Journal of Animal Breeding and Genetics最新文献

Genetic diversity is essential for the sustainability and adaptability of populations, and is thus a central pillar of the agro-ecological transition. However, within a population, it is inevitable that some amount of genetic variability is lost, and efforts must be made to limit this as much as possible. A valuable tool in this endeavour could be the use of cryopreserved genetic resources in cryobanks, which could assist in the management of various animal populations in the contexts of both selection and conservation. We performed simulations that revealed that the most appropriate use of ex situ genetic resources depends on characteristics of the target population and its management objectives. For populations under conservation, the aim is to maintain genetic diversity, which was best achieved by the regular use of cryopreserved genetic resources at each generation. For populations under selection, instead, the concern is the addition of additive genetic variability, which benefited from the use of cryopreserved collections over only a few generations based primarily on the genetic values of donors. The use of cryopreserved semen had a beneficial effect when breeding objectives were changed. In both cases, the use of cryopreserved individuals in animal populations requires a large amount of reproductive material: for breeds under selection because the number of offspring is high, and for breeds under conservation because the frozen semen is used repeatedly over a long period. The use of cryopreserved material appears to be an effective means of managing the genetic variability of an animal population, either by slowing down the erosion of variability or by helping to redirect a selection objective. However, care must be taken with populations under selection to limit the disadvantages associated with the reintroduction of old genetic material, in particular the gap in breeding values for traits of interest. Finally, our study highlights the need for a sufficiently large stock of cryopreserved material in collections (e.g., number of doses, straws) to ensure the most efficient use.

Meiotic recombination is an essential process for shuffling genetic diversity in sexually reproducing organisms, can vary within and between individuals in response to intrinsic and extrinsic factors, and can be heritable. Interestingly, recombination rate has been found to vary with age in some species, but to date, there have been no assessments of the heritability and genetic architecture of this age effect. Here, we leverage a large pedigree of SNP chip-genotyped Aotearoa New Zealand Holstein-Friesian and Jersey dairy cattle to test for an effect of age on male recombination rate, the heritability of recombination rate and of any such age effect on recombination, and the genetic architecture underlying these two phenotypes. We found a significant, albeit small, increase in the average number of male autosomal recombinations with age. Consistent with previous studies, we found moderate heritability (h² ≈ 0.15) of sire recombination rate and detected association with several regions on chromosome 10 encompassing genes such as REC8, REC114, RNF212B and NEK9. Further, we found novel evidence of some heritability (h² ≈ 0.05) in the rate of change in recombination with age in sires. Variation in the rate of change with age is likely also polygenic, but there is a region on chromosome 1 that is weakly associated with the rate of change. It is unclear whether the heritability of age-related recombination rate change is widespread across species, and we encourage studies in other taxa to assess its prevalence and evolutionary significance.

Missing pedigrees are a common problem in most populations. Animals with unknown ancestors are usually treated as founders; however, this can underestimate inbreeding, not properly account for different base populations, and bias breeding values. We aimed to assess the use of unknown parent groups (UPG) or metafounders (MF) to model missing pedigrees in a beef cattle population. Phenotypic and genotypic data from the Nellore improvement programme of the Brazilian Breeders and Researchers Association were used. The pedigree contained 3.8 M animals born between 1970 and 2022, of which 51,752 were genotyped. Records for scrotal circumference at 365 days old (SC365, N = 239,806), age at first calving (AFC, N = 560,785) and accumulated cow productivity (ACP, N = 269,330) were used. Four models were implemented: single-step GBLUP without explicitly dealing with missing pedigree (G0), with UPG (G1), with MF (G2) and with $��G�$ accounting for group-specific allele frequencies (G3). UPG and MF were assigned based on commercial and registered herds (S1), uncertain paternity (S2) and patriarchs (S3). The accuracy and bias of predictions were assessed using the linear regression (LR) method. Linear, single-trait animal models were used for SC365 and AFC, and multi-trait for ACP. Heritability estimates ranged from 0.07 to 0.40. Compared to G0, accuracy was slightly higher in G2_S2 and G2_S3 (0.70 vs. 0.71) for SC365, G2_S3 (0.49 vs. 0.51) for AFC, G1_S2 for ACP (0.67 vs. 0.71). Bias was small in all the scenarios (≤ 0.06 SD), except of ACP that presented a great bias, including MF. Overall, G1 and G2 had similar accuracy, possibly because of the limited number of genotyped animals linked to MF. Centring the genomic relationship matrix by patriarchs' allelic frequencies resulted in similar accuracy and bias to the MF models. Replicating the study with a larger database containing more genotyped animals connected to MF could help improve the MF estimates, and thus, prediction accuracy and bias.

In this study, we aimed to evaluate the genetic association between fertility traits, milk yield and the fat: protein ratio (FPR) on the test day in primiparous Holstein cows. The analysed traits were milk yield (TDMY) and FPR assessed on the test day, as well as the following fertility traits: period from calving to first service (CFS), days open (DO) and calving interval (CI). Genetic parameters were estimated through bivariate analysis, using a random regression model (considering fourth-order Legendre polynomials) and the Bayesian method, with GIBBS2F90 software. Heritability estimates varied between 0.11 and 0.22 for TDMY, between 0.16 and 0.30 for FPR and between 0.03 and 0.05 for the fertility traits. Correlation estimates between TDMY and fertility traits tended to increase from early lactation until approximately day 100, then decreased slightly before continuing to grow until the end of lactation. Genetic correlations between TDMY and FPR were negative throughout lactation, ranging from −0.04 on day 5 to −0.37 in the final third of this period. The genetic correlations between FPR and fertility traits were positive in early lactation and negative in late lactation (except for CFS). These results indicate that TDMY and FPR are heritable and can be used as selection criteria in Holstein cows in Brazil. However, for fertility traits, genetic gains through direct selection may be slow. Additionally, a high level of milk production and FPRs in early lactation negatively impact fertility traits.

Traits related to growth, carcass quality and stayability are key components in enhancing the profitability and sustainability of Nelore cattle production systems. This study aimed to estimate heritabilities and genetic and environmental correlations for these traits using a Bayesian approach. Data from 94,703 females were analysed for weights at 210, 365 and 450 days of age (W210, W365 and W450), loin eye area (LEA), subcutaneous fat thickness in the loin (LFT) and rump (REFT) and stayability at 48, 54 and 72 months (STAY48, STAY54 and STAY72). Heritability estimates (± standard error) were 0.14 ± 0.03 for LEA, 0.20 ± 0.03 for LFT, 0.43 for REFT, 0.12 ± 0.02 for STAY54, and 0.18 ± 0.02 for STAY72. Moderate heritabilities for W210, W365, W450, LFT and REFT indicate a substantial additive genetic component, whereas lower estimates for LEA and stayability suggest a predominant influence of environmental factors. Genetic trends were generally positive but moderate: 0.14 kg/generation (W210), 1.40 kg/generation (W365), 1.77 kg/generation (W450), 0.016 cm²/generation (LEA) and 0.0081 months/generation (STAY72). In contrast, STAY48 showed a slightly negative trend (−0.0073 months/generation). Direct selection for W450 yielded a genetic gain of 9.837 kg, whereas indirect selection via correlated traits resulted in gains ranging from 0.125 to 9.272 kg. These findings highlight the relevance of environmental effects on traits with low heritability, such as LEA and stayability, and reinforce the effectiveness of selection for weight-related traits due to their moderate heritability and favourable genetic trends.