Approaches to the management of inbreeding and relationship in the German Holstein dairy cattle population

The aim of this study was to estimate the current level of inbreeding in the German cow population and for bull dams born in Germany, to find out sires most related to different subsets of their breed and to demonstrate the negative effect of homozygosity in the case of complex vertebral malformation (CVM). Further on, the application of optimum genetic contribution (OGC) theory for the selection of bull dams and bull sires in different breeding scenarios was investigated. Levels of inbreeding for the cow population were in a low range from 0.97% to 1.70% evaluating birth years from 1996 to 1999 in a total dataset of 244,427 registered Holstein cows. The inbreeding coefficient of 8030 bull dams was much higher, i.e. 3.71%, for the birth year 1999. Increases in inbreeding of 0.19% per year indicated an effective population size of only 52 animals. Individual sires like R.O.R.A. Elevation and Hannoverhill Starbuck were highly related to potential bull dams with coefficients of relationship of 13.4% and 12.9%, respectively, whereas P.F. Arlinda Chief (16.3%) and Carlin-M Ivanhoe Bell (16.1%) were highest related to the best available AI sires. Coefficients of relationship were calculated by classes of estimated breeding values (EBV) for production traits showing highest values above 7% in the two highest EBV-classes. The optimum genetic contribution theory using official EBVs and approximative, for zero inbreeding corrected EBVs, was applied for elite matings in a breeding program embracing 30 young bulls per year to find the optimal allocations of bull sires and bull dams. Compared with the actual breeding program applied in practice, OGC-theory has the potential to increase genetic gain under the same constraint for the increase of average relationship by 13.1%. A more relaxed constraint on increase in inbreeding allowed even higher expected genetic gain whereas a more severe constraint resulted in more equal contributions of selected bull sires. Contributions from 21 selected bull sires and 30 selected bull dams for a scenario at 5% constrained relationship were used to develop a specific mating plan to minimise inbreeding in the short term in the following generation applying a simulated annealing algorithm. The expected coefficient of inbreeding of progeny was 66.3% less then the one resulting from random mating. Mating programs can address inbreeding concerns on the farm, at least in the short term, but long-term control of inbreeding in a dairy population requires consideration of relationships between young bulls entering AI progeny test programs. Significantly better EBVs of CVM-free bulls compared with CVM-carriers for the paternal fertility justify the application of OGC for elite matings.     

Optimal genetic contribution selection in Danish Holstein depends on pedigree quality

The aim of this study was to assess the importance of pedigree depth when performing optimal contribution selection as implemented in the software program EVA. This was done by applying optimal genetic contribution in the breeding program of the major Danish Dairy breed Danish Holstein. In the analyses earlier breeding decisions were considered by including all AI waiting- and young bulls and contract matings. Twenty potential sires, 2169 potential dams, 1421 AI-bulls and 754 contract matings plus pedigree animals were included. Results showed that the outcome was very dependent on quality of pedigree, also for information going more than 25 years (5–7 generations) back. The analyses showed that EVA works satisfactorily as a management tool for planning of breeding schemes with respect to contributions of sires of sons at population level in maximising the genetic gain, while controlling the increase in future inbreeding. The more weight put on the average additive genetic relationship in next generation relative to genetic merit, the lower the average merit of the matings, and the lower average additive genetic relationship among the chosen matings and the present breeding animals. Furthermore more weight on average additive genetic relationship gives a more diverse use of sires of sons. Given the potential sires and dams the average additive genetic relationship among the selected matings and the present breeding animals can be reduced from 0.1621 to 0.1495 at the cost of 0.7 genetic S.D. units at the total merit index. This reduction was obtained when selection was only on reduction of average relationship compared to selection only on genetic merit. Optimal genetic contribution selection is a promising tool for managing breeding schemes for populations facing inbreeding problems, such as Danish Holstein and other dairy breeds. However sufficient pedigree information is a necessity.     

