Ant colony optimization as a method for strategic genotype sampling.

A simulation study was carried out to develop an alternative method of selecting animals to be genotyped. Simulated pedigrees included 5000 animals, each assigned genotypes for a bi-allelic single nucleotide polymorphism (SNP) based on assumed allelic frequencies of 0.7/0.3 and 0.5/0.5. In addition to simulated pedigrees, two beef cattle pedigrees, one from field data and the other from a research population, were used to test selected methods using simulated genotypes. The proposed method of ant colony optimization (ACO) was evaluated based on the number of alleles correctly assigned to ungenotyped animals (AK(P)), the probability of assigning true alleles (AK(G)) and the probability of correctly assigning genotypes (APTG). The proposed animal selection method of ant colony optimization was compared to selection using the diagonal elements of the inverse of the relationship matrix (A(-1)). Comparisons of these two methods showed that ACO yielded an increase in AK(P) ranging from 4.98% to 5.16% and an increase in APTG from 1.6% to 1.8% using simulated pedigrees. Gains in field data and research pedigrees were slightly lower. These results suggest that ACO can provide a better genotyping strategy, when compared to A(-1), with different pedigree sizes and structures.

The ant colony algorithm for feature selection in high-dimension gene expression data for disease classification.

The use of gene expression data to diagnose complex diseases represents an exciting area of medicine; however, such data sets are often noisy, requiring the selection of feature subsets to obtain maximum classification accuracy. Due to the high dimensions of many expression data sets, filter-based methods are commonly used, but often yield inconsistent results. Optimization algorithms can outperform filter methods, but often require preselection of features to achieve good results. To address the problems of many commonly used feature selection methods, the ant colony algorithm (ACA) is proposed for use on data sets with large numbers of features. The ACA is an optimization algorithm capable of incorporating prior information, allowing it to search the sample space more efficiently than other optimization methods. When applied to several high-dimensional data sets, the ACA was able to identify small subsets of highly predictive and biologically relevant genes without the need for extensive preselection of features. Using the selected genes to train a latent variable model yielded substantial increases in prediction accuracy when compared to several rank-based methods and results obtained in previous studies. The superiority of the ACA algorithm was validated through simulation.

Estimation of nutrient requirements using broken-line regression analysis.

We evaluated and compared various broken-line regression models and SAS (SAS Inst. Inc., Cary, NC) procedures for estimating nutrient requirements from nutrient dose response data. We used the SAS (Version 9) procedures NLIN and NLMixed and the response data of Parr et al. (2003), who evaluated the isoleucine requirement of growing swine. The SAS NLIN was used to fit 2 different broken-line regression models: a simple 2 straight-line, one-breakpoint model and a quadratic broken-line model in which the response below the single breakpoint was quadratic; there was a plateau above the breakpoint. The latter was fit using 2 different approaches in NLIN. We also used SAS NLMixed to fit 3 different broken-line models: the 2 straight-line, one-breakpoint model that included a random component for the plateau; the quadratic broken-line model that included a random component for the plateau; and the quadratic broken-line model that included random components for both the plateau and the slope of the curve below the requirement. The best fit (greater adjusted R2; least log likelihood) was achieved using SAS NLMixed and the quadratic model with a random component for asymptote included in the model. Model descriptions, SAS code, and output are presented and discussed. Additionally, we provide other examples of possible models and discuss approaches to handling difficult-to-fit data.

Joint longitudinal modeling of age of dam and age of animal for growth traits in beef cattle.

Two methods to jointly model age of dam (AOD) and age of animal in random regression analyses of growth in Gelbvieh cattle were examined. The first method (M1) was analogous to the multiple-trait analysis and consisted of AOD as a nested class variable and a cubic polynomial regression on age nested within birth, weaning, and yearly weights. The second method (M2) used two-dimensional splines, with age knots at 150, 205, 270, 340, and 390 d. The AOD knots were placed at 725, 1,464, and 2,189 d. These selected knots were used to form a two-dimensional grid containing 15 knots, each representing a specific age and AOD combination. A data set containing Gelbvieh growth records was split along contemporary groups into two data sets. Data set 1 contained 316,078 records and was used for prediction by mixed-model equations. Data set 2 contained 164,167 records and was used for cross validation. In the complete data set, only 90 and 30% of animals with birth weight had records on weaning and yearling weights, respectively. Models were evaluated based on R2, average squared error (ASE), percent bias, and plots of solutions. The ASE for weights associated with birth weight, weaning weight, and yearling weight for M1 were 15, 505, and 703 kg2. With M2, large jumps in fixed-effect estimates were observed outside the two-dimensional grid. To eliminate this problem, weighted one-dimensional splines were used for extrapolation beyond the two-dimensional grid. For M2 with weighted spline extrapolation, the ASE were 15, 542, and 777 kg2 for birth weight, weaning weight, and yearling weight, respectively. Creation of optimal two-dimensional splines is difficult when data are clustered. Despite such difficulties, the two-dimensional spline was capable of jointly and continuously modeling AOD and age of animal.

