Accurate pedigree reconstruction is critical for genetic evaluation in admixed cattle populations, yet the relative performance of microsatellite and genome-wide SNP markers in twin-rich herds with incomplete pedigree records remains unclear. We compared 12 ISAG-recommended microsatellite markers with whole-genome SNP data for dam–calf assignment in a Simmental crossbred population (n = 43, 13 dam–calf groups) from southern China. Twin zygosity was determined from SNP identity-by-descent (PI_HAT) values: nine calf pairs were dizygotic, one pair was monozygotic (20A/21A), and one adult pair was composed of dizygotic twin sisters (31A/34A). Admixture analysis at K = 3 revealed ancestry proportions of 50.7% European taurine, 28.9% Chinese indicine and 20.4% East Asian taurine. The SNP-based neighbor-joining tree correctly recovered 12 of 13 groups (92.3%, 95% CI: 64.0–99.8%), whereas the microsatellite-based tree recovered 11 (84.6%, 95% CI: 54.6–98.1%); the difference was not statistically significant (exact McNemar test, p = 1.0). Locus INRA023 was monomorphic (PIC = 0), reducing the effective number of markers to 11. These results indicate that genome-wide SNPs show a favourable trend in accuracy and are less prone to false-positive clustering than a standard microsatellite panel in admixed, twin-rich cattle populations.

IntroductionPrecision livestock farming requires decision support systems (DSS) that can translate biologically rich but small feeding-trial datasets into transparent and actionable nutritional evidence. This study developed a proof-of-concept hybrid knowledge-based DSS using a controlled silage ramie substitution trial in Xiangxi Yellow Cattle.MethodsTwenty-one cattle were allocated to five dietary treatments. The system integrated an experiment-derived evidence-rule engine, a 21-record case library for case-based reasoning (CBR), and ensemble machine-learning predictors based on Random Forest and Gradient Boosting. Module outputs were combined through a confidence-aware meta-reasoning layer. Ramie versus control contrasts were adjusted using the Benjamini-Hochberg false-discovery-rate procedure, and machine-learning performance was internally assessed using leave-one-out cross-validation.ResultsUnder the tested conditions, complete substitution of silage corn with silage ramie was associated with improved serum antioxidant and immune biomarkers and lower lipid peroxidation: CAT +15.4% (P = 0.0005; q = 0.0011), SOD +174.5% (P = 0.0002; q = 0.0011), T-AOC +14.7% (P = 0.0008; q = 0.0014), MDA -51.5% (P = 0.0065; q = 0.0097), IgA +45.1% (P = 0.0005; q = 0.0011), and IgG +41.8% (P = 0.0005; q = 0.0011). Carcass-yield indicators declined modestly. Internal cross-validation suggested that ensemble learning captured diet-sensitive serum biomarkers better than complex production traits (SOD: R2 = 0.791; CAT: R² = 0.545; net meat rate: R² = -0.263).DiscussionThe proposed framework provides a transparent evidence-translation workflow for converting small-sample feeding-trial results into computable, case-specific decision-support assets. However, the system should be interpreted as a proof-of-concept prototype rather than an externally validated feeding recommendation; larger multi-batch validation and economic modeling are required before farm-level deployment.

Heat stress (HS) poses a major environmental issue that negatively impacts the reproductive efficiency of bulls. However, the complex interactions among HS-induced declines in semen quality, sperm metabolism, and semen microbiota remain inadequately understood. The study explored the effects of HS on the quality of bull semen, sperm metabolic profiles, and semen microbiota composition by employing 16S sequencing and metabolomics. The findings revealed that HS significantly compromised semen quality and altered the semen microbiota composition, as evidenced by increased abundances of Acholeplasma and Oceanivirga, and decreased abundances of Lactobacillus, Ruminococcaceae UCG-005, and Ruminococcaceae UCG-010. Metabolomic analysis indicated that HS predominantly affected the metabolic pathways of amino acids and carbohydrates in sperm. Spearman's correlation analysis suggested that HS-induced sperm metabolic disorders may be associated with dysbiosis in the semen microbiota composition in bulls. The study reveals new perspectives on the microbiota-metabolism relationship in semen quality impacted by HS, indicating potential approaches to counteract HS-related fertility reductions in bulls through microbiota interventions.