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.     

Candidate genes for resistance to Salmonella enteritidis colonization in chickens as detected in a novel genetic cross

Salmonellosis is a zoonotic disease that is problematic for both animal production and food safety. A novel genetic cross, named the Iowa Salmonella response resource population (ISRRP), was established to elucidate the genetic control of resistance to Salmonella enteritidis (SE) colonization in young chicks, to characterize unique resistance alleles, and to estimate gene interaction effects. Outbred broiler sires were mated with dams of diverse, highly inbred, light-bodied lines to produce an F(1) generation that was informative for all heterozygous alleles of the sires. Mating F(1) sires back to dams of the corresponding inbred line produced a backcross generation. To mimic the natural route of exposure and thus afford the opportunity to investigate mucosal immunity, pathogenic SE were inoculated into the esophagus of day-old chicks. After 1 week, the SE colonizing the cecal lumen and the spleen were enumerated. Candidate genes were selected for analysis based upon one of the two criteria. Functional candidates were genes with reported activity related to the tested traits. Positional candidates were genes mapped near microsatellites that were linked, in other phases of this project, with antibody levels to SE vaccine. Broiler sire alleles of the MHC class I, NRAMP1, PSAP, and IAP1 genes showed association with SE colonization in the F(1) generation of this novel disease resistance resource population.     

Genetic and phenotypic parameter estimates for body weights and egg production in Horro chicken of Ethiopia

A breeding program has been established in 2008 to improve productivity of Horro chicken, an indigenous population in the western highlands of Ethiopia. The pedigree descended from 26 sires and 260 dams. Body weights were measured every 2 weeks from hatch to 8 weeks then every 4 weeks for the next 8 weeks. Egg production was recorded to 44 weeks of age for one generation. Genetic parameters were estimated using animal model fitted with common environmental effects for growth traits and ignoring common environment for egg production traits. Direct heritabilities ranged from low (0.15 ± 0.08), for body weight at 6 weeks, to moderate (0.40 ± 0.23), for hatch weight. Heritabilities of common environmental effects on growth were high at hatch (0.39 ± 0.10) and remained low afterwards. Age at first egg showed a very low heritability (0.06 ± 0.15). Heritabilities of egg numbers in the first, second, third, and fourth months of laying were 0.32 (±0.13), 0.20 (±0.16), 0.56 (±0.15), and 0.25 (±0.14), respectively. Heritabilities of cumulative of monthly records of egg numbers were from 0.24 ± 0.16 (for the first 2 months, EP12) to 0.35 ± 0.16 (over the 6 months, EP16). Body weight at 16 weeks of age (BW16) has a strong genetic correlation with the cumulative of monthly records: 0.92 (with EP12), 0.69 (with EP36), and 0.73 (with EP16). Besides their strong association, BW16 and EP16 showed higher heritability, relative to their respective trait categories. These two traits seemed to have common genes and utilizing them as selection traits would be expected to improve both egg production and growth performance of local chicken. However, the standard errors of estimates in this study were mostly high indicating that the estimates have low precision. Parameter estimations based on more data are needed before applying the current results in breeding programs.     

