Theoretical efficiency of multiple-trait quantitative trait loci-assisted selection

The effectiveness of five selection methods for genetic improvement of net merit comprising trait 1 of low heritability (h² = 0.1) and trait 2 of high heritability (h² = 0.4) was examined: (i) two‐trait quantitative trait loci (QTL)‐assisted selection; (ii) partial QTL‐assisted selection based on trait 1; (iii) partial QTL‐assisted selection based on trait 2; (iv) QTL‐only selection; and (v) conventional selection index without QTL information. These selection methods were compared under 72 scenarios with different combinations of the relative economic weights, the genetic correlations between traits, the ratio of QTL variance to total genetic variance of the trait, and the ratio of genetic variances between traits. The results suggest that the detection of QTL for multiple‐trait QTL‐assisted selection is more important when the index traits are negatively correlated than when they are positively correlated. In contrast to literature reports that single‐trait marker‐assisted selection (MAS) is the most efficient for low heritability traits, this study found that the identified QTL of the low heritability trait contributed negligibly to total response in net merit. This is because multiple‐trait QTL‐assisted selection is designed to maximize total net merit rather than the genetic response of the individual index trait as in the case of single‐trait MAS. Therefore, it is not economical to identify the QTL of the low heritability traits for the improvement of total net merit. The efficient, cost‐effective selection strategy is to identify the QTL of the moderate or high heritability traits of the QTL‐assisted selection index to facilitate total economic returns. Detection of the QTL of the low h² traits for the QTL‐assisted index selection is justified when the low h² traits have high negative genetic correlation with the other index traits and/or when both economic weights and genetic variances of the low h² traits are larger as compared to the other index traits of higher h². This study deals with theoretical efficiency of QTL‐assisted selection, but the same principle applies to SNP‐based genomic selection when the proportion of the genetic variance ‘explained by the identified QTLs’ in this study is replaced by ‘explained by SNPs’.     

Comparison of High Performance Liquid Chromatography and Immunoassay Methods for Measurement of Cyclosporine A Blood Concentrations After Feline Kidney Transplantation

Objective —To compare two methods of whole blood cyclosporine A (CsA) measurement in cats.
Study Design —Whole blood samples were analyzed for CsA concentrations with use of high performance liquid chromatography (HPLC) and monoclonal immunoassay methods.
Animals —Blood (n = 36 samples) was obtained from six cats after renal transplantation.
Methods —Results were compared by linear regression analysis using both pooled and individual patient data. Eight samples were off-scale on the immunoassay and were excluded.
Results —There was significant correlation between CsA measured using HPLC and immunoassay methods ( P < .001; r = .942; r²= .887). However, individuals varied nonrandomly from the mean pooled patient data. Correlation between the assay methods was higher for individual patients using data only from that specific individual (mean r value = .976; r²= .955). Clinical utility of the immunoassay (ie, results would prompt an appropriate CsA dosage adjustment) was good when based on individually derived conversion factors (27 of 28 [96.5%] of decision events).
Conclusion—HPLC is superior for measurement of blood CsA concentrations in cats after kidney transplantation. However, an immunoassay may provide reliable information for CsA management if a comparative database (HPLC v immunoassay) has been previously determined in a specific patient.
Clinical Relevance —Locally available monitoring of CsA by immunoassay in cats may provide significant advantages when shipping of blood samples to distant locations is required to obtain analysis by HPLC. These advantages may include cost and timeliness of results in circumstances where daily blood CsA concentrations may be desired, such as when managing an acute rejection reaction.     

Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

In fine mapping of a large‐scale experimental population where collection of phenotypes are very expensive, difficult to record or time‐demanding, selective phenotyping could be used to phenotype the most informative individuals. Linkage analyses based sampling criteria (LAC) and linkage disequilibrium‐based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However, in order to estimate unbiased QTL parameters based on LAC in a large half‐sib family, prior information on QTL position was required. The LDC improved the accuracy to estimate the QTL position but not significantly compared to random phenotyping with the same sample size. When applying LDC (all phenotyping levels), the estimated QTL effect were closer to the true value in comparison to LAC. The results showed that the LDC were better than the LAC to select individuals for phenotyping and contributed to detection of the QTL.     

