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PubMed2026

A genome-wide assessment of the population structure of thirteen admixed and pure Australian beef cattle breeds.

Knowledge of population structure is a key factor for successful multi-breed genomic prediction, especially in single-step analysis when metafounders are considered. In Australia, current assessments mostly focus on single breeds using a single-step genomic prediction method. However, the effective integration of pedigree, phenotypic, and genomic data in a multi-breed framework still requires further research, especially for combined analyses including admixed and multi-breed populations. This study began with 602,952 genotyped individuals with 8K SNPs in common from 13 beef cattle breeds (Alexandria, Angus, Brahman, Brangus, Charolais, Droughtmaster, Hereford, Kynuna, Limousin, Santa Gertrudis, Shorthorn, Speckle Park, and Wagyu). Due to different numbers of animals being genotyped in each breed, a representative subset of animals was chosen by employing a validated sampling strategy using Gaussian Mixture Models (GMM) complemented by Principal Component Analysis (PCA) within each breed. Subsequently, a specific number of animals in each cluster were randomly selected to capture the entire genetic diversity per breed, with a total of 260 animals from each breed. The first three principal components explained 59.89% of the total variation, with PC1 (33.54%) clearly separating Bos indicus from Bos taurus lineages. Admixture analysis identified stable ancestral components and defined the genetic makeup of both pure and composite populations. The results showed extensive genetic diversity in some breeds and highlighted distinct genetic differences between Bos indicus and Bos taurus breeds. In addition, six composite breeds' admixture levels confirmed their origin and breed history, revealing a directional shift in ancestry proportions by a longitudinal increase in Brahman ancestry within tropical composites over time. Thus, the findings pave the way for more effective utilization of genetic diversity both within and across populations and provide a framework for designing multi-breed genetic evaluations and breeding programs to improve productivity and profitability in Australian beef production.

Animals↗
PubMed2026

Genome Wide Analysis Reveals Divergence and Ancestral Origins of Min Pigs.

The Min pig, a representative northern Chinese indigenous breed, carries a unique ancestral background shaped by the historical phylogeography of Northeast Asia. This study aimed to dissect the population structure, temporal genetic divergence, and ancestral composition of Min pigs, trace their evolutionary origin, and identify trait-linked functional genes, providing information regarding their evolutionary history and conservation. We analyzed 61 Min pigs sampled across nearly 20 years and 701 reference pigs comprising other Chinese indigenous breeds, Western commercial lines, and Chinese wild boars, using PCA, NJ phylogenetic analysis, Admixture, TreeMix, D-statistic, f4-ratio, and combined selection signature scans (sliding-window FST, XP-EHH, and π-ratio). Clear genetic stratification was observed among Min pig subpopulations, reflecting long-term divergence under natural and artificial selection. PCA and Admixture (K = 2-4) separated East Asian indigenous and Western ancestral components, verifying an admixed Northeast Asian origin with a dominant ancient East Asian component and a Western component. Compared with early-2000s Min pigs, contemporary individuals are genetically closer to Western breeds and exhibit a more scattered structure due to shifted ancestral component proportions, further confirmed by D-statistic and f4-ratio values. We identified 321 differentiated SNP loci based on the Animal QTL database, corresponding to core candidate genes (AKT3, ACACA, MAP3K5, FGFR4, C3, and SERPINC1) enriched for meat quality, growth, reproduction, immunity, energy metabolism, and MAPK/PI3K-Akt/AMPK pathways. This study reveals Min pigs' admixed origin and temporal divergence, clarifying their Northeast Asian evolution and providing molecular markers for genetic monitoring and conservation.

Animals↗
PubMed2026

The paradoxical extinction: Exploring signatures of assortative mating as a possible mechanism that maintains canonical Red Wolf genetic ancestry in the American Gulf Coast canids.

Admixed genomes, particularly those with an evolutionary history of genetic exchange with an endangered or extinct species, are valued for innovative and unconventional conservation actions. Here, we show the substantial conservation value that the admixed canids of the Gulf Coast have as they retain high amounts of contemporary Red Wolf ancestry and unique genetic variation of past Red Wolf lineages (e.g. ghost ancestry). We analyzed 54,439 loci genotyped across the genome of 413 North American canids and investigated the role that assortative mating with respect to ancestry proportions played in the retention of endangered genetic variation. We report high correlations of inter-chromosomal ancestry proportions that varied with geographic location along Texas and Louisiana Gulf Coast populations, with the stronger signatures reported in the latter. We found that models of assortative mating promoted greater ancestry variance compared with random mating leading to increased efficiency of selection for Red Wolf and ghost alleles. Despite the Red Wolf being extinct in the wild, original, and ghost genomic variation persists in Gulf Coast admixed canids. We suggest two conservation strategies that value and preserve this unique and endangered genomic variation through designed breeding programs. Ultimately the incorporation of this ghost genetic variation would be valuable to boost the genetic viability of the ex situ Red Wolf breeding program, create in situ redundancy, and avoid extinction for this endemic American wolf species.

Animals↗
PubMed1979

[Current zoonoses from the food hygiene point of view (author's transl)].