Performance of Duroc and Yorkshire boars and gilts and reciprocal breed crosses

Analyses of variance were computed for records on growth and body composition traits made in 1983 by 255 boars and gilts in selected and control lines of Durocs and Yorkshires and their reciprocal crossbreds. Previous selection over a period of several generations was mainly on an index of sow productivity including preweaning litter sizes and weight. Animals in the select lines were selected for high index values; animals in the control lines were selected to average near the mean index values of that year and line. Breeding animals in all four lines during that period were basically randomly selected with regard to growth rate or body composition traits. The same boars sired both purebred and crossbred litters in 1983. Traits analyzed were average daily gain (ADG) during a standard test period from 56 d of age to 90.7 kg and average backfat thickness (ABF) and longissimus muscle area (LMA) from ultrasonic scans at 90.7 kg. Crossbred pigs had greater (P less than .01) ADG than purebred pigs, but did not differ (P greater than .05) in ABF or LMA. Heterosis was 8.2% for ADG. Crossbreds with Yorkshire dams had thinner (P less than .01) ABF and larger (P less than .01) LMA than crossbreds with Duroc dams. Boars had greater (P less than .05) ADG, thinner (P less than .01) ABF and smaller (P less than .01) LMA than gilts. Correlations between 38 half-sib family averages of purebred and crossbred pigs of the same sex and the same sires were .07, .37 and .24 for ADG, ABF and LMA, respectively. Implications of the above and additional findings for swine breeding strategies are discussed.     

Inheritance of proportionate dwarfism in Angus cattle

OBJECTIVE: To determine the mode of inheritance of congenital proportionate dwarfism in Angus and Angus crossbred cattle, initially detected in two commercial beef herds in northern New South Wales. DESIGN: Matings of normal carrier sires to unrelated cows of diverse breeds, and of one carrier sire to his unaffected daughters. An unrelated Piedmontese bull was also mated to unaffected daughters of the carrier sires. PROCEDURE: Two carrier Angus bulls and nine unaffected daughters, all of whom were completely indistinguishable from normal animals, were purchased for controlled breeding studies under known nutritional and disease conditions. Affected and carrier individuals were examined for the presence of obvious chromosomal abnormalities. RESULTS: Angus dwarfism has been successfully reproduced under controlled experimental conditions over successive years using unrelated dams and is undoubtedly heritable. The high frequency of occurrence of affected individuals (23/61 = 0.38 +/- .06) among the progeny of matings of the Angus sires to unrelated females of diverse breeding is not compatible with recessive inheritance, because of the negligible frequency of proportionate dwarfism in the breeds of the dams. Both paternal and maternal transmission of the defect was demonstrated, so that imprinting in the strict sense of a gene that is only expressed when received from the male parent appears not to be involved. Tested individuals showed no evidence of gross chromosomal abnormality. Dominant autosomal inheritance with incomplete penetrance was indicated by the lack of expression of the defective gene in the two Angus sires and in three unaffected daughters who produced dwarf calves from matings to the Piedmontese bull. CONCLUSIONS: The mode of inheritance is that of a single autosomal dominant gene with a penetrance coefficient of 0.75 +/- 0.12, estimated from the observed incidence of 23/61 affected offspring of the two carrier Angus bulls mated to unrelated dams. Simple genetic models involving either (i) an unstable mutant which changes at high frequency to the expressed dominant dwarfing allele during gametogenesis, or (ii) a dominant allele with penetrance determined by an unlinked modifying locus, are shown to be compatible with the experimental data. Both models indicate that penetrance of the dwarfing gene may possibly be higher in matings involving carrier daughters of the two Angus bulls.     

Characterization of breeds of Bos indicus and Bos taurus cattle for maternal and individual traits