A practical longitudinal model for evaluating growth in Gelbvieh cattle.

Genetic evaluation of growth in Gelbvieh beef cattle was examined by multiple-trait (MTM) and random regression (RRM) analysis. The data set comprised 541,108 animals with 1,120,086 records. Approximately 15% of the animals in the data set had at least one record measured outside of the accepted MTM age ranges for weaning weight (Wwt) and yearling weight (Ywt). Fourteen percent of Wwt records and 19% of Ywt records were measured outside the accepted ranges for MTM analysis, and thus were excluded from MTM evaluations. Two RRM evaluations were performed using cubic Legendre polynomials (RRML) and linear splines (RRMS) with three knots at 1, 205, and 365 d of age. Data Set 1 (d1) utilized all available records, whereas Data Set 2 (d2) included only records measured within MTM ranges (1 d, 160 to 250 d, and 320 to 410 d). The RRML models did not reach convergence until diagonalization was imposed. After diagonalization, it was found that all longitudinal models required fewer iterations to converge than the MTM. Correlations between the MTM, RRML-d2, and RRMS-d2 evaluations were >or=0.99 for all three traits, indicating that these models were equivalent when predicting breeding values from data within the MTM age ranges. Correlations between MTM, RRML-d1, and RRMS-d1 were >0.99 for Bwt and >0.95 for Wwt and Ywt. The lower correlations for Wwt and Ywt indicate that the added information does affect breeding value prediction. The RRM has the capability to incorporate records measured at all ages into genetic evaluations at a computing cost similar to the MTM.

Environmental heat stress does not reduce blood ionized calcium concentration in hens acclimated to elevated temperatures.

Changes in blood concentrations of ionized calcium and total calcium were measured in broiler breeder hens (42 wk old) relative to egg cycle and environmental temperatures. Two environmental temperature treatments were used: 1) temperature cycled daily from a low of 10 C at 0300 h to a high of 25 C at 1600 h; and 2) temperature cycled from a low of 21 C at 0300 h to a high of to a high of 39 C at 1600 h. Serial blood samples were collected from five laying hens per temperature treatment via cutaneous ulnar vein cannula beginning at the time of oviposition and every 4 h thereafter until the next oviposition. Neither blood concentration of ionized calcium nor total plasma calcium was affected by temperature. Results suggest that the supply of calcium available in blood for shell deposition is not diminished in hens acclimated to high environmental temperatures.

Interaction of feeding time and temperature and their relationship to performance of the broiler breeder hen.

Experiments with broiler breeder hens were undertaken to determine effect of feeding time and environmental temperature on various production variables, body weight, and feed consumption. Two temperature treatments were used: low cyclic temperature (10 to 25 C), and high cyclic temperature (21 to 39 C). The three feeding treatments were: fed one daily meal either at 0700 h (Treatment 1) or 1800 h (Treatment 2), or one-half the daily amount at 0700 h and the other half at 1800 h (Treatment 3). In another experiment, hens were assigned to feeding times of either 0700 or 1800 h. Feeding time and temperature did not markedly affect rate of egg production; however, hens at high temperature fed two meals per day produced the fewest eggs. High temperature caused significant reductions in egg weight, specific gravity, and shell thickness. Feeding time and temperature had no effect on time of oviposition, ovulation, or the transit time of the egg through the oviduct. Significant body weight loss occurred in hens at high temperature and fed at 0700 h. Both high temperature and feeding one-half of the daily feed at 0700 and the other half at 1800 h caused a reduction in feed consumption.

Relative biological availability of manganese from manganese proteinate, manganese sulfate, and manganese monoxide in broilers reared at elevated temperatures.

