Analysis of the genetic structure and selection signature of Xiangyang Black pigs using whole-genome resequencing data

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To explore the genetic diversity, population structure, and selection signatures of XYB in the context of Chinese and Western pig breeds, we performed whole-genome resequencing on 15 pig breeds, involving 225 individuals. Results After quality control, 20,479,203 high-quality single-nucleotide polymorphisms (SNPs) were retained for subsequent analysis. Genetic diversity analysis revealed that XYB exhibited relatively high genetic diversity (Ho = 0.38, pi = 0.35) and a low inbreeding coefficient (F ROH = 0.001–0.090), indicating its strong potential for genetic improvement and conservation. Population structure analyses—including neighbor-joining tree, principal component analysis, and ADMIXTURE—revealed a distinct genetic structure and verified the rationality of XYB’s status as a unique genetic resource at the molecular level. Selection signature detection using three complementary methods (Fst, θπ ratio, and XP-EHH) identified 1080 significant selected regions and 951 candidate genes in XYB compared with Western breeds. Functional annotation showed that these genes were enriched in pathways related to meat quality (e.g., FABP2 , PPARG , C/EBPα , and THRSP ), reproduction (e.g., GNRH1 , CENPE , and CCDC112 ), and disease resistance (e.g., CCL17 , CCL22 , and CX3CL1 ). Conclusions Our results provide insights into the genetic basis of phenotypic traits in XYB pigs and offer a theoretical foundation for their conservation, breeding, and genetic improvement. Xiangyang Black pig whole-genome resequencing genetic diversity population structure selection signature Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Background The diversity of local pig breeds is of strategic significance for enriching China's livestock industry and constitutes a key component of the agricultural economy. The domestication of wild boars, which began approximately 10,000 years ago, has led to the development of around 300 distinct pig breeds globally as a result of sustained natural and human-driven selection [ 1 ]. Such prolonged selective pressure has not only modified phenotypic traits but also profoundly influenced genomic architecture, affecting variations in morphology, physiology, and behavior. Advances in sequencing technology, reductions in sequencing costs, and improvements in bioinformatics have enabled many studies to explore evolutionary selection, clarifying the genetic mechanisms of different morphologies, physiologies, and behaviors in pigs and providing new insights for their further improvement. Advances in sequencing technology and the concurrent reduction in associated costs have greatly promoted the application of whole-genome resequencing in studies of genetic diversity and selection signatures in pigs [ 2 – 4 ]. Genomic analyses have uncovered numerous candidate genes and markers associated with important economic traits, as well as adaptive and phenotypic characteristics [ 5 ]. These results not only enhance our understanding of pig origin, domestication, and selective breeding history, but also offer valuable insights for future genetic improvement efforts. Xiangyang Black (XYB) represents a valuable indigenous pig breed resource in China, primarily distributed within the Xiangyang City region of Hubei Province. It has been raised for over 300 years and is known for its tender meat (intramuscular fat content ~ 3.5%), early sexual maturity, and tolerance to harsh feeding conditions. However, with the large-scale introduction of Western commercial breeds, the XYB population has declined, and its genetic characteristics remain poorly understood. Moreover, there is currently insufficient evidence to prove that it is a unique genetic resource. Therefore, determining whether XYB represents a distinct genetic resource that is separate from other breeds in Hubei Province and the western region is of great significance for the protection of genetic resources and biodiversity. In this study, we integrated whole-genome resequencing data from XYB and 14 other pig breeds—10 Chinese indigenous and four Western commercial—to (1) evaluate the genetic diversity and inbreeding status of XYB, (2) clarify its genetic relationship with other Chinese and Western breeds, and (3) identify genomic regions and candidate genes under selection associated with its key phenotypic traits. Our findings aim to provide a scientific basis for the conservation, utilization, and genetic improvement of XYB. Methods Sample collection and sequencing In this study, ear tissue was collected from 59 Xiangyang blcak pigs, 10 Qingping pigs, and 10 Jianli pigs for high-throughput resequencing. Xiangyang Black pig comes from Xiangyang Wanfengyuan Ecological Agricultural Science and Technology Development Co., Ltd., the Qingping pig was sourced from Qingping Pig Breeding Farm, and Jianli pig was provided by Hubei Tianmu Livestock Co., Ltd. Genomic DNA was isolated from ear tissue samples employing the Qiagen DNeasy Tissue Kit (Qiagen, Germany), in accordance with a conventional phenol-chloroform extraction method. For each individual, paired-end sequencing libraries (read length: 2×150 bp) were prepared and sequenced on an Illumina HiSeq 2000 platform, achieving an average coverage of approximately 11× coverage. Whole-genome sequencing data from 146 additional individuals were obtained from publicly accessible databases. These datasets represented eight indigenous pig breeds from China, one Asian wild boar population, and three Western commercial breeds (Table 1 ). The analyzed data were sourced from the following BioProject entries: PRJNA213179[ 6 ], PRJNA488960[ 7 ], PRJNA524263[ 8 ], and PRJNA260763[ 9 ]. In total, this study included whole-genome sequences from a total of 225 pigs, covering 15 distinct populations. Genetic variation detection and annotation Clean sequencing reads were aligned to the Sscrofa11.1 reference genome using BWA (v0.7.12) [ 10 ] under default parameters, while sorted BAM files were produced with SAMtools (v1.9) [ 11 ]. SNP calling was carried out using GATK (v4.1.4.1) [ 12 ] via the “HaplotypeCaller” and “GenotypeGVCFs” modules for gVCF generation and joint-genotyping, respectively. Hard filtering was then applied based on the following criteria: QUAL < 30.0, QD 60.0, MQ 3.0, MQRankSum < -12.5, or ReadPosRankSum < -8.0, using the VariantFiltration function in GATK. The vcftools v0.1.15 [ 13 ] was used to filter out SNP loci with an minor allele frequency less than 0.05 and a call rate less than 0.9. Finally, SNPs were annotated using SnpEff software (v4.3) [ 14 ] based on the Ensembl database. Genotype imputation was conducted using the Beagle software package [ 15 ]. Genetic diversity analysis To assess genomic variability, key diversity parameters—including expected heterozygosity (H E ), observed heterozygosity (H O ), and nucleotide diversity (p i )—were computed with PLINK v1.9 [ 16 ]. The level of runs of homozygosity (ROH) were performed using the same software following a pipeline similar to that described in our previous publication [ 17 ]: a sliding window of 50 SNPs permitting one heterozygous and up to five missing calls per window; a minimum of 100 consecutive SNPs required to define an ROH; and a minimum physical length of 1 Mb to exclude regions likely reflecting strong linkage disequilibrium. The inbreeding coefficient (F ROH ) was derived as the combined length of all ROH segments divided by the total length of the autosomes covered by SNPs. Pairwise population differentiation (Fst) was computed using vcftools v0.1.15 [ 13 ] and visualized as a heatmap using the "corrplot" package in R. Population structure analysis Principal component analysis (PCA) was carried out with GCTA v1.91.7 [ 19 ] to reduce dimensionality, and the first three principal components were retained for further interpretation. Ancestral genetic structure and individual admixture proportions were inferred through the ADMIXTURE program (v1.3) [ 20 ]. To elucidate genetic relationships among populations, a neighbor-joining tree (NJ) was built employing identity-by-state (IBS) genetic distances, computed with MEGA v5.0 [ 18 ] and graphically represented using FigTree v1.4.3 ( http://tree.bio.ed.ac.uk/software/figtree/ ). Principal component analysis (PCA) was performed using GCTA v1.91.7 [ 19 ] to reduce dimensionality. ADMIXTURE v1.3 [ 20 ] was used to infer ancestral components. Selection signature detection Selection signatures in Xiangyang Black pig were detected by comparing with Western commercial breeds (LW, LR, DU) using three methods: population differentiation coefficient (Fst), polymorphism levels statistic (θπ) and cross-population extended haplotype homozygosity (XP-EHH). Fst and π ratio were calculated using a 100 kb sliding window with a 50 kb step size in VCFtools v0.1.15 [ 13 ]. XP-EHH statistics were computed using selscan v1.3.0 [ 21 ]. Regions with values in the top 5% of at least two methods were considered significant selected regions. Functional