Breeding Practices Research Articles

Genome‐Wide Association Mapping and Genomic Prediction of Septoria nodorum Blotch Resistance in Central European Winter Wheat (Triticum aestivum L.)

ABSTRACTSeptoria nodorum blotch (SNB) is a fungal disease of wheat caused by the necrotrophic fungus Parastagonospora nodorum (Berk.), considered as one of the most devastating fungal diseases affecting winter wheat (Triticum aestivum L.). The complex inheritance of resistance to SNB poses significant challenges to breeding programmes. Improving selection precision and identifying novel resistance QTLs are crucial for enhancing SNB resistance. This study investigated strategies for crop genetic improvement, including genome‐wide association mapping (GWAS) and genomic prediction (GP), within a practical breeding programme. A population of 1500 winter wheat breeding lines was phenotyped for SNB resistance over 5 years across 19 geographical locations under natural infection conditions. Despite highly unbalanced breeder's data, medium to high heritabilities for SNB resistance were achieved. GWAS identified 11 significant marker‐trait associations for SNB resistance across Chromosomes 2A, 2B, 4B, 4D, 5D and 7B. GP fivefold cross‐validation analysis revealed a predictive ability of 0.52 for SNB resistance. The resistant wheat genotypes and SNP markers identified in this study will be valuable assets for future breeding efforts to enhance SNB resistance in wheat.

YOLOX-S-TKECB: A Holstein Cow Identification Detection Algorithm

Accurate identification of individual cow identity is a prerequisite for the construction of digital farms and serves as the basis for optimized feeding, disease prevention and control, breed improvement, and product quality traceability. Currently, cow identification faces challenges such as poor recognition accuracy, large data volumes, weak model generalization ability, and low recognition speed. Therefore, this paper proposes a cow identification method based on YOLOX-S-TKECB. (1) Based on the characteristics of Holstein cows and their breeding practices, we constructed a real-time acquisition and preprocessing platform for two-dimensional Holstein cow images and built a cow identification model based on YOLOX-S-TKECB. (2) Transfer learning was introduced to improve the convergence speed and generalization ability of the cow identification model. (3) The CBAM attention mechanism module was added to enhance the model’s ability to extract features from cow torso patterns. (4) The alignment between the apriori frame and the target size was improved by optimizing the clustering algorithm and the multi-scale feature fusion method, thereby enhancing the performance of object detection at different scales. The experimental results demonstrate that, compared to the traditional YOLOX-S model, the improved model exhibits a 15.31% increase in mean average precision (mAP) and a 32-frame boost in frames per second (FPS). This validates the feasibility and effectiveness of the proposed YOLOX-S-TKECB-based cow identification algorithm, providing valuable technical support for the application of dairy cow identification in farms.

Yield of winter soft wheat varieties of different ecological and geographical origin and their adaptability in the conditions of the Central Nonblack Earth Region

When creating new varieties, it is necessary to pay attention not only to high yields and the quality of the original parent forms, but also to be guided by knowledge about their reaction to changing growing environment conditions. The article presents the results of a comprehensive assessment of 15 varieties of different ecological and geographical origin. The methods of S.A. Eberhart and W.A. Russell, A.A. Rossielle and J. Hamblin, L.A. Zhivotkov, E.D. Nettevich were used in the analysis of adaptability indicators. The research was carried out in the northwestern part of the Ryazan region in the fields of ISA – a branch of the Federal State Budgetary Educational Institution FNAC VIM in 2019–2023, of which two years were unfavorable – the index of environmental conditions (Ij) –2,54 – –1,87, three years favorable Ij was 0,84–2,24. It was found that, on average, over 5 years of research, the highest yield potential was possessed by the varieties of winter wheat Danaya – 5,79 t/ha, Isktar – 6,36 t/ha, Nebokrat and Slavna – 5,81 t/ha and 6,09 t/ha, which is higher than the average annual indicator by experience by 11,1%, 22,1%, 11,5% and 16,9%, respectively. The group of the most plastic varieties includes: Danaya and Lavina (Russia), Nebokrat and Slavna (Ukraine), Isztar (Germany). High responsiveness to improving environmental conditions was noted in winter wheat varieties Moskovskaya 39 (Russia) – 1,22, Fantasia (Belarus) – 1,23, Saturnus and Tambor (Germany) – 1,17 and 1,41, respectively. According to the complex of adaptive properties, the Isztar (Germany) and Nebokrat (Ukraine) varieties were distinguished as genetically flexible ((Ymin + Ymax)/2 from 5,56 to 6,26), with a high level of stability (PUSS from 103,28% to 113,12%), good adaptability to environmental conditions (KA – 1,15% and 1,26%, respectively) and resistance to stress ((Ymin – Ymax) from –4,23 to –4,68). The research results can be used in practical breeding.