The relative biological availabilities of Mn from Mn proteinate, MnSO4, and MnO were compared under two different environmental conditions. Commercial broilers were reared in brooder batteries between Days 1 and 21 and fed diets containing 0, 1,000, 2,000, or 3,000 mg supplemental Mn/kg diet. On Day 22, birds were transferred to individual cages in two environmental chambers maintaining the same dietary Mn sources and supplemental levels. The temperature in one chamber cycled between 18 and 23.9 C (thermoneutral, TN), and in the other chamber cycled between 23.9 and 35 C (heat distress, HD). Birds in the HD environment were exposed to 8 h of 23.9 C, 4 h of 23.9 to 35 C, 4 h of 35 C, and 8 h of 35 to 23.9 C. Tibia Mn increased linearly (P < .05) with level of supplementation when measured on Days 22 and 47. Based on ratios of slopes from multiple linear regression analysis of bone Mn on Mn intake from various sources, the biological availabilities of Mn proteinate and MnO relative to MnSO4 (100%) were 120 and 91%, respectively, in 21-d-old chicks. In 49-d-old birds, corresponding relative biological availabilities of Mn from proteinate and oxide were 125 and 83%, respectively, in birds reared under TN, and 145 and 82%, respectively, for HD birds.

Light and feed management of broiler breeders reared under short versus natural day length.

A series of four experiments was conducted to determine the response of meat-type breeder pullets to various light and feed management systems during the rearing, developing, and laying periods. Pullets reared under a short-day (8 h) lighting regimen entered lay at a significantly younger age and lighter body weight than did pullets reared under natural day length. When reared under short days, pullets subjected to light and feed stimulation earlier than 18 wk of age entered lay at a slightly younger age and significantly heavier body weight and produced fewer eggs through 45 wk of age. When pullets were reared under natural day length and photostimulated at 14 wk of age, incremental reductions in age (from 24 to 15 wk of age) at which feed stimulation was initiated resulted in proportionate reductions in age at first egg but had no effect on body weight at first egg. Results suggest that egg production by commercial meat-type females is optimum when managed to begin lay at 24 wk of age. Pullets reared under short days will enter lay at 24 wk if photostimulation is begun at 18 wk and feed stimulation is initiated not later than 24 wk. Pullets reared under natural day length will enter lay at 24 wk if photostimulation is begun at 14 wk and feed stimulation is initiated at 15 wk.

Effects of ad libitum versus restricted feeding on body composition and egg production of broiler breeders.

A 64-wk experiment was conducted in which the effects of ad libitum vs. restricted feeding were studied during the pullet-layer transition and laying periods. Broiler breeder females were reared through 23 wk of age according to the breeder's recommendation. At 24 wk of age the following four treatments were imposed: T1, fed restricted amounts of feed according to the breeder's management guide; T2, feed restricted from 24 to 32 wk of age (as in T1), then fed ad libitum; T3, fed ad libitum from 24 to 64 wk of age; and T4, fed ad libitum from 24 to 32 wk of age, then restricted to 85% of the average 24 to 32-wk consumption. Birds fed ad libitum during the pullet-layer transition period (T3 + T4) consumed an average of 37 g more feed per day and reached sexual maturity 14 days earlier than restricted birds (T1 + T2). Live body weight, carcass weight, carcass weight corrected to zero fat content, and percentage carcass fat were all significantly higher at first egg in ad libitum vs. restricted birds, but these differences were small. Birds fed ad libitum during lay (T2 + T3) produced more eggs, achieved a higher peak percentage hen-day production, consumed more feed, and contained more body fat at last egg than hens restricted during lay (T1 + T4). However, neither mortality, feed efficiency, egg weight, egg fertility, nor egg specific gravity was affected by treatment.

Threonine requirement of the broiler chick as affected by protein level and source.

The threonine requirement of the young broiler chick was estimated in two experiments. In Experiment 1, a threonine-deficient corn-peanut meal-amino acid mixture was included in a basal diet at levels equivalent to 15 and 20% crude protein. In Experiment 2, a purified crystalline amino acid mixture, also limiting in threonine, was included in a basal diet at levels equivalent to 10.98 and 18.3% crude protein. When expressed as a percent of diet, the estimated threonine requirements increased as dietary protein content increased. However, when expressed as a percent of dietary protein, the estimated threonine requirements were not significantly affected by dietary protein content, and were similar for the two experiments. It was concluded that the threonine requirement is 3.7% of dietary crude protein, and is little affected by dietary protein content.

Effects of dietary crude protein, electrolyte balance, and photoperiod on growth of broiler chickens.

