The c-Myc oncogene is a critical regulator of viral oncogenesis and immune evasion in multiple cancers. However, its modulation by long noncoding RNAs (lncRNAs) during retroviral infection remains poorly understood. Here, we show that ch-MYC-AS1, a novel lncRNA, restricts avian leukosis virus subgroup J (ALV-J) replication by targeting c-Myc protein expression using chicken macrophage HD11 cells. Mechanistically, ch-MYC-AS1 binds to annexin A2 (ANXA2) and impedes its nuclear translocation, preventing its collaboration with c-Myc to promote glycolysis. This dual inhibition suppresses c-Myc-driven metabolic reprogramming essential for viral proliferation. Our findings reveal ch-MYC-AS1 as a key suppressor of retroviral replication through coordinated disruption of c-Myc/ANXA2 signaling, providing a potential therapeutic strategy for antiviral and anticancer drug development.IMPORTANCEAvian leukosis virus subgroup J (ALV-J) is an oncogenic retrovirus that causes tumors and immunosuppression in chickens, leading to significant economic losses in poultry industries. This study identifies a host-derived long noncoding RNA (lncRNA), ch-MYC-AS1, which suppresses ALV-J replication by disrupting the ANXA2-c-Myc signaling axis. These findings unveil a novel layer of antiviral defense mediated by an epigenetically regulated lncRNA and highlight a potential RNA-based strategy to combat retroviral infections. Moreover, targeting the ANXA2-c-Myc interaction may offer therapeutic insights for controlling ALV-J and other MYC-driven diseases.

In recent years, real-time monitoring of broiler chicken weight has become crucial for assessing growth and health status. Currently, obtaining weight data often relies on manual collection. However, this process is cumbersome, labor-intensive, and inefficient. This paper proposes a broiler carcass weight detection model based on deep learning image segmentation and regression to address these issues. The model first segments broiler carcasses and then uses the pixel area of the segmented region as a key feature for a regression model to predict weight. A custom dataset comprising 2709 images from 301 Taihu yellow chickens was established for this study. A novel segmentation network, AR2U-AtNet, derived from R2U-Net, is proposed. To mitigate the interference of background color and texture on target carcasses in slaughterhouse production lines, the Convolutional Block Attention Module (CBAM) is introduced to enable the network to focus on areas containing carcasses. Furthermore, broilers exhibit significant variations in size, morphology, and posture, which impose high demands on the model’s scale adaptability. Selective Kernel Attention (SKAttention) is therefore integrated to flexibly handle broiler images with diverse body conditions. The model achieved an average Intersection over Union (mIoU) score of 90.45%, and Dice and F1 scores of 95.18%. The regression-based weight prediction achieved an R2 value of 0.9324. The results demonstrate that the proposed method can quickly and accurately determine individual broiler carcass weights, thereby alleviating the burden of traditional weighing methods and ultimately improving the production efficiency of yellow-feather broilers.

Waxy corn and sweet corn represent 2 major classes of fresh-eating corn, each with distinct sensory attributes and nutritional compositions. Developing a new variety that combines both waxy and sweet traits would address rising consumer demand and expand new market potential. From a fast neutron-mutagenized population of the waxy corn inbred line HB522, we isolated a novel mutant, designated as wx-sweet, whose kernels simultaneously exhibit waxy and sweet characteristics at the milk-filling stage. Through bulked segregant analysis combined with fine mapping, we mapped the causal locus to SHRUNKEN1 (Sh1) on chromosome 9, which was confirmed by an allelism test with a characterized Mu-insertion allele of Sh1. A 7,227-bp Copia-type long terminal repeat retrotransposon insertion was identified in exon 2 of Sh1 in the wx-sweet mutant by long-read sequencing. Consistently, the novel sh1 allele significantly reduced sucrose synthase activity. Genetic and physiological analyses demonstrate that sh1 and wx1 act synergistically to fine-tune carbohydrate metabolism in the endosperm. Integrated transcriptomic and metabolomic profiling uncover extensive transcriptional reprogramming and redirected metabolic flux, leading to substantial accumulation of sucrose and a range of oligosaccharides. These metabolic shifts underlie the unique simultaneous dual waxy-sweet texture in fresh-eating wx-sweet kernels. In summary, our work not only provides valuable genetic resources for breeding next-generation fresh-eating corn but also, for the first time, elucidates the molecular mechanism by which the sh1 and wx1 mutations cooperatively shape the waxy-sweet endosperm phenotype.