Rediscovering and Unrediscovering Gregor Mendel: His Life, Times, and Intellectual Context.

Two things about Mendel were "rediscovered" in 1900: His famous paper of 1865 and the story of his life and long neglect. Unlike the paper, which anyone could read in its entirety, the story came out only gradually, and many of its elements were misconstrued by Western European scientists. They pictured him as a pure scientist like themselves and were puzzled by or disinterested in his career as a clergyman, his intellectual community in far-off Moravia, and the importance to him of practical plant breeding. This paper recapitulates the process of mythmaking that followed the rediscovery, then shows how more recent historical research has been able to undo it and, in a sense, "unrediscover" Mendel.

Exploring Genomic Regions Associated with Fruit Traits in Pepper: Insights from Multiple GWAS Models

This study utilized 303 pepper accessions from diverse Capsicum species to explore fruit traits, including length, width, wall thickness, and weight. Descriptive statistics revealed a mean fruit length of 66.19 mm, width of 23.48 mm, wall thickness of 1.89 mm, and weight of 15.29 g, with significant variability, particularly in fruit weight. Correlation analysis demonstrated strong positive relationships between fruit width, weight, and fruit wall thickness (r = 0.89 and r = 0.86, respectively), while fruit length showed weaker correlations with these traits. Analysis of fruit positions revealed that the majority of accessions had a pendent fruit position (156), followed by erect (85) and intermediate (8). In terms of fruit shape, triangular and narrow triangular shapes were the most common, observed in 102 and 98 accessions, respectively. Genome-wide association studies (GWAS) identified significant single nucleotide polymorphisms (SNPs) associated with fruit traits across four models (Blink, FarmCPU, MLM, MLMM). The number of significantly associated SNPs were as follows: fruit length (89), fruit width (55), fruit weight (63), fruit wall thickness (48), fruit shape (151), and fruit position (51). Several genes were also identified where the SNPs are located or adjacent to, providing candidate genes for further exploration of the genetic basis of fruit morphology. Notably, genes such as E3 ubiquitin-protein ligase RGLG1 (associated with fruit width), Homeobox-leucine zipper protein HDG11 (involved in fruit width), Auxin response factor 23 (linked to fruit shape), and ATP-dependent zinc metalloprotease FtsH (related to fruit weight) were identified. These findings enhance our understanding of the genetic basis of fruit morphology in Capsicum, offering valuable insights for breeding and agricultural practices.

Historic breeding practices contribute to germplasm divergence in leaf specialized metabolism and ecophysiology in cultivated sunflower (Helianthus annuus).