Artemisinin (ART) is known to alleviate inflammation in mastitis, but its effect on ferroptosis in mammary epithelial cells and the associated regulatory mechanisms has not been fully clarified. Here, we demonstrate that ART markedly attenuates inflammatory injury and ferroptosis in Staphylococcus aureus-induced mastitis models both in vivo and in vitro. ART treatment reduces iron accumulation and lipid peroxidation while restoring antioxidant capacity, accompanied by improved mitochondrial integrity. Mechanistically, ART upregulates the palmitoyltransferase ZDHHC12, which promotes palmitoylation of nuclear factor erythroid 2-related factor 2 (Nrf2) and facilitates its nuclear translocation. Activation of Nrf2 subsequently enhances heme oxygenase-1 (HO-1) signaling, leading to suppression of inflammation and ferroptosis. Collectively, these findings reveal that ART exerts protective effects against mastitis by activating the ZDHHC12/Nrf2/HO‑1 axis, highlighting ART as a potential therapeutic agent for mastitis through coordinated inhibition of inflammation and ferroptosis.

The paradigm of precision livestock farming (PLF) demands intelligent decision support systems (DSS) capable of translating complex, multi-dimensional biological data into actionable nutritional strategies, yet such systems are frequently constrained by small-sample, high-dimensional datasets typical of controlled feeding trials. This paper presents an integrated knowledge-based DSS for optimizing livestock nutrition, demonstrated through a case study on substituting silage corn with silage ramie (Boehmeria nivea L.) in the diet of Xiangxi Yellow Cattle. The system employs a hybrid reasoning framework synergistically combining three inference paradigms: a forward-chaining production rule engine grounded in statistically validated findings, a case-based reasoning (CBR) module leveraging individual animal records, and an ensemble machine learning (ML) predictor utilizing Random Forest and Gradient Boosting algorithms, with a meta-reasoning layer dynamically fusing outputs via context-dependent confidence assessments. The knowledge base was constructed from a controlled trial involving 21 cattle across five dietary groups, yielding 11 production rules and a 21-record case library. Leave-one-out cross-validation confirmed strong ML predictive performance for diet-sensitive serum biomarkers (SOD: R2=0.791; CAT: R2=0.545) but poor generalization for complex production traits (net meat rate: R2=−0.263), empirically validating the hybrid architecture. The system confirmed that complete silage ramie substitution significantly enhances antioxidant capacity (CAT: +15.4%, P=0.0005; SOD: +174.5%, P=0.0002; T-AOC: +14.7%, P=0.0008) and immune function (IgA: +45.1%; IgG: +41.8%, P=0.0005) while reducing lipid peroxidation (MDA: −51.5%, P=0.0065), alongside a modest decrease in slaughter rate (−3.2%, P=0.0255). The system is deployed as a RESTful API, providing a replicable framework for transforming experimental findings into dynamic decision-support assets.

Livestock sex control is one of the core bioengineering technologies for improving quality and efficiency in modern animal husbandry, holding profound practical significance for sex-limited livestock production systems. Precise identification of fetal sex at the early gestational stage constitutes a key prerequisite for achieving targeted sex regulation. The discovery of cell-free fetal DNA (cffDNA) in the peripheral blood of pregnant cows has paved an important technical avenue for establishing a non-invasive and high-precision diagnostic system for early fetal sex identification. In this study, plasma and serum samples collected from pregnant cows were used as experimental materials, and three protocols-phenol-chloroform extraction, heat-based extraction, and a commercial kit specifically designed for isolating cffDNA from plasma/serum-were employed for cffDNA purification and isolation. Y-chromosome-specific genes (either the TSPY or SRY gene) were selected as molecular markers, and optimised detection systems were established by integrating polymerase chain reaction (PCR), real-time quantitative PCR (RT-qPCR), and loop-mediated isothermal amplification (LAMP) techniques. A systematic comparison was conducted to evaluate the efficacy and accuracy of different cffDNA extraction methods combined with various amplification technologies for fetal sex identification in both early and late stages of gestation. The actual calving outcomes were used as the standard for validation. The results demonstrated that the quality of cffDNA templates extracted by the commercial kit method was significantly superior to that obtained by the heat-based and phenol-chloroform methods, with the corresponding sex identification accuracy reaching the highest level. Notably, the LAMP technique exhibited unique advantages in detecting fetal sex in extremely early gestational samples (at 1-2 months of pregnancy). Characterised by its simplicity of operation, rapid reaction kinetics, and elimination of the need for sophisticated instrumentation, LAMP is particularly well-suited for on-site large-scale rapid primary screening of fetal sex in livestock farms. It enables the efficient exclusion of male foetuses within a short timeframe, thereby substantially improving the efficiency of breeding selection. Based on the aforementioned findings, this study proposes a combined detection model of "LAMP-based primary screening plus PCR-based confirmation", which can effectively balance detection efficiency and identification accuracy. The research outcomes provide empirical data and methodological references for constructing a non-invasive, early-stage, and high-precision technical system for fetal sex identification in dairy cows. This holds great value for promoting the implementation of precise early reproductive management in dairy farms and enhancing the economic benefits of the livestock industry.