Goose yolk, the primary source of nutrients and flavor, is particularly susceptible to quality deterioration during storage, yet its metabolic dynamics remain poorly characterized. To elucidate these changes, we combined physicochemical assays with untargeted LC-MS/MS metabolomics to systematically profile the temporal metabolic alterations in goose egg yolks stored at 4 °C for up to 60 days, using day-1 yolks as fresh controls. Our analysis quantified 1005 metabolites and identified a critical metabolic shift occurring after 30 days of storage. Among 21 significantly altered metabolites, the sustained decline of adenosine and 2-aminopurine, alongside the accumulation of 4-hydroxyretinoic acid, strongly correlated with the loss of egg freshness. Interaction network and pathway analyses pinpointed purine metabolism—with adenosine and 2-aminopurine as central nodes—as a core pathway impaired in yolk during storage. Crucially, we identify 2-aminopurine as a novel, storage-sensitive biomarker for goose egg freshness derived from yolk metabolomics, directly linking intracellular metabolic dysregulation to observable quality decline. This study deciphers the metabolic landscape of goose egg yolk aging and provides a targeted, mechanism-based strategy for yolk-centric quality monitoring and preservation, offering new insights for food composition analysis and safety assurance.

In large-scale caged broiler farms, daily inspection of dead broilers is essential for flock health management and disease prevention. To address the significant performance degradation of existing methods under challenging conditions such as poor lighting, severe occlusion, and complex backgrounds, this paper proposes a dual-modal dynamic hybrid convolutional feature fusion method for dead bird detection based on an improved YOLO11 framework, termed YOLO11-DualDynConv-FF. First, a dual-modal fusion network architecture was developed to combine RGB and infrared (IR) images, enabling the model to simultaneously process both modalities. By integrating complementary information from RGB and IR data, the proposed method significantly improved detection accuracy and efficiency under low-light conditions. Second, a dynamic hybrid convolution feature fusion module was designed to merge multi-scale feature maps with contextual information, allowing the network to capture fine-grained details and adapt better to complex farming environments. In addition, an occlusion-aware module was introduced to specifically address the physical occlusion challenges prevalent in crowded cage settings. Comparative experiments and ablation studies involving multiple object detection networks were conducted to evaluate the proposed method. The results show that the improved YOLO11 model achieves superior performance, with precision, recall, F1-score, and mAP@0.5 reaching 92.6%, 79.0%, 0.85, and 80.1%, respectively. These results represent improvements of 2.0%, 5.0%, 0.17, and 12.1%, respectively, over the original YOLO11 model. Compared with existing approaches, the proposed model is better suited to complex real-world poultry farming environments and achieves higher detection accuracy, providing a valuable reference for intelligent monitoring in caged poultry farming.

Goose astrovirus (GAstV) is an important pathogen associated with visceral gout, growth retardation, and mortality in goslings, whereas the splenic response to infection remains poorly understood. In this study, GAstV-infected goslings showed positive viral RNA detection in spleen tissues, obvious splenomegaly, and histopathological lesions. Transcriptomic analysis identified 383 differentially expressed genes, including 243 upregulated and 140 downregulated genes. Functional enrichment analyses showed that these genes were mainly involved in antiviral defense, innate immune responses, complement and coagulation cascades, and the RIG-I-like receptor signaling pathway. GSEA further supported the enrichment of the RIG-I-like receptor signaling pathway in infected spleens. Notably, several genes related to this pathway, including DDX58, IFIH1, TRIM25, and IRF3, were markedly upregulated and were also identified as hub genes in the protein–protein interaction network. RT-qPCR validation further confirmed the upregulation of these hub genes in GAstV-infected spleens, corroborating the transcriptomic findings. Collectively, these findings indicate that GAstV infection is associated with splenic lesions and extensive transcriptional reprogramming in goslings, and suggest that RIG-I-like receptor-related antiviral signaling may be involved in the splenic innate immune response to GAstV infection. This study provides new transcriptomic insight into the innate immune responses associated with GAstV infection.

