The purpose of the project:
Project objectives:
– Creation of a biobank of DNA and RNA of breeding animal tissues with target features.
– Search for informative biomarkers associated with resistance and exposure to economically significant diseases and economically valuable traits using GWAS methods, genome and transcriptome sequencing.
– Identification of genes involved in the formation of economically valuable animal traits using combined genome-wide and transcriptomic studies.
– Development of approaches to improving the economic characteristics of animals using methods of genetic engineering and genomic editing.
– Development of complementary approaches to classical genomic breeding for selecting animals based on post-genomic data, including biochemical, proteomic and transcriptomic markers and alleles directly related to the control of genetic expression.
– Development of the new SwineTSS_Russia digital platform, which is a collection of multimix data: genetic digital atlases of gene expression, allele-specific expression and activity of regulatory elements of the genome associated with beneficial traits of pigs.
– A retrospective analysis of metadata databases on phenotypes and other characteristics of pigs to isolate and subsequent genomic and postgenomic analysis of the most contrasting animals to identify the genetic basis of phenotypic manifestations.
– Preparation of educational programs and internships for training young specialists in modern methods of targeted breeding, transcriptomic analysis and genomic editing.
Scientific results in 2024:
In 2024, as part of a scientific project, the staff of the Laboratory of Genomic and Post-Genomic Technologies in Animal Husbandry, together with the project's industrial partner (Tavros Group), began creating a biobank of breeding animals.
Biomaterials were collected, and DNA and RNA were isolated from over 2,200 Duroc, Landrace, and Yorkshire pigs. The creation of such a biomaterial collection from breeding pigs has significant scientific and practical significance, not only preserving information on the genetic diversity of breeds but also significantly contributing to the rapid implementation of genomic selection.
To identify genetic markers for economically valuable traits, a genome-wide association study was conducted on 7,985 breeding pigs of three breeds. Genetic loci associated with reproductive traits (average number of piglets born, average number of live births, proportion of stillborn pigs, average litter weight, etc.), production traits (fat thickness, eye muscle depth), and fattening performance (average body length, metacarpal girth) were identified.
The first version of a catalog of significant genetic loci associated with economically valuable traits in Yorkshire, Duroc, and Landrace pigs has been created. Currently, the catalog contains systematized information on 402 significant associations with 15 economically valuable traits. Pilot programs for incorporating research results into the Tavros Group breeding program are being developed in collaboration with an industrial partner.
A functional annotation of the genetic loci associated with the studied traits was conducted using available databases. Loci associated with the development of several key traits were identified. For example, the locus in the kinesin transport protein 1 gene, TRAK1 (rs80952748), was associated with the highest level of significance with productive qualities (average piglet birth weight, average number of piglets born, and proportion of live born piglets).
Проведена функциональная аннотация ассоциированных с изучаемыми признаками генетических локусов с использованием доступных баз данных. Обнаружены локусы, связанные с развитием нескольких ключевых признаков. Например, с продуктивными качествами (средним весом поросёнка при рождении, средним количеством рожденных поросят, долей живорожденных поросят) с наиболее высоким уровнем значимости ассоциирован локус в гене транспортного белка кинезина 1 TRAK1 (rs80952748).
An analysis of the association of causal mutations and polymorphic variants associated with diseases and economically useful traits in Yorkshire, Landrace and Duroc pigs was performed in the study sample.
As part of the internship of the project team members (students, graduate students) at the Kazan Federal University on the topic “Basic principles and skills of histological technology”, a study was conducted on the morphology of defective (crater) nipples of pigs in comparison with healthy ones.
A review of current literature on current research areas in pig farming, identified by an industrial partner, was conducted. These include pig lameness, aggressive behavior and cannibalism, congenital malformations of piglets, infectious diseases of pigs, etc., as well as methods for addressing them, including genomic editing and the implementation of modern methods of animal identification in production.
The results of the work for 2024 were presented in the form of oral presentations by the project manager and implementers at five scientific events at the All-Russian and international level, two of which were organized within the framework of the project.
All objectives set for the first year of the project were successfully achieved, and the results obtained serve as the basis for the effective implementation and further development of the project in subsequent years.
The 2024 project marked an important step in creating a modern scientific infrastructure that will enable Russian researchers to participate in international collaborations and develop cutting-edge technologies. The laboratory continues to refine computational methods, modeling of physical processes, and hardware solutions, remaining at the forefront of science.
