Due to its high efficiency and safety, oocyte vitrification finds broad application in many fields of life sciences, such as clinical assisted reproduction and conservation of animal genetic resources. However, vitrification may cause cellular damage and reduce the quality of oocytes and their cumulus cells (CCs), which could be closely related to disorders in lipid metabolism. At present, the impact of vitrification upon the lipid profile of oocytes and CCs has not been systematically elucidated. In this study, we used porcine germinal vesicle cumulus-oocyte complexes (COCs) as a model to analyze their lipid characteristics after vitrification and in vitro maturation (IVM), utilizing untargeted lipid metabolomics. Our results showed that an overall count of 37 down-regulated and 8 up-regulated differential lipids was identified in the vitrified oocytes. Pathway analysis confirmed the enrichment in glycerophospholipid metabolism and fat digestion and absorption, etc. Combined with transcriptomic analysis, three enriched pathways were revealed, including the AMPK signaling pathway, metabolic pathways, and fatty acid elongation. On the other hand, a total of four down-regulated and eight up-regulated differential lipids were detected in the vitrified CCs. Pathway enrichment implicated autophagy, glycerophospholipid metabolism, etc. A joint analysis of metabolomic and transcriptomic data revealed four enrichment pathways, including cholesterol metabolism, fat digestion and absorption, regulation of lipolysis in adipocytes, and metabolic pathways. Notably, the supplementation of lysophosphatidylcholine during IVM attenuated oxidative stress, enhanced mitochondrial activity, and enhanced the viability and embryonic development of cryopreserved porcine oocytes. The results indicate that vitrification alters lipids in oocytes and CCs, and the supplementation of lipids plays a role in improving the quality of vitrified oocytes.

Objective: This study evaluated the greasy fleece weight (GFW) and shearing live weight at shearing (SLW) of the Kaçeli sheep breed conserved under Türkiye’s National Animal Genetic Resources Conservation Program.Materials and Methods: The animal material for this study consisted of 291 Kaçeli sheep (283 females and 8 males) raised under semi-intensive conditions on the Çeşme Peninsula. The animals ranged in age from 2 to 7 years. Dirty fleece weights were recorded during shearing in May, and live weights at shearing were measured using digital scales. Due to the small sample size and physiological differences in males, ram data were evaluated only descriptively and were excluded from statistical models. Descriptive statistics, general linear models, least squares means, and phenotypic correlation analyses were performed on the ewe data using SAS software. Farm, age, and live weight were included as fixed effects in the models, and between-group differences were determined using the Duncan Multiple Range Test.Results: Mean GFW was 1.70 kg in rams and 1.26 kg in ewes, while mean SLW was 57.61 kg and 41.40 kg, respectively. Farm effects were significant; Farm 2 showed the highest SLW (45.38 kg). Each 1 kg increase in SLW resulted in a 0.020 kg rise in GFW. Age negatively affected GFW (–0.046) but positively influenced SLW (1.112).Conclusion: Kaçeli sheep display moderate productivity, broad phenotypic diversity, and strong adaptability, providing key data for sustainable breeding and conservation strategies.

Wild relatives of domestic animals are crucial reservoirs of genetic diversity, yet pervasive hybridization with domestic animals poses significant conservation challenges. Here, we developed a deep learning-based pipeline, consisting of a multi-layer perceptron for SNP panel selection and a Deep & Cross Network for model training, to discern wild relatives from their closely related domestic animals using genomic SNP data. Leveraging the 1960 genomes from 164 red jungle fowl (RJF; Gallus gallus) and 1796 domestic chicken samples, we applied this pipeline to yield the RJF identification model based on a 285-SNP panel. We employed this model to characterize domestic chickens, RJF, and hybrids in the independent genomic datasets from contemporary samples and historical specimens, respectively. The accuracy was 97.8% for historical samples with missing genotypes. The benchmarking multiple hybrid detection tools indicated that the RJF identification model was effective and practical. The further application to the genomic data from wild boar (Sus scrofa), domestic pigs, and their hybrids validated the pipeline. Our method has potential in not only monitoring genetic diversity in wild relatives of domestic animals but also supporting animal genetic resource conservation and management.

