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1.
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2.
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   

3.
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   

4.
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   

5.
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   

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.
Finnish Spitz is 130‐year‐old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (fa) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis () is 168, whereas the genetic effective population size (Neg) computed the decay of linkage disequilibrium (r2) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had fa of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz ( = 98 and Neg = 49). Interestingly, the r2 data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed.  相似文献   

8.
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   

9.
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   

10.

This study assessed daily milk yield (DMY), 100-day (MY100), and 305-day (MY305) milk yield, and lactation length (LL) in purebred Ankole cattle and Ankole crossbreds, and the influence of environmental factors on these traits. Milk yield data were obtained for 865 cows and 1234 lactations and analyzed using a mixed linear model. The overall least squares mean of DMY, MY100, and MY305 across breed groups was 2.7 L (N = 1234, SD = 1.7), 262 L (N = 959, SD = 176), and 759 L (N = 448, SD = 439), respectively, while the average lactation length was 256 days (N = 960, SD = 122). All factors included (breed group, season and year of calving, and parity) were significant for yield traits, except season of calving for MY305. First-parity cows had the lowest milk production, and fourth-parity cows the highest. For all traits, pure Ankole cows had the lowest milk yield. Among the crossbreds, there was no significant difference between Ankole × Friesian, Ankole-Jersey mother × Sahiwal sire, and Ankole-Sahiwal mother × Jersey sire, or between Ankole × Sahiwal and Ankole-Sahiwal mother × Sahiwal sire. It was concluded that Ankole crosses with Friesian or Jersey can be beneficial, even under a management system of limited nutrition as in Rwanda.

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11.
Economically important traits are usually complex traits influenced by genes, environment and genotype-by-environment (G × E) interactions. Ignoring G × E interaction could lead to bias in the estimation of breeding values and selection decisions. A total of 1,778 pigs were genotyped using the PorcineSNP80 BeadChip. The existence of G × E interactions was investigated using a single-step reaction norm model for growth traits of days to 100 kg (AGE) and backfat thickness adjusted to 100 kg (BFT), based on a pedigree-based relationship matrix (A) or a genomic–pedigree joint relationship matrix (H). In the reaction norm model, the herd-year-season effect was measured as the environmental variable (EV). Our results showed no G × E interactions for AGE, but for BFT. For both AGE and BFT, the genomic reaction norm model (H) produced more accurate predictions than the conventional reaction norm model (A). For BFT, the accuracies were greater based on the reaction norm model than those based on the reduced model without exploiting G × E interaction, with EV ranging from 0.5 to 1, and accuracy increasing by 3.9% and 4.6% in the reaction norm model based on A and H matrices, respectively, while reaction norm model yielded approximately 8.4% and 7.9% lower accuracy for EVs ranging from 0 to 0.4, based on A and H matrices, respectively. In addition, for BFT, the highest accuracy was obtained in the BJLM6 farm for realizing directional selection. This study will help to apply G × E interactions to practical genomic selection.  相似文献   

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13.
Heritabilities were estimated from sire and dam components for egg production traits in four generations of two pure‐lines and their reciprocal crosses. Heritabilities in cross‐breds, as estimated from the sire components of variance, were larger than in pure‐breds for production and sexual maturity. Heritabilities estimated from dam components were larger than the sire estimates, thus indicating the presence of maternal and/or dominance effects. Again, heritabilities in cross‐breds were larger than in pure‐breds for production and sexual maturity as well as for specific gravity. Heritabilities were also estimated for disease traits in material from one generation. Cross‐line values were as large or larger than those estimated from pure‐lines but the standard errors of the estimates were quite large.

Genetic correlations were estimated between pure‐line and cross‐line performance using both sire and dam covariances. These approached unity for body weight, egg quality traits and adult mortality but were considerably less than unity for production, sexual maturity, blood spots and mortality during growth and mortality due to Marek's disease.

The possible bias due to genotype x environment interaction is discussed and it is concluded that such a bias, if present, is small, and that in spite of possible G × E interaction effect the genetic correlations between pure‐line and cross‐line performance for production and sexual maturity are less than one. The same holds true of mortality during growth and to Marek's disease although these estimates are much less precise.

The genetic correlation between pure‐breds and cross‐breds appears to decrease over the span of the five generations.

Use of cross‐line performance will permit more efficient selection for traits when the genetic correlations are much less than one.  相似文献   


14.
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   

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16.
Our objective was to evaluate changes in breeding values for carcass traits of two meat‐type quail (Coturnix coturnix) strains (LF1 and LF2) to changes in the dietary (methionine + cystine):lysine ([Met + Cys]:Lys) ratio due to genotype by environment (G × E) interaction via reaction norm. A total of 7000 records of carcass weight and yield were used for analyses. During the initial phase (from hatching to day 21), five diets with increasing (Met + Cys):Lys ratios (0.61, 0.66, 0.71, 0.76 and 0.81), containing 26.1% crude protein and 2900 kcal ME/kg, were evaluated. Analyses were performed using random regression models that included linear functions of sex (fixed effect) and breeding value (random effect) for carcass weight and yield, without and with heterogeneous residual variance adjustment. Both fixed and random effects were modelled using Legendre polynomials of second order. Genetic variance and heritability estimates were affected by both (Met + Cys):Lys ratio and strain. We observed that a G × E interaction was present, with changes in the breeding value ranking. Therefore, genetic evaluation for carcass traits should be performed under the same (Met + Cys):Lys ratio in which quails are raised.  相似文献   