Опубликованные в 2024 г. статьи
1. Kravchik M., Subbot A., Bilyalov A., Novikov I., Deviatiiarov R., Yusef Y., Gusev O. Neodymium-Facilitated Visualization of Extreme Phosphate Accumulation in Fibroblast Filopodia: Implications for Intercellular and Cell–Matrix Interactions // International Journal of Molecular Sciences. 2024. V. 25(20). P. 11076. https://doi.org/10.3390/ijms252011076 WoS Q1
2. Чубукова О.В., Хакимова Л.Р., Вершинина З.Р., Михайлова Е.В., Гусев О.А. Сравнительный анализ выделения ДНК из ушных тканей и хвостов свиней (Sus scrofa domesticus) // Известия уфимского научного центра РАН 2024. № 4. С. 18–24. https://doi.org/10.31040/2222-8349-2024-0-4-136-140 РИНЦ. К2 (ВАК)
Scientific results in 2025:
A second version of the biobank was created, including 10,432 DNA samples and 145 RNA samples from Duroc, Yorkshire, and Landrace pigs. Additionally, phenotypic information for 4,664 individuals with available grading data per 100 kg (muscle depth, body length, number of teats, metatarsal girth, metacarpal girth, and backfat thickness) was uploaded to the catalog. Samples of pigs with contrasting phenotypes for the presence/absence of limb diseases, as well as samples of piglets with congenital malformations, were collected for genome-wide association analysis and whole-genome and transcriptome sequencing.
A new, highly accurate computational approach has been developed to identify significant associations between individual genome variants and phenotypic traits. Further development of this approach and its application to an expanded sample of pigs from three breeds—Yorkshire, Landrace, and Duroc—will enable the development of reliable markers for agricultural traits.
A GWAS analysis of 13 economically valuable traits was conducted in over 16,000 Duroc, Yorkshire, and Landrace pigs. Genes associated with economically valuable traits were identified and described, including average piglet birth weight, litter weight, backfat thickness, muscle depth, conformation-based culling, and others.
An analysis of metadatabases was conducted on phenotypes - weight, length, muscle depth, fat thickness and reasons for culling pigs to identify and subsequently analyze animals with the most contrasting characteristics.
DNA samples from 23 healthy animals and 33 animals with limb disease were collected for whole-genome sequencing. Thirty of these passed quality control and were sent for sequencing. Three pathogenic variants were identified in the TRIM44, BMP5, and ENSSSCG00000040861 genes, dysfunction of which can cause lameness in pigs.
When analyzing the transcriptome, the most statistically significant differences in expression levels between paired samples of healthy and affected limbs were found for the TPM2, TACC2, and EIF4A2 genes, which play an important role in the formation and development of muscle tissue.
To create genetically engineered constructs suitable for use in pig genome editing, a high-copy plasmid was created. The required guide RNA spacer sequence will then be cloned into it using the GoldenGate method with negative selection on streptomycin. Schemes for creating AAV vectors for in vivo pig genome editing, including RNA editing, as well as for editing embryonic DNA by introducing the vector into the oviduct, were developed. As part of an internship for the project team at the Institute of Cytology and Genetics SB RAS on the topic "Application of the CRISPR/Cas9 System for Animal Genome Editing," a trial genome editing of pig cells was conducted.
Whole genome sequencing of DNA samples from pigs with congenital malformations and primary processing of sequencing data were carried out.
As part of the development of predictive models for assessing selection traits of pigs using the BLUP and SS-G-BLUP methods, cross-validation was carried out for 14 traits of animals of three breeds: Yorkshire, Landrace and Duroc.
The results of the work for 2025 were presented in the form of oral reports by the project manager and executors at 5 scientific events of the All-Russian and International level, 2 of which were organized within the framework of the project.
All objectives set for the second year of the project were successfully completed.
Articles published in 2025:
1. Kazantseva A., Bilyalov A., Filatov N., Perepechenov S., Gusev O. Genetic Contributions to Aggressive Behaviour in Pigs: A Comprehensive Review // Genes. 2025. V. 16. P. 534. https://doi.org/10.3390/genes16050534 («Белый список» К2).
2. Белова М.В., Рудь А.И., Хайдаров А.А., Самойлов А.Д., Стручалин М.В., Рукин И.В., Мифтахов И.Р., Гусев О.А. Валидация результатов прогноза племенной ценности // Свиноводство. 2025. № 6. С. 4-7. https://doi.org/10.37925/0039-713X-2025-6-4-7 («Белый список» К3).
3. Mikhaylova E., Khusnutdinov E., Terekhov M., Pozdeev D., Gusev O. Pig genome editing for agriculture: achievements and challenges // Int. J. Mol. Sci. 2025. N. 26. P. 12140. https://doi.org/10.3390/ijms262412140 2025 («Белый список» К1).
4. Kazantseva A., Bilyalov A., Filatov N., Perepechenov S., Gusev O. Genetic Contributions to Aggressive Behaviour in Pigs: A Comprehensive Review // Genes. 2025. V. 16. P. 534. https://doi.org/10.3390/genes16050534 («Белый список» К2).