annotation and enrichment analysis of candidate genes Candidate genes under selection were identified based on the Ensembl database. Genes within significant selected regions were annotated using the Ensembl database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted with DAVID 6.8. Terms with a p-value below 0.05 were deemed statistically significant and included in the results. Results Sequencing data and SNP characteristics To gain comprehensive genomic insights, we conducted whole-genome resequencing of 59 Xiangyang Black pigs, 10 Qingping pigs, and 10 Jianli pigs, achieving an average coverage of 11×. Furthermore, to contextualize the genetic diversity and population structure of Xiangyang Black pigs within a broader genetic landscape, we integrated publicly available sequencing data from 146 additional individuals, encompassing eight Chinese indigenous breeds, one Asian wild boar population, and three European commercial breeds (Table 1 ). We then performed variant calling on these 225 pigs and identified 20,479,203 SNPs. Generally speaking, SNPs are evenly distributed across each chromosome, except for some sites at the telomeres of the chromosomes (Figure S1 ). Of these, 23% were identified as novel variants, since they were not present in the dbSNP pig database ( https://ftp.ncbi.nih.gov/snp/organisms/archive/pig_9823/VCF/ ). In line with earlier investigations, the majority of SNPs were located in intergenic regions and introns—accounting for 51.9% and 43.7%, respectively—while only 2.6% were located in exonic regions, comprising 79,448 synonymous mutations and 30,938 missense mutations. Table 1 Samples and genetic diversity of Xiangyang Black and other pigs Population Abbreviation Size P N H O H E pi Xiangyang Blcak XYB 59 0.96 0.38 0.36 0.35 Qingping QP 10 0.61 0.29 0.33 0.20 Jianli JL 10 0.51 0.3 0.33 0.17 Tongcheng TC 10 0.60 0.31 0.33 0.20 Asian Wild Boar AWB 15 0.74 0.27 0.33 0.25 Erhualian EHL 5 0.52 0.37 0.35 0.19 Jinhua JH 24 0.54 0.26 0.31 0.17 Laiwu LWU 6 0.68 0.36 0.34 0.23 Luchuan LC 6 0.49 0.39 0.35 0.17 Bamaxiang BMX 6 0.61 0.38 0.35 0.21 Anqing Six-End-White ASW 18 0.97 0.31 0.35 0.34 Wannan Blcak WNH 20 0.68 0.26 0.30 0.20 Duroc DU 8 0.62 0.34 0.34 0.22 Landrace LR 13 0.81 0.31 0.35 0.28 Large white LW 15 0.83 0.32 0.35 0.29 Genetic diversity of the Xiangyang Black pig Of the 15 breeds, Chinese indigenous breeds generally showed higher genetic diversity than Western commercial breeds (Table 1 ). XYB pigs exhibited high P N (0.96), H O (0.38), and pi (0.35), indicating a relatively healthy population structure. To evaluate genetic diversity, pairwise genetic differentiation was quantified using the fixation index (Fst), as summarized in Fig. 1 A. The Fst values between XYB pigs and commercial lean-type breeds ranged from 0.20 to 0.27, which were comparable to those between XYB and other Chinese indigenous pig populations (ranging from 0.10 to 0.30), indicating no significant difference in the levels of genetic distinction across these groups. Pairwise Fst analysis showed that XYB pigs had the lowest genetic differentiation from ASW pigs (Fst = 0.10) and the highest from JH pigs (Fst = 0.30) (Fig. 1 A). To assess the genomic inbreeding level of XYB, the ROH was calculated for each pig breed. The average ROH-based inbreeding coefficient (F ROH ) of XYB ranged from 0.001 to 0.090, indicating a low level of inbreeding and high genetic diversity (Fig. 1 B). Population Structure To evaluate the evolutionary relationships across the 15 pig populations, a NJ tree was generated using IBS distances for all individuals (Fig. 2 A). The phylogenetic reconstruction showed that all XYB individuals were clustered together and formed an independent branch, indicating that XYB can serve as an independent resource population with unique genetic characteristics. The NJ tree also revealed a pronounced phylogenetic split between Chinese indigenous breeds and Western commercial breeds (DU, LR, LW). Interestingly, XYB was positioned intermediately between these two groups, suggesting that it is closer to Western breeds than to other Chinese indigenous breeds. The PCA results supported this pattern, with PC1 (60.5% contribution rate) separating the Chinese and Western breeds, and XYB pigs clustered in an intermediate position between these two distinct groups (Fig. 2 B). To further explore the admixture history and ancestral contributions across populations, we conducted ADMIXTURE analysis under a range of hypothetical ancestral population numbers (K = 2 to 5) (Fig. 2 C, Figure S2 ). At a K of 2, XYB contained ancestral components from both Western breeds and Chinese indigenous pig breeds. At a K of 4, XYB was independently separated and formed a unique genetic structure. Therefore, the results of the PCA and the ADMIXTURE analysis revealed the clustering trends of the tested populations, highlighting that XYB is a unique population. Selection signature detection of the Xiangyang Black pig population To uncover the genomic regions under selection in XYB pigs during their adaptation, we executed a comparative population genomic analysis between XYB and Western commercial breeds. Three complementary methods—Fst, θπ, and XP-EHH—were employed to identify putative selection signatures in the XYB genome. The distribution of candidate regions identified through various methods is illustrated in Fig. 3 . Based on their respective top 5% thresholds, Fst (≥ 0.444; Table S1 ), π ratio (≥ 1.095; Table S2 ), and XP-EHH (≥ 0.185; Table S3) each identified 2263 windows. To improve reliability and minimize false positives, we focused on regions that were simultaneously identified by at least two of these approaches. This integrative strategy yielded 1080 high-confidence candidate regions (Fig. 4 , Table S4). Functional enrichment analysis of candidate genes A total of 951 genes were located within the candidate selective sweep regions (Table S5). Functional enrichment identified 30 GO terms (Table S6) and 12 KEGG pathways (Table S7) were significantly enriched (FDR < 0.05), including response to endogenous stimulus (GO:0009719) and anatomical structure development (GO:0048856), as well as the calcium signaling pathway (ssc04020), and the cAMP signaling pathway (ssc04024) (Fig. 5 ). Discussion Although XYB pigs and other pig populations in nearby areas have different morphologies, they share similar characteristics, such as high reproductive capacity, strong disease resistance, high fat deposition rate, and tolerance to coarse feed. To explore XYB’s unique genetic structure and genetic relationship with Chinese and Western breeds, we conducted analyses of genetic distance, genetic differentiation, and population structure for these groups to further clarify the rationality of XYB as an independent genetic resource. From an NJ tree based on the genetic distance between individuals and the PCA results, all XYB individuals were clustered together, while the other groups were relatively independent. From the perspective of the population structure of ADMIXTURE, the XYB pig population became independent very early (K = 4). This indicates that XYB differs from Western breeds and other local breeds due to its unique genetic structure and confirms the rationality of the breed as a unique genetic resource at the molecular level. XYB exhibited the highest P N , H O , H E , and pi among the 15 breeds, indicating that it has higher genetic diversity and better breed conservation effectiveness. In addition, we used ROH to calculate the inbreeding coefficient. Compared with other pig breeds, the coefficient of XYB was generally lower (0.001–0.090), consistent with the finding that XYB pigs have high genetic diversity. Analyzing the selection characteristics of the genome can provide a deeper understanding of the genetic mechanism of adaptive phenotypes in pigs and identify important candidate genes related to excellent economic traits. In this paper, we focused on the selection of signature regions containing important candidate genes associated with specific traits related to livestock breeding. Several candidate genes related to meat quality traits were identified, including FABP2 , which encodes intestinal fatty acid binding protein 2 and has been studied in various livestock species for its potential influence on meat quality traits, particularly fatty acid composition and related characteristics [ 22 – 24 ]; PPARG , which is one of the differentiation markers in preadipocyte differentiation that drives the conversion of preadipocytes to mature adipocytes by activating transcription factors such as C/EBPα and plays an important role in adipose deposition [ 25 , 26 ]; CIDEC gene, which is involved in lipid droplet formation in adipocytes and has been shown in both pigs [ 27 ] and cattle [ 28 ] to be more highly expressed in the muscles of animals with high intramuscular fat (IMF) content; and THRSP , which plays an important role in adipogenesis. For instance, through ATAC-seq and RNA-seq analyses, Xu et al. identified THRSP as a key gene influencing intramuscular fat content traits in Xidu Black pigs [ 29 ]; while transcriptome