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

Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows

We assessed the performance of single-step genomic prediction of breeding values for superovulatory response traits in Japanese Black donor cows. A total of 25,332 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) per flush for 1874 Japanese Black donor cows were collected during 2008 and 2022. Genotype information on 36,426 autosomal single-nucleotide polymorphisms (SNPs) for 575 out of the 1,874 cows was used. Breeding values were predicted exploiting a two-trait repeatability animal model. Two genetic relationship matrices were used, one based on pedigree information (A matrix) and the other considering both pedigree and SNP marker genotype information (H matrix). Estimated heritabilities of TNE and NGE were 0.18 and 0.11, respectively, when using the H matrix, which were both slightly lower than when using the A matrix (0.26 for TNE and 0.16 for NGE). Estimated genetic correlations between the traits were 0.61 and 0.66 when using H and A matrices, respectively. When the variance components were the same in breeding value prediction, the mean reliability was greater when using the H matrix than when using the A matrix. This advantage seems more prominent for cows with low reliability when using the A matrix. The results imply that introducing single-step genomic prediction could boost the rate of genetic improvement of superovulatory response traits, but efforts should be made to maintain genetic diversity when performing selection.

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.

The Use of Genomic Information for the Conservation of Animal Genetic Diversity

The conservation of genetic diversity, both among and within breeds, is a costly process. Therefore, choices between breeds and animals within breeds are unavoidable, either for conservation in vitro (gene banks) or in vivo (maintaining small populations alive). Nowadays, genomic information on breeds and individual animals is the standard for the choices to be made in conservation. Genomics may accurately measure the genetic distances among breeds and the relationships among animals within breeds. Homozygosity at loci and at parts of chromosomes is used to measure inbreeding. In addition, genomics can be used to detect potentially valuable rare alleles and haplotypes, their carriers in these breeds and can facilitate in vivo or in vitro conservations of these genomic regions.

Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe

Background

Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful.

Results

Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility.

Conclusions

This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.

Heterosis and Hybrid Crop Breeding: A Multidisciplinary Review

Although hybrid crop varieties are among the most popular agricultural innovations, the rationale for hybrid crop breeding is sometimes misunderstood. Hybrid breeding is slower and more resource-intensive than inbred breeding, but it allows systematic improvement of a population by recurrent selection and exploitation of heterosis simultaneously. Inbred parental lines can identically reproduce both themselves and their F1 progeny indefinitely, whereas outbred lines cannot, so uniform outbred lines must be bred indirectly through their inbred parents to harness heterosis. Heterosis is an expected consequence of whole-genome non-additive effects at the population level over evolutionary time. Understanding heterosis from the perspective of molecular genetic mechanisms alone may be elusive, because heterosis is likely an emergent property of populations. Hybrid breeding is a process of recurrent population improvement to maximize hybrid performance. Hybrid breeding is not maximization of heterosis per se, nor testing random combinations of individuals to find an exceptional hybrid, nor using heterosis in place of population improvement. Though there are methods to harness heterosis other than hybrid breeding, such as use of open-pollinated varieties or clonal propagation, they are not currently suitable for all crops or production environments. The use of genomic selection can decrease cycle time and costs in hybrid breeding, particularly by rapidly establishing heterotic pools, reducing testcrossing, and limiting the loss of genetic variance. Open questions in optimal use of genomic selection in hybrid crop breeding programs remain, such as how to choose founders of heterotic pools, the importance of dominance effects in genomic prediction, the necessary frequency of updating the training set with phenotypic information, and how to maintain genetic variance and prevent fixation of deleterious alleles.

Long-Term Evaluation of Breeding Scheme Alternatives for Endangered Honeybee Subspecies

Modern breeding structures are emerging for European honeybee populations. However, while genetic evaluations of honeybees are becoming increasingly well understood, little is known about how selection decisions shape the populations' genetic structures. We performed simulations evaluating 100 different selection schemes, defined by selection rates for dams and sires, in populations of 200, 500, or 1000 colonies per year and considering four different quantitative traits, reflecting different genetic parameters and numbers of influential loci. Focusing on sustainability, we evaluated genetic progress over 100 years and related it to inbreeding developments. While all populations allowed for sustainable breeding with generational inbreeding rates below 1% per generation, optimal selection rates differed and sustainable selection was harder to achieve in smaller populations and for stronger negative correlations of maternal and direct effects in the selection trait. In small populations, a third or a fourth of all candidate queens should be selected as dams, whereas this number declined to a sixth for larger population sizes. Furthermore, our simulations indicated that, particularly in small populations, as many sires as possible should be provided. We conclude that carefully applied breeding provides good prospects for currently endangered honeybee subspecies, since sustainable genetic progress improves their attractiveness to beekeepers.