The large Japanese field mouse, Apodemus speciosus, is a rodent species endemic to Japan and is widely distributed throughout the country. It has been extensively used as a model organism in studies of geographic isolation and as an environmental bioindicator. However, there have been no reports on the establishment of pluripotent stem cells from this species that could be applied to developmental engineering. In this study, we attempted to generate induced pluripotent stem cells (iPSCs) from A. speciosus and successfully obtained cells that formed dome-shaped colonies and expressed pluripotency markers. These cells were capable of forming embryoid bodies that expressed markers of the three germ layers, and in vivo analysis using immunodeficient mice confirmed their ability to form teratomas. A. speciosus iPSCs established in this study not only contribute to the conservation of Japan's valuable animal genetic resources, but also provide a novel platform for investigating various biological processes that remain unexplored in this wild species.

The genetic diversity of multiple animal species is now declining rapidly, highlighting the need for action to protect and preserve animal genetic resources for the long term. The Nordic countries house a broad range of farm and companion animal breeds and subspecies that play a critical role in environmental sustainability, food safety and security, and human activities. Unfortunately, close to 80% of these breeds and subspecies are either endangered or critically endangered, with population sizes too small to ensure their long-term survival. In addition, almost half of them have either a declining or unknown demographic trend, and many of them suffer from high inbreeding. Emerging pressures such as climate change, infectious diseases and public unrest further threaten the status of the populations, and urgent action is necessary to ensure their future survival. Consequently, efforts for safeguarding the genetic diversity of animal genetic resources (AnGR) with additional in vitro or cryoconservation efforts need further consideration. The Nordic conservation strategies for AnGR have traditionally been based on in vivo or live conservation. Although cryoconservation efforts are in place for some species, the number of donors and doses varies considerably between breeds and species. Due to the increasing demand for additional measures for safeguarding AnGR, this document discusses the status of active AnGR conservation measures in the Nordic countries and emphasize the central role of regional cooperation in ensuring AnGR sustainability and long-term viability. Further, the contributions of cryoconservation in mitigating genetic losses are discussed.

Molecular-genetic methods are essential tools for the utilization and conservation of animal genetic resources. These methods facilitate more efficient management and control of breeding programs within livestock production systems. For studying the genetic diversity of a population, the use of STR markers is relevant due to the high variability of repeats. This study presents a genetic characterization of a Holstein and Black Pied cattle population (n = 10233) in Western Siberia using 12 microsatellite loci (BM1818, BM1824, BM2113, ETH10, ETH225, ETH3, INRA023, SPS115, TGLA126, TGLA122, TGLA227, TGLA53). A total of 145 alleles were identified across all loci, with frequencies ranging from 0.00005 to 0.68961. The highest level of genetic diversity was observed at the TGLA122 locus (25 alleles) with an average number of effective alleles (Ne) of 4.5. The least polymorphic locus was BM1824 (7 alleles) with an average Ne of 3.27. The average observed (Ho) and expected (He) heterozygosity across all loci was 0.6. The highest variability was observed at the TGLA53 locus, with a Wright’s fixation index (Fis) of 0.161, indicating a heterozygote deficiency. A similar deficiency was observed at the BM1818 locus. All other loci exhibited a positive Fis, with the highest value observed at the ETH3 locus (-0.074), indicating an excess of heterozygotes. The average Fis across all loci was -0.02, suggesting a sufficient level of heterozygosity within the studied population. These findings provide valuable information for population studies and practical breeding programs aiming to manage genetic diversity and improve selection efficiency in this cattle population.