and metabolome analyses by Hou et al. confirmed its role in Beijing Black pigs [ 30 ]. XYB pigs have good meat quality, with an IMF content of over 3.5%, which may be related to these genes. Candidate genes identified for reproduction included GNRH1 , which encodes a gonadotropin-releasing hormone and directly regulates the secretion of luteinizing and follicle-stimulating hormones in the pituitary gland, thereby influencing the estrous cycle and ovulation frequency of sows [ 31 ], and CENPE , a centromeric kinesin, which affects gonadotropin secretion by regulating the hypothalamic–pituitary–gonadal axis. Studies using transcriptome-wide association study analysis have revealed that the expression of CENPE is strongly associated with mean litter weight and influences embryo implantation efficiency [ 32 ]. Also identified in this category was CCDC112 , which is crucial for male fertility [ 33 ], is associated with reproductive traits in pigs [ 34 ], and has been reported to be a stage-specific marker in spermatocytes of humans [ 35 ] and buffalo [ 36 ]. In terms of disease resistance, genes identified included CCL17 , CCL22 , and CX3CL1 , which belong to the chemokine family and are responsible for recruiting monocytes and T cells to sites of infection. CCL17 is a chemokine produced by epithelial cells and participates in the immune response within the mesenteric lymph nodes of pigs infected with Ascaris suum [ 37 ]. Studies have shown that CCL22 is associated with the inflammatory responses involved in the development of asthma in Meishan pigs [ 38 ]. Finally, CX3CL1 is the only member of the CX3C chemokine subfamily and plays a crucial role in the immune response to respiratory syncytial virus infection [ 39 ]. We speculate that these genes may be associated with XYB pigs’ adaptability to harsh environments. Conclusions This study systematically analyzed the genomic characteristics of XYB and 14 other Chinese and Western pig breeds. XYB pigs were found to exhibit high genetic diversity, a unique population structure, and strong selection signatures associated with meat quality, disease resistance, and reproduction. The candidate genes identified provide insights into the genetic basis of XYB’s phenotypic traits and offer practical markers for breeding and conservation. These findings contribute to the understanding of pig adaptive evolution and support the sustainable utilization of XYB pig germplasm resources. Abbreviations SNP Single nucleotide polymorphism He Expected heterozygosity Ho Observed heterozygosity IBS Identical-by-state NJ Neighbor-joining PCA Principal component analysis ROH Runs of homozygosity GO Gene Ontology KEGG Kyoto Encyclopedia of Genes and Genomes XP-EHH Cross-population extended haplotype homozygosity Declarations Acknowledgments We are grateful to the global scientific community for generating and sharing publicly available whole-genome sequencing data from pigs, which were instrumental for this study. Author Contributions XWP, SQM and JJW designed the study. ZX, ZPL, JWZ, YZ and MQ performed the data collection. ZX performed the analyses under the assistance and guidance of HS, YF, TC, DKC and FOO. ZX drafted the manuscript. All authors read and approved the final manuscript. Funding This research was funded by the Major Program (JD) of Hubei Province (2023BAA029), National Key R&D Program of China (2021YFD1301105), Hubei Province Science and Technology Innovation Team Project, the Innovation Team of the Hubei Agricultural Science and Technology Innovation Center (2024-620-000-001-014), National Pig Industry Technology System (CARS-35). Data Availability The raw sequencing reads generated for Xiangyang Black, Qingping, and Jianli pigs in this study have been deposited in the NCBI Sequence Read Archive under BioProject accession number PRJNA1310513. Additionally, publicly available sequencing datasets were retrieved from the NCBI SRA under the following BioProject accessions: PRJNA488960, PRJNA524263, PRJNA213179, and PRJNA260763. Ethics approval and consent to participate The animal study was reviewed and approved by the Institutional Animal Care and Use Committee of the Hubei Academy of Agricultural Sciences (Permit Number: 36/2016). All procedures involving pigs were conducted in strict compliance with the ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) version 2.0. The ear tissue samples of Xiangyang Black pig, Qingping pig, and Jianli pig were provided by Xiangyang Wanfengyuan Ecological Agricultural Science and Technology Development Co., Ltd., Qingping Pig Breeding Farm, and Hubei Tianmu Livestock Co., Ltd. respectively, which authorized us to use the samples for research purposes. No animals were euthanized or sacrificed in this study. Consent for publication This section is not applicable to this study. Conflict of Interest The authors declare that they have no competing interests. References Rischkowsky B, Pilling D, Commission on Genetic Resources for Food and Agriculture. The state of the world's animal genetic resources for food and agriculture. Rome: Commission on Genetic Resources for Food and Agriculture, Food and Agriculture Organization of the United Nations; 2007. 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Gene. 2024;893:147950. https://doi.org/10.1016/j.gene.2023.147950 . Wang M, Liu X, Chang G, Chen Y, An G, Yan L, et al. Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis. Cell Stem Cell. 2018;23(4):599–e6144. https://doi.org/10.1016/j.stem.2018.08.007 . Huang L, Zhang J, Zhang P, Huang X, Yang W, Liu R, et al. Single-cell RNA sequencing uncovers dynamic roadmap and cell-cell communication during buffalo spermatogenesis. iScience. 2023;26(1):105733. https://doi.org/10.1016/j.isci.2022.105733 . Skallerup P, Nejsum P, Cirera S, Skovgaard K, Pipper CB, Fredholm M, et al. Transcriptional immune response in mesenteric lymph nodes in pigs with different levels of resistance to Ascaris suum. Acta Parasitol. 2017;62(1):141–53. https://doi.org/10.1515/ap-2017-0017 . Tu W, Wang H, Zhang Y, Huang J, Diao Y, Zhou J, et al. Investigation of the Molecular Mechanism of Asthma in Meishan Pigs Using Multi-Omics Analysis. Anim (Basel). 2025;15(2). https://doi.org/10.3390/ani15020200 . Rivas-Fuentes S, Salgado-Aguayo A, Santos-Mendoza T, Sevilla-Reyes E. The Role of the CX3CR1-CX3CL1 Axis in Respiratory Syncytial Virus Infection and the Triggered Immune Response. Int J Mol Sci. 2024;25(18). https://doi.org/10.3390/ijms25189800 . Additional Declarations No competing interests reported. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7454947","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":513334665,"identity":"2242dca4-1d20-4762-9d68-ca208679389a","order_by":0,"name":"Zhong Xu","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAsklEQVRIie3RMQrCQBCF4YSFrZ5s6xIPMVgoYtCrJARSeYgBwcoDxItYb1iwNAdI4xGSC4gpbYRJZzFfPX8xM0mi1F8y7at853COxYmtaLD1yjdBnGDjGxtz4kIYUPeoM6ADJSEdxpMg8RzjHsseW8PG3+6CxKWXsgf12HGwZiFJrAFlKJ6gUAgTZ7GejhVmJP46HXnkCr5pz7JdqIvTK/lwdO7cDqMk+ZLyvHmllFK/fQC3wzPTIpYrMgAAAABJRU5ErkJggg==","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":true,"prefix":"","firstName":"Zhong","middleName":"","lastName":"Xu","suffix":""},{"id":513334666,"identity":"5cfe8c1f-d548-4fa7-ad90-a7a559282f8d","order_by":1,"name":"Zipeng Li","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Zipeng","middleName":"","lastName":"Li","suffix":""},{"id":513334667,"identity":"87a2b74f-81f9-4ae1-a6d4-a5b8f41b7773","order_by":2,"name":"Mu Qiao","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Mu","middleName":"","lastName":"Qiao","suffix":""},{"id":513334668,"identity":"fdf3b0fd-f8a5-45d1-935d-e777ee140cd7","order_by":3,"name":"Jiawei Zhou","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Jiawei","middleName":"","lastName":"Zhou","suffix":""},{"id":513334669,"identity":"ee9b7f65-b342-4b87-b0f5-329a588fd8db","order_by":4,"name":"Yu Zhang","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Yu","middleName":"","lastName":"Zhang","suffix":""},{"id":513334670,"identity":"247f23d0-33bb-423d-924b-7f35daab9255","order_by":5,"name":"Yue Feng","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Yue","middleName":"","lastName":"Feng","suffix":""},{"id":513334671,"identity":"d6163a08-e08f-4b10-a658-cd0052fb9ff5","order_by":6,"name":"Hua Sun","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Hua","middleName":"","lastName":"Sun","suffix":""},{"id":513334672,"identity":"09bc17e5-7b6c-4c63-9bf2-fbda114f829e","order_by":7,"name":"Tong Chen","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Tong","middleName":"","lastName":"Chen","suffix":""},{"id":513334673,"identity":"595431fa-4da6-4234-992f-1577ab048e10","order_by":8,"name":"Dake Chen","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Dake","middleName":"","lastName":"Chen","suffix":""},{"id":513334674,"identity":"fe0399be-b100-45b1-9ea8-53c81da5c3ff","order_by":9,"name":"Favour Oluwapelumi Oyelami","email":"","orcid":"","institution":"The John Curtin School of Medical Research, Australian National