Selection Programs Research Articles

Identification of genomic regions associated with fatty acid metabolism across blood, liver, backfat and muscle in pigs

BackgroundThe composition and distribution of fatty acids (FA) are important factors determining the quality, flavor, and nutrient value of meat. In addition, FAs synthesized in the body participate in energy metabolism and are involved in different regulatory pathways in the form of signaling molecules or by acting as agonist or antagonist ligands of different nuclear receptors. Finally, synthesis and catabolism of FAs affect adaptive immunity by regulating lymphocyte metabolism. The present study performed genome-wide association studies using FA profiles of blood, liver, backfat and muscle from 432 commercial Duroc pigs.ResultsTwenty-five genomic regions located on 15 Sus scrofa chromosomes (SSC) were detected. Annotation of the quantitative trait locus (QTL) regions identified 49 lipid metabolism-related candidate genes. Among these QTLs, four were identified in more than one tissue. The ratio of C20:4n-6/C20:3n-6 was associated with the region on SSC2 at 7.56–14.26 Mb for backfat, liver, and muscle. Members of the fatty acid desaturase gene cluster (FADS1, FADS2, and FADS3) are the most promising candidate genes in this region. Two QTL regions on SSC14 (103.81–115.64 Mb and 100.91–128.14 Mb) were identified for FA desaturation in backfat and muscle. In addition, two separate regions on SSC9 at 0 – 14.55 Mb and on SSC12 at 0–1.91 Mb were both associated with the same multiple FA traits for backfat, with candidate genes involved in de novo FA synthesis and triacylglycerol (TAG) metabolism, such as DGAT2 and FASN. The ratio C20:0/C18:0 was associated with the region on SSC5 at 64.84–78.32 Mb for backfat. Furthermore, the association of the C16:0 content with the region at 118.92–123.95 Mb on SSC4 was blood specific. Finally, candidate genes involved in de novo lipogenesis regulate T cell differentiation and promote the generation of palmitoleate, an adipokine that alleviates inflammation.ConclusionsSeveral SNPs and candidate genes were associated with lipid metabolism in blood, liver, backfat, and muscle. These results contribute to elucidating the molecular mechanisms implicated in the determination of the FA profile in different pig tissues and can be useful in selection programs that aim to improve health and energy metabolism in pigs.

Genetic Parameter Estimates for Growth of Hāpuku (Groper, Polyprion oxygeneios) in Land-Based Aquaculture Using Random Regression Models

Hāpuku (Polyprion oxygeneios) is a promising candidate for aquaculture production in New Zealand. Methods for spawning, juvenile production, and growout to harvest entirely on land, where water quality, pathogens, environmental impacts, and genetic “pollution” can be tightly controlled, have been developed, and genetic improvement to optimise land-based production is the obvious next step. However, estimates of genetic parameters are required to design a rigorous, disciplined, and effective selective breeding program. By using existing data consisting of irregularly spaced repeated measurements of fork length and live body weight collected on wild-collected founders and two generations of captively reared progeny, we evaluated the species’ genetic potential for improvement in growth. We first tested a range of univariate random regression models to identify the best-fitting models for these data. Subsequently, using a bivariate model, we estimated variance components for growth trajectories of fork length and whole body weight. With one to six records available per fish, the best-fitting univariate models included only a fixed effect for contemporary groups and fixed and random genetic third-order Legendre polynomials. More complex models that included full-sib family and/or permanent environmental effects produced unacceptable constrained and/or non-positive-definite solutions. Both traits are moderately heritable at all stages of the growout phase (~0.4–0.5), and the genetic correlation patterns between daily breeding values estimated via the covariance function are different for length and weight. Genetic correlations for length between all pairs of age-specific breeding values are positive and strong (>0.7) and change gradually and smoothly with increasing temporal separation. For weight, these correlations deteriorate more rapidly with increasing time lags between measurements and become negative for some age pairings. We conclude that random regression analyses are a valuable tool for extracting genetic information from irregularly spaced repeated measurements of fish size, speculate that emerging technologies for high-throughput genotyping and phenotyping will add to the value of this approach in the near future, and reason that a breeding strategy that rigorously takes into account the potentially unfavourable genetic correlations between breeding values for weight at some ages will further adapt hāpuku to land-based systems and enhance the profitability commercial-scale production.

Identification of Genetic Associations of IDH2, LDHA, and LDHB Genes with Milk Yield and Compositions in Dairy Cows.