The use of hybrid breeding systems to increase crop yields has been the cornerstone of modern agriculture and is exemplified in the breeding and improvement of cultivated sunflower (Helianthus annuus). However, it is poorly understood what effect supporting separate breeding pools in such systems, combined with continued selection for yield, may have on leaf ecophysiology and specialized metabolite variation. We analyzed 288 lines of cultivated H. annuus to examine the genomic basis of several specialized metabolites and agronomically important traits across major heterotic groups. Heterotic group identity supports phenotypic divergences between fertility restoring and cytoplasmic male-sterility maintainer lines in leaf ecophysiology and specialized metabolism. However, the divergence is not associated with physical linkage to nuclear genes that support current hybrid breeding practices in cultivated H. annuus. Additionally, we identified four genomic regions associated with leaf ecophysiology and specialized metabolism that colocalize with previously identified QTLs for quantitative self-compatibility traits and with S-protein homolog (SPH) proteins, a recently discovered family of proteins associated with self-incompatibility and self/nonself recognition in Papaver rhoeas (common poppy) with suggested conserved downstream mechanisms among eudicots. Further work is necessary to confirm the self-incompatibility mechanisms in cultivated H. annuus and their relationship to the integrative and polygenic architecture of leaf ecophysiology and specialized metabolism in cultivated sunflower. However, because self-compatibility is a derived quantitative trait in cultivated H. annuus, trait linkage to divergent phenotypic traits may have partially arisen as a potential unintended consequence of historical breeding practices and selection for yield.

The adoption non-adoption dichotomy: Why do smallholder producers dis-adopt improved chicken breeds?

Adopting agricultural technologies is crucial to improve productivity and livelihoods in developing countries. While much research has focused on adoption decisions, understanding dis-adoption, when farmers stop using technology, is equally important. Studies on agricultural technology adoption often treat dis-adopters (those who initially adopted but later discontinued to use) and never-adopters (those who never adopted) as the same, using binary models to analyze farmers' decisions. We argue that a better understanding of these decisions can be achieved by separately analyzing 'never-adoption', 'dis-adoption', and 'adoption.' Using nationally representative data from three African countries, Ethiopia, Nigeria, and Tanzania, we developed a multinomial logit model to analyze the adoption of improved chicken breeds. Our findings show that dis-adopters of improved chicken are different from never-adopters. Factors associated with dis-adoption include gender and education of household heads, access to training and extension services, breeding and culling practices, access to markets, use of complementary inputs, production objectives, landholding size, income diversity, and access to finance. Policies and strategies that aim to enhance sustained adoption and use of improved chicken breeds should promote a bundle of technologies, including tailored training, women empowerment, locally adapted and farmer-preferred chicken breeds, complementary inputs and services, innovative marketing strategies, and delivery models for bundles of technologies.

Opportunities for CRISPR-Cas9 application in farm animal genetic improvement.

CRISPR-Cas9 has emerged as a powerful tool in livestock breeding, enabling precise genetic modifications to address genetic diseases, enhance productivity, and develop disease-resistant animal breeds. A thorough analysis of previous research highlights the potential of CRISPR-Cas9 in overcoming genetic disorders by targeting specific mutations in genes. Furthermore, its integration with reproductive biotechnologies and genomic selection facilitates the production of gene-edited animals with high genomic value, contributing to genetic enhancement and improved productivity. Additionally, CRISPR-Cas9 opens new avenues for developing disease-resistant livestock and creating innovative breeding models for high-quality production. A key trend in the field is the development of multi-sgRNA vectors to correct mutations in various genes linked to productivity traits or certain diseases within individual genomes, thereby increasing resistance in animals. However, despite the potential advantages of CRISPR-Cas9, public acceptance of genetically modified agricultural products remains uncertain. Would consumers be willing to purchase such products? It is essential to advocate for bold and innovative research into genetically edited animals, with a focus on safety, careful promotion, and strict regulatory oversight to align with long-term goals and public acceptance. Continued advancements in this technology and its underlying mechanisms promise to improve poultry products and genetically modified livestock. Overall, CRISPR-Cas9 technology offers a promising pathway for advancing livestock breeding practices, with opportunities for genetic improvement, enhanced disease resistance, and greater productivity.