"Quasi-REML" correlation estimates between production and health traits in the presence of selection and confounding: a simulation study

Performance of the "quasi-REML" method for estimating correlations between a continuous trait and a categorical trait, and between two categorical traits, was studied with Monte Carlo simulations. Three continuous, correlated traits were simulated for identical populations and three scenarios with either no selection, selection for one moderately heritable trait (Trait 1, h2 = .25), and selection for the same trait plus confounding between sires and management groups. The "true" environmental correlations between Traits 2 (h2 = .10) and 3 (h2 = .05) were always of the same absolute size (.20), but further data scenarios were generated by setting the sign of environmental correlation to either positive or negative. Observations for Traits 2 and 3 were then reassigned to binomial categories to simulate health or reproductive traits with incidences of 15 and 5%, respectively. Genetic correlations (r(g12), r(g13), and r(g23) and environmental correlations (r(e12), r(e13), and r(e23)) were estimated for the underlying continuous scale (REML) and the visible categorical scales ("quasi-REML") with linear multiple-trait sire and animal models. Contrary to theory, practically all "quasi-REML" genetic correlations were underestimated to some extent with the sire and animal models. Selection inflated this negative bias for sire model estimates, and the sign of r(e23) noticeably affected r(g23) estimates for the animal model, with greater bias and SD for estimates when the "true" r(e23) was positive. Transformed "quasi-REML" environmental correlations between a continuous and a categorical trait were estimated with good efficiency and little bias, and corresponding correlations between two categorical traits were systematically overestimated. Confounding between sires and contemporary groups negatively affected all correlation estimates on the underlying and the visible scales, especially for sire model "quasi-REML" estimates of genetic correlation. Selection, data structure, and the (co)variance structure influences how well correlations involving categorical traits are estimated with "quasi-REML" methods.     

COMPARISON OF PER-RECTAL PORTAL SCINTIGRAPHY USING 99mTECHNETIUM PERTECHNETATE TO MESENTERIC INJECTION OF RADIOACTIVE MICROSPHERES FOR QUANTIFICATION OF PORTOSYSTEMIC SHUNTS IN AN EXPERIMENTAL DOG MODEL

Per-rectal portal scintigraphy using tech-netium-99m pertechnetate (^99mTcO₄^-) was performed in 8 normal dogs before and after surgical creation of a portacaval shunt. Shunt fractions were calculated by computer assisted analysis of dynamic images (IMG) and compared to shunt fractions determined by mesenteric venous injection of radioactive microspheres (MIC). The mean pre-operative shunt fraction was 1.59% using IMG and 3.00% using MCI. The mean postoperative shunt fraction was 64.56% using IMG and 69.56% using MIC. There was excellent correlation between both methods (r² 0.94). Per-rectal portal scintigraphy is an easily performed, inexpensive method to diagnose and quantify portosystemic shunts in dogs.     

Determination of Safe Depth of Pin Penetration for Repair of Distal Femoral Physeal Fractures in Immature Dogs: A Comparison of Normograde and Retrograde Pin Placement

Objective —The purpose of this study was to determine the depth that implants may be safely placed into the distal femoral epiphysis (DFE) for the repair of distal femoral physeal fractures.
Study Design —The depth of the DFE was related to the radiographic thickness of the patella in this experimental study.
Animals or Sample Population —Twenty immature canine cadavers.
Methods —Patella thicknesses were measured from lateral radiographs. Actual DFE depths were determined for pins driven in normograde fashion and for pins driven retrograde from the central depression between the metaphyseal pegs and from the cranial pegs. The association of DFE depth and patella thickness was evaluated using linear regression analysis. Using 95% confidence intervals, rules for estimating the safe depth of implant placement into the DFE were determined.
Results —DFE depth had significant correlation with patella thickness for pins placed in retrograde fashion from the central depression between the metaphyseal pegs (r²= .83) and from the cranial pegs (r²= .82) and for pins placed in normograde fashion (r²= .65).
Conclusions —Based on 95% confidence intervals, pins placed in retrograde fashion from the central depression between the metaphyseal pegs may be safely driven into the DFE a distance equal to 140% of patella thickness. Pins placed from the cranial metaphyseal pegs may be driven to a depth equal to 80% of patella thickness, and pins placed in normograde fashion may be driven to a depth equal to 30% of patella thickness.
Clinical Relevance —Measurement of patella thickness assists the surgeon in determining the approximate depth that pins may be driven into the DFE without penetrating the articular surface of the stifle joint.     