Previous study revealed that isocitrate dehydrogenase (NADP (+)) 2, mitochondrial (IDH2), lactate dehydrogenase A (LDHA), and lactate dehydrogenase B (LDHB) genes were significantly differentially expressed in liver tissues of Holstein cows among different lactation periods and associated with lipid and protein metabolism; hence, they were considered as candidates for milk production traits. Herein, the genetic effects of the three genes on milk yield, fat, and protein traits were studied by association analysis using 926 Chinese Holstein cows from 45 sire families. As a result, five single nucleotide polymorphisms (SNPs) in IDH2, one in LDHA, and three in LDHB were identified by re-sequencing, and subsequently, they were genotyped in 926 Chinese Holstein cows by genotyping by target sequencing (GBTS). With the animal model, single-locus association analysis revealed that four SNPs in IDH2 and one SNP in LDHA were significantly associated with milk, fat, and protein yields (p ≤ 0.0491), and three SNPs in LDHB were associated with milk yield, milk fat yield, and fat percentage (p ≤ 0.0285). Further, four IDH2 SNPs were found to form a haplotype block significantly associated with milk yield, fat yield, protein yield, and protein percentage (p ≤ 0.0249). In addition, functional predictions indicated that one SNP in LDHA, g.26304153G>A, may affect transcription factor binding and two SNPs, g.88544541A>G and g.88556310T>C could alter LDHB mRNA secondary structure. In summary, this study profiled the significant genetic effects of IDH2, LDHA, and LDHB on milk yield and composition traits and provided referable genetic markers for genomic selection programs in dairy cattle.

A machine learning and linear programming aided approach to wine ranking and selection

PurposeThis paper aims to mitigate the subjective nature of wine rating by introducing statistical and optimization tools for analysis, providing a unique approach not found in existing literature.Design/methodology/approachThe research uses an unsupervised machine learning algorithm, k-means, to cluster wines based on their chemical characteristics, followed by the application of the PROMETHEE II multicriteria decision-making model to rank the wines based on their sensorial characteristics and selling price. Lastly, a linear programming model is used to optimize the selection of wines under different scenarios and constraints.FindingsThe study presents a method to rank wines based on both chemical and sensorial characteristics, providing a more comprehensive assessment than traditional subjective ratings. Clustering wines based on their characteristics and ranking them according to sensorial characteristics provides the user/consumer with meaningful information to be used in an optimization model for wine selection.Practical implicationsThe proposed framework has practical implications for wine enthusiasts, makers, tasters and retailers, offering a systematic approach to ranking and selecting/recommending wines based on both objective and subjective criteria. This approach can influence pricing, consumption and marketing strategies within the wine industry, leading to more informed and precise decision-making.Originality/valueThe research introduces a novel framework that combines machine learning, decision-making models and linear programming for wine ranking and selection, addressing the limitations of subjective ratings and providing a more objective approach.

Predicting special forces dropout via explainable machine learning.

Selecting the right individuals for a sports team, organization, or military unit has a large influence on the achievements of the organization. However, the approaches commonly used for selection are either not reporting predictive performance or not explainable (i.e., black box models). In the present study, we introduce a novel approach to selection research, using various machine learning models. We examined 274 special forces recruits, of whom 196 dropped out, who performed a set of physical and psychological tests. On this data, we compared four machine learning models on their predictive performance, explainability, and stability. We found that a stable rule-based (SIRUS) model was most suitable for classifying dropouts from the special forces selection program. With an averaged area under the curve score of 0.70, this model had good predictive performance, while remaining explainable and stable. Furthermore, we found that both physical and psychological variables were related to dropout. More specifically, a higher score on the 2800m time, need for connectedness, and skin folds was most strongly associated with dropping out. We discuss how researchers and practitioners can benefit from these insights in sport and performance contexts.

Genetic Programming for Automatically Evolving Multiple Features to Classification

Abstract Performing classification on high-dimensional data poses a significant challenge due to the huge search space. Moreover, complex feature interactions introduce an additional obstacle. The problems can be addressed by using feature selection to select relevant features or feature construction to construct a small set of high-level features. However, performing feature selection or feature construction only might make the feature set suboptimal. To remedy this problem, this study investigates the use of genetic programming for simultaneous feature selection and feature construction in addressing different classification tasks. The proposed approach is tested on 16 datasets and compared with seven methods including both feature selection and feature constructions techniques. The results show that the obtained feature sets with the constructed and/or selected features can significantly increase the classification accuracy and reduce the dimensionality of the datasets. Further analysis reveals the complementarity of the obtained features leading to the promising classification performance of the proposed method.