As an elite indigenous poultry breed under national protection in China, the Xupu goose is renowned for its large body size, superior fatty liver production, premium meat quality, and high tolerance to roughage. To elucidate its genomic architecture, genetic diversity, and evolutionary selection signatures, we conducted whole-genome resequencing on 15 purposively selected, unrelated male Xupu geese. An average of 6.79 Gb of high-quality sequence data was generated per individual, yielding approximately 4.27 million single-nucleotide polymorphisms (SNPs) with a transition/transversion (Ti/Tv) ratio of 2.49. Population genomic analyses revealed that while the population retains a moderate genetic reservoir (HE = 0.298), it exhibits a distinct heterozygote deficit (HO = 0.217) and a moderate genomic inbreeding coefficient FROH = 0.204). This structural pattern underscores the genetic impact of historical ex situ closed-flock conservation and the consequent formation of cryptic family lineages. Furthermore, genome-wide integrated haplotype score (iHS) scans detected distinct regions under recent positive selection. Functional annotation of these regions highlighted candidate genes tightly associated with the breed's hallmark traits, specifically lipid metabolism and hepatic fat deposition (ACSS2, ACSS3, PECR), alongside muscle development (CMYA5, MTPN, LEPR). Conclusively, this study delineates a comprehensive genomic landscape of the Xupu goose, providing a robust foundational resource for future germplasm conservation, molecular marker development, and precision breeding programs.

Background: During maize anthesis, heat stress severely limits productivity—particularly under humid conditions where high humidity suppresses transpirational cooling, forcing tissues to endure direct thermal load. Methods: Using field enclosures to impose enclosure-imposed humid heat shock (EHS), we screened 135 maize inbred lines for flowering-stage yield resilience, using grain weight per ear at maturity under EHS relative to the corresponding control (CK) condition as the primary selection criterion. Based on this screen, we selected two tolerant (R025, R100) and two sensitive (R133, R135) genotypes for data-independent acquisition mass spectrometry (DIA-MS) profiling of the tassel-subtending leaf. Results: At baseline, the selected tolerant lines exhibited a constitutively distinct proteomic state, including lower abundance of light-harvesting complex components and higher abundance or detection frequency of several regulatory proteins, including SRK2E/OST1 and HSF-B2a. Under sustained EHS, the selected sensitive lines showed extensive proteomic disruption, including reduced abundance of photosynthesis-related proteins and oxidative phosphorylation, together with increased abundance of proteins associated with endoplasmic reticulum stress responses and protein turnover. In contrast, the selected tolerant lines displayed a more constrained acclimation response, characterized by relative maintenance of photosynthesis-related proteins together with selective increases in chaperone systems (HSP90/sHSPs) and benzoxazinoid biosynthesis-related proteins. Several proteins showed switch-like detection patterns between the selected tolerant and sensitive lines, including TMEM97-like and a peptidyl-prolyl isomerase, indicating potentially distinct regulatory states. Conclusions: These findings suggest that tolerant performance under enclosure-imposed heat stress is associated with a pre-conditioned proteomic state and enhanced protein homeostasis (proteostasis) buffering capacity that may help preserve photosynthetic function during flowering-stage stress. The identified proteins should be regarded as candidate markers requiring further functional validation before any application in breeding programs aimed at improving adaptation to increasingly frequent heat-stress events.

Cryopreservation plays a critical role in the long-term preservation of biological materials and has become an indispensable technology in biomedicine, agriculture, animal breeding, and biodiversity conservation. Despite substantial advances in cryobiology, the preservation of cells and tissues at ultra-low temperatures remains limited by cryoinjuries associated with ice crystal formation, osmotic stress, oxidative damage, and cellular dehydration. This review provides an overview of the historical development and fundamental principles of cryopreservation and critically summarizes the key factors affecting cryopreservation efficiency, including cryoprotective agents, antioxidants, osmotic balance, freezing and thawing protocols, and emerging ice-controlling materials. In addition, recent advances in the cryopreservation of diverse biological materials—such as sperm, oocytes, embryos, stem cells, and gonadal tissues from different animal species—are critically discussed, with particular attention to species-specific differences and the distinction between post-thaw survival and functional recovery. Finally, the current limitations of existing cryopreservation technologies and future research directions are highlighted to facilitate the development of safer and more effective preservation strategies for animal genetic resource conservation and biomedical applications.

