Value of the Dutch Holstein Friesian germplasm collection to increase genetic variability and improve genetic merit

Use of the flavonoid taxifolin for sperm cryopreservation from the threatened Bermeya goat breed

Taxifolin is a plant flavonoid effective as an antioxidant. This study aimed to assess the effect of adding taxifolin to the semen extender during the cooling period before freezing on the overall post-thawing sperm variables of Bermeya goats. In the first experiment, a dose-response experiment was performed with four experimental groups: Control, 10, 50, and 100 μg/ml of taxifolin using semen from 8 Bermeya males. In the second experiment, semen from 7 Bermeya bucks was collected and extended at 20 °C using a Tris-citric acid-glucose medium supplemented with different concentrations of taxifolin and glutathione (GSH): control, 5 μM taxifolin, 1 mM GSH, and both antioxidants. In both experiments, two straws per buck were thawed in a water bath (37 °C, 30 s), pooled, and incubated at 38 °C. Motility (CASA) was assessed at 0, 2, and 5 h, and sperm physiology was assessed at 0 and 5 h by flow cytometry (viability, intact acrosome membrane, mitochondria membrane potential, capacitation, intracellular reactive oxygen species -ROS-, mitochondrial superoxide, and chromatin status). In experiment 2, an artificial insemination trial (AI) was included with 29 goats for testing the taxifolin 5-μM treatment on fertility. Data were analyzed with the R statistical environment using linear mixed-effects models. In experiment 1 and compared to the control, T10 increased progressive motility (P < 0.001) but taxifolin decreased total and progressive motility at higher concentrations (P < 0.001), both post-thawing and after the incubation. Viability decreased post-thawing in the three concentrations (P < 0.001). Cytoplasmic ROS decreased at 0 and 5 h at T10 (P = 0.049), and all doses decreased mitochondrial superoxide post-thawing (P = 0.024). In experiment 2, 5 μM taxifolin or 1 mM GSH (alone or combined) increased total and progressive motility vs. the control (P < 0.01), and taxifolin increased kinematic parameters such as VCL, ALH, and DNC (P < 0.05). Viability was not affected by taxifolin in this experiment. Both antioxidants did not significantly affect other sperm physiology parameters. The incubation significantly affected all the parameters (P < 0.004), overall decreasing sperm quality. Fertility after artificial insemination with doses supplemented with 5 μM taxifolin was 76.9% (10/13), not significantly different from the control group (69.2%, 9/13). In conclusion, taxifolin showed a lack of toxicity in the low micromolar range and could benefit goat semen cryopreservation.

Reintroducing genetic diversity in populations from cryopreserved material: the case of Abondance, a French local dairy cattle breed

BACKGROUND

Genetic diversity is a necessary condition for populations to evolve under natural adaptation, artificial selection, or both. However, genetic diversity is often threatened, in particular in domestic animal populations where artificial selection, genetic drift and inbreeding are strong. In this context, cryopreserved genetic resources are a promising option to reintroduce lost variants and to limit inbreeding. However, while the use of ancient genetic resources is more common in plant breeding, it is less documented in animals due to a longer generation interval, making it difficult to fill the gap in performance due to continuous selection. This study investigates one of the only concrete cases available in animals, for which cryopreserved semen from a bull born in 1977 in a lost lineage was introduced into the breeding scheme of a French local dairy cattle breed, the Abondance breed, more than 20 years later.

RESULTS

We found that this re-introduced bull was genetically distinct with respect to the current population and thus allowed part of the genetic diversity lost over time to be restored. The expected negative gap in milk production due to continuous selection was absorbed in a few years by preferential mating with elite cows. Moreover, the re-use of this bull more than two decades later did not increase the level of inbreeding, and even tended to reduce it by avoiding mating with relatives. Finally, the reintroduction of a bull from a lost lineage in the breeding scheme allowed for improved performance for reproductive abilities, a trait that was less subject to selection in the past.

CONCLUSIONS

The use of cryopreserved material is an efficient way to manage the genetic diversity of an animal population, by mitigating the effects of both inbreeding and strong selection. However, attention should be paid to mating of animals to limit the disadvantages associated with incorporating original genetic material, notably a discrepancy in the breeding values for selected traits or an increase in inbreeding. Therefore, careful characterization of the genetic resources available in cryobanks could help to ensure the sustainable management of populations, in particular local or small populations. These results could also be transferred to the conservation of wild threatened populations.

Opportunities of Genomics for the Use of Semen Cryo-Conserved in Gene Banks

Shortly after the introduction of cryo-conserved semen in the main farm animal species, gene banks were founded. Safeguarding farm animal genetic diversity for future use was and is the main objective. A sampling of sires was based on their pedigree and phenotypic information. Nowadays, DNA information from cryo-conserved sires and from animals in the living populations has become available. The combination of their DNA information can be used to realize three opportunities: 1) to make the gene bank a more complete archive of genetic diversity, 2) to determine the history of the genetic diversity from the living populations, and 3) to improve the performance and genetic diversity of living populations. These three opportunities for the use of gene bank sires in the genomic era are outlined in this study, and relevant recent literature is summarized to illustrate the great value of a gene bank as an archive of genetic diversity.

Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection

Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (F_ROH). The average pedigree inbreeding was 0.07, while the average F_ROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for F_ped and F_ROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.

Quality Management Practices of Gene Banks for Livestock: A Global Review

The genetic diversity of livestock is decreasing and many countries have created gene banks for ex situ-in vitro conservation of animal genetic resources (AnGR). The collection, processing, and storage of animal germplasm require substantial investment and the material collected (and associated data) is highly valuable. Therefore, quality management systems (QMSs) and practices are important. The objective of this study was to review the quality management procedures of livestock gene banks around the world to identify the general strengths and weaknesses of quality control. A survey was administered by means of an online questionnaire consisting of 54 questions, most of which were yes/no with respect to the presence of a particular aspect of quality management. The survey was distributed through networks of the Food and Agriculture Organization of the United Nations that are associated with AnGR. Ninety responses were received from 62 countries. The gene banks were predominantly public institutions, with the main goal of preventing breed extinction. Approximately 30% of the banks reported having a QMS, 15 of which involved formal certification. Many other banks have plans to implement formal quality management within the next 5 years. Regarding specific aspects of quality management, more emphasis was placed on material entering the banks than on eventual utilization. Among the banks processing and freezing material, 90% followed specific standard operating procedures, but only 24% had policies regarding provision of access to external stakeholders. Increased cooperation among livestock gene banks could improve quality management. Sharing of knowledge could standardize procedures and cooperating peers could evaluate each other's QMSs.

Assessment of a germplasm bank for the autochthonous cattle breed Asturiana de la Montaña: Extender (Biociphos vs. BIOXCell) affected sperm quality but not field fertility

Semen banking is critical to preserving rare and autochthonous breeds. However, protocols can change with time, leaving heterogeneous semen batches. The objective of this study was to assess differences in sperm quality and field fertility. We report differences between batches frozen with the Biociphos and BIOXCell extenders in the Asturiana de la Montaña cryobank (autochthonous and endangered breed, Northern Spain). Doses from 48 bulls were analysed by CASA and flow cytometry. The 85-days non-return rates from AI records were used to assess the fertility of 23,853 AI. BIOXCell showed higher quality post-thawing. Differences increased after a 5-hr incubation at 37°C, and Biociphos yielded doses with lower resilience. Field fertility did not differ between extenders (Biociphos: 57.4% ± 1.2; BIOXCell: 56.6% ± 3.0), possibly because of AI protocols compensating for differences in quality. However, this needs to be confirmed by controlled intervention studies. In conclusion, batches frozen with Biociphos may require specific strategies for compensating for the lower sperm quality. Regular surveys and evaluation of cryobank procedures may be useful to characterizing stored batches and defining strategies to guaranteeing success in their future use.

Cryoconservation of Animal Genetic Resources in Europe and Two African Countries: A Gap Analysis

Cryoconservation is one of the main strategies to conserve farm animal genetic resources, providing opportunities for genetic improvement and adaptation to changes in production environments and consumer demands. In this study, we combine livestock breed-related data from the Domesticated Animal Diversity Information System (DAD-IS) and information provided by gene banks from 15 European and 2 non-European countries on material stored for livestock breeds to analyze the gaps in cryomaterial collections according to species, countries and various breed categories. Out of the 2949 breeds registered in DAD-IS for these countries, 15.9% have been reported to have material stored in gene banks, but only 4.3% have material sufficient to allow breed reconstitution. The proportion of breeds with stored cryomaterial was greater than 20% for ruminants and pigs, between 10% and 20% for equids, and below 10% for rabbit and avian species. According to the results of two logistic regressions, countries show significant differences in the proportion of populations collected for cryostorage, while breeds not-at-risk are more likely to have cryomaterial preserved than are other breeds. Also, a relatively larger proportion of transboundary breeds have cryomaterial in gene banks than do local breeds, likely due in part to the fact that multiple countries have the opportunity to collect this material. These results highlight the need for increased efforts in material collection for at-risk local breeds and regional coordination on cryoconservation of material from transboundary breeds.

Inference of Selection from Genetic Time Series Using Various Parametric Approximations to the Wright-Fisher Model

Detecting genomic regions under selection is an important objective of population genetics. Typical analyses for this goal are based on exploiting genetic diversity patterns in present time data but rapid advances in DNA sequencing have increased the availability of time series genomic data. A common approach to analyze such data is to model the temporal evolution of an allele frequency as a Markov chain. Based on this principle, several methods have been proposed to infer selection intensity. One of their differences lies in how they model the transition probabilities of the Markov chain. Using the Wright-Fisher model is a natural choice but its computational cost is prohibitive for large population sizes so approximations to this model based on parametric distributions have been proposed. Here, we compared the performance of some of these approximations with respect to their power to detect selection and their estimation of the selection coefficient. We developped a new generic Hidden Markov Model likelihood calculator and applied it on genetic time series simulated under various evolutionary scenarios. The Beta with spikes approximation, which combines discrete fixation probabilities with a continuous Beta distribution, was found to perform consistently better than the others. This distribution provides an almost perfect fit to the Wright-Fisher model in terms of selection inference, for a computational cost that does not increase with population size. We further evaluated this model for population sizes not accessible to the Wright-Fisher model and illustrated its performance on a dataset of two divergently selected chicken populations.