Signatures of selection analyses reveal genomic differences among three heavy pig breeds that constitute the genetic backbone of a dry-cured ham production system

The Italian pig farming industry is unique in its focus on raising heavy pigs primarily for the production of high-quality dry-cured hams. These products require pigs to be slaughtered at a live weight of around 170 kg at 9 months of age. The primary breeds used in this system are Italian Duroc, Italian Landrace, and Italian Large White which are crossed to produce lines that meet standard requirements. Over the past four decades, selection and breeding programmes for these breeds have been subjected to distinct selective pressures to highlight the characteristics of each breed. In this study, we investigated the genome of these breeds by analysing high-density single nucleotide polymorphism data from over 9 000 pigs to scan for signatures of selection using four different methods, two within breeds and two across breeds. This allowed to identify the genomic regions that differentiate these breeds as well as any relevant genes and biological terms. On a global scale, we found that the Italian Duroc breed exhibited a higher genetic differentiation from the Italian Landrace and Italian Large White breeds, with a pairwise FST value of 0.20 compared with the 0.13 between Italian Landrace and Italian Large White. This may reflect either their different origins or the different breeding goals, which are more similar for the Italian Landrace and Italian Large White breeds. Despite these genetic differences at a global level, few signatures of selection regions reached complete fixation, possibly due to challenges in detecting selection linked to quantitative polygenic traits. The differences among the three breeds are confirmed by the low level of overlap in the regions detected. Genetic enrichment analyses of the three breeds revealed pathways and genes related to various productive traits associated with growth and fat deposition. This may indicate a common selection direction aimed at enhancing specific production traits, though different biological mechanisms are likely targeted by the same directional selection in these three breeds. Therefore, these genes may play a critical role in determining the distinctive characteristics of Italian Duroc, Italian Landrace, and Italian Large White, and potentially influence the traits in crossbred pigs derived from them. Overall, the insights gained from this study will contribute to understanding how directional selection has shaped the genome of these heavy pig breeds and to better address selection strategies aimed at enhancing the meat processing industry linked with dry-cured ham production chains.

Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production.

Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.

A newly developed 20 K SNP array reveals QTLs for disease resistance to Cryptocaryon irritans in tiger pufferfish (Takifugu rubripes)

This study describes the development and application of a 20 K single nucleotide polymorphism (SNP) array in fugu (Takifugu rubripes). The main goal of this newly developed SNP array is to enhance selective breeding practice via the incorporation of genomic information. Fugu is one of the economic aquaculture species and mainly threatened by parasite disease. The performance of the array was evaluated in a farmed pufferfish population challenged with Cryptocaryon irritans and benchmarked against whole-genome sequencing of a subset of the animals. The array showed very high call rates, consistency between technical replicates, and concordance with genome-resequencing data. Heritability estimates using pedigree and SNP datasets demonstrated a significant genetic component of resistance to C. irritans, with heritability estimates ranging from 0.53 to 0.67, and prediction accuracies were significantly improved with the use of genomic data. Genome-wide association study identified two putative quantitative trait loci (QTLs) on chromosomes 3 and 17. Our findings suggest resistance to C. irritans can be rapidly increased in fugu populations by selective breeding, further expedited via the application of genetic markers. Therefore, they represent a valuable resource for selective breeding programmes aimed at enhancing disease resistance in fugu aquaculture.

Evaluating performance, intestinal lesions, and immunity related genes in heritage and modern broiler breeds during a necrotic enteritis challenge

