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1.
Single‐step genomic predictions need the inverse of the part of the additive relationship matrix between genotyped animals ( A 22). Gains in computing time are feasible with an algorithm that sets up the sparsity pattern of (SP algorithm) using pedigree searches, when is close to sparse. The objective of this study is to present a modification of the SP algorithm (RSP algorithm) and to assess its use in approximating when the actual is dense. The RSP algorithm sets up a restricted sparsity pattern of by limiting the pedigree search to a maximum number of searched branches. We have tested its use on four different simulated genotyped populations, from 10 000 to 75 000 genotyped animals. Accuracy of approximation is tested by replacing the actual by its approximation in an equivalent mixed model including only genotyped animals. Results show that limiting the pedigree search to four branches is enough to provide accurate approximations of , which contain approximately 80% of zeros. Computing approximations is not expensive in time but may require a great amount of memory (at maximum, approximately 81 min and approximately 55 Gb of RAM for 75 000 genotyped animals using parallel processing on four threads).  相似文献   

2.
The current study evaluates reliability of genomic predictions in selection candidates using multi‐trait random regression model, which accounts for interactions between marker effects and breed of origin in the Nordic Red dairy cattle (RDC). The population structure of the RDC is admixed. Data consisted of individual animal breed proportions calculated from the full pedigree, deregressed proofs (DRP) of published estimated breeding values (EBV) for yield traits and genotypic data for 37 595 single nucleotide polymorphic markers. The analysed data included 3330 bulls in the reference population and 812 bulls that were used for validation. Direct genomic breeding values (DGV) were estimated using the model under study, which accounts for breed effects and also with GBLUP, which assume uniform population. Validation reliability was calculated as a coefficient of determination from weighted regression of DRP on DGV (), scaled by the mean reliability of DRP. Using the breed‐specific model increased the reliability of DGV by 2 and 3% for milk and protein, respectively, when compared to homogeneous population GBLUP. The exception was for fat, where there was no gain in reliability. Estimated validation reliabilities were low for milk (0.32) and protein (0.32) and slightly higher (0.42) for fat.  相似文献   

3.
Models for genetic evaluation of feed efficiency ( FE ) for animals housed in groups when they are either fed ad libitum ( F ) or on restricted ( R ) feeding were implemented. Definitions of FE on F included group records of feed intake () and individual records of growth rate ( GF ) and metabolic weight ( MF ). Growth rate ( GR ) as FE measurement on R was used. Data corresponded to 5,336 kits from a rabbit sire line, from 1,255 litters in 14 batches and 667 cages. A five‐trait mixed model (also with metabolic weight on R, MR ) was implemented including, for each trait, the systematic effects of batch, body weight at weaning, parity order and litter size; and the random effects of litter, additive genetic and individual. A Bayesian analysis was performed. Conditional traits such as and were obtained from elements of additive genetics ( and ) or phenotypic ( and ) (co)variance matrices. In the first case, heritabilities were low (0.07 and 0.06 for and , respectively) but null genetic correlation between the conditional and conditioning traits is guaranteed. In the second case, heritabilities were higher (0.22 and 0.16 for and , respectively) but the genetic correlation between and was moderate (0.58). Heritability of GR was low (0.08). This trait was negatively correlated with and of animals on F, which indicate a different genetic background. The correlation between GR and GF was also low to moderate (0.48) and the additive variance of GF was almost four times that of GR, suggesting the presence of a substantial genotype by feeding regimen interaction.  相似文献   

4.
The availability of genomic information demands proper evaluation on how the kind (phenotypic versus genomic) and the amount of information influences the interplay of heritability (h2), genetic correlation () and economic weighting of traits with regard to the standard deviation of the index (σI). As σI is directly proportional to response to selection, it was the chosen parameter for comparing the indices. Three selection indices incorporating conventional and genomic information for a two trait (i and j) breeding goal were compared. Information sources were chosen corresponding to pig breeding applications. Index I incorporating an own performance in trait j served as reference scenario. In index II, additional information in both traits was contributed by a varying number of full‐sibs (2, 7, 50). In index III, the conventional own performance in trait j was combined with genomic information for both traits. The number of animals in the reference population (NP = 1000, 5000, 10 000) and thus the accuracy of GBVs were varied. With more information included in the index, σI became more independent of , and relative economic weighting. This applied for index II (more full‐sibs) and for index III (more accurate GBVs). Standard deviations of index II with seven full‐sibs and index III with NP = 1000 were similar when both traits had the same heritability. If the heritability of trait j was reduced ( = 0.1), σI of index III with NP = 1000 was clearly higher than for index II with seven full‐sibs. When enhancing the relative economic weight of trait j, the decrease in σI of the conventional full‐sib index was much stronger than for index III. Our results imply that NP = 1000 can be considered a minimum size for a reference population in pig breeding. These conclusions also hold for comparing the accuracies of the indices.  相似文献   

