The breeding of high-quality beef cattle breeds is crucial for the development of animal husbandry, and whole-genome resequencing is widely applicated in the field of molecular breeding. Advantages in growth and reproductive traits exist in Pinan cattle compared with other cattle breeds, but there is limited research on its genomic mechanism. Using whole-genome resequencing, the genetic structure and genomic selection signatures in Pinan cattle were investigated in this study. Phylogenetic, cluster, and admixture analysis results indicated that Pinan cattle have a closer genetic relationship with Kholmogory cattle and China north cattle breeds. Through a selective sweep strategy, 207 and 54 candidate genes related to growth and reproduction and immunity, respectively, were identified in the Pinan cattle population. Given the crucial role of the glutamate–cysteine ligase catalytic (GCLC) gene in muscle antioxidative defense, the high frequency of allele T of the GCLC c.429 C>T locus in the Pinan cattle population might partially contribute to the advantages of Pinan cattle in growth performance. This study laid the foundation for the genetic improvement in Chinese local beef cattle and provide background for the studies on the growth and development of Pinan cattle.

Beef cattle breed improvement holds strategic significance in the livestock industry. Pinan cattle, developed through years of selective breeding in Xinye County, Henan Province, exhibit superior traits including thin skin, fine bone structure, rapid growth, high dressing percentage, excellent meat yield, and superior feed efficiency. However, research on the genetic characteristics of Pinan cattle remains in its infancy. In this study, we investigated population genetic diversity and positive selection signals in Pinang cattle based on whole-genome resequencing data. Using a selective sweep approach, we identified 98 candidate genes associated with growth, reproduction, and immunity, along with 13 high-confidence missense mutations, which may underlie key traits in this population. Based on the critical roles of the NDN and PARVA genes in reproduction and muscle development, the predominant T allele at the NDN c.581T > A and PARVA c.893T > A loci in the Pinan cattle population may partially explain their advantages in sexual precocity and rapid growth compared to other breeds or populations. This study provides an important theoretical basis for the genetic improvement of native beef cattle and lays a scientific foundation for further investigation into the growth and development mechanisms of Pinan cattle.

Bovine respiratory disease (BRD) is a major cause of morbidity and mortality in cattle, and Klebsiella pneumoniae (K. pneumoniae) has emerged as an opportunistic pathogen that can colonize the bovine respiratory tract. However, epidemiological data on K. pneumoniae from cattle with BRD in Henan Province, central China, remain scarce. This study aimed to investigate the isolation rate, antimicrobial resistance profiles, resistance genes, virulence-associated genes, and genetic diversity of K. pneumoniae from BRD-affected calves in Henan. From 2021 to 2026, deep nasal swabs were collected once from 517 calves with clinical signs of BRD (Wisconsin score ≥5) across 38 farms in 13 cities over six years. A total of 87 K. pneumoniae isolates were obtained, giving an overall isolation rate of 16.8% (87/517), ranging from 13.8% to 22.6% across five geographic regions. Antimicrobial susceptibility was determined by disk diffusion using CLSI VET01S and CLSI M100-S26 criteria for 15 antimicrobials belonging to six classes. Resistance and virulence-associated genes were screened by PCR, and multilocus sequence typing (MLST) was performed. MLST revealed 34 sequence types (STs), with ST950 being the most prevalent (6.9%), followed by ST262, ST187, and ST306. Antimicrobial resistance was highest against ampicillin (94.3%), sulfisoxazole (79.3%), cefoxitin (73.6%), cefazolin (70.1%), and enrofloxacin (67.8%). Multidrug resistance (resistance to ≥3 classes) was observed in 96.6% (84/87; 95% CI 90.3–98.8%) of isolates. The most common resistance genes were blaTEM (72.4%), sul1 (39.1%), blaSHV (37.9%), and qnrB (14.9%). After Firth’s penalized logistic regression with farm-level cluster-robust standard errors and Benjamini–Hochberg FDR correction, no resistance gene was significantly associated with phenotypic resistance (all q > 0.05). Virulence-associated genes fimH, mrkD, uge, wabG, entB, iutA, and ureA were highly prevalent (>90%), whereas hypervirulence markers (rmpA and rmpA2) were absent. The most common virulence-associated gene combination (eight genes) was present in 35.6% of isolates. These findings indicate high genetic diversity, widespread multidrug resistance, and a broad virulence-associated gene repertoire among K. pneumoniae isolated from cattle with BRD in Henan. Because no healthy comparison group or etiological confirmation was included, the study does not establish K. pneumoniae as the causative agent of BRD. The high resistance rates to β-lactams, sulfonamides, and quinolones highlight the need for prudent antimicrobial use. Florfenicol showed the lowest in vitro resistance rate among the tested agents; however, clinical efficacy, treatment outcome, and safety were not evaluated. Continuous surveillance and molecular monitoring are essential to manage this pathogen in cattle populations.

