Hao Sun

In this study, we conducted a population genomic survey of two local pig breeds in Jilin Province, Dongliao Black (DLB) and Jilin Spotted (JLS) pigs, and evaluated their genetic relationships with 23 Northeastern Asian pig breeds, comprising 46 wild boars, 211 Chinese local pigs, 69 Russian pigs, 13 Korean pigs, and 107 commercial pigs. The results will be helpful for the conservation and utilization of these rare germplasm resources. The minor allele frequency of DLB and JLS pigs was 0.24 and 0.22, respectively. Both DLB and JLS pigs exhibited higher observed heterozygosity than expected values. Moreover, JLS pigs displayed the lowest excess of homozygosity inbreeding coefficient (−0.12 ± 0.07) among all studied populations. Additionally, population structure analyses indicated that DLB and JLS pigs possess admixed ancestries intermediate between Chinese and Western pigs, with DLB being closely related to Min pigs and both breeds showing admixture signals with neighboring Northeastern Chinese breeds, reflecting their distinct hybrid histories. Furthermore, 16 and 19 genes were identified as putative candidate genes in DLB and JLS pigs using Fst analyses, respectively. All these findings are consistent with a history of crossbreeding and with low levels of inbreeding in DLB and JLS pig populations. Additionally, it is hypothesized that DLB and JLS pig breeds may carry putative candidate genes during their breeding programs, which are associated with meat quality, reproduction, production, immunity, and environmental adaptation. Therefore, strengthening conservation and promotion efforts for DLB and JLS pigs is of great significance.

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

The Jishen Black pig is a synthetic breed incorporating the genetic backgrounds of Chinese indigenous pigs and Western lean-type pigs. The objective of this study was to characterize phenotypic variation, estimate genetic parameters, and identify genomic loci associated with rib number (NR) and the total number of thoracolumbar vertebrae (NTLV) in Jishen Black pigs. NR, NTLV, and lumbar vertebra number (NLV) were measured in 389 pigs, and genotyping was performed using a 70K SNP chip. Genetic parameters were estimated using HIBLUP, and genome-wide association studies (GWAS) were conducted using the MLM and BLINK models in GAPIT v3.0. The mean values of NR, NTLV, and NLV were 14.88, 20.94, and 6.05, respectively, and their heritability estimates were 0.568, 0.493, and 0.140, respectively. GWAS identified a shared major association peak for NR and NTLV on SSC7 at 91.19–98.15 Mb, centered on VRTN and the adjacent ABCD4-LTBP2-AREL1-PGF linkage region, among which the loci at 96.12 Mb, 96.56 Mb and 97.79 Mb are NR-specific loci. Additional signals included MIB1 on SSC6 and MMRN2 on SSC14 for NTLV, together with NR-specific loci on SSC7 at 111.59 Mb and on SSC8. Database annotation indicated that several significant SNPs overlapped with records for rib number, carcass length, loin muscle area, backfat thickness, or teat number. This study identifies major genomic regions associated with vertebral-number traits in Jishen Black pigs and expands current knowledge of their genetic basis.

Background: Reproduction traits constitute the primary objective of porcine genetic improvement programs, with litter size being the principal determinant of herd reproduction output. Relative to the intensively selected Large White line, as a breed derived from Large White (LW) and Beijing Black (BJB) pigs, Jishen Black (JSB) pigs exhibit markedly lower litter size, indicating substantial potential for genetic improvement. Results: Whole-genome resequencing data were obtained from 110 individuals of six pig populations differed in litter size: a Large White line with high litter size (> 16, LWH), cryopreserved Large White samples from 1977 (LW1977), dam-selected (LWD) and sire-selected (LWS) lines derived from LW1977, Berkshire (BKS), and Jishen Black pigs (JSB). Principal component analysis (PCA) captured clear population genetic structure along PC2, with the observed distribution pattern descriptively coinciding with litter size variation across populations, though such an association was not statistically verified. A composite selection-signature scan that integrated Fst , π-ratio, and XP-EHH was performed between multiple population groups. Candidate signals were filtered by excluding those also detected in a control comparison (Jishen Black vs. Berkshire) that showed minimal litter‑size difference, to screen selection signatures with potential relevance to reproductive trait differentiation at the population level. Twelve genes were identified as putative candidate genes for litter size, including PEX14 , CDK15 , KCNQ1 , SPAG17 , TTF2 , CD101 , CASQ2 , VANGL1 , ARID5B , KLHL32 , EML1 , and NAV1 . Functional enrichment analysis indicated that these genes significantly over-represented in microtubule-related biological processes. Among them, KCNQ1 was consistently detected by all methods and comparison groups. Further analysis of KCNQ1 revealed multiple SNPs with significant allele-frequency differentiation among populations; notably, two intronic variants (chr2:A1,861,604G and chr2:A1,867,076G) showed population-specific allele frequency patterns that descriptively aligned with the stratification of litter size performance. Conclusions: By comprehensively dissecting population genomic differentiation among multi-breed populations divergent in litter-size performance, this study implemented established a feasible framework for screening candidate loci associated with porcine prolificacy at the population level, expanded the gene list with suggestive selection signatures, and provided potential molecular markers requiring further independent cohort validation and functional verification to support future genetic improvement in swine reproduction efficiency.