Cadmium is a heavy metal used in industrial processes that can be released into the environment, where it accumulates in plants. When animals consume these plants, resistance to metabolic elimination results in cadmium accumulation in tissues, inducing damage to multiple organs, particularly the testes and ovaries, thereby impairing reproductive fitness. A substantial body of recent research has explored the ways in which this damage is passed down to the offspring of affected animals, resulting in transgenerational reproductive harm. In this review, we provide a brief overview of the ways in which cadmium disrupts the reproductive systems of male and female animals, as well as a detailed examination of the multigenerational effects of parental cadmium exposure on reproductive health in offspring. We highlight common themes among different animal models, potential biological pathways involved in multigenerational toxicity, and gaps in our current understanding of how cadmium toxicity is transmitted between generations. Finally, we present recommendations for future studies of the multigenerational effects of cadmium toxicity on the animal reproductive system.

Objective: Mulberry (Morus alba) leaf (ML) is a high-quality feed source for ruminants, while it is unclear whether it can enhance the growth performance and meat quality of Xiangdong black goats.Methods: In this study, we investigated the effects of ML supplementation (0%, 5%, 10%, 15%, and 20%) on the growth performance, serum variables, and the profiles of amino acids and fatty acids in the muscle of Xiangdong black goats.Results: Results showed that the final body weight, initial and final dry matter intake, and average daily gain increased linearly and quadratically with the increasing ML content (p<0.05). The serum concentrations of total antioxidant capacity (T-AOC) increased linearly, while immunoglobulin G (IgG) increased quadratically with the increasing ML content (p<0.05). Conversely, the saturated fatty acids (SFA) content in meat decreased linearly with the increasing ML content (p<0.05). Compared to goats without ML supplementation, goats fed with 15% ML showed significant increases in serum concentrations of T-AOC, superoxide dismutase, catalase, and IgG (p<0.05). Furthermore, goats fed with 20% ML displayed significant decreases in SFA (C18:0) content, compared to goats without ML supplementation (p<0.05).Conclusion: These results suggest that ML supplementation promotes the growth performance of goats. A diet containing 15% ML showed better effects in promoting antioxidant and immunomodulatory activities, while a diet with 20% ML was more effective in enhancing meat flavor in Xiangdong black goats.

Hunan Province, located in Central-South China, has a hot and humid climate, which has shaped the unique characteristics of its cattle. In this study, we analyzed the genomic diversity of 110 indigenous Hunan cattle using whole-genome sequencing and found that they have a mixed ancestry of indicine and taurine. By grouping the cattle based on their collection regions (western, central, southeastern, and southern Hunan), we used an unsupervised three-component Gaussian model to classify the runs of homozygosity (ROH) and calculated the genomic inbreeding coefficient based on runs of homozygosity (FROH) to assess inbreeding levels. The results showed that western Hunan cattle had the highest level of hybridization, while southern Hunan cattle had the lowest. Through selective sweep analysis, we identified candidate genes and pathways related to environmental adaptation and homeostasis. Notably, the SLC5A2 gene showed strong selection signals across all four regions and exhibited a distinct haplotype compared to other referenced cattle breeds. Additionally, we detected introgression from wild species into Hunan domestic cattle and analyzed their Y-chromosome haplotypes.

Cellulose-degrading bacteria play a crucial role in straw feed utilization, offering potential for the high-value conversion of straw resources. This paper reviews the screening methods and techniques for cellulose-degrading bacteria, analyzes the physiological and biochemical characteristics of highly efficient strains, and discusses their application effects and influencing factors in straw feed utilization. At the same time, commonly used physical, chemical, and microbial treatment technologies in straw feed processing are systematically summarized, with a comparison of their advantages, disadvantages, and applicability. Research indicates that microbial treatment technologies, especially the application of cellulose-degrading bacteria, can not only significantly improve the degradation efficiency of straw but also enhance the nutritional value and digestibility of the resulting feed. Furthermore, this paper outlines the main challenges in current studies and provides insights into future research directions and industrial application prospects, aiming to provide theoretical support and technical guidance for promoting sustainable development in grassland science and animal husbandry.