Angus, Boran and Red Poll sires were mated to Ankole, Boran and small East African Zebu (Zebu) females to produce the cows characterized in this study, which produced calves by Friesian, Brown Swiss, Simmental, Boran and Red Poll sires. Individual traits included cow parturition weight, cow weight at weaning, cow mean weight and cow weight change from parturition to weaning; maternal traits included calf crop born percentage, preweaning viability percentage, overall viability percentage, birth weight, weaning weight, weight at 12, 18 and 24 mo and calf weight weaned per cow exposed to breeding (productivity index). Cows by Angus and Red Poll sires significantly exceeded cows by Boran sires (all cows in this comparison had Ankole and Zebu dams) in weaning weight of progeny and in cow weight at parturition and at weaning. Cows by Red Poll sires significantly exceeded cows by Boran sires in birth weight of progeny. Progeny of cows by Boran sires significantly exceeded progeny of cows by Angus and Red Poll sires in 24-mo weight. Cows by Angus and Red Poll sires did not differ (P greater than .05) in any of the traits analyzed. Cows with Ankole and Boran dams significantly exceeded cows with Zebu dams (all cows in this comparison had Angus and Red Poll sires) in progeny weight at birth, 18 mo and 24 mo and in cow weight at parturition and at weaning. Cows with Boran dams significantly exceeded cows with Zebu dams in weaning and 12-mo weight of progeny and significantly exceeded cows with Ankole dams in weaning weight of progeny. The significantly heavier weaning weight and significantly lighter 24-mo weight of the 3/4 Bos taurus progeny of cows with Angus and Red Poll sires relative to the 1/2 Bos taurus progeny of cows with Boran sires suggest that cattle that are 1/2 Bos taurus breed composition have greater general adaptation than cattle with 3/4 Bos taurus breed composition in the postweaning nutritive and climatic environment under which this experiment was conducted. Significantly heavier weights of Angus and Red Poll crossbred cows relative to Boran crossbred cows (all breeds crossed on Ankole and Zebu cows) indicate that the two Bos taurus breeds exceed the Boran (Bos indicus) breed in additive direct genetic effects for size when they have general adaptation to the environment.     

Evaluation of expected response to selection for orthopedic health and performance traits in Hanoverian Warmblood horses

OBJECTIVE: To determine whether selection schemes accounting for orthopedic health traits were compatible with breeding progress in performance parameters in Hanoverian Warmblood horses. ANIMALS: 5,928 horses. PROCEDURE: Relative breeding values (RBVs) were predicted for osseous fragments in fetlock (metacarpo- and metatarsophalangeal) and tarsal joints, deforming arthropathy in tarsal joints, and pathologic changes in distal sesamoid bones. Selection schemes were developed on the basis of total indices for radiographic findings (TIR), dressage (TID), and jumping (TIJ). Response to selection was traced over 2 generations of horses for dressage and jumping ability and all-purpose breeding. Development of mean RBVs and mean total indices in sires and prevalences of orthopedic health traits in their offspring were used to assess response to selection. RESULTS: Giving equal weight toTIR andTID, TIJ, or a combined index of 60% TID and 40% TIJ, 43% to 53% of paternal grandsires and 70% to 82% of descending sires passed selection. In each case, RBVs and total indices increased by as much as 9% in selected sires, when compared with all sires, and prevalences of orthopedic health traits in offspring of selected sires decreased relatively by as much as 16%. When selection was exclusively based on TID, TIJ, or TID and TIJ, percentages of selected sires were 44% to 66% in the first and 73% to 84% in the second generation and TID and TIJ increased by 9% to 10% and 19% to 23%, respectively. CONCLUSIONS AND CLINICAL RELEVANCE: Compared with exclusively performance-based selection, percentages of selected sires changed slightly and breeding progress in TID, TIJ, or TID and TIJ was only slightly decreased; however, prevalences of orthopedic health traits decreased in offspring of TIR-selected sires.     

Evaluation of the efficiency of alternative two-tier nucleus breeding systems designed to improve meat sheep in Kenya

A deterministic approach was used to genetically and economically evaluate the efficiency of five two‐tier nucleus breeding systems for meat sheep in Kenya. The nucleus breeding systems differed in terms of whether the system was closed or open, in the type of animals that were involved in the movement of genetic superiority and in the number of selection pathways in each system. These systems were compared under four alternative breeding objectives based on monetary genetic gain and profit per ewe. The first objective simulated a situation where the flock size cannot be increased due to non‐feed related constraints (FLOCK). The second specifically assumed that the flock size is restricted due to limited amount of feed resources (FEED). The third and fourth objectives assumed that sheep performed only tangible roles (TR) and both tangible and intangible roles (IR) in the production system respectively. Monetary genetic gains were highest for all objectives in an open nucleus system with a certain proportion of commercial‐born ewes being introduced in the nucleus while at the same time utilizing young rams from the nucleus to breed sires and dams for the nucleus and commercial sector (ONyre). Utilizing young rams in a closed nucleus system for the dissemination of superior genes resulted in higher annual monetary genetic gain than utilization of old rams. Profit per ewe was significantly higher for FLOCK and IR in ONyre. In a closed system that allowed for downward movement of dams from the nucleus to the commercial sector to breed sires and dams, profit per ewe was highest for FEED and TR. The success of a nucleus breeding system should also focus on the profitability and logistics of establishing it. The implication of these results on the choice of two‐tier nucleus breeding systems for the improvement of meat sheep is discussed.     