5.
Investigation of genetic structure on the basis of pedigree information requires indicators adapted to the specific context of the populations studied. On the basis of pedigree‐based estimates of diversity, we analysed genetic diversity, mating practices and gene flow among eight cat populations raised in France, five of them being single breeds and three consisting of breed groups with varieties that may interbreed. When computed on the basis of coancestry rate, effective population sizes ranged from 127 to 1406, while the contribution of founders from other breeds ranged from 0.7 to 16.4%. In the five breeds, FIS ranged between 0.96 and 1.83%, with this result being related to mating practices such as close inbreeding (on average 5% of individuals being inbred within two generations). Within the three groups of varieties studied, FIT ranged from 1.59 to 3%, while values were estimated between 0.04 and 0.91%, which was linked to various amounts of gene exchanges between subpopulations at the parental level. The results indicate that cat breeds constitute populations submitted to low selection intensity, contrasting with relatively high individual inbreeding level caused by close inbreeding practices.  相似文献   

6.
In recent years, with development and validation of different genotyping panels, several methods have been proposed to build efficient similarity matrices among individuals to be used for genomic selection. Consequently, the estimated genetic parameters from such information may deviate from their counterpart using traditional family information. In this study, we used a pedigree-based numerator relationship matrix ( A ) and three types of marker-based relationship matrices () including two identical by descent, that is and and one identical by state, as well as four Gaussian kernel () similarity kernels with different smoothing parameters to predict yet to be observed phenotypes. Also, we used different kinship matrices that are a linear combination of marker-derived IBD or IBS matrices with A, constructed as , where the weight () assigned to each source of information varied over a grid of values. A Bayesian multiple-trait Gaussian model was fitted to estimate the genetic parameters and compare the prediction accuracy in terms of predictive correlation, mean square error and unbiasedness. Results show that the estimated genetic parameters (heritability and correlations) are affected by the source of the information used to create kinship or the weight placed on the sources of genomic and pedigree information. The superiority of GK -based model depends on the smoothing parameters (θ) so that with an optimum θ value, the GK -based model statistically yielded better performance (higher predictive correlation, lowest MSE and unbiased estimates) and more stable correlations and heritability than the model with IBD, IBS or kinship matrices or any of the linear combinations.  相似文献   

7.
Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect of the microbiota composition on the breeding value of an animal is the conditional expectation of its breeding value, given the vector with microbiota frequencies, that is The breeding value of an animal can therefore be decomposed into a heritable contribution that arises from an altered microbiota composition and a heritable contribution that arises from altered metabolic pathways within the animal, so Instead of selecting for breeding value , an index comprising the two components and with appropriate weights, that is , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.  相似文献   

8.
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9.
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10.
Supplementing ruminants with nitrate reduces their enteric methane (CH4) emissions; however, the greenhouse gas (GHG) mitigation achieved can be partially offset by small emissions of nitrous oxide (N2O), a more potent GHG. Sheep were dosed intraruminally with 15 to investigate whether dietary is a precursor of N2O and/or di‐nitrogen gas (N2), and to quantify the amounts of recovered as N2O and N2 in gas emissions from sheep adapted or not adapted to dietary . Ruminally cannulated sheep were adapted to a hay diet supplemented with (n = 3; 10 g /kg DM) or urea (n = 3; 5.3 g urea/kg DM). On the day of the experiment all sheep were dosed intraruminally with 15 and quickly moved into gas‐tight chambers to enable recovery of 15N in N2O and N2 to be measured. Measurements of gases accumulating in the chambers were made over 10 successive 50 min periods; this enabled the amount of N2O produced, and the recovery of 15‐N in N2O and N2 to be determined over a total of 10 hr. Only 0.04% of labelled ‐N was recovered as N2O, and this was not dependent (p > .05) on whether or not the animals had been adapted to dietary . Approximatively 3% of 15‐N was recovered as 15N2, which was also not dependent (p > .05) on whether sheep had been adapted to . Because the kinetics of rumen ammonia (NH3) were uncertain, the recovery of 15N from in rumen NH3 could not accurately be quantified, but our results suggest that approximately 76% of dietary was converted to NH3 in the rumen. We conclude that the small amount of recovered in N2 was evidence of denitrification, previously thought not to occur in the rumen.  相似文献   