Breeding programs for smallholder sheep farming systems: I. Evaluation of alternative designs of breeding schemes

Village‐ and central nucleus‐based schemes were simulated and evaluated for their relative bio‐economic efficiencies, using Ethiopia's Menz sheep as example. The schemes were: village‐based 2‐tier (Scheme‐1) and 1‐tier (Scheme‐2) cooperative village breeding schemes, dispersed village‐based nuclei scheme (Scheme‐3), conventional 2‐tier central nucleus‐based scheme (Scheme‐4), and schemes linking a central nucleus and village multiplier nuclei with selection in central nucleus (Scheme‐5) or in both central and village nuclei (Scheme‐6). Among village‐based schemes, Scheme‐1 gave the highest genetic progress, while Scheme‐2 was economically the most efficient with genetic gain in the breeding objective of Birr 5.6 and a profit of Birr 37.2/ewe/year. The central nucleus schemes were more efficient than the village schemes. Scheme‐4 was the most efficient with genetic gain in the breeding objective of Birr 13.5 and a profit of Birr 71.2, but is operationally more difficult as it requires a very large central nucleus. The choice between village and central nucleus‐based schemes would depend on local conditions (availability of infrastructure, logistics and technical knowhow and support). Linking central nucleus with village‐based nuclei (Scheme‐6) would be a feasible option to overcome the operational difficulties of the conventional central nucleus scheme. If a village‐based breeding program is envisaged as should be the 1st step in most low‐input systems, then Scheme‐2 is the most efficient. To scale out to an entire Menz breed level, Scheme‐3 would be recommended.     

One-generation divergent selection on large and small yolk proportions in a White Leghorn line

1. A striking change in egg consumption from shell eggs toward egg products is taking place. Consequently, internal egg quality traits must be seen in a different light, as they may affect the profitability of the egg processing industry. In order to study the possibility of using breeding as a means to alter yolk production, a one-generation divergent selection experiment was set up. The trait was yolk proportion. The effect of hen's age on egg composition was also studied. Genetic parameters for yolk proportion, yolk weight, egg weight and albumen weight were estimated, using a multiple trait animal model, and restricted maximum likelihood. 2. Selection response was obtained for yolk proportion and correlated selection responses for yolk weight and albumen weight. In the 'high line' a decrease in egg weight and an increase in yolk weight was established, whereas in the 'low line', egg weight remained more or less the same and yolk weight decreased slightly 3. Yolk proportion, yolk weight, egg weight and albumen weight all increased with increasing age of the hen in both selection lines. The difference between selection lines in yolk proportion, yolk weight and albumen weight persisted throughout the laying period. 4. Estimated heritabilities for yolk proportion, yolk weight, egg weight and albumen weight were 0.38, 0.22, 0.34 and 0.41 respectively. The genetic correlation between yolk proportion and yolk weight was 0.52, whereas the genetic correlations with egg weight and albumen weight were -0.51 and -0.74 respectively. 5. We conclude that selection can be used to alter yolk production. Selection can be at an early age with a sustained effect throughout the laying period.     

Estimation of genetic parameters and response to selection for a continuous trait subject to culling before testing

The consequences of assuming a zero environmental covariance between a binary trait 'test-status' and a continuous trait on the estimates of genetic parameters by restricted maximum likelihood and Gibbs sampling and on response from genetic selection when the true environmental covariance deviates from zero were studied. Data were simulated for two traits (one that culling was based on and a continuous trait) using the following true parameters, on the underlying scale: h2 = 0.4; r(A) = 0.5; r(E) = 0.5, 0.0 or -0.5. The selection on the continuous trait was applied to five subsequent generations where 25 sires and 500 dams produced 1500 offspring per generation. Mass selection was applied in the analysis of the effect on estimation of genetic parameters. Estimated breeding values were used in the study of the effect of genetic selection on response and accuracy. The culling frequency was either 0.5 or 0.8 within each generation. Each of 10 replicates included 7500 records on 'test-status' and 9600 animals in the pedigree file. Results from bivariate analysis showed unbiased estimates of variance components and genetic parameters when true r(E) = 0.0. For r(E) = 0.5, variance components (13-19% bias) and especially (50-80%) were underestimated for the continuous trait, while heritability estimates were unbiased. For r(E) = -0.5, heritability estimates of test-status were unbiased, while genetic variance and heritability of the continuous trait together with were overestimated (25-50%). The bias was larger for the higher culling frequency. Culling always reduced genetic progress from selection, but the genetic progress was found to be robust to the use of wrong parameter values of the true environmental correlation between test-status and the continuous trait. Use of a bivariate linear-linear model reduced bias in genetic evaluations, when data were subject to culling.     