Transcriptomic analysis reveals differentially expressed genes associated with meat quality in Chinese Dagu chicken and AA+ broiler roosters

BackgroundWith the improvement of living standards, the quality of chicken has become a significant concern. Chinese Dagu Chicken (dual-purpose type) and Arbor Acres plus broiler (AA+ broiler) (meat-type) were selected as the research subjects in this study, the meat quality of the breast and leg muscles were measured. However, the molecular mechanism(s) underlying regulation of muscle development are not yet fully elucidated. Therefore, finding molecular markers or major genes that regulate muscle quality has become a crucial breakthrough in chicken breeding. Unraveling the molecular mechanism behind meat traits in chicken and other domestic fowl is facilitated by identifying the key genes associated with these developmental events. Here, a comparative transcriptomic analysis of chicken meat was conducted on breast muscles (BM) and leg muscles (LM) in AA+ broilers (AA) and Dagu chicken (DG) to explore the differences in their meat traits employing RNA-seq.ResultsTwelve cDNA libraries of BM and LM from AA and DG were constructed from four experimental groups, yielding 14,464 genes. Among them, Dagu chicken breast muscles (DGB) vs AA+ broilers breast muscles (AAB) showed 415 upregulated genes and 449 downregulated genes, Dagu chicken leg muscles (DGL) vs AA+ broilers leg muscles (AAL) exhibited 237 upregulated genes and 278 downregulated genes, DGL vs DGB demonstrated 391 upregulated genes and 594 downregulated genes, and AAL vs AAB displayed 122 upregulated genes and 154 downregulated genes. 13 genes, including nine upregulated genes (COX5A, COX7C, NDUFV1, UQCRFS1, UQCR11, BRT-1, FGF14, TMOD1, MYOZ2) and four downregulated genes (MYBPC3, MYO7B, MTMR7, and TNNC1), were found to be associated with the oxidative phosphorylation signaling pathway. Further analysis revealed that the differentially expressed genes (DEGs) from muscle were enriched in various pathways, such as metabolic pathways, oxidative phosphorylation, carbon metabolism, glycolysis, extracellular matrix-receptor interaction, biosynthesis of amino acids, focal adhesion, vascular smooth muscle contraction, and cardiac muscle contraction, all of which are involved in muscle development and metabolism. This study also measured the meat quality of the breast and leg muscles from the two breeds, which demonstrated superior overall meat quality in Chinese Dagu Chicken compared to the AA+ broiler.ConclusionsOur findings show that the meat quality of dual-purpose breeds (Chinese Dagu chicken) is higher than meat-type (AA+ broiler), which may be related to the DEGs regulating muscle development and metabolism. Our findings also provide transcriptomic insights for a comparative analysis of molecular mechanisms underlying muscle development between the two breeds, and have practical implications for the improvement of chicken breeding practices.

Verification of the Fusarium‐Increasing Properties of the Dominant Dwarfing Gene Ddw1 in triticale (×Triticosecale)

ABSTRACTDwarfing genes that are considerably reducing plant height are used in many cereals. In triticale, the rye‐derived dominant dwarfing gene Ddw1 was introgressed in commercial varieties. It has already been shown that this gene increases Fusarium head blight (FHB) susceptibility in one segregating population. We aimed for verifying this effect in the genetically unrelated doubled haploid (DH) population Cando (Ddw1) × Tritikon (ddw1), with 182 progenies in an experiment with artificial inoculation across six location–year combinations (environments). Linkage mapping was performed with DArTseq markers. The progenies significantly (p < 0.001) varied for FHB severity, plant height and heading stage with high entry‐mean heritabilities (0.85–0.98). The population showed a bimodal distribution for plant height. A significant QTL on chromosome 5RL was found for all three traits explaining 38%, 62% and 43% of the genotypic variation for FHB severity, plant height and heading stage, respectively, and most likely representing Ddw1. This gene increased FHB severity by 5.6 percentage points, delayed heading by 2.7 EC stages and reduced plant height by 29.6 cm on average. To use this gene in practical triticale breeding, the genetic background must be enriched with FHB resistance QTL to counterbalance the negative effect of Ddw1 either by introgression of major FHB QTL from exotic sources or by genomic selection within the adapted gene pool.

GWAS for Drought Resilience Traits in Red Clover (Trifolium pratense L.)