11.
This study aimed to describe the population genetic structure and evaluate the state of conservation of the genetic variability of Santa Inês sheep in Brazil. We used pedigree data of the Santa Inês breed available in electronic processing of the Brazilian Association of Sheep Breeders. A file with 20,206 records, which enabled the calculation of the genetic conservation index (GCI), individual inbreeding coefficient (F), change in inbreeding (ΔF), effective population size (Ne), effective number of founders (?e), effective number of ancestors (?ɑ), generation interval (L), average relatedness coefficient of each individual (AR), and Wright’s F-statistics (F IT, F IS, and F ST). For pedigree analysis and calculation of population parameters, the program ENDOG was used. The average inbreeding coefficient (\( \overline{F} \)) was 0.97% and the mean average relatedness (\( \overline{\mathrm{AR}} \)) 0.49%. The effective numbers of founders and ancestors were, respectively, 199 and 161. The average values of F and AR increased significantly over the years. The effective population size fluctuated over the years concurrently to oscillations in inbreeding rates, wherein N e reached just 68 in the year 2012. The mean average generation interval was 5.3 years. The Santa Inês breed in Brazil is under genetic drift process, with loss of genetic variation. It requires the implementation of a genetic management plan in the herd, for conservation and improvement of the breed.  相似文献   

12.
Because of few available data on semen parameters in small breed dogs, the study aimed to analyse semen and measure testes of dogs ≤10.0 kg bodyweight. Semen was collected from 41 fertile stud dogs, which were divided based on bodyweight: group 1 ≤ 5.0 kg and group 2 between 5.1 and 10.0 kg. Median values for ejaculate volume (group 1: 1.2 ml; group 2: 2.2 ml), total sperm output (group 1: 110.7 × 106; group 2: 215.1 × 106) and testicular volume (group 1: left testicle 2.8 ml, right testicle 2.7 ml; group 2: left testicle 5.5 ml, right testicle 5.0 ml) were lower in group 1 compared to dogs of group 2 (p = .001; p = .001; both testes: p < .001). There was no difference in sperm concentration (p = .985). Based on these results, introduction of an additional weight group to the commonly used reference values is recommended, since values for ejaculate volume, total sperm output and testicular dimensions for dogs ≤5.0 kg bodyweight differed significantly from values of dogs with a bodyweight from 5.1 to 10.0 kg.  相似文献   

13.
SUMMARY: The population structure of two Finnish hunting dog breeds was examined, by calculating generation intervals and inbreeding coefficients. Data sets consisted of registers, including 84338 Finnish Hounds and 28370 Finnish Spitzes. The mean values for paternal generation intervals were 5.8 years in the Hound and 5.7 years in the Spitz. The mean values for maternal generation intervals were 5.0 and 4.5 years in the two breeds, respectively. The average inbreeding coefficient was 3.12% in the Finnish Hound and 7.16% in the Finnish Spitz. The use of intense inbreeding had decreased during the last few years, especially in the Spitz. The expected average inbreeding coefficients, calculated on the basis of random mating simulations, were usually somewhat lower than the observed in both breeds. This implies that linebreeding or mild inbreeding has been used as a breeding method. ZUSAMMENFASSUNG: Generationsintervall und Inzuschtkoeffizienten in Finnischen Spitz und Bracken Hunden Die Populationsstruktur der beiden Finnischen Jagdhunderassen wurde in Hinblick auf Generationsintervall und Inzucht untersucht. Die Daten umfa?ten Registration von 84338 Bracken und 28370 Spitz. Das v?terliche Generationsintervall war 5, 8 Jahre bei Bracken und 5, 7 bei Spitz, das mütterliche 5, 0 und 4, 7 Jahre. Der durchschnittliche Inzuchtkoeffizient war 3, 12% beim Finnischen Bracken und 7, 16% beim Finnischen Spitz. Enge Inzucht hat in den letzten Jahren abgenommen, besonders beim Spitz. Die erwartete Inzucht wurde anhand von Simulation zuf?lliger Paarung gesch?tzt und ergab etwas geringere Werte als die tats?chliche in beiden Rassen. Das deutet auf praktizierte Linienzucht und geringe Inzucht in der Zuchtarbeit.  相似文献   