The importance of haplotype length and heritability using genomic selection in dairy cattle

Reliabilities for genomic estimated breeding values (GEBV) were investigated by simulation for a typical dairy cattle breeding setting. Scenarios were simulated with different heritabilites ( h ²) and for different haplotype sizes, and seven generations with only genotypes were generated to investigate reliability of GEBV over time. A genome with 5000 single nucleotide polymorphisms (SNP) at distances of 0.1 cM and 50 quantitative trait loci (QTL) was simulated, and a Bayesian variable selection model was implemented to predict GEBV. Highest reliabilities were obtained for 10 SNP haplotypes. At optimal haplotype size, reliabilities in generation 1 without phenotypes ranged from 0.80 for h ² = 0.02 to 0.93 for h ² = 0.30, and in the seventh generation without phenotypes ranged from 0.69 for h ² = 0.02 to 0.86 for h ² = 0.30. Reliabilities of GEBV were found sufficiently high to implement dairy selection schemes without progeny testing in which case a data time-lag of two to three generations may be present. Reliabilities were also relatively high for low heritable traits, implying that genomic selection could be especially beneficial to improve the selection on, e.g. health and fertility.     

HIGH-RESOLUTION PARATHYROID SONOGRAPHY

The purpose of this study was to assess the diagnostic utility of parathyroid ultrasonography to differentiate causes of hypercalcemia in dogs. We analyzed qualitative and quantitative ultrasound imaging findings and clinical pathology data from 33 dogs that underwent parathyroid ultrasound examination as part of the diagnostic evaluation for hypercalcemia. Diagnoses of the diseases causing hypercalcemia included parathyroid carcinoma (n = S), parathyroid adenoma (n = 15), parathyroid adenomatous hyperplasia (n = 6), chronic renal insufficiency (n = 3), and hypercalcemia of malignancy (n = 4). All parathyroid lesions were round or oval and hypoechoic compared with surrounding thyroid parenchyma. Adenomatous and adenocarcinomatous glands were 4 mm or larger in longest linear measurement on US examination and were statistically significantly larger than hyperplastic glands. (p < 0.001) Linear measurements of parathyroid glands acquired at the time of ultrasound examination correlated well with direct siz determination after surgical excision. (r²= 0.9, p < 0.0001) Parathyroid lesions <4 mm are highly suspicious for parathyroid adenoma or carcinoma, while US lesions <4 mm most likely represent primary adenomatous hyperplasia or secondary parathyroid hyperplasia. Parathyroid size estimation from ultrasound examination is an accurate predictor of true size.     

Ovarian Structure in Mice Lines Selected for Weight

Selection for body weight at 49 day of age ( s and h , downward selected lines; s' and h' , upward selected lines) affected reproductive traits in CF1 mice lines. The objective of this study was to compare ovarian structures in females of these lines, as well as in unselected controls (Line t ). The number of ovarian follicles ( N ), follicle diameter (FD), number of corpora lutea (CL), litter size (LS), and body weight ( W ), were recorded. There were significant differences among lines for N , FD, CL, LS and W ; means values for the lines with the greatest difference for post-pubertal females were: N _s  = 19.3 and N _s'  = 32.7; FD _h'   = 161.7 and FD _s'  = 178.2; CL _h  = 10.3 and CL _s'  = 21.9; LS _s  = 6.0 and LS _h'  = 11.1; W _h  = 18.9 and W _s'  = 32.4. There were also differences between positive lines; Line s' had a higher proportion of large follicles in pre-pubertal females, a greater capacity to convert these follicles into CL, but a lower capacity to maintain embryos until term than Line h' . For negative lines, Line h apparently had a reduced incidence of embryonic loss when compared with Line s . In conclusion, selection for body weight modified ovarian structure, as well as reproductive efficiency.     