The Yan goose (YE, Anser cygnoides) is a valuable indigenous poultry genetic resource, renowned for its superior meat quality and environmental adaptability. Despite its economic importance, the genetic basis underlying these adaptive traits remains unclear. In this study, we employed whole-genome resequencing (WGS) to perform high-throughput sequencing on a conserved population of 15 samples. Bioinformatic analyses were conducted to systematically evaluate the population's genetic structure, and a genome-wide scan for selection signals related to economically significant traits was performed using the integrated haplotype score (iHS) method. An average of 4.43 million high-quality SNPs were identified, which were predominantly located in intergenic and intronic regions. Population structure analysis revealed a close genetic relationship within the conserved population of YE, with no significant lineage stratification observed. Pairwise sequentially Markovian coalescent (PSMC) analysis indicated that the YE underwent a severe genetic bottleneck during the Last Glacial Maximum (LGM), followed by gradual population recovery in the early Neolithic period. Genome-wide selection signal scanning identified multiple genomic regions under strong selection, annotating key genes associated with growth and development (e.g., GHRL, AKT1, and MAPK3), lipid deposition (e.g., PLPP4, SAMD8, and LPIN1), and disease resistance and stress resilience (e.g., TP53, STAT3). Functional enrichment analysis revealed significant enrichment of these genes in pathways related to glycerophospholipid metabolism (p < 0.01), purine metabolism (p < 0.01), and immune response (p < 0.01). This study not only provides a theoretical foundation for the scientific conservation of the YE germplasm resources but also offers valuable genomic resources for identifying functional genes underlying important economic traits and advancing molecular breeding strategies.

In recent years, the dwindling population of these endangered geese has hindered our understanding of their phenotypic variations and the genes associated with important traits. To investigate the population structure and genetic diversity of this breed, the whole-genome data of 90 individuals from a conservation farm were obtained using the Illumina 6000 paired-end platform. The research results indicate that each locally endangered goose variety has formed a monophyletic population. The Baizi (BZ), Lingxian White (LX), and Xupu (XP) geese exhibiting higher genetic diversity than the other goose breeds. Tree-Mix analysis revealed the presence of five gene flows events between goose populations, with Yangjiang (YJ) geese consistently exhibiting significant genetic distance from the other breeds. Under strong pressures from the natural environment and artificial selection, whole-genome selective scanning revealed 394 overlapping genes. Gene Ontology (GO) enrichment analysis of the putative candidate genes (PCGs) revealed significant enrichment of 20 terms (P < 0.05). Similarly, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed significant enrichment of PCGs in 23 terms (P < 0.05). Examination of overlapping genes identified through at least two selection methods revealed a set of genes associated with key traits, including growth and development (CCND1, DES, CCNO, SMC5, and NUBP1), immunity (ABCA2, ABCC8, UHRF2, and ABCA1), and body aging (KAT6B). Our findings provide insights into the genetic basis of endangered geese at the whole-genome level, laying the foundation for future molecular research on genetic variation and phenotypic changes. In summary, our results provide invaluable resources for delineating the uniqueness of endangered goose breeds.