14.
The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability of the Mazandaran native fowls in Iran by quantifying the pedigree completeness index, effective population size, genetic diversity, inbreeding level, and individual increase in inbreeding. The pedigree completeness analysis showed 3.31 full, 10.19 maximum, and 6.30 equivalent generations. The effective number of founders (f e) was 131, representing 5% of the potential number of founders. The effective number of ancestors (f a) was 81, and the genetic contribution of the 37 most influent ancestors explained 50% of the genetic variability in the population. The ratio f e/f a (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.62. The inbreeding coefficient increased over generations and the average was 1.93%. The average relatedness coefficient between individuals of the population was estimated to be 2.59%. The effective population size, based on the number of full generations, was 56. Family size analysis showed that fewer males than females were used, resulting in the observed levels of inbreeding. Average inbreeding coefficient in the Mazandaran native fowls can be regarded to be below critical levels. However, considering the relationship coefficients of individuals is recommended to aid maintaining genetic diversity of Mazandaran native fowls.  相似文献   

15.
The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (Nge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on Nge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.  相似文献   

16.
This study investigated genomic predictions across Nordic Holstein and Nordic Red using various genomic relationship matrices. Different sources of information, such as consistencies of linkage disequilibrium (LD) phase and marker effects, were used to construct the genomic relationship matrices (G‐matrices) across these two breeds. Single‐trait genomic best linear unbiased prediction (GBLUP) model and two‐trait GBLUP model were used for single‐breed and two‐breed genomic predictions. The data included 5215 Nordic Holstein bulls and 4361 Nordic Red bulls, which was composed of three populations: Danish Red, Swedish Red and Finnish Ayrshire. The bulls were genotyped with 50 000 SNP chip. Using the two‐breed predictions with a joint Nordic Holstein and Nordic Red reference population, accuracies increased slightly for all traits in Nordic Red, but only for some traits in Nordic Holstein. Among the three subpopulations of Nordic Red, accuracies increased more for Danish Red than for Swedish Red and Finnish Ayrshire. This is because closer genetic relationships exist between Danish Red and Nordic Holstein. Among Danish Red, individuals with higher genomic relationship coefficients with Nordic Holstein showed more increased accuracies in the two‐breed predictions. Weighting the two‐breed G‐matrices by LD phase consistencies, marker effects or both did not further improve accuracies of the two‐breed predictions.  相似文献   

17.
A pedigree including 1538 individuals of the endangered pig breed ‘Bunte Bentheimer’ and 3008 records of the fertility traits ‘number of piglets born alive’ (NBA) and ‘number of piglets weaned’ (NW) were used to i) characterize the population structure, ii) to estimate genetic (co)variance components and estimated breeding values (EBVs) and iii) to use EBVs for the application of the concept of optimal genetic contributions. The average coefficient of inbreeding increased from F = 0.103 to F = 0.121 within the two recent cohorts. Average rate of inbreeding amounted to 1.66%, which resulted in an effective population size of Ne = 30 animals in the recent cohort. Average generation interval was 3.07 years considering the whole pedigree, and in total, only 612 sows and boars generated offspring. Estimated heritabilities for both traits NBA and NW were 0.12, and the estimated genetic correlation between both traits was 0.96. The variance component due to the service sire was higher than in commercial pig breeds, presumably due to the widespread use of natural service boars. The EBVs for NBA from 333 selection candidates (63 boars and 270 sows) were used to determine optimal genetic contributions. Based on selected animals and their optimal genetic contributions, specific mating designs were evaluated to minimize inbreeding in the next generation. Best results were achieved when using a simulated annealing algorithm and allowing artificial insemination.  相似文献   

18.
The objective of this research was to examine the population structure of full‐blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full‐blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (FIT and FST) and the effective population size (Ne) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full‐blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (FROH) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (FROH) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full‐blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.  相似文献   

19.
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20.
The aim of this study was to establish heart rate as a measure of energy expenditure in large active kennel dogs (28 ± 3 kg bw). Therefore, the heart rate (HR)–oxygen consumption () relationship was analysed in Foxhound‐Boxer‐Ingelheim‐Labrador cross‐breds (FBI dogs) at rest and graded levels of exercise on a treadmill up to 60–65% of maximal aerobic capacity. To test for effects of training, HR and were measured in female dogs, before and after a training period, and after an adjacent training pause to test for reversibility of potential effects. Least squares regression was applied to describe the relationship between HR and . The applied training had no statistically significant effect on the HR– regression. A general regression line from all data collected was prepared to establish a general predictive equation for energy expenditure from HR in FBI dogs. The regression equation established in this study enables fast estimation of energy requirement for running activity. The equation is valid for large dogs weighing around 30 kg that run at ground level up to 15 km/h with a heart rate maximum of 190 bpm irrespective of the training level.  相似文献   

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