17.
In pork production, the efficiency of dietary protein (AA) use is low, resulting in urinary excretion of large quantities of nitrogen as urea. Use of AA and formation of urea are under enzymatic regulation, suggesting genetic regulation. The current study examined the effects of sire line, sire, and sex on growth characteristics and plasma urea nitrogen (PUN) concentrations in the offspring of 11 Duroc sires and 11 Landrace sires bred to Yorkshire-Landrace dams. Plasma samples were obtained at approximately 107 (age class = 107 d), 128 (age class = 128 d), and 149 (age class = 149 d) d of age from 511 boars, gilts, and barrows group-penned and fed standard finishing diets. Body weight and backfat (BF, mean of 3 measurements) were recorded at the time of blood sample collection. Sex, age class, and their interaction influenced (P < 0.01) BW, BF, and PUN. Predicted traits (i.e., ADG, BW at 21 wk, average daily change in BF, BF at 21 wk, and the mean of 3 PUN measures) were generated. Means (+/-SD) were: ADG, 888 +/- 204 g; BW at 21 wk, 94.2 +/- 12.5 kg; average daily change in BF, 0.083 +/- 0.052 mm; BF at 21 wk, 13.8 +/- 3.0 mm; and the mean of 3 PUN measures, 16.2 +/- 4.4 mg/dL. Predicted weight traits were influenced (P < 0.05) by sire line, and sex influenced (P < 0.01) all predicted traits. Heritability estimates for PUN at 107, 128, and 149 d of age were 0.35 +/- 0.15, 0.21 +/- 0.13, and 0.16 +/- 0.12, respectively. Phenotypic correlations of PUN with growth and fat traits were low. Genetic correlations of PUN measured at 107 d with growth and fat traits were low. However, genetic correlations of PUN measured at 128 or 149 d with growth and fat traits ranged from 0.81 to 0.95. Determination of PUN, as herein, may be of sufficient precision to allow its use in a selection protocol. Selection of pigs with superior growth performance and low PUN may result in a greater efficiency of dietary nitrogen use and a reduced negative environmental impact.  相似文献   

18.
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19.
The semen movement and sperm head size patterns of boar ejaculates were analysed using computer-assisted semen analysis (CASA)-Mot and -Morph systems. The aim of the present study was to compare morphometric and kinematics variables from boars and to determine the relationship with sow fertility variables related to litter size. The females were from maternal crossing schemes such as the continuous 3-generation cross between York (Y), Landrace (L), and Pietrain (P) hybrid sows and Pietrain boars. Semen samples were collected from 11 sexually mature boars from two sire lines. Samples were analysed using the ISAS®v1 system to evaluate eight kinematic variables of sperm velocity, progressiveness and undulations. Four morphometric parameters of sperm head size (length, width, area and perimeter) were analysed. Bayesian analysis revealed relevant differences in four kinematic variables (VSL, LIN, STR and WOB) between sire lines, with a probability of relevance (PR) of 0.79–0.91, and Pietrain boars were associated with higher progressive motility compared with Duroc x Pietrain boars. Moreover, there were relevant differences in all morphometric variables (PR = 0.82–0.85) between sire lines. The dam line Y-L-50 (½ Y × ½ L) had higher total born per litter and piglets born alive, and YLP-75 (1/8 Y × 1/8 L × 3/4 P) was associated with higher values of litter weight at birth (highest posterior density region at 95% = 9.92, 16.41 kg). There are relevant differences in kinematic variables between the assessed sire lines and the differences in morphometric and litter size variables were also relevant. The York-Landrace hybrid sows had higher total born per litter and piglets born alive, and there were relevant differences when compared with YLP-50 (¼ York × ¼ Landrace × ½ Pietrain). Differences in kinematic and morphometric variables between sire and dam lines related to fertility need to be further studied.  相似文献   

20.
This study conducted four experiments to assess preference of cattle between centipedegrass (Eremochloa ophiuroides; CG) and bahiagrass (Paspalum notatum; BG) under manipulated vegetation conditions. In each experiment, three Japanese Black cows (Bos taurus) were individually allowed to graze four plots of conterminous monocultures of CG and BG (30 min for each 10 × 10 m plot). Vegetation of the plots was the combinations of two patch sizes (coarse and fine; 5 × 10 m and 5 × 5 m, respectively) × two relative availabilities of the grasses (CGtall/BGshort and CGshort/BGtall). Tall and short patches were created by varying regrowth durations after cutting, and almost always offered a clear CG–BG contrast in availability (height and mass) and quality (digestibility and protein) with the trade‐off relationship. Cows always preferred or equally selected CG to BG, with the preference being affected by the relative availability of grasses in three of the four experiments but not by the patch size at all. Test of intake rate maximization on both short‐term and daily bases indicated that cows chose between the grasses to simultaneously enhance daily potential intake of dry matter, digestible energy and protein. The results strengthen the value of CG as a forage.  相似文献   

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