Selection for immune response in goats: the antibody response to diphtheria toxoid after 12 years of selection.

A herd of Norwegian dairy goats was subject to selection for high and low antibody response to diphtheria toxoid for 12 yr, or approximately 5.5 generations because sires were used for one mating season, whereas dams were used several years. The herd comprised approximately 100 milking goats. Only sires were tested and selected, five to seven sires were used in each line each year, and the percentage of male kids used for breeding varied between 15 and 50%. The mean phenotypic values of the lines diverged until the 4th yr, but the lines did not diverge any further. The means of both lines decreased during the experimental period. The restricted maximum likelihood (REML) estimate of the heritability of the trait in the base population was .19, whereas the realized heritability approached zero in the last six cycles of selection. Using the REML-estimate of heritability in an individual animal model, the mean breeding values (BLUP) of the lines were significantly different. The difference in mean BLUP values between the lines increased throughout the study. Yet, this increase was only 40% from the 2nd to the 12th yr. No effect of a major gene was observed in a test based on individual BLUP.     

Genetic and economic evaluation of a basic breeding programme for Kenya Boran cattle

The objective of this study is to describe the present organisational structure of Boran cattle breeding and develop a model breeding programme using a deterministic approach under the current structure of the Boran Cattle Breeders Society. A breeding unit of 13,000 cows supplying bulls to a commercial population of 39,000 cows was assumed. Selection criteria used were growth and reproduction traits while breeding objective traits targeted were growth, carcass, reproduction, survival, milk yield and feed intake traits. Higher selection intensity was possible for breeding sires resulting in higher genetic gains compared to dams even though selection accuracies were generally low. Annual genetic gains were positive except for dressing percentage, cow survival rate, and age at first calving. However, a reduction of age at first calving by 9.5 days obtained a return of Ksh 49.76. The overall monetary genetic gain obtained was Ksh 84.89 with a profit per cow per year of Ksh 377.98. The basic breeding programme could be expanded to accommodate a larger population of Boran cattle. The implications of the results are also discussed.     

Dam and Sire Effects on Sperm Penetration of the Perivitelline Layer of Eggs Produced by Two Strains of Commercial Turkeys

The reproductive performance of 2 commercial turkey breeder lines was examined using reciprocal crosses between sires and dams of each line. One line had been selected using artificial inseminations performed at biweekly intervals, whereas the second line had been selected using inseminations performed at weekly intervals. The hypothesis was proposed that sires and dams of the 2 lines differ because of different abilities for sperm to penetrate the inner perivitelline layer (IPVL) and fertilize eggs.Fertilized eggs to hatch poults for the experiment were obtained from the primary breeders and were incubated using conditions recommended by the industry. Hens (n = 72) and toms (n = 15) from each strain were identified and reared in preparation for a reproductive cycle using commercially accepted standards. Beginning just prior to the onset of egg production and at weekly intervals thereafter, half of the hens were inseminated with semen from males of the same line, whereas the remaining half received semen from the opposite line. Eggs were collected from the pens daily and set in incubators to determine fertility and embryo survival. At biweekly intervals 3 eggs per pen were used for counting sperm penetration holes in the IPVL. Data were collected for fertility, hatchability, and time that embryos died for each of the pens. Dam and sire affected IPVL penetration independently. A dam by sire interaction influenced fertility, whereas hatchability was affected only by dam. Thus, it is concluded that selection of dam and sires for commercial breeders alters IPVL sperm penetration ability of hens as well as egg-binding ability of sires.     