Junmu No.1 is a commercially important Chinese pig breed, yet stable in vitro models for investigating its muscle development mechanisms and genetic regulation remain lacking; this study aimed to establish an immortalized porcine satellite cell line from Junmu No.1 pigs to address this gap. Primary porcine satellite cells (PSCs) were isolated from a 2-day-old Junmu No.1 piglet and immortalized via lentiviral transduction using the pHAGE-EF1α-eGFP-SV40LT-BleoR vector. The resulting cell line (imPSC-JM) was characterized for morphology, satellite cell marker expression, karyotype stability, myogenic differentiation capacity, and long-term proliferative potential, and RNA sequencing combined with Gene Set Enrichment Analysis (GSEA) was performed to assess transcriptomic fidelity relative to primary PSCs. The imPSC-JM line retained characteristic spindle-shaped satellite cell morphology, consistently expressed PAX7, maintained a normal diploid karyotype (2n = 38, XY), and showed stable SV40 large T antigen expression, enabling sustained proliferation exceeding 100 cumulative population doublings while preserving myogenic differentiation and the formation of multinucleated myotubes expressing Desmin, MYHC, and DMD. Transcriptomic profiles were highly concordant with primary PSCs (Pearson r ≥ 0.95; R² = 0.9188; 83.8% of expressed genes unchanged), with key satellite-cell and myogenic regulator genes (PAX7, MYOD1, MYF5, MYOG, MYF6) unaltered, while GSEA revealed upregulation of autophagy and inflammatory signaling and downregulation of ribosome biogenesis. The imPSC-JM line thus provides a reliable experimental platform with high transcriptomic fidelity for studying muscle development and genetic regulation in Junmu No.1 pigs.

As an important reproductive trait, teat number plays a vital role in the pork industry, which is related to the ability of sows to host more piglets. However, the genetic mechanism of the teat number in pigs is still not very clear. We collected phenotype data, including the total teat number (TTN), left teat number (LTN), and right teat number (RTN), from 300 Jishen Black (JSB) sows and performed genotyping using a porcine SNP 50K panel. Most JSB sows exhibited 14, 15, or 16 TTN (259, 86%). Only 41 pigs (14%) had TTN values outside this range. Moreover, the LTN and TTN exhibited approximate frequency distribution in the studied population. Seven was the most common LTN and RTN in JSB sows, accounting for 181 (60%) and 173 (57%), respectively. Additionally, these traits exhibited low-to-medium heritability (0.14–0.22). Using the BLINK and FarmCPU models, three, six, and three key loci were identified in the GWAS of TTN, LTN, and RTN, respectively. Additionally, five key genes were detected to play vital roles in teat number traits, including ME1, SCN8A, EVC, UBC, and PDE4D. Our research provided efficient molecular markers and new insights into further improvement and understanding for teat number traits in Jishen Black pigs.

The Body Mass Index (BMI), integrating body weight and length, is a widely used metric for obesity assessment in humans. As pigs serve as crucial biomedical models, the application of BMI in swine and its genetic basis remain poorly explored. This study aimed to investigate the genetic architecture of pig BMI and compare two carcass-based BMI metrics (BMI-S and BMI-O) for breeding applicability. A total of 439 Landrace × Yorkshire crossbred pigs were genotyped with a 50 K SNP chip; heritability was estimated via a mixed linear model, and genome-wide association study (GWAS) was performed using the BLINK model. BMI-S and BMI-O exhibited moderate-to-high heritability of 0.55 and 0.47, respectively, with 17 genome-wide significant SNPs detected—including the top associated SNP rs81382440 on chromosome 4 and rs80898583 on chromosome 7. Key candidate genes (GPHN, ADAM33, KCNH8, PDCD4) and 5 SNP-trait associations validated in PigQTLdb were linked to lipid/energy metabolism and muscle development. Carcass-based BMI improved phenotypic accuracy, and our findings provide core genetic markers and a theoretical basis for molecular breeding of pig body conformation and lipid deposition traits.

Dorper sheep (DOR) are a commercially important mutton breed renowned for their high growth rate, favorable carcass composition, environmental adaptability, and natural wool shedding. In China, they are widely utilized as terminal sires to enhance growth and carcass yield in local breeds. To elucidate the genetic basis of these traits, we sequenced the genomes of 20 DOR and integrated the data with whole-genome sequences from 73 individuals representing four Chinese indigenous breeds. Analyses of genetic diversity, inbreeding coefficients, and population structure revealed reduced genomic diversity, elevated inbreeding levels, and clear genetic separation for DOR from other indigenous breeds. Selective sweep scans using F_ST, pi, and XP-EHH identified candidate genes involved in five major trait categories: growth performance and development (COL2A1, DAB2IP, EPYC, TSPAN18, WNT1, CTPS1, FBXW7, INSR, S100A6, SOCS2), energy metabolism (ACSS3, ADGRE3, CPT2, GCGR, PRKAA1), fat deposition and adipocyte differentiation (EHBP1, FOXP1, KLF12, PDGFD, RALGAPA2), immune response (CXCR6, IL17RB, NFKBIZ, TMEM154), and wool traits (CERS4, MITF). These results will provide novel insights into the genomic architecture of economically important traits in DOR and support their genetic improvement through informed crossbreeding with Chinese local breeds.