BackgroundAccurate breed identification is essential for the conservation and sustainable use of indigenous farm animal genetic resources. In this study, we evaluated the phylogenetic relationships and genomic breed compositions of 13 sheep breeds using SNP and InDel data from whole genome sequencing. The breeds included 11 Chinese indigenous and 2 foreign commercial breeds. We compared different strategies for breed identification with respect to different marker types, i.e. SNPs, InDels, and a combination of SNPs and InDels (named SIs), different breed-informative marker detection methods, and different machine learning classification methods.ResultsUsing WGS-based SNPs and InDels, we revealed the phylogenetic relationships between 11 Chinese indigenous and two foreign sheep breeds and quantified their purities through estimated genomic breed compositions. We found that the optimal strategy for identifying these breeds was the combination of DFI_union for breed-informative marker detection, which integrated the methods of Delta, Pairwise Wright's FST, and Informativeness for Assignment (namely DFI) by merging the breed-informative markers derived from the three methods, and KSR for breed assignment, which integrated the methods of K-Nearest Neighbor, Support Vector Machine, and Random Forest (namely KSR) by intersecting their results. Using SI markers improved the identification accuracy compared to using SNPs or InDels alone. We achieved accuracies over 97.5% when using at least the 1000 most breed-informative (MBI) SI markers and even 100% when using 5000 SI markers.ConclusionsOur results provide not only an important foundation for conservation of these Chinese local sheep breeds, but also general approaches for breed identification of indigenous farm animal breeds.

Accurate breed classification is required for the conservation and utilization of farm animal genetic resources. Traditional classification methods mainly rely on phenotypic characterization. However, it is difficult to distinguish between the highly similar breeds due to the challenges in qualifying the phenotypic character. Machine learning algorithms show unique advantages in breed classification using genomic information. To evaluate the classification methods for Chinese cattle breeds, this study utilized genomic SNP data from 213 individuals across seven Chinese local breeds and compared the classification accuracies of three feature selection methods (FST value sorting and screening, mRMR, and Relief-F) and three machine learning algorithms (Random Forest, Support Vector Machine, and Naive Bayes). Results showed that: 1) using the FST method to screen more than 1500 SNPs, or using the mRMR algorithm to screen more than 1000 SNPs, the SVM classification algorithm can achieve more than 99.47% classification accuracy; 2) the most effective algorithm was SVM, followed by NB, while the best SNP selection method was FST and mRMR, followed by Relief-F; 3) species misclassification often occurs between breeds with high similarity. This study demonstrates that machine learning classification models combined with genomic data are effective methods for the classification of local cattle breeds, providing a technical basis for the rapid and accurate classification of cattle breeds in China.

The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction. Creole cattle populations have suffered a drastic reduction in recent decades owing to absorbent crosses or replacement with commercial breeds of European or Indian origin. Genetic characterization can serve as a source of information for conservation strategies to maintain genetic variation. The objective of this work was to evaluate the levels of inbreeding and kinship through the use of genomic information. A total of 903 DNAs from 13 cattle populations from Argentina, Bolivia and Uruguay were genotyped using an SNP panel of 48 K. Also, a dataset of 76 K SNPs from Peruvian Creole was included. Two inbreeding indices (FROH and Fhat2) and kinship relationships were calculated. In addition, effective population size (Ne), linkage disequilibrium, population composition and phylogenetic relationships were estimated. In Creole cattle, FROH ranged from 0.14 to 0.03, and Fhat2 was close to zero. The inferred Ne trends exhibited a decline toward the present for all populations, whereas Creole cattle presented a lower magnitude of Ne than foreign breeds. Cluster analysis clearly differentiated the taurine and Zebu components (K2) and showed that Bolivian Creole cattle presented Zebu gene introgression. Despite the population reduction, Creole populations did not present extreme values of consanguinity and kinship and maintain high levels of genetic diversity. The information obtained in this work may be useful for planning conservation programmes for these valuable local animal genetic resources.

Extant diversity for phenotypic traits is an essential criterion to be considered when ordering priorities for conservation and improvement of animal genetic resources. Concretely, the characterisation of the distinctive body morphometry of a particular group of animals can aid in the design of selective breeding programs, given the strong correlation between body morphology and productive function. The present research aims to characterise an endangered autochthonous camel breed (Canarian camel), mainly relegated to leisure riding, for its body morphology, with a double objective: to explore the phenotypic diversity and structure of the breed for zoometric traits and assess the zoometric profile of this genetic resource that supports its differentiation from other camel breeds. Overall, the results highlight the existence of a high degree of diversity, which may be linked to genetic factors for zoometric traits in an endangered autochthonous breed with traditional in situ breeding schemes, which predicts the success of the implementation of genetic improvement schemes for such functional characteristics. This phenotypic diversity in body morphology could also be a tool for the evaluation of new functional niches within the efforts of functional valorisation of this camel breed for its sustainable conservation. Body morphology traits in the studied camel breed are significantly influenced by sex, physiological status and coat colour.