As a pigment-related trait, beak color is an important feature for duck breeds. Nowadays, several studies have been conducted on the genetic mechanisms and candidate markers of duck beak color. However, related loci which were mostly single base mutations could hardly explain the phenotype. To select greater structural mutations associated with beak color, all 308 birds of the F2 population of the Runzhou white crested ducks were selected to perform the genome-wide association studies to select key genes and differential InDels related to the formation of beak color in ducks. To verify the accuracy of the GWAS and to further select the candidate variants of beak colors, Line H (H1, H2, H3 and HF) was selected as black-beaked ducks along with yellow-beaked ducks which consist of CV ducks and Line E for genomic selection signatures by integrated analysis of FST and θπ. Genotyping was performed to verify the functions of the candidate sites. As the result, 2 InDels in the intronic region were selected as candidate variants by GWAS. Furthermore, eight genes were selected according to a standard FDR of <0.05 and MITF was finally selected based on a comparison of the FST values by genomic selection signature. After the selection of the loci, 1 bp insertion (InDel-4, at the position of 17829988 on chromosome 10 of ASM874695v1) in intron regions of MITF were selected as candidate sites. As the result of the genotyping, all yellow-beaked ducks were homozygous mutated individuals, while all individuals in Line H (black-beaked ducks) were found to have the RR (ref / ref) genotype. In addition, the relative expression of MITF from beak tissue of the H2 ducks was significantly higher than that of CV ducks(p < 0.001). Thus, MITF plays a critical role in melanogenesis and melanin deposition in duck beaks, which can affect beak color, and InDel-4 were significantly different in the yellow- and black-beaked individuals and could be used as markers to identify the beak colors of ducks.

Goose astrovirus (GAstV) infection has emerged as a prevalent cause of urate deposition and viral gout in major goose farming across China, leading to high mortality and substantial economic losses. However, the molecular mechanisms linking GAstV to gout pathogenesis remain elusive. Here, a total of 10 five-day-old Jiangnan white goslings were selected, and tissue damage and kidney gene expression profiles were investigated. The results showed multi-organ damage in GAstV-infected gosling, including kidney, liver, spleen, and lung. Also, 342 differentially expressed genes were identified in infected kidney tissues after 10 days post-infection using transcriptomic sequencing, including 185 upregulated and 157 downregulated genes. In addition, gene set enrichment analysis revealed significant positive correlations between GAstV infection and bile acid metabolism and fatty acid metabolism pathways. Notably, bile acid metabolism was implicated in uric acid regulation and gout progression. Protein–protein interaction network analysis identified AGXT as a central hub gene within the bile acid metabolic pathway, with key upregulated interactors including PIPOX, ALDH1A1, and CAT. AGXT, a critical enzyme in glyoxylate detoxification, directly modulates uric acid biosynthesis. Our findings propose that GAstV-induced activation of bile acid metabolism, particularly AGXT upregulation, drives hyperuricemia and subsequent gout pathology. This study elucidates a novel mechanism of GAstV-associated metabolic dysregulation and provides actionable genetic targets for antiviral breeding strategies in waterfowl.

Waxy corn and sweet corn are two major types of fresh-eating corn. Each has significant market value due to its unique sensory and nutritional profiles. Developing a variety that combines both traits would meet growing consumer demand and create new market opportunities. From a fast neutron-mutagenized population of the waxy corn inbred line HB522, we identified a mutant, wx-sweet , whose kernels exhibit both waxy and sweet properties at the filling stage. Using bulked segregant analysis (BSA) and fine mapping, we localized the causal locus to SHRUNKEN1 ( Sh1 ) on chromosome 9, which was confirmed by an allelic test with a known Mu-insertion mutant. PCR and sequencing indicated a putative large structural variation in the second and third exons of Sh1 in wx-sweet , likely disrupting the reading frame. This novel sh1 allele significantly reduced sucrose synthase activity. The sh1 and waxy1 mutant genes act synergistically to remodel carbohydrate metabolism in wx-sweet endosperms. This remodeling, revealed by integrated transcriptomic and metabolomic analyses, drives transcriptional reprogramming and restructures metabolic flux. These changes thereby enhance sucrose and raffinose accumulation, which underlies the unique waxy-sweet texture in fresh-eating maize endosperm. In summary, our work not provides valuable genetic resources for fresh-eating corn breeding, but also elucidates, for the first time, the molecular mechanism underlying the synergistic formation of waxy and sweet texture. Key message The novel allele of Sh1 acts synergistically with waxy1 to regulate carbohydrate metabolism, which elucidates the molecular mechanism for the unique waxy-sweet texture in fresh-eating corn endosperm. Our work provides new strategies for sweet-waxy maize breeding. ### Competing Interest Statement The authors have declared no competing interest. Agricultural Science and Technology Independent Innovation Fund Project of Jiangsu Province, CX [24]3090 “JBGS” Project of Seed Industry Revitalization in Jiangsu Province, JBGS [2021]012 National Natural Science Foundation of China, 32372101