Skin is a highly specialized barrier organ, which serves essential barrier, immune, and sensory functions and exhibits conserved structure. In addition, each species exhibits a unique skin transcriptional profile for adapting distinct environmental conditions and physiological demands. However, these transcriptional profiles across mammals remain incompletely understood. In this study, we integrated 61 publicly available skin RNA-seq datasets from eight mammalian species: human (Homo sapiens), macaque (Macaca fascicularis), mouse (Mus musculus), sheep (Ovis aries), goat (Capra hircus), donkey (Equus asinus), rabbit (Oryctolagus cuniculus), and pig (Sus scrofa). We identified a large number (2286 to 4588) of differentially expressed genes (DEGs) based on 10,504 one-to-one orthologous genes in all pairwise species comparisons. A total of 44 conserved genes were identified by integrating tissue specificity, expression variability, and mean expression level, which were enriched in epidermal development, keratinocyte differentiation, and desmosome organization. We also identified species-specific genes and transcription factors, such as STMN1 (donkey), COL1A1 (goat), and ACTN2 (mouse), which are associated with the cell cycle, extracellular matrix, and muscle contraction pathways, respectively. WGCNA further revealed goat-associated module 2 (M2) enriched in the negative regulation of angiogenesis. Collectively, this study provides a comprehensive cross-species transcriptional profile resource for mammalian skin, providing a valuable resource for understanding the regulatory plasticity underlying skin evolution across mammals.

The mammalian stomach has conserved digestive functions but also shows major anatomical and physiological differences among species. However, broad comparative transcriptomic analyses across mammals and across ruminant stomach chambers remain limited. Here, we collected and integrated 111 bulk RNA-seq datasets from 11 mammalian species (humans, mice, monkeys, dogs, horses, donkeys, pigs, cattle, deer, goats, and sheep) and analyzed 12,048 shared one-to-one orthologous genes. We identified 56 conserved genes mainly involved in translation, ribosome biogenesis, protein homeostasis, and mitochondrial function. Pairwise comparisons revealed extensive transcriptional differences, with 2070–7110 differentially expressed genes across species pairs, together with distinct species-associated transcription-factor activity patterns. We also identified 25 ruminant-enriched genes associated with epithelial differentiation, ion transport, mucosal defense, and metabolism. Analysis of 69 samples from the rumen, reticulum, omasum, and abomasum of sheep, goats, cattle, and deer showed clear chamber-associated transcriptomic differences. The abomasum had a distinct expression program, with 235 enriched genes related to hormone regulation, secretion, transport, and digestion. Weighted gene co-expression network analysis further identified different gene programs in the forestomach and abomasum. Together, these findings reveal conserved, species-associated, and chamber-associated transcriptional features of the mammalian stomach and provide a useful framework for understanding its molecular diversity.

Enterovirus71 (EV71) is a major etiological agent of severe hand, foot, and mouth disease (HFMD), which can lead to central nervous system damage in children. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) often produces false-negative results during the early stage of EV71 infection, attributable to the low viral load. To address this limitation, we developed a rapid, precise, and highly sensitive multiplex reverse transcription digital polymerase chain reaction (RT-dPCR) assay for differential diagnosis of EV71-induced HFMD and non-EV71 pathogens. The EV71 RT-dPCR assay targeted the viral structural protein VP2 using a TaqMan minor groove binder (MGB) probe. This method achieved a detection sensitivity of 7.406 copies per microliter. Specificity analysis confirmed no cross-reactivity with non-EV71 enteroviruses. When validated against 60 clinical samples, the assay demonstrated 100% overall agreement (60/60) with a kappa value of 1.0 (p < 0.001). The developed EV71 RT-dPCR assay may facilitate early diagnosis of severe EV71-associated HFMD, enabling timely intervention for affected children.