Molecular diagnosis of inherited neuromuscular disease.

Prevention of inherited disease in companion animals is largely dependent on prebreeding identification of carriers of autosomal recessive disease traits. Molecular diagnosis is emerging as a convenient and reliable method of carrier detection, but few molecular diagnostic tests of inherited neuromuscular disease are readily available. New test development depends on investigations to determine disease genes and the disease causing mutations. A general approach to molecular diagnosis of inherited disorders is discussed.     

Growth traits and composition of two- and three-way-cross intact male progeny of Bos taurus and Bos indicus X Bos taurus dams

Feedlot traits, carcass traits and distribution of commercial cuts of crossbred intact male progeny (n = 556) from young and mature Hereford, Red Poll, Hereford X Red Poll, Red Poll X Hereford, Angus X Hereford, Angus X Charolais, Brahman X Hereford and Brahman X Angus dams were evaluated. First-calf heifers were bred to Red Angus bulls; Santa Gertrudis sires were used for each cow's second and third breeding seasons. Calves from these young dams were slaughtered at 13 mo. Calves of mature dams were all sired by Limousin bulls and slaughtered at 12 mo. Dam breed was a major source of variation in most bull traits. Progeny of Brahman-cross dams were inferior (P less than .01) in daily gain, final weight, carcass weight and in edible cuts/day of age compared with progeny from Bos taurus dams. Intact male progeny of Angus X Charolais dams ranked highest in longissimus area, cutability, and edible cuts/day of age. The range of dam breed means in percentage of steak, roast, bone-in cuts (chuck short ribs and back ribs), short plate and thin cuts, and lean trim was just over 1%. Greater variation among dam breeds existed in fat measurements. Analyses in which Hereford-Red Poll diallel data for young dams and mature dams were combined showed positive maternal heterosis for dressing percentage (P less than .05), carcass weight (P less than .05), carcass weight/day of age (P less than .05), estimated carcass fat (P less than .05), fat thickness (P less than .01) and marbling score (P less than .01). Reciprocal effects were inconsequential. Results illustrate the importance of dam breed-type effects in formulating breeding strategies for commercial beef herds.     

Results from nine generations of selection for increased litter size in swine

Direct selection for increased litter size was done for nine generations. The select line consisted of approximately 15 sires and 60 dams per generation, and selection was based on estimated breeding values for number of live pigs. A control line of approximately 10 sires and 30 dams was maintained with stabilizing selection. Heritabilities estimated in the select line using restricted maximal likelihood procedures, daughter-dam regression within sires, and half-sib analysis were 0.01, 0.04, and 0.00 for number of pigs born alive (NBA) and 0.02, 0.16, and 0.00 for total born per litter (TB). Corresponding estimates for the control line were 0.01, 0.06, and 0.23 and 0.02, 0.07, and 0.09 for NBA and TB, respectively. Realized heritabilities for NBA from multiple regression were 0.09 +/- 0.08 in the select line and 0.11 +/- 0.166 in the control line. Heritability estimated from regression of differences in response between lines on differences in cumulative selection differentials was 0.13 +/- 0.07. At Generation 9, litter sizes, estimated breeding values, and cumulative selection differentials were 0.86 (P < 0.05), 0.63 (P < 0.01), and 9.05 (P < 0.01) pigs larger for the select line than for the control line. Phenotypic differences between lines for TB, adjusted backfat (BF), and days to 104 kg (DAYS) were not significant. Genetic trends in the select line were 0.053 +/- 0.002 pigs/yr for NBA, 0.054 +/- 0.013 mm/yr for BF, and 0.398 +/- 0.110 d/yr for DAYS. Corresponding phenotypic trends were 0.145 +/- 0.051 pigs/yr, -0.012 +/- 0.089 mm per yr, and 0.307 +/- 0.278 d/yr, respectively. Genetic trends in the control line were -0.026 +/- 0.004 pigs/yr for NBA, 0.026 +/- 0.022 mm/yr for BF, and -0.532 +/- 0.182 d/yr for DAYS. Corresponding phenotypic trends were 0.001 +/- 0.085 pigs/yr, -0.043 +/- 0.147 mm/yr, and -0.519 +/- 0.462 d/yr, respectively. Litter size can be increased by direct selection using breeding values estimated from an animal model, in conjunction with rearing selected gilts in litters of 10 pigs or less.     