A comparison of restricted selection procedures to control genetic gains

Using Monte Carlo simulation, two schemes of restricted selection were compared under various combinations of genetic parameters and constraints on the genetic gains. The first selection scheme is the combination of best linear unbiased prediction (BLUP) evaluation and linear programming technique (BLUP + LP), and the second one is based on the restricted BLUP selection (RBLUP). Selection for two traits was supposed, in which animals were selected to maximize the genetic gain in trait 2 (Δg₂) under a proportional restriction on the genetic gain in trait 1 (Δg₁) to satisfy the intended ratio (Δg₁:Δg₂). Little differences were found between the two selection schemes with respect to the genetic gains averaged over replicates. However, in all the cases studied, the variance of genetic gains among replicates under BLUP + LP selection was smaller and less sensitive to the genetic parameters and the intended restriction than RBLUP selection. Under the situations of antagonistic selection, the difference tended to be larger. When the heritabilities of the two traits were different, RBLUP selection remarkably increased the variance of genetic gain in a trait with a higher heritability. These results suggest that BLUP + LP selection should always be preferable to RBLUP selection because of the smaller risk of selection. This choice is especially important for the situation where the genetic parameters act as limiting factors for the achievement of intended genetic gains.     

Genetic Relations between Reproduction,Chick Weight and Maternal Egg Composition in a White Leghorn Line

Selection is a viable way to increase egg dry matter, an important trait for the egg processing industry, but simultaneously a change in the embryonic environment takes place. The main purpose of this study was to estimate genetic parameters for the percentage of fertile eggs of eggs set (FERT), percentage of eggs hatched of fertile eggs (HATCH), percentage of live chicks 2 weeks post-hatch of hatched eggs (SURV/h) and of fertile eggs (SURV), and their genetic correlations with egg weight, albumen weight, yolk weight, yolk proportion, albumen dry matter and mean chick weight in a White Leghorn selection line. Direct and maternal heritabilities were low for FERT, HATCH and SURV, and non-existent for SURV/h. All direct-direct genetic correlations between reproduction traits and egg composition traits were not significant. Maternal-direct genetic correlations between HATCH and egg weight, albumen weight, yolk weight, yolk proportion and albumen dry matter were - 0.22, - 0.30, 0.28, 0.52 and 0.26, respectively. Similar correlations were found between SURV and egg composition traits. No significant genetic relationship was found between chick weight and post-hatch survival. In conclusion, within the range of values for egg composition in this study, selection for an increased egg dry matter should not impair reproduction.     

Hematologic evaluation of normal and anemic lambs with the Technicon H*1 using EDTA or heparin as anticoagulants

Abstract: A study was performed to evaluate blood from young lambs using the Technicon H*1 hematology analyzer, with emphasis on RBC parameters, comparison of tripotassium EDTA and heparin, and the effects of storage on heparinized blood. Blood samples from lambs 2 days to 18 weeks of age were analyzed within 6 hours, revealing a high precision, except for WBC counts in heparinized blood. The HCT values estimated by the H*1 correlated well (r²= .90) with those obtained by the microhematocrit method. Mean hematologic values obtained for heparinized blood differed by up to 4% from values obtained for blood collected into EDTA. WBC counts decreased 8.4% in heparinized blood stored at 4°C for 1 day, but differences observed in RBC counts were ≤ 2%. Problems occurred when analyzing blood from young lambs with low hemoglobin values because the H*1 incorrectly counted microcytes with volumes of < 10 fL as platelets. When the necessary corrections were performed, the H*1 was useful for analyzing RBC parameters in lamb blood collected both into EDTA and into heparin.     

Validation of a Technique to Assess Radial Torsion in the Presence of Procurvatum and Valgus Deformity Using Computed Tomography: A Cadaveric Study

Objective— To validate a technique to assess radial torsion with and without procurvatum and valgus deformity using computed tomography (CT).
Study Design— Anatomic study.
Animals— Radii (n=3) from normal dogs.
Methods— Three cadaveric radii were scanned using CT (3 mm slices). Transverse image sections were assessed at the distal and proximal physeal scar parallel to the joint surface in both sagittal and dorsal planes. Anatomic landmarks of the radius were identified and torsion was measured. A hinged Ilizarov circular external skeletal fixator was constructed to create known procurvatum, valgus, and torsional deformities.
Results— Between observers results were highly correlated for calculation of torsion (r=0.972, r²=0.9448, P <.00001). Mean baseline torsion of the radius in the construct was 4.88°. At 20° procurvatum and valgus, mean calculated torsion was 5.07° (confidence interval [CI]=4.6–5.6°). At 20° procurvatum and valgus with 22.5°-induced torsion, mean measured torsion was 25.4° (expected=27.38°; CI=22.7–28.1°). At 40° procurvatum and valgus and 45°-induced torsion, mean measured torsion was 51.1° (expected=49.88°; CI=−49.2 to 53.0°).
Conclusion— Assessment of radial torsion by CT is reproducible and accurate in the presence of procurvatum and valgus antebrachial angular limb deformities in the dog.
Clinical Relevance— Despite complex presurgical planning, current measurements only allow for measurement of valgus and procurvatum deformities in the sagittal and dorsal planes, this method allows for more precise measurements of radial torsion in the transverse plane.     