The analysis of the genetic diversity and historical dynamics of endemic endangered goose breeds structure has attracted great interest. Although various aspects of the goose breed structure have been elucidated, there is still insufficient research on the genetic basis of endemic endangered Chinese goose breeds. In this study, we collected blood samples from Lingxiang White (LX), Yan (YE), Yangjiang (YJ), Wuzong (WZ), Xupu (XP), and Baizi (BZ) geese (Anser cygnoides) and used Sanger sequencing to determine the partial sequence of the cytochrome b (CYTB) gene in a total of 180 geese. A total of 117 polymorphic sites were detected in the 707 bp sequence of the mtDNA CYTB gene after shearing and correction, accounting for approximately 16.55% of the entire sequence. The AT content (51.03%) of the processed sequence was slightly higher than the GC content (48.97%), indicating a preference for purine bases. The YJ, YE, and WZ breeds had the highest population genetic diversity, with a haplotype diversity greater than 0.9 (Hd > 0.9) and average population nucleotide difference of 8.01 (K > 8.01). A total of 81 haplotypes were detected and divided into six major branches. Among the six goose breeds, there were frequent genetic exchanges among LX, YJ, YE, and WZ geese (Nm > 15.00). We analyzed the distribution of base-mismatch differences in goose breeds and tested their historical dynamics for neutrality in Tajima’s D and Fu’s Fs. For YJ and WZ geese, Tajima’s D > 0, but the difference was not significant (p > 0.05). The actual values for the two breeds exhibited multimodal Poisson distributions. The population patterns of the WZ and YJ geese are purportedly relatively stable, and the breeds have not experienced population expansions or bottleneck effects, which is consistent with the neutrality test results. This study provides new insights into the diverse genetic origins and historical dynamics that sustain endemic endangered goose breeds.

A floor egg is an egg that is not laid in the nest, which is a prevalent issue in many fowl breeder farms, lowering egg collection efficiency, hatching performance, and economic benefits. Although the pattern and influencing factors of floor laying have been extensively reported in chickens and ducks, it is not clear in geese. Herein, the Yangzhou goose breeders were selected, and the time and location preferences, genetic and environmental influences, and physiological indexes in floor laying were investigated. The results revealed distinct time and location preferences existed. More floor eggs were laid from 2:00 to 5:00 and 8:00 to 12:00 am, with a concentration observed in the feed trough. Moreover, the proportion of floor eggs was higher at the early stage than at other stages of the laying cycle, and the fast-growing line laid more floor eggs than dual-purpose and high-yielding lines (P < 0.05). In addition to genetic factors, the effect of environmental influences on floor eggs was also surveyed. More floor eggs were observed in the family housing system than in large-group and small-population housing systems, and geese who reared in north-facing houses laid more floor eggs than in south-facing houses (P < 0.05). Physiological indexes were compared between floor-laying and nest-laying geese. Significantly decreased serum progesterone and prolactin levels were detected, alongside down-regulated gene expressions of progesterone receptor in ovaries, oxytocin receptor in both pituitary and ovaries, corticotropin-releasing hormone in ovaries, and dopamine receptor D2 in hypothalamus and ovaries in floor-laying geese compared to nest-laying geese (P < 0.05). In addition, a practical and inexpensive approach of adding a single decoy egg to the nest box effectively reduced the proportion of floor eggs (P < 0.05). Taken together, these data provide scientific information for patterns, genetic and environmental influences, and physiological indexes of floor eggs, thereby contributing to effective control of floor laying in goose breeders' production.

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections and can profoundly affect the host antiviral innate immune response, although the mechanisms by which these changes occur are largely unknown. Here we report that chicken-specific ERVs exert genetic resistance to exogenous retrovirus infection. Mechanistically, chicken-specific ERVs activated the scavenger receptor MARCO (macrophage receptor with collagenous structure)-mediated TLR3-IL-1β inflammatory response in macrophages. Under the presence of MARCO, macrophages response to viral infection through inducing TLR3-IL-1β inflammatory response. Conversely, lack of MARCO increased the viral replication levels and attenuated the antiviral inflammatory response. MARCO-mediated ligand delivery enhances TLR3-IL-1β antiviral response, and IL-1β expression is responsible for viral inhibition. Restoring MARCO or IL-1β expression overcomes viral infection in macrophages. Our study provides new insights into the molecular mechanisms underlying the host defense against exogenous retroviruses infection and may have important implications for the development of novel therapeutic strategies against retroviruses infection.