In this comparative study, the differential responses of heritage (ACRB; Athens Canadian Random Bred) and modern (Cobb) broilers to a necrotic enteritis (NE) challenge were evaluated. The design was a 2×2 factorial with breed (ACRB and Cobb) and challenge (non-challenged and NE-challenged) as main factors. On day (d) of hatch, 96 male chicks (48 ACRB and 48 Cobb) were allocated to 4 experimental groups with 8 replicate cages and 3 birds/cage. On d 14, birds in the NE-challenged groups were orally gavaged with 3,000 Eimeria maxima sporulated oocysts followed by 2 doses of ∼1×108 CFU of Clostridium perfringens on d 19 and 20. On d 21, 2 birds/cage were necropsied to score NE lesions, and spleen and cecal tonsils (CT) samples were collected from 1 bird/cage for assessing mRNA abundance. Challenged ACRB birds exhibited reduced growth performance and relative growth performance compared to challenged Cobb birds. There was no significant interaction between breed and challenge during the challenge period (d 14-21) for mortality. However, there was a challenge main effect (P ≤ 0.05) on mortality as manifested by greater NE-associated mortality compared to non-challenged birds. No significant breed × challenge interaction or breed main effect on lesion scores were observed in the duodenum, jejunum, and ileum. NE-challenged Cobb birds exhibited greater mRNA abundance of IL-18, TNFα, TLR1.2, TLR2.1, CCR5, CCR6, CCL20, and AvBD1 in CT compared to NE challenged ACRB birds. There was a significant breed × challenge interaction effect on mRNA abundance of IL-10, AvBD13, NK-Lysin, and LEAP2 in the spleen. Moreover, a main effect of breed was observed in IL-1β, IL-18, TNFα, TLR2.1, CCR5, CCL20, and NK-Lysin where ACRB birds had higher mRNA abundance than Cobb birds (P ≤ 0.05). The observed differences in performance, pathology, and mRNA abundance between ACRB and Cobb broilers during the NE challenge highlight the distinct immune response profiles of heritage and modern breeds, emphasizing the need for breed-specific nutritional, managerial, and genetic selection programs for modulating immune responses during enteric disease challenges.

A Review and Meta-Analysis of Genotype by Environment Interaction in Commercial Shrimp Breeding.

(1) Background: Genotype-by-environment interaction (G×E) can adversely impact genetic improvement programs. The presence of G×E is mainly measured as the genetic correlation between the same trait measured in different environments where departure from unity can be taken as presence of G×E. (2) Methods: To understand the extent of G×E in shrimp production, a review and meta-analysis was conducted using the results from 32 peer-reviewed studies. (3) Results: Of these, 22 G×E studies were conducted on Pacific white shrimp (Litopenaeus vannamei) with fewer studies reported in other shrimp species. The most frequently studied traits were growth and survival, with relatively few studies on traits of economic importance. The meta-analysis demonstrated a moderately high genetic correlation (rg = 0.72 ± 0.05) for growth, indicating low to moderate levels of G×E with some re-ranking of breeding values across environments. However, substantial G×E was evident for survival where only a moderate genetic correlation (rg = 0.58 ± 0.07) was observed for survival across different environments. A re-ranking of breeding values is likely for this trait and genetic improvement of shrimp for survival in one environment may not be effective in other environments. The results from ANOVA-based studies show that G×E accounted for 6.42 ± 1.05% and 7.13 ± 3.46% of the variation for growth and survival traits, respectively. (4) Conclusion: The significance of G×E necessitates tailored genetic improvement programs in commercial shrimp breeding. We discuss the scope and challenges of G×E for shrimp breeding programs, including opportunities of implementing G×E in genomic selection programs.

452 Data-driven strategic sustainability initiatives of beef and dairy genetics consortiums: A comprehensive landscape analysis for USA, Brazil, and Europe