The regulation of gene expression is influenced by multiple factors, including species origin, tissue specificity, developmental stage, and sex differences. Therefore, gene expression sequencing data obtained from various tissues of different species at different time points are of immense significance for achieving a comprehensive and clear understanding of gene functions.Numerous pig breeds exist globally. In this report, the focus is on the Junmu No.1 White pig (Figure 1). It is a hybrid of Belgian Seghershybrid boars and Chinese Sanjiang hybrid sows, with strong artificial selection for growth traits. The Junmu No.1 White pig is primarily utilized as a terminal sire breed, selected specifically for superior growth rate and enhanced feed conversion efficiency (Bai et al., 2017).Generally speaking, sense of smell is closely related to its appetite, and appetite also determines the amount of feed intake, which further affects the animal's growth rate and the farm's economic efficiency. Meanwhile, there is limited information available on RNA-seq of olfactory tissues in pigs, despite a single recent RNA-seq survey of porcine olfactory epithelium (Yang et al., 2024) and its conspicuous absence from the Pig RNA Atlas, comprehensive transcriptomic data for this tissue remain markedly scarce, underscoring the need for the present multi-tissue dataset. Therefore, we collected RNA sequencing to profile the transcriptomes of 13 distinct tissues from growing Junmu No. 1 White pigs, with particular focus on olfactory receptor (OR) genes. By examining the relevant databases, we discovered that, for most available transcriptome data, there are few instances where so many tissues from a single pig breed have been measured simultaneously. As a result, the data we obtained is highly valuable and rich in information, and we present this data to offer valuable insights for other researchers to investigate the functions of pig genes.The Junmu No.1 White boars were obtained from the pig farm of Agriculture Experimental Base of Jilin University (Changchun, China). Three nursery finished healthy male piglets 70 days old with an average weight of 30 kg were randomly selected. The Spleen, ileum, brain, fat, kidney, duodenum, lung, heart, muscle, jejunum, liver, olfactory epithelium and testis tissues were collected. A small section was taken from a regular position of each tissue for each individual. Total RNA was extracted using a commercial kit (Tiangen), and sequencing was performed by Novogene Biotech (Beijing, China) using the Illumina Genome Analyzer platform.The FASTP (Chen et al., 2018) software was used to perform quality control. The clean reads were aligned to the pig reference genome (Sus scrofa 11.1) using HISAT2 (Kim et al., 2019) with default parameters. Then SAM files are converted to BAM files and sorted using the Sortsam command by GATK (Van der Auwera et al., 2013). The StringTie software (Shumate et al., 2022) was used for transcript assembly and quantification. The GFFCompare software (Pertea & Pertea, 2020) was used to annotate the transcripts. Principal component analysis (PCA) was performed using DESeq2 (Love et al., 2014).After filtering, the average quality value of the data was significantly improved, and low-quality reads and splice sequences were effectively removed. A total of 309.8 Gb clean data was obtained. Filtered data quality values (Q30) can reach an average of 93.32%. It shows that the quality of the data has been significantly improved, providing a high-quality data base for subsequent analyses. The clean reads were aligned to the pig reference genome using HISAT2, and the results showed that the overall alignment rate was 94.61%. The results showed that most of the reads could be successfully aligned to the reference genome, indicating that the alignment process was accurate and efficient. The sequence data were deposited in the NCBI Sequence Read Achieve (SRA) and the accession number of the sequencing data was PRJNA664265. The sequencing information of each sample was shown in Table S1.After assembly and quantification of transcripts using StringTie, a total of 115045 transcripts were detected with varying degrees of expression in 39 samples, these findings provided a standardised dataset for subsequent differential expression analysis.Subsequently, GFFCompare was used to annotate the transcripts, and those with a class code of"="were specifically retained. The transcript count data obtained can be found in the figshare (https://doi.org/10.6084/m9.figshare.29192831.v1).To elucidate the genetic distinctions between pig olfactory epithelial tissue and other tissues for future researchers, we conducted a comparison between pig olfactory epithelial tissue and the remaining 12 tissues. The results of the principal component analysis (PCA) are depicted in Figure 2. The PCA revealed that samples from the same tissue, such as liver and muscle, clustered closely together in two-dimensional space. This clustering indicates that samples from the same tissue exhibit highly similar gene expression patterns.In conclusion, this report provides 39 RNA-seq data from 13 tissues of three Junmu No.1 White boars, which can provide candidate targets and molecular mechanism clues for further functional validation experiments (gene knockout, overexpression or single-cell sequencing) in the future. These datasets support analysis of gene function in porcine olfactory epithelium, advancing understanding of olfactory biology and its physiological impacts.