Simple SummarySheep farming is crucial for preserving biodiversity, maintaining soil and water quality, and supporting local communities. Preserving genetic resources is vital for combating new diseases and tackling environmental changes. This study focuses on the Massese sheep, an indigenous breed which is primarily bred in Tuscany in extensive conditions using natural resources. The examination of their genealogy revealed that the data were incomplete, as a significant number of animals were recorded with one or two parents whose identity was unknown. This made it difficult to accurately evaluate the relationships among animals and to determine the extent of inbreeding. Breeders’ associations can play a crucial role in preserving genetic diversity; however, the completeness of the genealogical data needs improving.This study investigates the genealogical and demographic trends of the Massese sheep breed in Tuscany from 2001 to 2021. The Herd Book kept by the Italian Sheep and Goat Breeders Association (Asso.Na.Pa) provided the data. The descriptive statistics were analyzed using JMP software. The pedigree parameters of a total of 311,056 animals (whole population—WP) were analyzed using CFC, ENDOG, and Pedigree viewer software. A total of 24,586 animals born in the period 2007–2021 represented the Reference Population (RP), and 18,554 animals the Base Population (BP). The demographic results showed an inconsistent trend of offspring registration. This study showed a short period of productivity for both ewes and rams, with means of 1.47 and 19.2 registered newborn ewes and rams, respectively. The genealogical analysis revealed incomplete data, highlighting inaccurate assessments of the relationships among the animals, and inbreeding with large differences among provinces. The average inbreeding coefficient in the WP was 1.16%, and it was 2.26% in the RP. The total number of inbreds was 2790 in the WP, with an average FPED of 13.56%, and 2713 in the RP, with an average FPED of 12.82%. The use of pedigree data is a key and economical approach to calculating inbreeding and relationship coefficients. It is the primary step in genetic management, playing a crucial role in the preservation of a breed. The regular updating of genealogical data is the first step to ensuring the conservation of animal genetic resources, and this study is compromised by the lack of such updates.

The Gene bank for domestic animals in the Republic of Croatia is provided by the National Program for the conservation of local and endangered breeds of domestic animals from 2010. For this purpose, the National Gene bank Network was established, which consists of (i) the Gene bank for domestic animals as a central point under the jurisdiction of the Ministry of Agriculture, and (ii) Recognized Gene banks (authorized by the Ministry of Agriculture and operated by organizations, associations and/or authorized institutions). Until 2023, more than 32,000 samples from six types of domestic animals are stored in the Gene bank as follows: cattle (57.7%), horses (13.2%), sheep (12.1%), pigs (10%), donkeys (5%), and goats (1.9%). Tissue samples (29.2%), hair (28%), semen (42.2%) and blood (0.6%) are mainly stored in the Gene bank. The implementation of the National Program is supported by the Reference Expert Network for the Conservation of Animal Genetic Resources, which promotes greater collaboration with stakeholders. Future plans include further characterization of breeds with emphasis on adaptive traits, and the necessary monitoring and implementation of new and improved procedures in the conservation of local breeds.

Animal genetic resources in the world are rich and varied. Local species have strong adaptability to the local environment. They are precious resources, and need to be protected by the whole world. In this paper, we summarize the current situation of conservation activities of livestock and poultry resources abroad, including the relevant policies and measures, financial support, genetic material conservation, research projects, and the benefits of conservation animal genetic resources. The actions of conservation of animal genetic resources reflects the increasing recognition of the importance of biodiversity by people around the world. The variety of conservation activities of genetic materials in the world and its benefits reflect that the concept of biodiversity has already been accepted by public and the government. Conservation of animal genetic resources is the primary action for the revitalization of Chinese seed industry. This paper has enlightenment significance for strengthening the conservation of animal genetic resources in China.