University","correspondingAuthor":false,"prefix":"","firstName":"Favour","middleName":"Oluwapelumi","lastName":"Oyelami","suffix":""},{"id":513334675,"identity":"e1c98871-4649-48e0-9a74-f8f72dc1c370","order_by":10,"name":"Shuqi Mei","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Shuqi","middleName":"","lastName":"Mei","suffix":""},{"id":513334676,"identity":"92287d4e-b1d5-4205-9cbd-2919d1a8a59c","order_by":11,"name":"Junjing Wu","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Junjing","middleName":"","lastName":"Wu","suffix":""},{"id":513334677,"identity":"118e74d5-2d81-45a7-ba81-260fa95ec4db","order_by":12,"name":"Xianwen Peng","email":"","orcid":"","institution":"Hubei Provincial Academy of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Xianwen","middleName":"","lastName":"Peng","suffix":""}],"badges":[],"createdAt":"2025-08-25 14:53:20","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7454947/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7454947/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12864-025-12404-0","type":"published","date":"2025-12-18T15:57:29+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":91553197,"identity":"d2b7e13e-d1f3-4a66-9f4b-f00dda321484","added_by":"auto","created_at":"2025-09-17 16:28:44","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":365871,"visible":true,"origin":"","legend":"\u003cp\u003eGenetic diversity of the Xiangyang Black breed. (A) Heatmap of Fst distances between breeds. (B) Distribution of genomic inbreeding coefficients (F\u003csub\u003eROH\u003c/sub\u003e) across pig breeds.\u003c/p\u003e","description":"","filename":"image1.png","url":"https://assets-eu.researchsquare.com/files/rs-7454947/v1/b8d4ad92bf5c9e9d8dec017c.png"},{"id":91552294,"identity":"1aff66e1-e1b4-4ec6-b53f-764fc2e7a98b","added_by":"auto","created_at":"2025-09-17 16:12:44","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":693128,"visible":true,"origin":"","legend":"\u003cp\u003eGenetic relationships and population structure among Xiangyang Black and 14 other pig breeds. (A) Neighbor-joining tree constructed by an IBS matrix among 15 populations. (B) Principal component analysis of the first two principal components for 225 pigs. (C) ADMIXTURE analysis with four presumed ancestral groups (K = 4).\u003c/p\u003e","description":"","filename":"image2.png","url":"https://assets-eu.researchsquare.com/files/rs-7454947/v1/de54e88b4a02eb46a84833e9.png"},{"id":91552450,"identity":"7fb70988-c8cb-4da8-bac4-3c31d8f975d7","added_by":"auto","created_at":"2025-09-17 16:20:44","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":609901,"visible":true,"origin":"","legend":"\u003cp\u003eThe signature selection in XYB pigs and Western pigs. (A) Manhattan plot of selective sweeps by Fst in XYB pigs. (B) Manhattan plot of selective sweeps by θπ ratio (Western/XYB). (C) Manhattan plot of selective sweeps by XP-EHH in XYB pigs and Western pigs. The dashed line displays the threshold level of the top 5%.\u003c/p\u003e","description":"","filename":"image3.png","url":"https://assets-eu.researchsquare.com/files/rs-7454947/v1/d045fecfe3165d70cd0a7587.png"},{"id":91552297,"identity":"04b21738-1f7e-4513-8c34-ccceebe2ad34","added_by":"auto","created_at":"2025-09-17 16:12:44","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":425156,"visible":true,"origin":"","legend":"\u003cp\u003eVenn diagram showing the overlapping regions in the top 5% of Fst, θπ ratio and XP-EHH.\u003c/p\u003e","description":"","filename":"image4.png","url":"https://assets-eu.researchsquare.com/files/rs-7454947/v1/e0f41eef1117accc186bf3cf.png"},{"id":91552454,"identity":"8236b8f8-9f97-4b2e-a154-a3cbcfd5e51f","added_by":"auto","created_at":"2025-09-17 16:20:44","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":306345,"visible":true,"origin":"","legend":"\u003cp\u003eEnrichment analysis of candidate genes. (A) Significantly enriched GO terms. (B) Significantly enriched KEGG pathways. The size of each circle indicates the number of genes in a given pathway, and the color reflects the \u003cem\u003ep\u003c/em\u003e-value of each pathway.\u003c/p\u003e","description":"","filename":"image5.png","url":"https://assets-eu.researchsquare.com/files/rs-7454947/v1/3f6c1a21b025bc43690468e7.png"},{"id":98815117,"identity":"afaca2a5-df87-4f8a-b4f7-5f095d73b9b2","added_by":"auto","created_at":"2025-12-22 16:13:46","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3001684,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7454947/v1/f3c54132-6983-4a38-85b8-a391787cd885.pdf"},{"id":91552295,"identity":"a84b79a8-f3a3-4a4b-8979-a80919bd3918","added_by":"auto","created_at":"2025-09-17 16:12:44","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":219822,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryMaterial1.docx","url":"https://assets-eu.researchsquare.com/files/rs-7454947/v1/f34565322b8ba50bdb6796c6.docx"},{"id":91552451,"identity":"77193a3b-10fc-4a77-9439-f165d1229b59","added_by":"auto","created_at":"2025-09-17 16:20:44","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":295019,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementaryMaterial2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-7454947/v1/4c9e54a224c9c0b9fcfcfb81.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Analysis of the genetic structure and selection signature of Xiangyang Black pigs using whole-genome resequencing data","fulltext":[{"header":"Background","content":"\u003cp\u003e The diversity of local pig breeds is of strategic significance for enriching China's livestock industry and constitutes a key component of the agricultural economy. The domestication of wild boars, which began approximately 10,000 years ago, has led to the development of around 300 distinct pig breeds globally as a result of sustained natural and human-driven selection [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e]. Such prolonged selective pressure has not only modified phenotypic traits but also profoundly influenced genomic architecture, affecting variations in morphology, physiology, and behavior. Advances in sequencing technology, reductions in sequencing costs, and improvements in bioinformatics have enabled many studies to explore evolutionary selection, clarifying the genetic mechanisms of different morphologies, physiologies, and behaviors in pigs and providing new insights for their further improvement.\u003c/p\u003e\u003cp\u003eAdvances in sequencing technology and the concurrent reduction in associated costs have greatly promoted the application of whole-genome resequencing in studies of genetic diversity and selection signatures in pigs [\u003cspan additionalcitationids=\"CR3\" citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Genomic analyses have uncovered numerous candidate genes and markers associated with important economic traits, as well as adaptive and phenotypic characteristics [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. These results not only enhance our understanding of pig origin, domestication, and selective breeding history, but also offer valuable insights for future genetic improvement efforts.\u003c/p\u003e\u003cp\u003eXiangyang Black (XYB) represents a valuable indigenous pig breed resource in China, primarily distributed within the Xiangyang City region of Hubei Province. It has been raised for over 300 years and is known for its tender meat (intramuscular fat content\u0026thinsp;~\u0026thinsp;3.5%), early sexual maturity, and tolerance to harsh feeding conditions. However, with the large-scale introduction of Western commercial breeds, the XYB population has declined, and its genetic characteristics remain poorly understood. Moreover, there is currently insufficient evidence to prove that it is a unique genetic resource. Therefore, determining whether XYB represents a distinct genetic resource that is separate from other breeds in Hubei Province and the western region is of great significance for the protection of genetic resources and biodiversity.\u003c/p\u003e\u003cp\u003eIn this study, we integrated whole-genome resequencing data from XYB and 14 other pig breeds\u0026mdash;10 Chinese indigenous and four Western commercial\u0026mdash;to (1) evaluate the genetic diversity and inbreeding status of XYB, (2) clarify its genetic relationship with other Chinese and Western breeds, and (3) identify genomic regions and candidate genes under selection associated with its key phenotypic traits. Our findings aim to provide a scientific basis for the conservation, utilization, and genetic improvement of XYB.