The Zhashi Brown goat is native to Hengyang Municipality in Hunan Province in southern China and boasts a rich history. The goats exhibit exceptional traits, including heat and insect resistance, strong reproductive capabilities and superior meat production. Despite these merits, the currently limited population requires immediate conservation endeavors. In this study, we conducted whole-genome resequencing on 21 Zhashi Brown goats. Additionally, we performed a joint analysis using published whole-genome data from 119 goats, including Chengdu Brown goat, Matou goat, Wuxue goat, Xiangdong Black goat, Qaidam Cashmere goat, Ujumqin Cashmere goat and Shanbei Cashmere goat. The results revealed that the Zhashi Brown goat is genetically more pure than other Southern Chinese goat breeds. Furthermore, the genetic diversity (nucleotide diversity, linkage disequilibrium, runs of homozygosity and inbreeding coefficient) of the Zhashi Brown goat's genome is at a low level among the eight breeds, indicating the need for further conservation. Employing analytical methodologies such as composite likelihood ratio, nucleotide diversity, integrated haplotype score, the fixation index and cross-population extended haplotype homozygosity, we systematically scanned selective signals within the genomic landscape of Zhashi Brown goat. The outcomes underscore strong selection signals associated with genes implicated in immune response, heat tolerance, reproductive performance and meat quality. These findings make a significant contribution to our understanding of the genetics framework associated with adaptive traits in Zhashi Brown goat. Furthermore, this study explores the genetic diversity of the Zhashi Brown goat, which may contribute to the theoretical framework for conserving its genetic resources, while the identified trait-associated variations could inform future strategies to optimize selective breeding programs.

The world's buffaloes are primarily divided into two main categories: : swamp buffaloes and riverine buffaloes. Binhu buffaloes (BB) are Chinese indigenous swamp buffaloes, characterized as strong body vigor, fit for durable work with docile nature. However, there is literature void regarding genomic architecture and selective sweeps analysis for this breed. Herein we utilized 20 newly whole genome sequences (WGS) of BB together with published WGS data of seventy-four buffaloes [Upper Yangtze (UY) buffaloes; n = 30, Middle-Lower Yangtze (MLY) buffaloes; (n = 30) and River buffaloes (RB); (n = 14)] to elucidate population structure, genetic diversity and selection characteristics of the BB. The results showed that the BB originated from swamp buffalos. The genetic diversity of the BB was lower than that of the RB and higher than that of the UY and the MLY buffaloes. In addition, employing five selective sweep detection methods numerous genes related to immunity (RELT, TP73, C5, CHMP1A, CDK10, ANKRD17), heat tolerance (DNAJB4, DNAJA1, HSF4, HELB, DNAJC28), growth (LYN, DYNC1I2, PLAG1, ADAMTSL3, CHKB, PDE1A, RXFP2), carcass and metabolism (SIRT6, LYPLA1, FADS1), nervous system (KIRREL3, AUTS2), and reproduction (SMG6, TSNAXIP1, CACNB2, ERCC3, RAD51, GDF9, CAMK4, KALRN, FANCA, SPIRE2, ATP2B1, AREG, EREG) were found to be under selection. Taken together, current investigation provides a genetic basis for the characteristics specific to the BB, such as high body strength; tolerance to roughage and easy to gain weight; docile nature; ability to endure labor; strong adaptability; and low fecundity and offers new ideas for the conservation, development and utilization of this breed.

(1) Background: Matou goats, native to Hunan and Hubei provinces in China, are renowned for their exceptional meat and skin quality. However, a comprehensive whole-genome-based exploration of the genetic architecture of this breed is scant in the literature. (2) Methods: To address this substantial gap, we used whole-genome sequences of 20 Matou goats and compared them with published genomic data of 133 goats of different breeds across China. This comprehensive investigation sought to assess genetic diversity, population structure, and the presence of genomic selection signals. (3) Results: The whole genome of Matou goat populations yielded a substantial catalog of over 19 million single nucleotide polymorphisms (SNPs), primarily distributed within intergenic and intron regions. The phylogenetic tree analysis revealed distinct clades corresponding to each goat population within the dataset. Notably, this analysis positioned Matou goats in a closer genetic affinity with Guizhou White goats, compared to other recognized goat breeds. This observation was corroborated by principal component analysis (PCA) and admixture analysis. Remarkably, Matou goats exhibited diminished genetic diversity and a notable degree of inbreeding, signifying a reduced effective population size. Moreover, the study employed five selective sweep detection methods (including PI, CLR, PI-Ratio, Fst, and XP-EHH) to screen top signal genes associated with critical biological functions, encompassing cardiomyocytes, immunity, coat color, and meat quality. (4) Conclusions: In conclusion, this study significantly advances our understanding of the current genetic landscape and evolutionary dynamics of Matou goats. These findings underscore the importance of concerted efforts in resource conservation and genetic enhancement for this invaluable breed.