Abstract The past two decades have witnessed beef and dairy genetic consortiums implementing data-driven germplasm propagation programs in global cattle systems. These programs optimize for multi-dimensional economic, environmental, and animal welfare related sustainability goals and are driven by consumer demands and shifts in supply chains. To summarize these programs and gain insights into the sustainability journey of industry, we did a comprehensive landscape analysis of the strategic initiatives of key global genetics companies, their germplasm offerings, and data platforms offered in three major cattle producing geographies, namely the USA, Brazil, and Europe. Within these locales, they followed selection index-based genomic and reproductive management strategies for both beef, dairy, and beef-on-dairy production, tailored to relevant market and climatic conditions (Figure 1). While individual traits in selection indices ranged between 40 to 90 traits, all traits could be broadly grouped into three: namely production, longevity, health and reproduction. In the USA, companies like ABS Global, Select Sires, Genex Cooperative, STGenetics, Zoetis, Vytelle offer genomic selection programs encompassing germplasm products, and genetic and production data tracking platforms across the beef, dairy, and beef-on-dairy value chains. These companies have implemented reproductive management programs such as in-vitro fertilized embryo transfer, sexed semen, along with genomic selection with a focus on future replacements based on multi-trait sustainability indices. These initiatives are customized for each of the cow-calf, backgrounding, and feedlot sector of beef production. In dairy, these companies have diversified data-driven production programs customizable to conventional and organic production systems. In Europe, companies like CRV, Viking Genetics, and Alta Genetics prioritize traits related to resource efficiency, animal welfare and environmental impact. Semen companies also offer data management tools tailored to European market requirements, alongside services for on-farm semen production and storage to reduce transportation-related emissions. In Brazil, companies such as ABS Pecplan, CRV Brazil, and Semex Brazil, developed herd management solutions focusing on traits like heat tolerance, tropical environmental adaptability, and disease resistance. The landscape analysis revealed a dynamic industry, evolving to meet sustainability goals and market demands. These enterprises collaborate with stakeholders across the value chain, including producers, policymakers, and industry associations, to scale data-driven production systems that balance profitability and environmental footprint of cattle production. As such, they have positioned themselves to capitalize on the growing interest in sustainable livestock production practices worldwide by aligning scientific and technical strategies with evolving regulatory requirements and consumer demands. The global cattle industry is positioned to venture forward by leveraging niche carbon markets and new marketing channels propelled by emerging principles of environmental, social, and corporate governance. Strategic germplasm and data-tracking platform initiatives by these groups thus become an integral part of the livestock sustainability solution palette and will contribute its share to a climate-neutral Earth by 2050.

Genome-wide association studies for growth and feed efficiency traits in American mink

The objective of this study was to identify potential genetic variants and positional candidate genes associated with growth and feed efficiency traits in American mink. Genome-wide association studies (GWAS) were performed using deregressed estimated breeding values (DEBVs) of 1037 to 1872 individuals (as pseudophenotypes), genotyped with the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array. A total of 42 SNPs located on 11 different chromosomes were significantly (FDR<0.01) associated with six growth and feed efficiency traits. Furthermore, 153 genes were identified within 1-Mb windows flanking these significant SNPs. Several positional candidate genes such as TUBB, CDKN1A, SRSF3, GPRC6A, RFX6, and KPNA5 were previously associated with feed efficiency and growth traits in other livestock species. The Gene Ontology (GO) and KEGG analyses revealed that these genes were involved in lipid metabolism, hormone signaling and regulation, and muscle development. To our knowledge, this is the first GWAS to identify genetic variants and biological mechanisms associated with growth and feed efficiency traits in American mink. These findings provide a biological foundation for improving these traits using genomic selection programs to select more efficient mink.

Nineteen years of radiographic screening: Impact of sepsis and evolution of osteochondrosis dissecans prevalence in Walloon sport horses born between 2004 and 2022.

Osteochondrosis dissecans is a particularly common developmental orthopaedic disorder in equines. Among its causes, the hereditary component is no longer a matter of debate, and, for several decades, the various studbooks for sport horses have been selecting stallions in order to limit the prevalence of this condition in the population. However, to our knowledge, no study has evaluated changes in the prevalence of osteochondrosis dissecans over time through longitudinal monitoring of a population of sport horses. The study presented here is part of a large screening programme for developmental orthopaedic pathologies in Wallonia (Belgium) and assessed the presence of these lesions over a period of 19 years in the Walloon sport horse population according to constant and standardised sampling and diagnostic criteria. The effects of breeding conditions and infection in foals were also assessed by means of questionnaires. The results showed no significant change in the prevalence of osteochondrosis dissecans in a population of 1099 individuals born between 2004 and 2022. Furthermore, individuals who had suffered from sepsis during their growing period were very significantly predisposed (p < 0.001) to the development of osteochondrosis dissecans compared to a control group, with respectively 14/21 (67%) and 103/364 (28%) of individuals affected. This study suggests that the selection programmes applied to the population studied are not sufficiently strong or adapted to reduce the prevalence of osteochondrosis dissecans in the population over a period of 19 years. Moreover, this study confirms that foals with sepsis and concurrent osteochondrosis dissecans lesions should not necessarily be excluded from breeding programmes on this basis.