Relationships among measures of growth performance and efficiency with carcass traits, visceral organ mass, and pancreatic digestive enzymes in feedlot cattle

Ninety-three crossbred steer calves (BW+/-SD=385+/-50 kg) were used (n=48 steers in yr 1, n=45 steers in yr 2) to examine the relationship among carcass traits, lean, bone, and fat proportions, visceral tissue weights, and pancreatic digestive enzyme activity with DMI, ADG, G:F, and residual feed intake. Calves were progeny from crossbred dams predominantly of Angus and Simmental breeding and were sired by Angus, Simmental, crossbred (predominantly of Angus and Simmental breeding), Charolais, or Piedmontese bulls. Steers were fed a high-moisture corn-based diet for an average of 112 d. Partial correlation analysis accounting for year, pen within year, week of slaughter within year, and sire breed was conducted. Gain:feed was negatively correlated (P 0.10) between performance measures and the pancreatic proportional content of alpha-amylase and trypsin activity (units/kg of BW). These data indicate that carcass fatness traits and changes in the proportional weight of total viscera may be negatively associated with G:F and that visceral fat weight proportion and trim and kidney fat weight proportion may be important factors influencing this relationship.     

Partitioning of genetic values associated with identified genotype and residual genotype

A simplified partition procedure was developed to partition the genetic value associated with the identified genotype (a combined genotype of all quantitative trait loci (QTL) identified) and residual genotype. The simplified partition procedure does not require the construction of mixed model equations for both identified and residual genotypes, and therefore drastically reduces the computing requirements as compared with the direct partition procedure. Both the simplified and the direct partition procedures were shown to be equivalent theoretically and experimentally. The simplified partition procedure also applies to the partitioning of other random effects such as the partition of sire effect into two components (constant and interaction sire effects) without actually solving the mixed model equations of the partitioned sire model. The relative contribution of the identified loci and the residual genotypes to the genetic value of a trait depends on their correlation (ρ _qr ) and the ratio of their genetic variances (σ² _q/ σ² _r ). Identifying more QTL or increasing QTL variance would add to the contribution of identified QTL to the total genetic value of a quantitative trait. However, the additional contribution of identifying each extra QTL increases at a decreasing rate when the correlation between identified and residual genotypes is positive, but at an increasing rate when the correlation is negative. An effective QTL-assisted selection program should consider both direct and associated effects of the identified loci.     

Genetic and economic evaluation of Japanese Black (Wagyu) cattle breeding schemes

Deterministic simulation was used to evaluate 10 breeding schemes for genetic gain and profitability and in the context of maximizing returns from investment in Japanese Black cattle breeding. A breeding objective that integrated the cow-calf and feedlot segments was considered. Ten breeding schemes that differed in the records available for use as selection criteria were defined. The schemes ranged from one that used carcass traits currently available to Japanese Black cattle breeders (Scheme 1) to one that also included linear measurements and male and female reproduction traits (Scheme 10). The latter scheme represented the highest level of performance recording. In all breeding schemes, sires were chosen from the proportion selected during the first selection stage (performance testing), modeling a two-stage selection process. The effect on genetic gain and profitability of varying test capacity and number of progeny per sire and of ultrasound scanning of live animals was examined for all breeding schemes. Breeding schemes that selected young bulls during performance testing based on additional individual traits and information on carcass traits from their relatives generated additional genetic gain and profitability. Increasing test capacity resulted in an increase in genetic gain in all schemes. Profitability was optimal in Scheme 2 (a scheme similar to Scheme 1, but selection of young bulls also was based on information on carcass traits from their relatives) to 10 when 900 to 1,000 places were available for performance testing. Similarly, as the number of progeny used in the selection of sires increased, genetic gain first increased sharply and then gradually in all schemes. Profit was optimal across all breeding schemes when sires were selected based on information from 150 to 200 progeny. Additional genetic gain and profitability were generated in each breeding scheme with ultrasound scanning of live animals for carcass traits. Ultrasound scanning of live animals was more important than the addition of any other traits in the selection criteria. These results may be used to provide guidance to Japanese Black cattle breeders.