Xiangdong black goats, indigenous to Hunan Province, China, exhibit remarkable adaptation to challenging environments and possess distinct black coat coloration alongside exceptional meat quality attributes. Despite their significance, comprehensive genomic investigations of this breed have been notably lacking. This study involved a comprehensive examination of population structure, genomic diversity, and regions of selection in Xiangdong black goats utilizing whole-genome sequencing data from 20 samples of this breed and 139 published samples from six other Chinese goat breeds. Our genomic analysis revealed a total of 19,133,125 biallelic single nucleotide polymorphisms (SNPs) within the Xiangdong black goat genome, primarily located in intergenic and intronic regions. Population structure analysis indicated that, compared with Jintang, Guizhou and Chengdu goats, Xiangdong black goats exhibit a reduced level of genetic differentiation but exhibit relatively greater divergence from Jining goats. An examination of genetic diversity within Xiangdong black goats revealed a moderate level of diversity, minimal inbreeding, and a substantial effective population size, which are more reflective of random mating patterns than other Chinese goat breeds. Additionally, we applied four distinct selective sweep methods, namely, the composite likelihood ratio (CLR), fixation index (FST), θπ ratio and cross-population extended haplotype homozygosity (XP-EHH), to identify genomic regions under positive selection and genes associated with fundamental biological processes. The most prominent candidate genes identified in this study are involved in crucial aspects of goat life, including reproduction (CCSER1, PDGFRB, IFT88, LRP1B, STAG1, and SDCCAG8), immunity (DOCK8, IL1R1, and IL7), lactation and milk production (SPP1, TLL1, and ERBB4), hair growth (CHRM2, SDC1, ITCH, and FGF12), and thermoregulation (PDE10A). In summary, our research contributes valuable insights into the genomic characteristics of the Xiangdong black goat, underscoring its importance and utility in future breeding programs and conservation initiatives within the field of animal breeding and genetics.

(1) Background: Buffaloes are crucial livestock species for food and service in tropical and subtropical regions. Buffalo genetics, particularly in indigenous Chinese breeds such as the Xiangxi white buffalo (XWB), remains an intriguing area of study due to its unique traits and regional significance. (2) Methods: This investigation utilized the whole-genome sequences of twenty XWBs (newly sequenced), along with eighty published whole-genome sequences of other buffalo breeds (including Guizhou white buffalo, river buffalo, and Chinese buffalo in the Yangtze River). Using whole-genome sequencing analysis technology, the population structure, genomic diversity, and selection signatures of XWB were determined. (3) Results: This study revealed that the XWB, being phylogenetically positioned in the middle and lower reaches of the Yangtze River, exhibited substantial genomic diversity. Employing four selection sweep detection methods (CLR, iHS, π-ratio, and FST), several genes were positively identified for adaptive traits in the XWB, including coat color phenotypes (ASIP, KIT), the nervous system (GRIK2), reproduction (KCNIP4), growth and development (IFNAR1, BMP6, HDAC9, MGAT4C, and SLC30A9), the body (LINGO2, LYN, and FLI1), immunity (IRAK3 and MZB1), and lactation (TP63, LPIN1, SAE1). (4) Conclusions: In conclusion, this study enhances our understanding of the genetic distinctiveness and adaptive traits of XWB, highlighting selection signatures crucial for future breeding and conservation and ensuring sustainable use of this vital livestock resource.