Early impact of domestication on aggressiveness, activity, and stress behaviors in zebrafish (Danio rerio) using mirror test and automated videotracking

Fish domestication progresses through five levels: from the initial acclimatization to captivity (Level 1), to the life cycle completion in captivity (Level 4), and even to the implementation of selective breeding programs (Level 5). Domestication leads to phenotypic changes over generations, sometimes from the very first generation. Behavioral traits are among the first to change. However, in fish, potential behavioral changes during early domestication have been little studied. Therefore, we studied potential behavioral changes among early and advanced levels of domestication in a model species, the zebrafish (Danio rerio), using a mirror test experiment, commonly used to assess traits involved in activity, aggressiveness, and stress in this species. We compared these traits between wild zebrafish in captivity (F0; Level 1), the first generation of their captive-born offspring (F1; Level 4), and three laboratory strains (AB, TU, and WIK; Level 5). Each fish was individually filmed and tracked using an automated procedure for 5 min. Nine behavioral traits and one activity-related trait were characterized for each individual based on the movements and positioning of the fish. We applied a principal component analysis (PCA) and tested the significance of potential differences between groups using an analysis of similarities (ANOSIM). We applied an indicator value analysis (IndVal) to determine which traits were most expressed by each group. We detected differences between groups and across domestication levels. More specifically, we highlighted differentiations between different levels of domestication (e.g. between F1, AB, TU, and WIK) as early as the beginning of the domestication process (i.e. F0 vs. F1), but also within the same level of domestication (i.e. AB vs. TU). Based on PCA and IndVal, (i) F0 and F1 tended to show stronger expression of stress-related traits than the other groups, (ii) F0 was more active than others, and (iii) TU was more aggressive than AB. Our results confirmed that domestication can change fish behavior, even in the first generation born in captivity, although these modifications remain limited. In contrast, we did not observe any general trends correlated with domestication levels, given that AB and TU diverged in their aggressiveness levels, and WIK differed only from F1. This result needs to be generalized to other species but also considered for domestication for aquaculture. If future studies confirm that the changes observed at the beginning of the domestication process remain limited and that there is no consistent evolutionary trend across generations in fish, this would highlight the crucial importance of selecting the right species from the outset of domestication. It would also emphasize the need to design selective breeding programs that shape fish stocks with the most desirable characteristics. To our knowledge, this study is one of the few to examine the behavior of wild zebrafish alongside laboratory strains, offering a unique insight into the early stages of domestication.

Genetic diversity and evolutionary significance of Cahi-DRB1 gene in Indian goat from semi-arid regions

Unlocking the genetic diversity of the Cahi-DRB1 gene in Indian goat breeds sheds light on their immune system's resilience. While extensive studies have elucidated MHC diversity in cattle and sheep, research on goats remains limited. Thus, this study aimed to investigate the genetic diversity of cahi-DRB1 across five goat breeds in India, encompassing a total of 233 individual goats. Using a PCR sequence-based typing approach, DRB1 fragments (285 bp) were amplified and sequenced. The PCR products were purified and sequenced. Amino acid variability within breeds was evaluated using the Wu-Kabat index at peptide-binding pockets. Selection analysis included assessing positive selection through relative rates of nonsynonymous and synonymous mutations, Z-test, and Tajima's test of neutrality. The findings revealed notable heterozygosity across breeds (mean: 100 %), with nucleotide content averaging 22.51 % for A, 18.62 % for T, 24.33 % for C, and 34.35 % for G. The GC content was rich (59.26 %) across breeds for the DRB1 region. The mean distance for DRB1 was highest in Barbari (0.20) and lowest in Osmanabadi goat (0.12), with a higher rate of transversions observed. The Wu-Kabat index assessments underscored substantial genetic variation within the peptide binding sites (PBS) of DRB1, with specific residues (12, 14, 33, 58, and 87) showing polymorphism relevant to antigen presentation. Positive selection pressure was evident across all breeds for the DRB1 locus (dN>dS), highlighting its evolutionary significance. The rich diversity of the DRB1 gene underscores the fitness of the population and the significance of this locus for future selection programs. These results highlight the highly polymorphic nature of the DRB1 locus in Indian goat breeds, emphasizing its crucial role in modulating immune responses. Consequently, our study offers valuable insights for developing targeted breeding strategies to enhance disease resistance in goats, thereby providing practical implications for sustainable livestock management.