\u003c/p\u003e"},{"header":"Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\u003ch2\u003eSample collection and sequencing\u003c/h2\u003e\u003cp\u003eIn this study, ear tissue was collected from 59 Xiangyang blcak pigs, 10 Qingping pigs, and 10 Jianli pigs for high-throughput resequencing. Xiangyang Black pig comes from Xiangyang Wanfengyuan Ecological Agricultural Science and Technology Development Co., Ltd., the Qingping pig was sourced from Qingping Pig Breeding Farm, and Jianli pig was provided by Hubei Tianmu Livestock Co., Ltd. Genomic DNA was isolated from ear tissue samples employing the Qiagen DNeasy Tissue Kit (Qiagen, Germany), in accordance with a conventional phenol-chloroform extraction method. For each individual, paired-end sequencing libraries (read length: 2\u0026times;150 bp) were prepared and sequenced on an Illumina HiSeq 2000 platform, achieving an average coverage of approximately 11\u0026times; coverage. Whole-genome sequencing data from 146 additional individuals were obtained from publicly accessible databases. These datasets represented eight indigenous pig breeds from China, one Asian wild boar population, and three Western commercial breeds (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The analyzed data were sourced from the following BioProject entries: PRJNA213179[\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e], PRJNA488960[\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e], PRJNA524263[\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e], and PRJNA260763[\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. In total, this study included whole-genome sequences from a total of 225 pigs, covering 15 distinct populations.\u003c/p\u003e\u003c/div\u003e\n\u003ch3\u003eGenetic variation detection and annotation\u003c/h3\u003e\n\u003cp\u003eClean sequencing reads were aligned to the Sscrofa11.1 reference genome using BWA (v0.7.12) [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e] under default parameters, while sorted BAM files were produced with SAMtools (v1.9) [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. SNP calling was carried out using GATK (v4.1.4.1) [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e] via the \u0026ldquo;HaplotypeCaller\u0026rdquo; and \u0026ldquo;GenotypeGVCFs\u0026rdquo; modules for gVCF generation and joint-genotyping, respectively. Hard filtering was then applied based on the following criteria: QUAL\u0026thinsp;\u0026lt;\u0026thinsp;30.0, QD\u0026thinsp;\u0026lt;\u0026thinsp;2.0, FS\u0026thinsp;\u0026gt;\u0026thinsp;60.0, MQ\u0026thinsp;\u0026lt;\u0026thinsp;40.0, SOR\u0026thinsp;\u0026gt;\u0026thinsp;3.0, MQRankSum \u0026lt; -12.5, or ReadPosRankSum \u0026lt; -8.0, using the VariantFiltration function in GATK. The vcftools v0.1.15 [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e] was used to filter out SNP loci with an minor allele frequency less than 0.05 and a call rate less than 0.9. Finally, SNPs were annotated using SnpEff software (v4.3) [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e] based on the Ensembl database. Genotype imputation was conducted using the Beagle software package [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e].\u003c/p\u003e\n\u003ch3\u003eGenetic diversity analysis\u003c/h3\u003e\n\u003cp\u003eTo assess genomic variability, key diversity parameters\u0026mdash;including expected heterozygosity (H\u003csub\u003eE\u003c/sub\u003e), observed heterozygosity (H\u003csub\u003eO\u003c/sub\u003e), and nucleotide diversity (p\u003csub\u003ei\u003c/sub\u003e)\u0026mdash;were computed with PLINK v1.9 [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. The level of runs of homozygosity (ROH) were performed using the same software following a pipeline similar to that described in our previous publication [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]: a sliding window of 50 SNPs permitting one heterozygous and up to five missing calls per window; a minimum of 100 consecutive SNPs required to define an ROH; and a minimum physical length of 1 Mb to exclude regions likely reflecting strong linkage disequilibrium. The inbreeding coefficient (F\u003csub\u003eROH\u003c/sub\u003e) was derived as the combined length of all ROH segments divided by the total length of the autosomes covered by SNPs. Pairwise population differentiation (Fst) was computed using vcftools v0.1.15 [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e] and visualized as a heatmap using the \"corrplot\" package in R.\u003c/p\u003e\n\u003ch3\u003ePopulation structure analysis\u003c/h3\u003e\n\u003cp\u003ePrincipal component analysis (PCA) was carried out with GCTA v1.91.7 [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e] to reduce dimensionality, and the first three principal components were retained for further interpretation. Ancestral genetic structure and individual admixture proportions were inferred through the ADMIXTURE program (v1.3) [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. To elucidate genetic relationships among populations, a neighbor-joining tree (NJ) was built employing identity-by-state (IBS) genetic distances, computed with MEGA v5.0 [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e] and graphically represented using FigTree v1.4.3 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://tree.bio.ed.ac.uk/software/figtree/\u003c/span\u003e\u003cspan address=\"http://tree.bio.ed.ac.uk/software/figtree/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). Principal component analysis (PCA) was performed using GCTA v1.91.7 [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e] to reduce dimensionality. ADMIXTURE v1.3 [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e] was used to infer ancestral components.\u003c/p\u003e\n\u003ch3\u003eSelection signature detection\u003c/h3\u003e\n\u003cp\u003eSelection signatures in Xiangyang Black pig were detected by comparing with Western commercial breeds (LW, LR, DU) using three methods: population differentiation coefficient (Fst), polymorphism levels statistic (θπ) and cross-population extended haplotype homozygosity (XP-EHH). Fst and π ratio were calculated using a 100 kb sliding window with a 50 kb step size in VCFtools v0.1.15 [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. XP-EHH statistics were computed using selscan v1.3.0 [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. Regions with values in the top 5% of at least two methods were considered significant selected regions.\u003c/p\u003e\u003cdiv id=\"Sec8\" class=\"Section2\"\u003e\u003ch2\u003eFunctional annotation and enrichment analysis of candidate genes\u003c/h2\u003e\u003cp\u003eCandidate genes under selection were identified based on the Ensembl database. Genes within significant selected regions were annotated using the Ensembl database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted with DAVID 6.8. Terms with a p-value below 0.05 were deemed statistically significant and included in the results.\u003c/p\u003e\u003c/div\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec10\" class=\"Section2\"\u003e\u003ch2\u003eSequencing data and SNP characteristics\u003c/h2\u003e\u003cp\u003eTo gain comprehensive genomic insights, we conducted whole-genome resequencing of 59 Xiangyang Black pigs, 10 Qingping pigs, and 10 Jianli pigs, achieving an average coverage of 11\u0026times;. Furthermore, to contextualize the genetic diversity and population structure of Xiangyang Black pigs within a broader genetic landscape, we integrated publicly available sequencing data from 146 additional individuals, encompassing eight Chinese indigenous breeds, one Asian wild boar population, and three European commercial breeds (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). We then performed variant calling on these 225 pigs and identified 20,479,203 SNPs. Generally speaking, SNPs are evenly distributed across each chromosome, except for some sites at the telomeres of the chromosomes (Figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e). Of these, 23% were identified as novel variants, since they were not present in the dbSNP pig database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://ftp.ncbi.nih.gov/snp/organisms/archive/pig_9823/VCF/\u003c/span\u003e\u003cspan address=\"https://ftp.ncbi.nih.gov/snp/organisms/archive/pig_9823/VCF/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). In line with earlier investigations, the majority of SNPs were located in intergenic regions and introns\u0026mdash;accounting for 51.9% and 43.7%, respectively\u0026mdash;while only 2.6% were located in exonic regions, comprising 79,448 synonymous mutations and 30,938 missense mutations.