A future EU overall strategy for agriculture and forest genetic resources management: Finding consensus through policymakers’ participation

This research seeks to deepen the current economic and structural aspects of the livestock farms in the rural territory “Casacastra” (Cilento area), to identify critical issues and development opportunities with the intention to enhance and protect the territory under study also through strengthening forms of local economy. Information about the consistency and the typology of livestock farms present in the study area, and the trend in the last twelve years, were acquired thought the consultation of the national livestock register of the Italian Ministry of Health. Subsequently, a questionnaire was submitted to a sample of farmers to better know the characteristics of the breeders and of the husbandries. The results showed that in the study area, there are 4% of the cattle and sheep herds of the Campania Region, and 7% of those with goats. The most representative farm size is the class with less than 20 animals per breeding type, and between 2010 and 2022, there has been a reduction in the number of all types of analyzed husbandries. The most represented productive orientation is that for meat, while the specialization in the production of milk in sheep and goat breeding is completely absent. The interviews revealed that the breeders are almost all over 40 years of age, with middle and high school qualifications and consolidated experience. The workforce involved in the farms is mainly the family one and often breeders are people engaged in other non-agricultural activities. Despite the permanence in some cases of archaic husbandry methods, the breeders play a key role in the study area for the protection of the territory, and the conservation and enhancement of local animal and plant genetic resources are at risk of extinction. Moreover, the survival of this rural context is linked to the development of new forms of local economy, such as the definition of an experiential rural tourist offer, in which the presence of institutions plays a fundamental role.

Last October 12 and 13, 2022, the VII American Rabbit Congress took place within the framework of the 2022 Animal Production and Agro-Development Convention, which was held from October 10 to 14, 2022 at the Plaza América Convention Center in Varadero, Matanzas, Cuba. The VII American Rabbit Congress was developed in a hybrid way (in person and online) with specialists, researchers, professors, students, breeders and producers from different latitudes related to rabbit farming and science. Throughout the conference, a total of 50 people attended in person and 15 online, mainly from Cuba, Mexico, Argentina and Spain. The objective of the meeting was to "Motivate the exchange of experiences and results in rabbit production systems in the Americas, their technical, economic, environmental and social sustainability, and strategies for the improvement, conservation, use and characterization of animal genetic resources" for rabbit farming. The congress opened with a lecture by Juan José Pascual, president of the World Rabbit Science Association (WRSA) on the current state of rabbit farming, followed by three other invited lectures, 18 scientific communications, and a round table on viral hemorrhagic disease, as well as a total of 21 posters. These scientific contributions were directed both to the fundamental areas of knowledge (feeding, genetics, reproduction, pathology), but also to other important aspects of America such as socioeconomics, the value chain, and the use of rabbit farming as a tool to fight against hunger. During the first working day, aspects of the vertical integration of rabbit production, the production and commercialization of rabbits in Cuba, feeding costs and limitations for obtaining raw materials, concern for not total slaughtering rabbits where the virus outbreaks occurred, the political will to eradicate this disease and increase the productivity of the species, the components of the value chains and the need for a correct articulation between all the links in the chain were discussed. On the other hand, during the second working day, there was a debate mainly on aspects related to the role of rabbit farming in society, not only for the production of quality meat, but also for its gender approach, the use of existing local resources in the Latin American countries, and the positive experiences of producers in the promotion of rabbit breeding. The congress closed with good attendance in the room, with a representation of students, producers, specialists, researchers and representatives of state production units and the Cuban Ministry of Agriculture (Director of the National Center for Animal Health and President of the livestock business group).

