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

International audienceBackground : 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 ( FPED ) was computed and 75 k geno-type data were used to compute genomic inbreeding, among others based on regions of homozygosity (ROH) in the genome ( FROH).Results : Inbreeding depression was observed, e.g. a 1% increase in 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, respec-tively. When FPED was split into generation-based components, inbreeding on recent generations was more harmful than inbreeding on more distant generations for yield traits. When 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

Trends in genome-wide and region-specific genetic diversity in the Dutch-Flemish Holstein-Friesian breeding program from 1986 to 2015

Background: In recent decades, Holstein-Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal composition (around 2000) and the implementation of genomic selection (GS; around 2010). These changes are expected to have influenced genetic diversity trends. Our aim was to evaluate genome-wide and region-specific diversity in HF artificial insemination (AI) bulls in the Dutch-Flemish breeding program from 1986 to 2015. Methods: Pedigree and genotype data (~ 75.5 k) of 6280 AI-bulls were used to estimate rates of genome-wide inbreeding and kinship and corresponding effective population sizes. Region-specific inbreeding trends were evaluated using regions of homozygosity (ROH). Changes in observed allele frequencies were compared to those expected under pure drift to identify putative regions under selection. We also investigated the direction of changes in allele frequency over time. Results: Effective population size estimates for the 1986-2015 period ranged from 69 to 102. Two major breakpoints were observed in genome-wide inbreeding and kinship trends. Around 2000, inbreeding and kinship levels temporarily dropped. From 2010 onwards, they steeply increased, with pedigree-based, ROH-based and marker-based inbreeding rates as high as 1.8, 2.1 and 2.8% per generation, respectively. Accumulation of inbreeding varied substantially across the genome. A considerable fraction of markers showed changes in allele frequency that were greater than expected under pure drift. Putative selected regions harboured many quantitative trait loci (QTL) associated to a wide range of traits. In consecutive 5-year periods, allele frequencies changed more often in the same direction than in opposite directions, except when comparing the 1996-2000 and 2001-2005 periods. Conclusions: Genome-wide and region-specific diversity trends reflect major changes in the Dutch-Flemish HF breeding program. Introduction of OCS and the shift in breeding goal were followed by a drop in inbreeding and kinship and a shift in the direction of changes in allele frequency. After introduction of GS, rates of inbreeding and kinship increased substantially while allele frequencies continued to change in the same direction as before GS. These results provide insight in the effect of breeding practices on genomic diversity and emphasize the need for efficient management of genetic diversity in GS schemes.</p

Domesticated Animal Biobanking : Land of Opportunity

In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals.Peer reviewe

Whole-genome sequence data uncover loss of genetic diversity due to selection

Background: Whole-genome sequence (WGS) data give access to more complete structural genetic information of individuals, including rare variants, not fully covered by single nucleotide polymorphism chips. We used WGS to investigate the amount of genetic diversity remaining after selection using optimal contribution (OC), considering different methods to estimate the relationships used in OC. OC was applied to minimise average relatedness of the selection candidates and thus miminise the loss of genetic diversity in a conservation strategy, e.g. for establishment of gene bank collections. Furthermore, OC was used to maximise average genetic merit of the selection candidates at a given level of relatedness, similar to a genetic improvement strategy. In this study, we used data from 277 bulls from the 1000 bull genomes project. We measured genetic diversity as the number of variants still segregating after selection using WGS data, and compared strategies that targeted conservation of rare (minor allele frequenc

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.</p

The impact of using old germplasm on genetic merit and diversity - A cattle breed case study

Artificial selection and high genetic gains in livestock breeds led to a loss of genetic diversity. Current genetic diversity conservation actions focus on long-term maintenance of breeds under selection. Gene banks play a role in such actions by storing genetic materials for future use and the recent development of genomic information is facilitating characterization of gene bank material for better use. Using the Meuse-Rhine-Issel Dutch cattle breed as a case study, we inferred the potential role of germplasm of old individuals for genetic diversity conservation of the current population. First, we described the evolution of genetic merit and diversity over time and then we applied the optimal contribution (OC) strategy to select individuals for maximizing genetic diversity, or maximizing genetic merit while constraining loss of genetic diversity. In the past decades, genetic merit increased while genetic diversity decreased. Genetic merit and diversity were both higher in an OC scenario restricting the rate of inbreeding when old individuals were considered for selection, compared to considering only animals from the current population. Thus, our study shows that gene bank material, in the form of old individuals, has the potential to support long-term maintenance and selection of breeds.</p

Domesticated Animal Biobanking: Land of Opportunity

In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals

Domesticated Animal Biobanking: Land of Opportunity

<div><p>In the past decade, biobanking has fuelled great scientific advances in the human medical sector. Well-established domesticated animal biobanks and integrated networks likewise harbour immense potential for great scientific advances with broad societal impacts, which are currently not being fully realised. Political and scientific leaders as well as journals and ethics committees should help to ensure that we are well equipped to meet future demands in livestock production, animal models, and veterinary care of companion animals.</p></div

European genetic resources conservation in a rapidly changing world

Even though genetic resources represent a fundamental reservoir of options to achieve sustainable development goals in a changing world, they are overlooked in the policy agenda and severely threatened. The conservation of genetic resources relies on complementary in situ and ex situ approaches appropriately designed for each type of organism. Environmental and socioeconomic changes raise new challenges and opportunities for sustainable use and conservation of genetic resources. Aiming at a more integrated and adaptive approach, European scientists and genetic resources managers with long experience in the agricultural crop, animal and forestry domains joined their expertise to address three critical challenges: (1) how to adapt genetic resources conservation strategies to climate change, (2) how to promote in situ conservation strategies and (3) how can genetic resources conservation contribute to and benefit from agroecological systems. We present here 31 evidence-based statements and 88 key recommendations elaborated around these questions for policymakers, conservation actors and the scientific community. We anticipate that stakeholders in other genetic resources domains and biodiversity conservation actors across the globe will have interest in these crosscutting and multi-actor recommendations, which support several biodiversity conservation policies and practices