Red clover (Trifolium pratense L.) is a well-appreciated grassland crop in temperate climates but suffers from increasingly frequent and severe drought periods. Molecular markers for drought resilience (DR) would benefit breeding initiatives for red clover, as would a better understanding of the genes involved in DR. Two previous studies, as follows, have: (1) identified phenotypic DR traits in a diverse set of red clover accessions; and (2) produced genotypic data using a pooled genotyping-by-sequencing (GBS) approach in the same collection. In the present study, we performed genome-wide association studies (GWAS) for DR using the available phenotypic and genotypic data. Single nucleotide polymorphism (SNP) calling was performed using GBS data and the following two red clover genome assemblies: the recent HEN-17 assembly and the Milvus assembly. SNP positions with significant associations were used to delineate flanking regions in both genome assemblies, while functional annotations were retrieved from Medicago truncatula orthologs. GWAS revealed 19 significant SNPs in the HEN-17-derived SNP set, explaining between 5.3 and 23.2% of the phenotypic variation per SNP–trait combination for DR traits. Among the genes in the SNP-flanking regions, we identified candidate genes related to cell wall structuring, genes encoding sugar-modifying proteins, an ureide permease gene, and other genes linked to stress metabolism pathways. GWAS revealed 29 SNPs in the Milvus-derived SNP set that explained substantially more phenotypic variation for DR traits, between 5.3 and 42.3% per SNP–trait combination. Candidate genes included a DEAD-box ATP-dependent RNA helicase gene, a P-loop nucleoside triphosphate hydrolase gene, a Myb/SANT-like DNA-binding domain protein, and an ubiquitin–protein ligase gene. Most accessions in this study are genetically more closely related to the Milvus genotype than to HEN-17, possibly explaining how the Milvus-derived SNP set yielded more robust associations. The Milvus-derived SNP set pinpointed 10 genomic regions that explained more than 25% of the phenotypic variation for DR traits. A possible next step could be the implementation of these SNP markers in practical breeding programs, which would help to improve DR in red clover. Candidate genes could be further characterized in future research to unravel drought stress resilience in red clover in more detail.

Anatomy of the uterus of sheep of the Edilbaev breed in the age aspect

Sheep farming is one of the key branches of animal husbandry in the Russian Federation. Various measures aimed at further increasing the useful qualities in sheep breeding are based not only on breeding principles, but also on the achievements of veterinary sciences. It is quite understandable that the special attention of biological science and agricultural practice to the breed, age, and species characteristics of animals, namely to the reproduction system, allows us to scientifically and correctly raise issues in breeding, care, feeding, exploitation and reproduction. Not knowing the issues of anatomical topography, the structure of organs in animals of different age groups, it is difficult to carry out various medical manipulations in surgical or obstetric and gynecological practice. The study was conducted at the Department of Animal Anatomy of the St. Petersburg State University of Veterinary Medicine. Cadaveric material for the study was delivered to the Department of Animal Anatomy of the St. Petersburg State University of Veterinary Medicine from a farm in the Leningrad Region. Female sheep of the Edilbaev breed served as the object of the study. Three age groups were selected for the study. The study established the anatomical features of the uterus in the age aspect in sheep of the Edilbaev breed, and morphometric measurements were carried out in three age-related physiological groups (fetuses, newborns, young). Skeleto- and syntopia of all parts of the uterus was determined in different age groups. It was established that the uterus of sheep of the Edilbaevsky breed belongs to mobile organs, that is, depending on physiological conditions, it can change its topographic location points. Morphometry has determined that there is an uneven increase in the components of all parts of the uterus from the fetal period to the age stage of the young. The results of the study can be used by veterinary specialists, in particular obstetricians, surgeons to establish operative access to the uterus and in obstetric and gynecological practice in sheep breeding.

