specific X-chromosome linkage group includes 3960 markers with 2389 positions, resulting in an average interval size of 1.4 cM. More than half (51%) of the total length of the map is covered with intervals of 2.0 cM or less, and the largest gap is a 10.2-cM interval on the X-linkage group. The new map should accelerate fine mapping and positional cloning of genes for genetic diseases and economically important traits in cattle, as well as related livestock species, such as sheep and goat.[Supplemental material is available online at www.genome.org. Marker information of new microsatellites is available from DDBJ under accession nos. AB164707 to AB166543 including flanking sequences and AB166544 to AB166659 for only primer sequences. Linkage groups for all autosomes and X-and Y-chromosomes are presented at

Chromosomal regions harboring variation affecting cattle birth weight and BW gain to 1 yr of age were identified by marker association using the highly parallel BovineSNP50 BeadChip (50K) assay composed of 54,001 individual SNP. Genotypes were obtained from progeny (F(1); 590 steers) and 2-, 3-, and 4-breed cross grandprogeny (F(1)(2) = F(1) x F(1); 1,306 steers and 707 females) of 150 AI sires representing 7 breeds (22 sires per breed; Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental). Genotypes and birth, weaning, and yearling BW records were used in whole-genome association analyses to estimate effects of individual SNP on growth. Traits analyzed included growth component traits: birth weight (BWT), 205-d adjusted birth to weaning BW gain (WG), 160-d adjusted postweaning BW gain (PWG); cumulative traits: 205-d adjusted weaning weight (WW = BWT + WG) and 365-d adjusted yearling weight (YW = BWT + WG + PWG); and indexes of relative differences between postnatal growth and birth weight. Modeled fixed effects included additive effects of calf and dam SNP genotype, year-sex-management contemporary groups, and covariates for calf and dam breed composition and heterosis. Direct and maternal additive polygenic effects and maternal permanent environment effects were random. Missing genotypes, including 50K genotypes of most dams, were approximated with a single-locus BLUP procedure from pedigree relationships and known 50K genotypes. Various association criteria were applied: stringent tests to account for multiple testing but with limited power to detect associations with small effects, and relaxed nominal P that may detect SNP associated with small effects but include excessive false positive associations. Genomic locations of the 231 SNP meeting stringent criteria generally coincided with described previously QTL affecting growth traits. The 12,425 SNP satisfying relaxed tests were located throughout the genome. Most SNP associated with BWT and postnatal growth affected components in the same direction, although detection of SNP associated with one component independent of others presents a possible opportunity for SNP-assisted selection to increase postnatal growth relative to BWT.