Animal Genetic Resources (AnGR) are a warranty for future unknown conditions and needs. Due to this fact, sustainable use and conservation of AnGR have special importance, and to achieve reliable programs for these goals, the risk status of AnGR should be estimated accurately. The aim of this study was to estimate the risk status for three widely used domesticated livestock species of cattle, sheep, and goat in animal production: 6 cattle, 33 sheep, and 15 goat breeds were included in the analysis. Extinction probability (z) was taken as a criterion for the risk status of each breed. Data collection based on survey realized with 215 farmers, field observations and personal interviews were performed for different provinces between 2014 and 2017. Extinction probabilities estimated were ranged from 0.53 to 0.90 with an average of 0.71 for native cattle breeds. Çine Çaparı sheep and Abaza goat had the highest extinction probabilities of 0.97 and 0.87, respectively, while Kıl goat and İvesi sheep breeds had the lowest probabilities of 0.37 and 0.40, respectively. Present study demonstrated that risk analyses of survey data sets may provide useful information concerning the decision-making on conservation efforts for endangered breeds. It should be monitored risk status for breeds to create efficient conservation investments. Considering the limited resources, it is undeniable that while some breeds continued to protect, some others would be removed from conservation programs. To make this task an appropriate manner extinction probability may be used as a criterion for decision-making.

To effectively conserve animal genetic resources, countries need to periodically review their conservation efforts and reflect on actual problems and challenges. This study provides a review of animal genetic resources conservation activities, as well as the related existing legislative measures, strategies and funding in Slovakia. We present the development of endangered and supported breeds, discuss the impact of subsidies and the importance of awareness raising, and provide a SWOT analysis of the current animal genetic resources conservation framework in the country. In Slovakia, conservation is primarily based on animal breeding in natural conditions (in situ) without any limitations to breed improvement, and cryoconservation of animal genetic resources is in its initial phase. Most of the funding for conservation measures is provided by the Rural Development Programme. In general, the animal genetic resources system in Slovakia is open in terms of including new breeds eligible for support and this paper shows that the provided subsidies helped to stabilize most of the supported populations. Promoting the presence, characteristics and advantages of local breeds in times of intensive import of exotic breeds into the country is crucial to motivate breeders to prefer local livestock breeds. While the future challenge for the government is to improve conservation and facilitate related activities, research should address not only diversity, pedigree studies and cryoconservation, but also focus on the characterization of animal genetic resources for food security and climate change.

<p>Breeds contain the genetic diversity of domesticated species; hence conserving breeds conserve this diversity. Breeds are stable genetic resources that enable the matching of animals with various environments and production goals. Breeds were created by a process involving foundation, isolation and selection. Breed types that are considered genetic resources include "landraces" (local breeds), standard breeds, commercial production breeds and feral livestock that has converted to a free-living state.</p>

This review explores innovative and sustainable strategies for conservation and use of village or indigenous chickens (IC) ( Gallus domesticus) in Zambia with lessons in Sub-Saharan Africa (SSA). Small scale farmers (SSF) have kept IC for hundreds of years to meet their households’ nutritional needs, incomes, social-cultural and religious uses. The commitment exhibited by SSF to keeping indigenous animals has made them the major custodians of essential animal genetic resources in most low-income regions. Between 1991 and 2012, private breeders invested over US$95 million in Zambia’s commercial poultry sector resulting in over 100% increase in the annual production of day-old chicks to 65 million. However, high production costs and low market access hindered the participation of rural farmers hence their continued dependence on IC breeds. The future of IC genetic resources is threatened due to their rapid erosion. In the 2015 biodiversity status report, the Food and Agriculture Organisation, an international body of the United Nations highlighted that over 3.5% of chicken breeds were extinct, nearly 33% were at high risk, and over 67% were of unknown status. Poultry diseases, lack of sustainable conservation strategies and poor use have significantly contributed to these losses. For example, in 2012, 60% of village chickens were reportedly diseased in parts of SSA. If these challenges are not mitigated, the loss of IC genetic resources and the adverse impact on rural communities is inevitable. Further, future research and breeding programs on commercial chickens may be limited due to the erosion of IC genetic resources. This paper reviews lessons and contributes to previous studies that demonstrated how community-based breeding programs and researcher-community-stakeholder engagements potentially enhanced sustainability, adoption of innovative ideas and conservation of local animal genetic resources in selected low-income countries. Further, suggest strategies to promote judicious use and conservation of IC breeds in Zambia.