Optimized breeding strategies to harness genetic resources with different performance levels

Background

The narrow genetic base of elite germplasm compromises long-term genetic gain and increases the vulnerability to biotic and abiotic stresses in unpredictable environmental conditions. Therefore, an efficient strategy is required to broaden the genetic base of commercial breeding programs while not compromising short-term variety release. Optimal cross selection aims at identifying the optimal set of crosses that balances the expected genetic value and diversity. We propose to consider genomic selection and optimal cross selection to recurrently improve genetic resources (i.e. pre-breeding), to bridge the improved genetic resources with elites (i.e. bridging), and to manage introductions into the elite breeding population. Optimal cross selection is particularly adapted to jointly identify bridging, introduction and elite crosses to ensure an overall consistency of the genetic base broadening strategy.

Results

We compared simulated breeding programs introducing donors with different performance levels, directly or indirectly after bridging. We also evaluated the effect of the training set composition on the success of introductions. We observed that with recurrent introductions of improved donors, it is possible to maintain the genetic diversity and increase mid- and long-term performances with only limited penalty at short-term. Considering a bridging step yielded significantly higher mid- and long-term genetic gain when introducing low performing donors. The results also suggested to consider marker effects estimated with a broad training population including donor by elite and elite by elite progeny to identify bridging, introduction and elite crosses.

Conclusion

Results of this study provide guidelines on how to harness polygenic variation present in genetic resources to broaden elite germplasm.

Conservation and Utilization of Livestock Genetic Diversity in the United States of America through Gene Banking

A germplasm collection curated by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Animal Germplasm Program contains of over one million samples from over 55,000 animals, representing 165 livestock and poultry breeds. The collection was developed to provide genetic conservation and security for the U.S. livestock sector. Samples in the collection span 60 years, suggesting a wide range of genetic diversity and genetic change is represented for rare and major breeds. Classifying breeds into four groups based upon registration or census estimates of population size of < 1000, < 5000, < 20,000, and > 20,000 indicated that 50% of the collection is comprised of rare breeds in the < 1000 category. As anticipated, collections for breeds in the < 20,000 and > 20,000 are more complete (86% and 98%, respectively) based upon an index combining the number of germplasm samples and the number of animals. For the rarest breeds (< 1000), collection completeness was 45%. Samples from over 6000 animals in the collection have been used for adding diversity to breeds, genomic evaluation, reconstituting populations, or various research projects. Several aspects of collecting germplasm samples from rare breeds are discussed. In addition, approaches that could be used to enhance the status of rare breeds via the repository use are presented. However, given the array of obstacles confronting rare breeds, the gene bank may be the most secure prospect for the long-term conservation of rare breed genetics.

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.

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

National gene bank collections for Holstein Friesian (HF) dairy cattle were set up in the 1990s. In this study, we assessed the value of bulls from the Dutch HF germplasm collection, also known as cryobank bulls, to increase genetic variability and improve genetic merit in the current bull population (bulls born in 2010-2015). Genetic variability was defined as 1 minus the mean genomic similarity (SIM_SNP) or as 1 minus the mean pedigree-based kinship (f_PED). Genetic merit was defined as the mean estimated breeding value for the total merit index or for 1 of 3 subindices (yield, fertility, and udder health). Using optimal contribution selection, we minimized relatedness (maximized variability) or maximized genetic merit at restricted levels of relatedness. We compared breeding schemes with only bulls from 2010 to 2015 with schemes in which cryobank bulls were also included. When we minimized relatedness, inclusion of genotyped cryobank bulls decreased mean SIM_SNP by 0.7% and inclusion of both genotyped and nongenotyped cryobank bulls decreased mean f_PED by 2.6% (in absolute terms). When we maximized merit at restricted levels of relatedness, inclusion of cryobank bulls provided additional merit at any level of mean SIM_SNP or mean f_PED except for the total merit index at high levels of mean SIM_SNP. Additional merit from cryobank bulls depended on (1) the relative emphasis on genetic variability and (2) the selection criterion. Additional merit was higher when more emphasis was put on genetic variability. For fertility, for example, it was 1.74 SD at a mean SIM_SNP restriction of 64.5% and 0.37 SD at a mean SIM_SNP restriction of 67.5%. Additional merit was low to nonexistent for the total merit index and higher for the subindices, especially for fertility. At a mean SIM_SNP of 64.5%, for example, it was 0.60 SD for the total merit index and 1.74 SD for fertility. In conclusion, Dutch HF cryobank bulls can be used to increase genetic variability and improve genetic merit in the current population, although their value is very limited when selecting for the current total merit index. Anticipating changes in the breeding goal in the future, the germplasm collection is a valuable resource for commercial breeding populations.