ABSTRACT To analyze the characteristics of Mycoplasma pneumoniae as well as macrolide antibiotic resistance through whole-genome sequencing and comparative genomics. Thirteen clinical strains isolated from 2003 to 2019 were selected, 10 of which were resistant to erythromycin (MIC >64 µg/mL), including 8 P1-type I and 2 P1-type II. Three were sensitive (<1 µg/mL) and P1-type II. One resistant strain had an A→G point mutation at position 2064 in region V of the 23S rRNA, the others had it at position 2063, while the three sensitive strains had no mutation here. Genome assembly and comparative genome analysis revealed a high level of genome consistency within the P1 type, and the primary differences in genome sequences concentrated in the region encoding the P1 protein. In P1-type II strains, three specific gene mutations were identified: C162A and A430G in L4 gene and T1112G mutation in the CARDS gene. Clinical information showed seven cases were diagnosed with severe pneumonia, all of which were infected with drug-resistant strains. Notably, BS610A4 and CYM219A1 exhibited a gene multi-copy phenomenon and shared a conserved functional domain with the DUF31 protein family. Clinically, the patients had severe refractory pneumonia, with pleural effusion, necessitating treatment with glucocorticoids and bronchoalveolar lavage. The primary variations between strains occur among different P1-types, while there is a high level of genomic consistency within P1-types. Three mutation loci associated with specific types were identified, and no specific genetic alterations directly related to clinical presentation were observed. IMPORTANCE Mycoplasma pneumoniae is an important pathogen of community-acquired pneumonia, and macrolide resistance brings difficulties to clinical treatment. We analyzed the characteristics of M. pneumoniae as well as macrolide antibiotic resistance through whole-genome sequencing and comparative genomics. The work addressed primary variations between strains that occur among different P1-types, while there is a high level of genomic consistency within P1-types. In P1-type II strains, three specific gene mutations were identified: C162A and A430G in L4 gene and T1112G mutation in the CARDS gene. All the strains isolated from severe pneumonia cases were drug-resistant, two of which exhibited a gene multi-copy phenomenon, sharing a conserved functional domain with the DUF31 protein family. Three mutation loci associated with specific types were identified, and no specific genetic alterations directly related to clinical presentation were observed.

Accurate gender identification is crucial for the study of bird reproduction and evolution. The current study aimed to explore and evaluate the effectiveness of a noninvasive method for gender identification in Yangzhou geese. In this experiment, 600 goose eggs were collected. Hair root tissues were used for PCR amplification, molecular sequencing, and anal inversion for early sex recognition in goslings. According to the DNA amplification results for the feather pulp tissue of 2-wk-old geese, bands appeared at 436 bp (CHD1-Z) and 330 bp (CHD1-W) upon gel electrophoresis. This method considered the base of goose feathers to accelerate the process of gender recognition. By examining the sex of anatomized poultry for verification, the accuracy rate of PCR gel electrophoresis and molecular sequencing sex identification was 100%, whereas the average accuracy rate of anal inversion was 97.41%. In the comparison of feather growth trends at 0 to 18 wk of age, the feather root weight (FRW), feather root length (FRL), feather branch length (FBL), and feather shaft diameter (FSD) of Yangzhou goose of the same age were not significantly different between males and females (P > 0.05). At 6 wk of age, the FRW, FRL, and FSD in males and FRL in females increased rapidly; their growth increased by 84.43, 67.58, 45.10, and 69.42%, respectively. At 10 wk of age, the male FRL, male FBL, and female FBL increased by 37.31, 34.81, and 21.72, respectively. The Boltzmann model was found to be the best-fitting model for the feathers of male Yangzhou geese. Early sex identification based on feather growth trends between the sexes is not feasible. This study provides a convenient and reliable technical means for early sex identification of waterfowl and serves as an ecological strategy for protecting the reproduction of poultry populations.