\u003c/p\u003e\u003cp\u003e\u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e\u003ccaption language=\"En\"\u003e\u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e\u003cdiv class=\"CaptionContent\"\u003e\u003cp\u003eSamples and genetic diversity of Xiangyang Black and other pigs\u003c/p\u003e\u003c/div\u003e\u003c/caption\u003e\u003ccolgroup cols=\"7\"\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e\u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e\u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e\u003cthead\u003e\u003ctr\u003e\u003cth align=\"left\" colname=\"c1\"\u003e\u003cp\u003ePopulation\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c2\"\u003e\u003cp\u003eAbbreviation\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c3\"\u003e\u003cp\u003eSize\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c4\"\u003e\u003cp\u003eP\u003csub\u003eN\u003c/sub\u003e\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c5\"\u003e\u003cp\u003eH\u003csub\u003eO\u003c/sub\u003e\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c6\"\u003e\u003cp\u003eH\u003csub\u003eE\u003c/sub\u003e\u003c/p\u003e\u003c/th\u003e\u003cth align=\"left\" colname=\"c7\"\u003e\u003cp\u003epi\u003c/p\u003e\u003c/th\u003e\u003c/tr\u003e\u003c/thead\u003e\u003ctbody\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eXiangyang Blcak\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eXYB\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e59\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.96\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.38\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.36\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.35\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eQingping\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eQP\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.61\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.29\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.33\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.20\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eJianli\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eJL\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.51\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.3\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.33\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.17\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eTongcheng\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eTC\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e10\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.60\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.31\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.33\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.20\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eAsian Wild Boar\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eAWB\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e15\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.74\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.27\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.33\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.25\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eErhualian\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eEHL\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e5\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.52\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.37\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.35\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.19\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eJinhua\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eJH\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e24\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.54\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.26\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.31\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.17\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eLaiwu\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLWU\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.68\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.36\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.34\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.23\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eLuchuan\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLC\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.49\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.39\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.35\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.17\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eBamaxiang\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eBMX\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e6\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.61\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.38\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.35\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.21\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eAnqing Six-End-White\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eASW\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e18\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.97\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.31\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.35\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.34\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eWannan Blcak\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eWNH\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e20\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.68\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.26\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.30\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.20\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eDuroc\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eDU\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e8\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.62\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.34\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.34\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.22\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eLandrace\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLR\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e13\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.81\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.31\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.35\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.28\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003ctr\u003e\u003ctd align=\"left\" colname=\"c1\"\u003e\u003cp\u003eLarge white\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"left\" colname=\"c2\"\u003e\u003cp\u003eLW\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c3\"\u003e\u003cp\u003e15\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c4\"\u003e\u003cp\u003e0.83\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e\u003cp\u003e0.32\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e\u003cp\u003e0.35\u003c/p\u003e\u003c/td\u003e\u003ctd align=\"char\" char=\".\" colname=\"c7\"\u003e\u003cp\u003e0.29\u003c/p\u003e\u003c/td\u003e\u003c/tr\u003e\u003c/tbody\u003e\u003c/colgroup\u003e\u003c/table\u003e\u003c/div\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e\u003ch2\u003eGenetic diversity of the Xiangyang Black pig\u003c/h2\u003e\u003cp\u003eOf the 15 breeds, Chinese indigenous breeds generally showed higher genetic diversity than Western commercial breeds (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). XYB pigs exhibited high P\u003csub\u003eN (0.96),\u003c/sub\u003e H\u003csub\u003eO\u003c/sub\u003e (0.38), and pi (0.35), indicating a relatively healthy population structure. To evaluate genetic diversity, pairwise genetic differentiation was quantified using the fixation index (Fst), as summarized in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA. The Fst values between XYB pigs and commercial lean-type breeds ranged from 0.20 to 0.27, which were comparable to those between XYB and other Chinese indigenous pig populations (ranging from 0.10 to 0.30), indicating no significant difference in the levels of genetic distinction across these groups. Pairwise Fst analysis showed that XYB pigs had the lowest genetic differentiation from ASW pigs (Fst\u0026thinsp;=\u0026thinsp;0.10) and the highest from JH pigs (Fst\u0026thinsp;=\u0026thinsp;0.30) (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA). To assess the genomic inbreeding level of XYB, the ROH was calculated for each pig breed. The average ROH-based inbreeding coefficient (F\u003csub\u003eROH\u003c/sub\u003e) of XYB ranged from 0.001 to 0.090, indicating a low level of inbreeding and high genetic diversity (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec12\" class=\"Section2\"\u003e\u003ch2\u003ePopulation Structure\u003c/h2\u003e\u003cp\u003eTo evaluate the evolutionary relationships across the 15 pig populations, a NJ tree was generated using IBS distances for all individuals (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eA). The phylogenetic reconstruction showed that all XYB individuals were clustered together and formed an independent branch, indicating that XYB can serve as an independent resource population with unique genetic characteristics. The NJ tree also revealed a pronounced phylogenetic split between Chinese indigenous breeds and Western commercial breeds (DU, LR, LW). Interestingly, XYB was positioned intermediately between these two groups, suggesting that it is closer to Western breeds than to other Chinese indigenous breeds. The PCA results supported this pattern, with PC1 (60.5% contribution rate) separating the Chinese and Western breeds, and XYB pigs clustered in an intermediate position between these two distinct groups (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB). To further explore the admixture history and ancestral contributions across populations, we conducted ADMIXTURE analysis under a range of hypothetical ancestral population numbers (K\u0026thinsp;=\u0026thinsp;2 to 5) (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eC, Figure \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e). At a K of 2, XYB contained ancestral components from both Western breeds and Chinese indigenous pig breeds. At a K of 4, XYB was independently separated and formed a unique genetic structure. Therefore, the results of the PCA and the ADMIXTURE analysis revealed the clustering trends of the tested populations, highlighting that XYB is a unique population.