Cadmium (Cd) is a toxic heavy metal contaminant in agricultural soils. Phytoremediation using hyperaccumulator plants is a promising remediation strategy. This study investigated the effects of TiO2 NPs on Cd uptake and accumulation in the hyperaccumulator ramie (Boehmeria nivea L.) grown in Cd-spiked soil. The aim was to evaluate the potential application of TiO2 NPs to enhance the phytoextraction efficiency of ramie for removing Cd from contaminated soils. Ramie was cultivated in soil spiked with 5 mg/kg Cd, with or without 500 mg/kg TiO2 NPs. The results showed TiO2 NPs significantly increased Cd concentrations in roots, stems, and leaves of ramie by 35%, 75%, and 278% respectively, compared to control plants. Cd levels reached 146 mg/kg in roots and 102 mg/kg in leaves with TiO2 NPs. The bioconcentration factor rose from 21.6 to 29.2 and translocation factor from 0.3 to 0.7 with nanoparticles. This indicates TiO2 NPs increased Cd bioavailability in soil and translocation to shoots. The higher Cd accumulation, especially in leaves, demonstrates the potential of TiO2 NPs to improve ramie's phytoextraction capacity. With TiO2 NP treatment, soil Cd levels decreased by an estimated 20–30% after 8 weeks of ramie cultivation, indicating enhanced phytoextraction. This study provides evidence that the application of TiO2 NPs can enhance the efficiency of phytoremediation using hyperaccumulator plants like ramie for remediation of Cd-contaminated soils.

Abstract Background Acephalic spermatozoa syndrome is a rare but severe type of teratozoospermia. The familial trait of acephalic spermatozoa syndrome suggests that genetic factors play an important role. However, known mutations account for only some acephalic spermatozoa syndrome patients, and more studies are needed to elucidate its pathogenesis. The current study aimed to elucidate the pathogenesis of acephalic spermatozoa syndrome caused by PMFBP1 mutation. Results We identified a homozygous splice site mutation (NM_031293.2, c.2089-1G > T) in PMFBP1 through Sanger sequencing. Western blotting and immunofluorescence analyses revealed that this splice site mutation resulted in the absence of PMFBP1 protein expression in the patient's sperm cells. We generated an in vitro model carrying the splice site mutation in PMFBP1 and confirmed, through RT‒PCR and Sanger sequencing, that it led to a deletion of 4 base pairs from exon 15. Conclusion A homozygous splice site mutation results in a deletion of 4 bp from exon 15 of PMFBP1, thereby affecting the expression of the PMFBP1 protein. The absence of PMFBP1 protein expression can lead to acephalic spermatozoa syndrome. This finding elucidates the underlying cause of acephalic spermatozoa syndrome associated with this specific mutation (NM_031293.2, c.2089-1G > T) in PMFBP1.

Heat stress (HS) poses a substantial challenge to livestock. Studies have demonstrated that HS reduces fertility and leads to gut microbiota dysbiosis in bulls. However, the impact of the gut microbiota on fertility in bulls during HS is still unclear. Our research revealed that HS exposure decreased semen quality in bulls, and fecal microbiota transplantation (FMT) from heat-stressed bulls to recipient mice resulted in a significant decrease in number of testicular germ cells and epididymal sperm. Untargeted metabolomics methodology and 16S rDNA sequencing conjoint analysis revealed that Akkermansia muciniphila (A. muciniphila) seemed to be a key bacterial regulator of spermatogenesis after HS exposure. Moreover, the research indicated that A. muciniphila regulated secondary bile acid metabolism by promoting the colonization of bile salt hydrolase (BSH)-metabolizing bacteria, leading to increase of retinol absorption in the host gut and subsequently elevation of testicular retinoic acid level, thereby improving spermatogenesis. This study sheds light on the relationship between HS-induced microbiota dysbiosis and spermatogenesis, offering a potential therapeutic approach for addressing bull spermatogenic dysfunction triggered by HS exposure.

Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives.

Exploring the genetic landscape of native cattle is an exciting avenue for elucidating nuanced patterns of genetic variation and adaptive dynamics. Xiangnan cattle, a native Chinese cattle breed mainly produced in Hunan Province, are well adapted to the high temperature and humidity of the local environment and exhibit strong disease resistance. Herein, we employed whole-genome sequences of 16 Xiangnan cattle complemented by published genome data from 81 cattle. Our findings revealed that Xiangnan cattle are pure East Asian indicine cattle with high genetic diversity and low inbreeding. By annotating the selection signals obtained by the CLR, θπ, FST, and XP-EHH methods, genes associated with immunity (ITGB3, CD55, OTUD1, and PRLH) and heat tolerance (COX4I2, DNAJC18, DNAJC1, EIF2AK4, and ASIC2) were identified. In addition, the considerable introgression from banteng and gaur also contributed to the rapid adaptation of Xiangnan cattle to the environment of Southern China. These results will provide a basis for the further conservation and exploitation of Xiangnan cattle genetic resources.