Identification of High-Photosynthetic-Efficiency Wheat Varieties Based on Multi-Source Remote Sensing from UAVs

Breeding high-photosynthetic-efficiency wheat varieties is a crucial link in safeguarding national food security. Traditional identification methods necessitate laborious on-site observation and measurement, consuming time and effort. Leveraging unmanned aerial vehicle (UAV) remote sensing technology to forecast photosynthetic indices opens up the potential for swiftly discerning high-photosynthetic-efficiency wheat varieties. The objective of this research is to develop a multi-stage predictive model encompassing nine photosynthetic indicators at the field scale for wheat breeding. These indices include soil and plant analyzer development (SPAD), leaf area index (LAI), net photosynthetic rate (Pn), transpiration rate (Tr), intercellular CO2 concentration (Ci), stomatal conductance (Gsw), photochemical quantum efficiency (PhiPS2), PSII reaction center excitation energy capture efficiency (Fv’/Fm’), and photochemical quenching coefficient (qP). The ultimate goal is to differentiate high-photosynthetic-efficiency wheat varieties through model-based predictions. This research gathered red, green, and blue spectrum (RGB) and multispectral (MS) images of eleven wheat varieties at the stages of jointing, heading, flowering, and filling. Vegetation indices (VIs) and texture features (TFs) were extracted as input variables. Three machine learning regression models (Support Vector Machine Regression (SVR), Random Forest (RF), and BP Neural Network (BPNN)) were employed to construct predictive models for nine photosynthetic indices across multiple growth stages. Furthermore, the research conducted principal component analysis (PCA) and membership function analysis on the predicted values of the optimal models for each indicator, established a comprehensive evaluation index for high photosynthetic efficiency, and employed cluster analysis to screen the test materials. The cluster analysis categorized the eleven varieties into three groups, with SH06144 and Yannong 188 demonstrating higher photosynthetic efficiency. The moderately efficient group comprises Liangxing 19, SH05604, SH06085, Chaomai 777, SH05292, Jimai 22, and Guigu 820, totaling seven varieties. Xinmai 916 and Jinong 114 fall into the category of lower photosynthetic efficiency, aligning closely with the results of the clustering analysis based on actual measurements. The findings suggest that employing UAV-based multi-source remote sensing technology to identify wheat varieties with high photosynthetic efficiency is feasible. The study results provide a theoretical basis for winter wheat phenotypic monitoring at the breeding field scale using UAV-based multi-source remote sensing, offering valuable insights for the advancement of smart breeding practices for high-photosynthetic-efficiency wheat varieties.

The Influence of Different Factors on the Metabolism of Capsaicinoids in Pepper (Capsicum annuum L.)

Pepper is a globally cultivated vegetable known for its distinct pungent flavor, which is derived from the presence of capsaicinoids, a class of unique secondary metabolites that accumulate specifically in pepper fruits. Since the accumulation of capsaicinoids is influenced by various factors, it is imperative to comprehend the metabolic regulatory mechanisms governing capsaicinoids production. This review offers a thorough examination of the factors that govern the metabolism of capsaicinoids in pepper fruit, with a specific focus on three primary facets: (1) the impact of genotype and developmental stage on capsaicinoids metabolism, (2) the influence of environmental factors on capsaicinoids metabolism, and (3) exogenous substances like methyl jasmonate, chlorophenoxyacetic acid, gibberellic acid, and salicylic acid regulate capsaicinoid metabolism. The findings of this study are expected to enhance comprehension of capsaicinoids metabolism and aid in the improvement of breeding and cultivation practices for high-quality pepper in the future.