\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec13\" class=\"Section2\"\u003e\u003ch2\u003eSelection signature detection of the Xiangyang Black pig population\u003c/h2\u003e\u003cp\u003eTo uncover the genomic regions under selection in XYB pigs during their adaptation, we executed a comparative population genomic analysis between XYB and Western commercial breeds. Three complementary methods\u0026mdash;Fst, θπ, and XP-EHH\u0026mdash;were employed to identify putative selection signatures in the XYB genome. The distribution of candidate regions identified through various methods is illustrated in Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e. Based on their respective top 5% thresholds, Fst (\u0026ge;\u0026thinsp;0.444; Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e), π ratio (\u0026ge;\u0026thinsp;1.095; Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e), and XP-EHH (\u0026ge;\u0026thinsp;0.185; Table S3) each identified 2263 windows. To improve reliability and minimize false positives, we focused on regions that were simultaneously identified by at least two of these approaches. This integrative strategy yielded 1080 high-confidence candidate regions (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Table S4).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e\u003cdiv id=\"Sec14\" class=\"Section2\"\u003e\u003ch2\u003eFunctional enrichment analysis of candidate genes\u003c/h2\u003e\u003cp\u003eA total of 951 genes were located within the candidate selective sweep regions (Table S5). Functional enrichment identified 30 GO terms (Table S6) and 12 KEGG pathways (Table S7) were significantly enriched (FDR\u0026thinsp;\u0026lt;\u0026thinsp;0.05), including response to endogenous stimulus (GO:0009719) and anatomical structure development (GO:0048856), as well as the calcium signaling pathway (ssc04020), and the cAMP signaling pathway (ssc04024) (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e).\u003c/p\u003e\u003cp\u003e\u003c/p\u003e\u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eAlthough XYB pigs and other pig populations in nearby areas have different morphologies, they share similar characteristics, such as high reproductive capacity, strong disease resistance, high fat deposition rate, and tolerance to coarse feed. To explore XYB\u0026rsquo;s unique genetic structure and genetic relationship with Chinese and Western breeds, we conducted analyses of genetic distance, genetic differentiation, and population structure for these groups to further clarify the rationality of XYB as an independent genetic resource. From an NJ tree based on the genetic distance between individuals and the PCA results, all XYB individuals were clustered together, while the other groups were relatively independent. From the perspective of the population structure of ADMIXTURE, the XYB pig population became independent very early (K\u0026thinsp;=\u0026thinsp;4). This indicates that XYB differs from Western breeds and other local breeds due to its unique genetic structure and confirms the rationality of the breed as a unique genetic resource at the molecular level.\u003c/p\u003e\u003cp\u003eXYB exhibited the highest P\u003csub\u003eN\u003c/sub\u003e, H\u003csub\u003eO\u003c/sub\u003e, H\u003csub\u003eE\u003c/sub\u003e, and pi among the 15 breeds, indicating that it has higher genetic diversity and better breed conservation effectiveness. In addition, we used ROH to calculate the inbreeding coefficient. Compared with other pig breeds, the coefficient of XYB was generally lower (0.001\u0026ndash;0.090), consistent with the finding that XYB pigs have high genetic diversity.\u003c/p\u003e\u003cp\u003eAnalyzing the selection characteristics of the genome can provide a deeper understanding of the genetic mechanism of adaptive phenotypes in pigs and identify important candidate genes related to excellent economic traits. In this paper, we focused on the selection of signature regions containing important candidate genes associated with specific traits related to livestock breeding. Several candidate genes related to meat quality traits were identified, including \u003cem\u003eFABP2\u003c/em\u003e, which encodes intestinal fatty acid binding protein 2 and has been studied in various livestock species for its potential influence on meat quality traits, particularly fatty acid composition and related characteristics [\u003cspan additionalcitationids=\"CR23\" citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e]; \u003cem\u003ePPARG\u003c/em\u003e, which is one of the differentiation markers in preadipocyte differentiation that drives the conversion of preadipocytes to mature adipocytes by activating transcription factors such as C/EBPα and plays an important role in adipose deposition [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e, \u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]; \u003cem\u003eCIDEC\u003c/em\u003e gene, which is involved in lipid droplet formation in adipocytes and has been shown in both pigs [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e] and cattle [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e] to be more highly expressed in the muscles of animals with high intramuscular fat (IMF) content; and \u003cem\u003eTHRSP\u003c/em\u003e, which plays an important role in adipogenesis. For instance, through ATAC-seq and RNA-seq analyses, Xu et al. identified \u003cem\u003eTHRSP\u003c/em\u003e as a key gene influencing intramuscular fat content traits in Xidu Black pigs [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]; while transcriptome and metabolome analyses by Hou et al. confirmed its role in Beijing Black pigs [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. XYB pigs have good meat quality, with an IMF content of over 3.5%, which may be related to these genes.\u003c/p\u003e\u003cp\u003eCandidate genes identified for reproduction included \u003cem\u003eGNRH1\u003c/em\u003e, which encodes a gonadotropin-releasing hormone and directly regulates the secretion of luteinizing and follicle-stimulating hormones in the pituitary gland, thereby influencing the estrous cycle and ovulation frequency of sows [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e], and \u003cem\u003eCENPE\u003c/em\u003e, a centromeric kinesin, which affects gonadotropin secretion by regulating the hypothalamic\u0026ndash;pituitary\u0026ndash;gonadal axis. Studies using transcriptome-wide association study analysis have revealed that the expression of \u003cem\u003eCENPE\u003c/em\u003e is strongly associated with mean litter weight and influences embryo implantation efficiency [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. Also identified in this category was \u003cem\u003eCCDC112\u003c/em\u003e, which is crucial for male fertility [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e], is associated with reproductive traits in pigs [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e], and has been reported to be a stage-specific marker in spermatocytes of humans [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e] and buffalo [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e].\u003c/p\u003e\u003cp\u003eIn terms of disease resistance, genes identified included \u003cem\u003eCCL17\u003c/em\u003e, \u003cem\u003eCCL22\u003c/em\u003e, and \u003cem\u003eCX3CL1\u003c/em\u003e, which belong to the chemokine family and are responsible for recruiting monocytes and T cells to sites of infection. \u003cem\u003eCCL17\u003c/em\u003e is a chemokine produced by epithelial cells and participates in the immune response within the mesenteric lymph nodes of pigs infected with \u003cem\u003eAscaris suum\u003c/em\u003e [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e]. Studies have shown that \u003cem\u003eCCL22\u003c/em\u003e is associated with the inflammatory responses involved in the development of asthma in Meishan pigs [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. Finally, \u003cem\u003eCX3CL1\u003c/em\u003e is the only member of the CX3C chemokine subfamily and plays a crucial role in the immune response to respiratory syncytial virus infection [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e]. We speculate that these genes may be associated with XYB pigs\u0026rsquo; adaptability to harsh environments.