Three experiments were conducted with broiler chicks to study the effects of dietary electrolyte balance, dietary crude protein level, and photoperiod on performance. Increasing the electrolyte balance (Na + K -Cl) from about 200 meq/kg to 350 meq/kg or more improved gain and feed consumption of chicks fed high protein (28.6%) diets but depressed gain and feed consumption of chicks fed low protein (14.3%) diets. Neither sex nor photoperiod affected to nature or magnitude of the crude protein X electrolyte balance interaction, although birds housed under 16L:8D had significantly higher concentrations of plasma ammonia than did those housed under 23L:1D. Chicks fed diets containing a high vs. a low electrolyte balance had significantly higher concentrations of plasma uric acid and significantly lower kidney asparaginase activities. Electrolyte effects on kidney asparaginase activity were not affected by diet crude protein content. Results indicate that the electrolyte balance that provides for optimum growth is dependent upon dietary crude protein concentration. Further, diet electrolyte effects on metabolic acid-base homeostasis are not related to their effects on growth.

Effect of feed restriction on growth, body composition, and egg production of broiler females through 68 weeks of age.

Effects of ad libitum and restricted (50% of ad libitum) feeding on performance of female broilers were assessed in a 68-week experiment. The treatments imposed were AA, fed ad libitum throughout; RR, fed restricted amounts of feed throughout; RA restricted through 24 weeks of age and ad libitum thereafter; and AR, fed ad libitum through 24 weeks and restricted thereafter. Average age at first egg was delayed by 17 days in RA hens compared with AA hens. Average body weight at first egg was 3.9 kg for RA birds and 4.5 kg for AA birds. Peak production was higher for RA birds (71 vs. 59%), but age at peak production was similar for both AA and RA hens. Through 68 weeks, AR birds produced 50% more eggs than AA birds (159 vs. 106). Cumulative number of eggs produced for RR and AR birds were 37 and 47, respectively. Mortality was similar for RR, RA, and AR birds but was approximately fourfold greater in AA birds. At 68 weeks of age, live body, carcass, abdominal fat pad, and estimated fat-free carcass weights were similar for AA and RA birds. Although abdominal fat as a percent of carcass weight was similar for AR and RR birds, average live weight, carcass weight, and fat-free carcass weight were higher for AR than RR birds at 68 weeks.

Utilization of energy for maintenance and gain in broilers and Leghorns at two ages.

Regression equations describing the relationship between energy gain and metabolizable energy intake per unit metabolic weight were derived for 8- to 22-day-old and 28- to 42-day-old broilers and 14- to 28-day-old and 28- to 42-day-old Leghorns. The estimated maintenance energy requirements were lower in the 28- to 42-day-old birds than in the younger birds, but the decreases were small. Maintenance energy requirements of Leghorns were 36% less than those of broilers. Age had no effect on the efficiency of energy utilization above maintenance in broilers. However, the efficiency of energy utilization above maintenance in Leghorns was 43% lower in the older birds. This was correlated with a lower percentage fat gain in the older Leghorns. The percentage fat gain in broilers was substantially higher in the older birds, but this was not correlated with changes in energetic efficiency.

Relationship of sex and body growth rate with daily accretion rates of fat, protein and ash in chickens.

A series of serial slaughter experiments was conducted with three strains of chickens of greatly different rates of body growth through 49 days of age. During the first week of life, the body weight of the rapidly growing strain increased from hatching at a rate twice that observed in either the medium or slowly growing strain of chicken. The percentage increase in body weight which occurred during the seventh week of life (i.e., gain from day 42 to day 49 as a percentage of 42-day body weight) was similar for all three strains. Daily gains in crude protein and ash, expressed as percentages of daily carcass weight gain, were similar among strains. However, daily fat gain, expressed as a percentage of daily carcass weight gain, decreased slightly in the slow growing strain during the last two weeks of the study, remained relatively constant in the medium growing strain, but increased linearly and substantially in the rapid growing strain. It is hypothesized that the biological factors which facilitate the very rapid early rate of growth in the rapid growing breed also result in excessive energy consumption as the bird ages and the rate of proportional increase in body weight declines.

The effect of light regime on growth and pattern of body fat accretion of broiler chickens.