Animal breeding and feeding tools may close human nutrition gaps

The last century has witnessed many innovations in agriculture and food technologies that have ensured the production of sufficient quantities of good hygienic food. Animal scientists have contributed substantially to efficient breeding and feeding practices by adapting animals for faster growth and improving feed efficiency and utilization. Breeding goals and feeding recommendations have been proposed with a primary focus on profitability to promote significant changes in the macronutrient content, i.e., animal body protein and fat reduction. However, improving the nutritional quality of meat was not included in the profit assessment. Increasing the lean meat fraction is consistent with the goal of public dietary guidelines for human nutrition proposed in 1980, emphasizing the importance of reducing the consumption of animal fat, particularly saturated fat. The application of breeding and feeding tools to modify and improve the fatty acid composition has been partly implemented in pigs and broiler chickens to supplement the dietary recommendations for humans. The health benefits of lean “red meat” have been questioned in recent years, with dietary guidelines and upper limits being introduced for human intake. Animal breeding indirectly reduces the total and heme iron (the redness generator) content in meat, due to covariation with priority breeding goals. Two micronutrients play important roles in the human diet and are derived largely from meat (selenium) and milk (iodine) if the amount provided and absorbed is sufficient and predictable. The iodine content can be highly dependent on the use of novel (more sustainable) feeds. The micronutrients discussed in this study (Fe, Se, I, and vitamin D) highlight opportunities for the utilization of breeding and feeding knowledge to adjust their levels to procure meat with a high nutrient density. The gaps in micronutrient levels in humans must be addressed by navigating within approved animal feeding levels. Animal scientists must recognize the nutritional impact of breeding and feeding and advertise them. In addition, human nutritionists must acknowledge the existing and potential changes in animal production to meet the dietary guidelines. Sustainable food production within the “One Health” concept can only be achieved through cooperation.

Genetic structure of cattle of the siberian branch by microsatellite loci

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.

Environmental Impact of the Hungarian Swine Sector during the PRRS Eradication Program with Full Herd Replacement (2014-2022).

The Porcine Reproductive and Respiratory Syndrome (PRRS) eradication program in Hungary, implemented between 2014 and 2022, utilized complete herd replacement and the introduction of high-performance breeds to enhance production efficiency and environmental sustainability in the swine sector. As a result, the sow population was reduced by 26.2% while maintaining nearly the same number of slaughter pigs. This led to significant reductions in ammonia emissions (-145,857 kg), slurry production (-153,879 m3), nitrogen emissions (-1,409,951 kg), and overall greenhouse gas emissions (91,768,362 kg CO2eq). Additionally, the feed and water consumption were substantially decreased by 53,237,805 kg and 292,978,094 L, respectively, further lowering the sector's environmental footprint. The study demonstrates the effectiveness of customized eradication strategies and advanced breeding practices in reducing the environmental impact of animal husbandry. These findings underscore the necessity for ongoing collaboration among scientists, policymakers, and industry stakeholders to develop and implement sustainable livestock production methods. The Hungarian experience provides valuable insights into how targeted interventions can simultaneously improve production outcomes and reduce the environmental burden in the swine industry.

V. Introduction and selection of a new species of Clarkia (C. purpurea) and development of a method for evaluating Clarkia pursh varieties for distinctiveness, uniformity and stability

During 2011–2023 in the south of Western Siberia, with the aim of introducing and selecting a new species of clarkia (C. purpurea), its biological characteristics and morphological characteristics were studied. Based on the data obtained and the use of other species and varieties of the genus Clarkia Pursh. For the first time, a methodology for conducting tests for distinctiveness, uniformity and stability (DUS) for this crop was developed. This technique is applicable to all varieties of the genus Clarkia Pursh, classified into sections: Godetia (C. purpurea (Curtis) A. Nelson & J. F. Macbr.), Phaeostoma (C. unguiculata Lindl.), Rhodanthos (C. amoena (Lehm.) A . Nelson & J. F. Macbr., Clarkia amoena ssp. lindleyi (Douglas) H. F. Lewis & M. Е. Lewis), fireweed family (Onagraceae Juss.). Many species of clarkia are characterized by long-lasting flowering and are promising for floral decoration of urban spaces, as well as for cutting. Most varieties are from very low – up to 25 cm tall, to very high – 96 cm or more; leaves are simple, lanceolate, narrow-lanceolate, wide-lanceolate, ovate, smooth, pubescent. The flowers are very decorative, varying in size from 2.0 to 8.0 cm tall, simple, semidouble, terry and strongly terry with or without fragrance, with a large variability of colors and types of floral pigmentation. Based on the study of the bioecological and morphological properties of the crop under study and in accordance with the rules approved by the Federal State Budgetary Institution “State Varietal Commission”, 36 characteristics were selected by which it is possible to test clarkey varieties. As a result of breeding work, a new variety of C. purpurea, Lilac Fairy, was created. When analyzing crossing, it was established that the lilac (violet) color of flowers is dominant in relation to pale pink (almost white), and when crossing F1 hybrids with light purple color, splitting 15:1 (15 violet from dark purple to pale purple was obtained and 1 is pale pink), which confirms the hypothesis about the polygenic nature of the inheritance of the main color of flowers in C. purpurea. The national methodology RTG/1157/1, created for the first time, for testing the DUS of Clarkia Pursh varieties will serve as a scientific basis for practical breeding.

AMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research.

As the largest family of dicotyledon, the Asteraceae family comprises a variety of economically important crops, ornamental plants and numerous medicinal herbs. Advancements in genomics and transcriptomic have revolutionized research in Asteraceae species, generating extensive omics data that necessitate an efficient platform for data integration and analysis. However, existing databases face challenges in mining genes with specific functions and supporting cross-species studies. To address these gaps, we introduce the Asteraceae Multi-omics Information Resource (AMIR; https://yanglab.hzau.edu.cn/AMIR/), a multi-omics hub for the Asteraceae plant community. AMIR integrates diverse omics data from 74 species, encompassing 132 genomes, 4 408 432 genes annotated across seven different perspectives, 3897 transcriptome sequencing samples spanning 131 organs, tissues and stimuli, 42 765 290 unique variants and 15 662 metabolites genes. Leveraging these data, AMIR establishes the first pan-genome, comparative genomics and transcriptome system for the Asteraceae family. Furthermore, AMIR offers user-friendly tools designed to facilitate extensive customized bioinformatics analyses. Two case studies demonstrate AMIR's capability to provide rapid, reproducible and reliable analysis results. In summary, by integrating multi-omics data of Asteraceae species and developing powerful analytical tools, AMIR significantly advances functional genomics research and contributes to breeding practices of Asteraceae.

Genomic Sequencing to Detect Cross-Breeding Quality in Dogs: An Example Studying Disorders in Sexual Development.

Disorders of sexual development (DSDs) in dogs, similar to humans, arise from genetic mutations, gonadal differentiation, or phenotypic sex development. The French Bulldog, a breed that has seen a surge in popularity and demand, has also shown a marked increase in DSD incidence. This study aims to characterize the genetic underpinnings of DSDs in a French Bulldog named Brutus, exhibiting ambiguous genitalia and internal sexual anatomy, and to explore the impact of breeding practices on genetic diversity within the breed. We utilized a comprehensive approach combining conventional cytogenetics, molecular techniques, and deep sequencing to investigate the genetic profile of Brutus. The sequence data were compared to three other male French Bulldogs' genome sequences with typical reproductive anatomy, including Brutus's father and the canine reference genome (CanFam6). We found a Robertsonian fusion involving chromosome 23 previously reported in dogs as a causative mutation responsible for sex reversal syndrome. Our findings revealed a 22% mosaicism (78,XX/77,XX), the absence of the sex-determining region (SRY) gene, and the presence of 43 unique Single Nucleotide Variants (SNVs) not inherited from the father. Notably, the run of homozygosity (ROH) analysis showed Brutus has a higher number of homozygous segments compared to other Bulldogs, with a total length of these fragments 50% greater than the average, strongly suggesting this dog is the product of the mating between siblings. Although no direct causative genes for the DSD phenotype were identified, four candidate loci warrant further investigation. Our study highlighted the need for a better annotated and curated reference dog genome to define genes causative of any specific phenotype, suggests a potential genetic basis for the DSD phenotype in dogs, and underscores the consequences of uncontrolled breeding practices in French Bulldogs. These findings highlight the importance of implementing strategic genetic management to preserve genetic health and diversity in canine populations.