\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eThis study systematically analyzed the genomic characteristics of XYB and 14 other Chinese and Western pig breeds. XYB pigs were found to exhibit high genetic diversity, a unique population structure, and strong selection signatures associated with meat quality, disease resistance, and reproduction. The candidate genes identified provide insights into the genetic basis of XYB\u0026rsquo;s phenotypic traits and offer practical markers for breeding and conservation. These findings contribute to the understanding of pig adaptive evolution and support the sustainable utilization of XYB pig germplasm resources.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eSNP Single nucleotide polymorphism\u003c/p\u003e\u003cp\u003eHe Expected heterozygosity\u003c/p\u003e\u003cp\u003eHo Observed heterozygosity\u003c/p\u003e\u003cp\u003eIBS Identical-by-state\u003c/p\u003e\u003cp\u003eNJ Neighbor-joining\u003c/p\u003e\u003cp\u003ePCA Principal component analysis\u003c/p\u003e\u003cp\u003eROH Runs of homozygosity\u003c/p\u003e\u003cp\u003eGO Gene Ontology\u003c/p\u003e\u003cp\u003eKEGG Kyoto Encyclopedia of Genes and Genomes\u003c/p\u003e\u003cp\u003eXP-EHH Cross-population extended haplotype homozygosity\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe are grateful to the global scientific community for generating and sharing publicly available whole-genome sequencing data from pigs, which were instrumental for this study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eXWP, SQM and JJW designed the study. ZX, ZPL, JWZ, YZ and MQ performed the data collection. ZX performed the analyses under the assistance and guidance of HS, YF, TC, DKC and FOO. ZX drafted the manuscript. All authors read and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis research was funded by the Major Program (JD) of Hubei Province (2023BAA029), National Key R\u0026amp;D Program of China (2021YFD1301105), Hubei Province Science and Technology Innovation Team Project, the Innovation Team of the Hubei Agricultural Science and Technology Innovation Center (2024-620-000-001-014), National Pig Industry Technology System (CARS-35).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData Availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe raw sequencing reads generated for Xiangyang Black, Qingping, and Jianli pigs in this study have been deposited in the NCBI Sequence Read Archive under BioProject accession number PRJNA1310513. Additionally, publicly available sequencing datasets were retrieved from the NCBI SRA under the following BioProject accessions: PRJNA488960, PRJNA524263, PRJNA213179, and PRJNA260763.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe animal study was reviewed and approved by the Institutional Animal Care and Use Committee of the Hubei Academy of Agricultural Sciences (Permit Number: 36/2016). All procedures involving pigs were conducted in strict compliance with the ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) version 2.0. The ear tissue samples of Xiangyang Black pig, Qingping pig, and Jianli pig were provided by Xiangyang Wanfengyuan Ecological Agricultural Science and Technology Development Co., Ltd., Qingping Pig Breeding Farm, and Hubei Tianmu Livestock Co., Ltd. respectively, which authorized us to use the samples for research purposes. No animals were euthanized or sacrificed in this study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis section is not applicable to this study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflict of Interest\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eRischkowsky B, Pilling D, Commission on Genetic Resources for Food and Agriculture. The state of the world's animal genetic resources for food and agriculture. Rome: Commission on Genetic Resources for Food and Agriculture, Food and Agriculture Organization of the United Nations; 2007.\u003c/span\u003e\u003c/li\u003e\u003cli\u003e\u003cspan\u003eHuang M, Zhang H, Wu ZP, Wang XP, Li DS, Liu SJ, et al. Whole-genome resequencing reveals genetic structure and introgression in Pudong White pigs. 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The Role of the CX3CR1-CX3CL1 Axis in Respiratory Syncytial Virus Infection and the Triggered Immune Response. Int J Mol Sci. 2024;25(18). \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3390/ijms25189800\u003c/span\u003e\u003cspan address=\"10.3390/ijms25189800\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"Xiangyang Black pig, whole-genome resequencing, genetic diversity, population structure, selection signature","lastPublishedDoi":"10.21203/rs.3.rs-7454947/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7454947/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e\u003cp\u003eXiangyang Black (XYB) is a valuable indigenous pig breed from Hubei Province, China, renowned for its excellent meat quality, strong disease resistance, and adaptability to local environments. To explore the genetic diversity, population structure, and selection signatures of XYB in the context of Chinese and Western pig breeds, we performed whole-genome resequencing on 15 pig breeds, involving 225 individuals.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e\u003cp\u003eAfter quality control, 20,479,203 high-quality single-nucleotide polymorphisms (SNPs) were retained for subsequent analysis. Genetic diversity analysis revealed that XYB exhibited relatively high genetic diversity (Ho\u0026thinsp;=\u0026thinsp;0.38, pi\u0026thinsp;=\u0026thinsp;0.35) and a low inbreeding coefficient (F\u003csub\u003eROH\u003c/sub\u003e = 0.001\u0026ndash;0.090), indicating its strong potential for genetic improvement and conservation. Population structure analyses\u0026mdash;including neighbor-joining tree, principal component analysis, and ADMIXTURE\u0026mdash;revealed a distinct genetic structure and verified the rationality of XYB\u0026rsquo;s status as a unique genetic resource at the molecular level. Selection signature detection using three complementary methods (Fst, θπ ratio, and XP-EHH) identified 1080 significant selected regions and 951 candidate genes in XYB compared with Western breeds. Functional annotation showed that these genes were enriched in pathways related to meat quality (e.g., \u003cem\u003eFABP2\u003c/em\u003e, \u003cem\u003ePPARG\u003c/em\u003e, \u003cem\u003eC/EBPα\u003c/em\u003e, and \u003cem\u003eTHRSP\u003c/em\u003e), reproduction (e.g., \u003cem\u003eGNRH1\u003c/em\u003e, \u003cem\u003eCENPE\u003c/em\u003e, and \u003cem\u003eCCDC112\u003c/em\u003e), and disease resistance (e.g., \u003cem\u003eCCL17\u003c/em\u003e, \u003cem\u003eCCL22\u003c/em\u003e, and \u003cem\u003eCX3CL1\u003c/em\u003e).\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e\u003cp\u003eOur results provide insights into the genetic basis of phenotypic traits in XYB pigs and offer a theoretical foundation for their conservation, breeding, and genetic improvement.\u003c/p\u003e","manuscriptTitle":"Analysis of the genetic structure and selection signature of Xiangyang Black pigs using whole-genome resequencing data","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-17 16:12:39","doi":"10.21203/rs.3.rs-7454947/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-08T10:33:55+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-08T07:36:47+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-05T15:55:58+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-03T08:49:25+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-24T01:58:43+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"324491025089386142780187682607986761217","date":"2025-09-23T23:59:18+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"216979202195350470585297697168638473402","date":"2025-09-23T17:22:30+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"4903176390765514277782785648361188864","date":"2025-09-23T11:34:03+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"132427240096464679030302046790070569207","date":"2025-09-11T00:12:22+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-09-10T11:19:41+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-08-29T05:46:11+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-08-28T09:22:06+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Genomics","date":"2025-08-28T09:17:29+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-genomics","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"gics","sideBox":"Learn more about [BMC Genomics](http://bmcgenomics.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/gics","title":"BMC Genomics","twitterHandle":"#BMCGenomics","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"aafe4587-187d-41d6-8e2e-dc6a0d154a30","owner":[],"postedDate":"September 17th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-12-22T16:10:14+00:00","versionOfRecord":{"articleIdentity":"rs-7454947","link":"https://doi.org/10.1186/s12864-025-12404-0","journal":{"identity":"bmc-genomics","isVorOnly":false,"title":"BMC Genomics"},"publishedOn":"2025-12-18 15:57:29","publishedOnDateReadable":"December 18th, 2025"},"versionCreatedAt":"2025-09-17 16:12:39","video":"","vorDoi":"10.1186/s12864-025-12404-0","vorDoiUrl":"https://doi.org/10.1186/s12864-025-12404-0","workflowStages":[]},"version":"v1","identity":"rs-7454947","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7454947","identity":"rs-7454947","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}