Current Advances in the Black Tiger Shrimp Penaeus monodon Culture: A Review

ABSTRACTThe increasing high‐end market demand for the black tiger shrimp Penaeus monodon has brought tremendous industry opportunities. Although the industry has tried its best to increase production, according to the report data from the Food and Agriculture Organization (FAO), annual global production has shown no significant upward trend over the past decade. Besides that, newly implemented policies such as seafood safety and food security negatively impacted the industry and reduced production. However, P. monodon cultivation is still promising due to its larger body size and higher market acceptance as a premium product. Over the years, numerous studies have been conducted to increase the production of P. monodon by optimizing its culture conditions, implementing new culture system, increasing disease resistance to disease such as WSSV, AHPND, WFD, implementation of pre‐ and probiotics in feed, and selective breeding programs to increase genetic diversity and population of P. monodon broodstock. This review provides an overview of the current advances in P. monodon broodstock cultivation, thereby providing an essential baseline for P. monodon aquaculture. Areas needing urgent research focus are also highlighted. Future research should take great strides and take into account the impact of future climate change scenario during P. monodon culture and optimization, and increase biosecurity measures to prevent its introduction as an alien species in wild settings.

PSIII-3 Evaluation of low-cost cow-side tests in developing a selective dry cow therapy program

PSIII-3 Evaluation of low-cost cow-side tests in developing a selective dry cow therapy program

Improving Safety and Comfort of Healthcare Workers Caring for Patients With High-Consequence Infectious Diseases in a High-Level Isolation Unit Using Innovative Approaches.

Patients with high-consequence infectious diseases (HCIDs) require high-quality care by specially trained staff in a high-level isolation unit (HLIU) that follows strict infection prevention and control (IPC) measures. Caring for patients with (suspected) HCID is challenging, mainly because of the strict personal protective equipment (PPE) and IPC protocols healthcare workers (HCW) must adhere to for protection. The Radboud University Medical Center, located in Nijmegen, the Netherlands, has been a dedicated HLIU facility since 2008. A newly built HLIU opened in May 2022, and encouraged us to review the existing PPE selection, IPC protocols, and HCID training program to improve safety and comfort for HCWs working in the HLIU. Based on a systematic search through (inter)national HCID PPE guidelines and semistructured interviews with end users, we selected an improved, more comfortable set of PPE. Additionally, we developed a more concise and easier-to-use patient care process flow and implemented a new teaching strategy. The new way of working was tested in October 2022 when the first 2 patients with suspected HCID were admitted to our unit. We used surveys to evaluate the experiences of HCWs involved in this care to further improve the workflow of the unit. When optimizing safety and comfort for HCWs, it is important to consider (inter)national guidelines as well as user preferences. By systematically evaluating recent experiences of patient admission to the HLIU and then adjusting protocols and training, we can ensure that the quality of provided healthcare and the safety of HCWs working in the HLIU remains high.

The highly dynamic satellitomes of cultivated wheat species.

Durum wheat, Triticum turgidum, and bread wheat, Triticum aestivum, are two allopolyploid species of very recent origin that have been subjected to intense selection programs during the thousands of years they have been cultivated. In this paper, we study the durum wheat satellitome and establish a comparative analysis with the previously published bread wheat satellitome. We revealed the durum wheat satellitome using the satMiner protocol which is based on consecutive rounds of clustering of Illumina reads by RepeatExplorer2, and estimated abundance and variation for each identified satDNA with RepeatMasker v4.0.5. We have also performed a deep satDNA families characterization including chromosomal location by Fluorescence In Situ Hybridization (FISH) in durum wheat and its comparison with FISH patterns in bread wheat. Basic Local Alignment Search Tool (BLAST®) was used for trailing each satDNA in the assembly of durum wheat genome through NCBI's Genome Data Viewer (GDW) and the genome assemblies of both species were compared. Sequence divergence and consensus turnover rate (CTR) between homologous satDNA families of durum and bread wheat were estimated using MEGA11. This study reveals that in an exceedingly short period, significant qualitative and quantitative changes have occurred in the set of satellite DNAs (satDNAs) of both species, with expansions/contractions of the number of repeats and the loci per satellite, different in each species, and a high rate of sequence change for most of these satellites, in addition to the emergence/loss of satDNAs not shared between the two species analysed. These evolutionary changes in satDNA are common between species but what is truly remarkable and novel about this study is that these processes have taken place in less than the last ~8000 years separating the two species, indicating an accelerated evolution of their satDNAs. These results, together with the relationship of many of these satellites with transposable elements and the polymorphisms they generate at the level of centromeres and subtelomeric regions of their chromosomes, are analysed and discussed in the context of the evolutionary origin of these species and the selection pressure exerted by man throughout the history of their cultivation.