Optimum contribution selection using traditional best linear unbiased prediction and genomic breeding values in aquaculture breeding schemes

The aim of this study was to compare genetic gain for a traditional aquaculture sib breeding scheme with breeding values based on phenotypic data (TBLUP) with a breeding scheme with genome-wide (GW) breeding values. Both breeding schemes were closed nuclei with discrete generations modeled by stochastic simulation. Optimum contribution selection was applied to restrict pedigree-based inbreeding to either 0.5 or 1% per generation. There were 1,000 selection candidates and a sib test group of either 4,000 or 8,000 fish. The number of selected dams and sires to create full sib families in each generation was determined from the optimum contribution selection method. True breeding values for a trait were simulated by summing the number of each QTL allele and the true effect of each of the 1,000 simulated QTL. Breeding values in TBLUP were predicted from phenotypic and pedigree information, whereas genomic breeding values were computed from genetic markers whose effects were estimated using a genomic BLUP model. In generation 5, genetic gain was 70 and 74% greater for the GW scheme than for the TBLUP scheme for inbreeding rates of 0.5 and 1%. The reduction in genetic variance was, however, greater for the GW scheme than for the TBLUP scheme due to fixation of some QTL. As expected, accuracy of selection increased with increasing heritability (e.g., from 0.77 with a heritability of 0.2 to 0.87 with a heritability of 0.6 for GW, and from 0.53 and 0.58 for TBLUP in generation 5 with sib information only). When the trait was measured on the selection candidate compared with only on sibs and the heritability was 0.4, accuracy increased from 0.55 to 0.69 for TBLUP and from 0.83 to 0.86 for GW. The number of selected sires to get the desired rate of inbreeding was in general less in GW than in TBLUP and was 33 for GW and 83 for TBLUP (rate of inbreeding 1% and heritability 0.4). With truncation selection, genetic gain for the scheme with GW breeding values was nearly twice as large as a scheme with traditional BLUP breeding values. The results indicate that the benefits of applying GW breeding values compared with TBLUP are reduced when contributions are optimized. In conclusion, genetic gain in aquaculture breeding schemes with optimized contributions can increase by as much as 81% by applying genome-wide breeding values compared with traditional BLUP breeding values.     

Broomfield Corriedales: a strain of sheep selectively bred for resistance to footrot

Broomfield Corriedales originate from a 15-year programme of selective breeding from sheep that evaded footrot when deliberately subjected to field challenge. To determine whether this policy may have resulted in improved resistance to footrot, trials were set up in which representative animals from the Broomfield blood-line were challenged with footrot by either experimental or natural infection, together with Corriedale sheep of similar age and sex but from flocks in which the disease is not known to occur. In another approach, the occurrence of footrot was compared in the offspring of Broomfield and of non-Broomfield sires mated with randomly selected ewes in a commercial Corriedale flock in which the condition was prevalent. Finally, the effects of natural challenge in Broomfield lambs were compared with those in a selection line of Corriedale lambs of which both parents had a history of chronic footrot disease. Footrot affected significantly fewer sheep of the Broomfield blood-line and to a markedly lesser degree than those chosen for comparison under identical challenge conditions. Where present, foot infections in Broomfield animals also tended to be less invasive and less persistent. Reduced footrot prevalence was also demonstrated in three birth cohorts of first-cross offspring of Broomfield sires relative to the offspring of other sires, though differences were not significant at all inspections. These findings, considered as a supplement to the historical development of the Broomfield flock, offer encouraging prospects for breeding programmes to enhance the resistance of sheep to footrot disease.     