Of the numerous zoonoses part of which are reportable, according to the Federal Communicable Diseases Act, the food hygienist attributes topicality at present to salmonellosis, brucellosis, toxoplasmosis, taeniasis (T. saginata), trichinellosis, and sarcosporidiosis. In salmonellosis, combating is directed to breeding and keeping of Salmonella-free flocks, poultry offering favourable conditions for this purpose. Moreover, one tries to decontaminate feeds through certain pelleting machines with the aid of friction heat or by admixing propionic acid. In brucellosis, the possibility of infection by tourism, but also that through ingestion of imported dairy products (like soft cheese) play a certain role. Instruction of tourists and advising foreign labour from endemic areas are essential contributions to combating. Another important infection source of toxoplasmosis is infected raw pig meat. As the agent does not survive freezing temperatures under certain conditions, the decontamination procedure is particularly suitable. In pregnancy advising, the role of raw pig meat for development of congenital toxoplasmosis should be clearly explained. In trichinellosis, apart from the traditional examination by the trichinoscope, the modified digestion procedure using pepsin as a digestive fluid was successful. Moreover, it is suitable for detecting weakly infected swine. The importance of systematic examinations of all domestic and wild pigs became evident only recently in 1977, when in Bavaria an epidemic of trichinellosis occurred following the ingestion of undetected Trichinella containing wild pig meat. According to most recent knowledge on the cycle of development of sarcosporidia, the studies showed that the species Sarc. bovihominis and suihominis were pathogens for human beings. Quite apart from necessary supplementary examinations, the freezing procedure would here too, warrant an effective protection for the raw meat consuming population.

Animals↗
PubMed2026

Genomic Insights Into Heterosis: Dominance or Additive × Additive Interaction?

Heterosis was documented in the 18th century, but its biological basis has been debated since. The theoretical framework proposed by Hill, and adapted by Lynch, is based on two central parameters: admixed composition (S), and the heterozygosity (H). Using genomic information, it is now possible to estimate independently the individual realized Si and Hi. In this research, a methodology for estimating the contribution of dominance and additive &#xd7; additive effects to heterosis is proposed. This approach would be especially relevant in cases where there is insufficient phenotypic information available, or an adequate genetic group experimental design, common in humans, wild species and other admixed populations. We also provide theoretical arguments highlighting the enhanced precision of the estimations of heterosis parameters through this method. Furthermore, we exemplify this procedure by analysing data from an experimental F2 pig population, which was initially designed for QTL mapping. Notably, all animals in this population were genotyped (including F1 and parental breeds), but phenotypic information was only available for F2 individuals and included 13 traits related to growth, fat deposition, carcass characteristics and meat quality. Significant additive effects (p&#x2009;<&#x2009;0.05) were detected for longissimus muscle area and carcass temperature, suggesting complementary additive effects for these traits. Significant dominance and additive &#xd7; additive effects were also detected for birth weight and carcass length, respectively (p&#x2009;<&#x2009;0.05), indicating that heterosis for these traits is primarily attributable to dominance and additive &#xd7; additive interactions. These results demonstrate that the proposed methodology can successfully estimate the genetic components underlying heterosis and underscores the utility of this approach in&#xa0;situations where we possess genomic data but limited phenotypic data.

SNP↗
PubMed2026

Dissecting genetic architecture of growth and yield traits in horsegram using GWAS.

Horsegram (Macrotyloma uniflorum), a member of the Fabaceae family, is a nutritious and low-cost legume used for both grain and fodder. This study employed a genome-wide association approach to identify loci linked to key agronomic traits in horsegram. Plant height, seed size, and shoot fresh weight were evaluated in a panel of 96 diverse genotypes. GBS was performed using the Illumina HiSeq platform, yielding 20,241 high-quality SNPs after filtering at a 5% minor allele frequency. Population structure analysis classified genotypes into three admixed subgroups. Phenotyping was conducted over three consecutive years at two locations in Himachal Pradesh (Palampur and Bajaura) using a randomized block design with two replications. GWAS analyses using GLM, MLM, FarmCPU, and BLINK models identified eight markers for plant height, three for seed size, and five for shoot fresh weight across different chromosomes. These markers provide valuable tools for accelerating trait improvement in future horsegram breeding programs.

Genome-Wide Association Study↗
PubMed2026

Genome-wide association studies reveal genetic variants associated with antineoplastic monoterpenoid indole alkaloid accumulation in Catharanthus roseus.

Catharanthus roseus produces pharmacologically important monoterpenoid indole alkaloids (MIAs), yet their natural accumulation is low, limiting therapeutic exploitation. To dissect the genetic basis of natural variation in MIA accumulation, we integrated phenotypic, chemotypic, and genomic analyses of 93&#xa0;C. roseus accessions sampled from six locations across India, including New Delhi, Lucknow, Jodhpur, Bangalore, and two locations in Gujarat: Navsari and Bardoli. Morphological characterization showed limited differentiation among locations, whereas accessions from Gujarat tended to be taller compared to other locations and more frequently white-flowered. Quantitative HPLC profiling revealed substantial accession- and location-dependent variation in total indole alkaloid levels, with Gujarat accessions showing the highest accumulation, largely driven by vindoline and catharanthine. Genotyping-by-sequencing generated 10,801 high-quality variants comprising 10,087 SNPs and 714 InDels corresponding to an average density of 19.34 variants per Mbp of the genome, revealing three genetic subgroups with overall admixed ancestry and weak geographic stratification. Genome-wide association study (GWAS) using five benchmark models identified 47 variants potentially associated with catharanthine, vindoline, and vinblastine content. These putative candidate loci were located near genes implicated in hormone signaling, mitochondrial function, nitrogen metabolism, and RNA processing, suggesting complex regulatory control of MIA biosynthesis. Notably, two missense variants in a carboxylesterase-like gene were associated with vindoline accumulation, and highly significant intergenic SNP clusters suggested putative regulatory hotspots for vinblastine biosynthesis. These results provide GWAS-based insights into the genetic architecture of MIA metabolism in C. roseus and nominate candidate variants for precision breeding and metabolic engineering to enhance pharmaceutical alkaloid production.

Catharanthus roseus↗