A seven week serial slaughter experiment was conducted with male and female broiler chickens to determine the effect of photoperiod on body growth rate and pattern and rate of fat deposition. The two light regimes compared were constant light and a 16 hour light:8 hour dark photoperiod. Males grown under the 16L:8D photoperiod consumed less feed and grew less rapidly than males under constant light. The slower rate of growth was apparently due entirely to less feed consumption, since feed efficiency of males was unaffected by light treatment. Females reared under 16L:8D also grew less rapidly than under constant light. However, the difference was much more pronounced than in males, and was not due to reduced feed consumption, rather to less efficient feed utilization. Females grown under 16L.8D exhibited a slower rate of increase in percent daily fat gain than did females grown under constant light. At seven weeks of age, total body fat content of females averaged 12% less when grown under 16L:8D. Rat and pattern of fat gain in males was unaffected by light treatment. The incidence of leg abnormalities was substantially lower for both sexes reared under 16L:8D.

Potassium-induced changes in muscle free amino acid concentrations in chicks.

Two experiments with purified crystalline amino acid diets were conducted to determine the effect of dietary potassium level on chick breast muscle free amino acid concentrations. In both experiments, concentrations of muscle free glutamine, lysine and arginine increased as dietary potassium increased from 0.12 to 0.18% and decreased as dietary potassium exceeded 0.18%. As dietary potassium increased, muscle potassium concentration increased linearly with an equivalent linear decrease in muscle sodium concentration. Peak concentration of muscle free glutamine, lysine and arginine occurred in muscle with a K+:Na+ ratio of approximately 1:4. Concentrations of the three amino acids were less in muscle with K4:Na+ ratios either less than or greater than 1.4. Breast muscle concentrations of free histidine decreased slightly, while muscle free carnosine increased substantially when dietary potassium exceeded 0.18%.

Amino acid utilization as influenced by antibacterial and anticoccidial drugs.

Utilization of amino acids, sulfur-containing amino acid (SAA) in particular, is little affected by antibiotic and anticoccidial compounds. Coccidiosis (i.e., Eimeria acervulina infection) likewise seems to have little effect on SAA utilization. Copper sulfate, a commonly used antibacterial-antifungal compound (used at levels of 100-250 mg/kg diet), interacts with SAA. Hence, at upper levels of copper ingestion (i.e., 250 mg/kg and higher), copper binds SH compounds such as cysteine and reduced glutathione. Dietary SAA requirements are increased in both chicks and rats by dietary copper levels of 250 or 500 mg/kg. Hepatic copper deposition is enhanced by copper feeding and also by E. acervulina infection. These two effects, moreover, appear to be additive. The organic arsenic compound, roxarsone, interacts with SAA also, but in a different way. Thus, whereas added dietary cysteine partially ameliorates copper toxicity due to the binding of copper by cysteine-SH with subsequent excretion, roxarsone toxicity (i.e., 500 mg/kg diet) is exacerbated by supplemental cysteine.

Kidney arginase activity in chicks fed diets containing deficient or excessive concentrations of lysine, arginine, histidine, or total nitrogen.

Three experiments were conducted with 1 to 2-week-old chicks fed purified crystalline amino acid diets. Kidney arginase activity increased substantially when total dietary nitrogen exceeded the dietary requirement for maximal chick weight gain. Single deficiencies of either histidine or lysine in nitrogen-adequate diets also resulted in marked increases in enzyme level. Arginine deficiency resulted in a slight increase in arginase activity, but the magnitude of the increase appeared to have little effect on efficiency of arginine utilization. Further, the response could be prevented by making lysine and arginine equally limiting. Increasing the lysine:arginine ratio to two in a nitrogen-deficient diet did not increase arginase activity. The same ratio in a arginine- and nitrogen-adequate diet resulted in a twofold increase in arginase activity accompanied by reductions in rate and efficiency of weight gain.

Xanthophyll bioavailability in dehydrated turf grass.

In a 16-day experiment involving 270 32-week-old laying hens, dehydrated turf grass (DTG) and corn gluten meal (CGM) were compared as xanthophyll sources for egg yolk pigmentation. Experimental diets were formulated to contain, 0, 5, 10, 15 and 20 mg total xanthophyll/kg diet, provided as either DTG or CGM. Neither egg production nor feed consumption was affected by diet. Egg yolk color dominant wavelength increased slightly with increasing dietary xanthophyll and did not differ with source. Egg yolk color excitation purity increased quadratically (P less than .001) with dietary xanthophyll. The response was similar for both DTG and CGM. It was concluded that the xanthophyll in DTG is 100% bioavailable relative to CGM.