Selection in Hereford cattle. I. Selection intensity, generation interval and indexes in retrospect

Selection intensity and generation interval were evaluated in a Hereford cattle herd made up of 14 inbred lines and 14 linecross groups corresponding to the lines of inbred sires at the Suan Juan Basin Research Center, Hesperus, Colorado. Selection indexes practiced were calculated in retrospect. Analyses of the records collected from 1946 through 1973 involved weaning weight (WW) and postweaning traits in males and females. Analyses by line were performed for the inbreds, while pooled analyses were done on the inbred and linecross populations. From records of 1,239 calves weaned, age of sire averaged 3.75 yr compared with 4.52 yr for age of dam, showing faster generation turnover for sires than for dams. Generation interval determined as actual age of midparent was 4.13 yr. Selection applied for WW, evaluated as annual selection differentials within inbred lines and then pooled over all lines, averaged .55 standard deviations (sigma)/generation for sires. For females, selection was much less intense. Midparent selection differential amounted to .33 sigma/generation. For sires, pooled standardized selection differentials per generation over all lines during the postweaning gain period were .49 sigma, .46 sigma, .40 sigma, -.20 sigma, -.10 sigma and .69 sigma, respectively, for initial weight, final weight, feed consumed, feed efficiency (FE, unadjusted and adjusted) and average daily gain (ADG). Selection of females for postweaning traits was not intense. Selection index actually practiced in retrospect for sires was: IS = .4461 (WW) - .0092 (FE) + .6126 (ADG). The indexes for dams included WW, 12-mo weight (12W), 18-mo weight (18W), mature spring weight (SPW) and mature fall weight (FAW) and were: for inbred dams, ID = .1824 (WW) - .0284 (12W) + .0736 (18W) - .1097 (SPW) - .1097 (FAW); for linecross dams, ID = .2693 (WW) - .2960 (12W) + .0147 (18W) + .1185 (SPW) - .0354 (FAW). The corresponding index selection differentials were .818, .203 and .209. Sire index selection differentials represent about 79% of the total selection differentials.     

Heritability and epidemiology of canine hip-dysplasia score in flat-coated retrievers and Newfoundlands in the United Kingdom

Hip dysplasia (malformation of the coxofemoral joint) in dogs is a major health problem for which the British Veterinary Association (BVA) had set up a control scheme in 1965. Based on scoring nine components of the radiographs of both the left and right joints, the degree of hip joint malformation is now quantified by an overall hip score (a measure of the condition of the hip joint). The hip scores of 1258 flat-coated retrievers and 1566 Newfoundlands (registered with The Kennel Club in the United Kingdom) were analysed after merging with Kennel Club pedigree data for 19036 flat-coated retrievers registered by 1995 and 14336 Newfoundlands registered by 1997. The merged data included the animal's identity, date of birth, sex and hip scores and also similar records for the dog's relatives including the hip score if the relative had been tested. In recent years, breeding has been increasingly from tested parents. There has been some reduction in offspring hip scores - presumably because breeders avoided breeding from males with very high scores. However, a much greater reduction in offspring hip score would be achieved by stricter science-based selection of potential sires and dams. Regression modelling quantified the positive relationship between offspring and parental hip scores. The genetic heritability of hip scores was large and significant in both breeds (particularly from dams). The breeders in UK tended to use healthy sires for breeding but they have taken less care in selecting dams. Our regression models emphasise the need for both sires and dams, particularly dams, to be healthy with very small hip scores.