Characterization of Genetic Diversity Conserved in the Gene Bank for Dutch Cattle Breeds

In this study, we characterized genetic diversity in the gene bank for Dutch native cattle breeds. A total of 715 bulls from seven native breeds and a sample of 165 Holstein Friesian bulls were included. Genotype data were used to calculate genetic similarities. Based on these similarities, most breeds were clearly differentiated, except for two breeds (Deep Red and Improved Red and White) that have recently been derived from the MRY breed, and for the Dutch Friesian and Dutch Friesian Red, which have frequently exchanged bulls. Optimal contribution selection (OCS) was used to construct core sets of bulls with a minimized similarity. The composition of the gene bank appeared to be partly optimized in the semen collection process, i.e., the mean similarity within breeds based on the current number of straws per bull was 0.32% to 1.49% lower than when each bull would have contributed equally. Mean similarity could be further reduced within core sets by 0.34% to 2.79% using OCS. Material not needed for the core sets can be made available for supporting in situ populations and for research. Our findings provide insight in genetic diversity in Dutch cattle breeds and help to prioritize material in gene banking.

Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle

Background

Inbreeding decreases animal performance (inbreeding depression), but not all inbreeding is expected to be equally harmful. Recent inbreeding is expected to be more harmful than ancient inbreeding, because selection decreases the frequency of deleterious alleles over time. Selection efficiency is increased by inbreeding, a process called purging. Our objective was to investigate effects of recent and ancient inbreeding on yield, fertility and udder health traits in Dutch Holstein–Friesian cows.

Methods

In total, 38,792 first-parity cows were included. Pedigree inbreeding (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{PED}$$\end{document}FPED) was computed and 75 k genotype data were used to compute genomic inbreeding, among others based on regions of homozygosity (ROH) in the genome (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{ROH}$$\end{document}FROH).

Results

Inbreeding depression was observed, e.g. a 1% increase in \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{ROH}$$\end{document}FROH was associated with a 36.3 kg (SE = 2.4) decrease in 305-day milk yield, a 0.48 day (SE = 0.15) increase in calving interval and a 0.86 unit (SE = 0.28) increase in somatic cell score for day 150 through to 400. These effects equalled − 0.45, 0.12 and 0.05% of the trait means, respectively. When \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{PED}$$\end{document}FPED was split into generation-based components, inbreeding on recent generations was more harmful than inbreeding on more distant generations for yield traits. When \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$F_{PED}$$\end{document}FPED was split into new and ancestral components, based on whether alleles were identical-by-descent for the first time or not, new inbreeding was more harmful than ancestral inbreeding, especially for yield traits. For example, a 1% increase in new inbreeding was associated with a 2.42 kg (SE = 0.41) decrease in 305-day fat yield, compared to a 0.03 kg (SE = 0.71) increase for ancestral inbreeding. There were no clear differences between effects of long ROH (recent inbreeding) and short ROH (ancient inbreeding).

Conclusions

Inbreeding depression was observed for yield, fertility and udder health traits. For yield traits and based on pedigree, inbreeding on recent generations was more harmful than inbreeding on distant generations and there was evidence of purging. Across all traits, long and short ROH contributed to inbreeding depression. In future work, inbreeding depression and purging should be assessed in more detail at the genomic level, using higher density information and genomic time series.

Genetic parameters for mastitis incidence and its indicators based on somatic cell score for Holsteins in Hokkaido, Japan

The objectives of this study were to estimate the heritability of mastitis incidence and genetic correlations between the mastitis and the somatic cell score (SCS) statistics, and to compare the practicability between different models. We used test-day records with the mastitis incidence and SCS collected from Holstein cows calving from 1988 to 2015 in Hokkaido, Japan. As indicators of mastitis, the average SCS (avSCS), the standard deviation of SCS (sdSCS), and the maximum SCS (maxSCS) were calculated using test-day records up to the first 305 days in milk within a lactation. We compared a four-trait repeatability animal model (MTRP) with a four-trait multiple-lactation animal model (MTML). The heritability for mastitis was equal to or lower than 0.05 in all the models. Genetic correlations between lactations with MTML within the same trait were positive and close to 1. With MTRP, the estimated genetic correlations of the mastitis incidence with avSCS, sdSCS, and maxSCS were 0.66, 0.79, and 0.82, respectively. A joint evaluation with SCS statistics is expected to give an extra reliability for mastitis because of high and positive genetic correlations among the traits.