Animal genetics最新文献

{"title":"Untangling the Copy Number Variation at the Basis of Belted Phenotypes in Cattle Using Long-Read Sequencing","authors":"Rensco A. H. Hogers,&nbsp;Mirte Bosse,&nbsp;Annemieke P. Rattink,&nbsp;Rayner González-Prendes,&nbsp;Marta Gòdia,&nbsp;Kimberley Laport,&nbsp;Martien A. M. Groenen,&nbsp;Richard P. M. A. Crooijmans,&nbsp;Aniek C. Bouwman","doi":"10.1002/age.70159","DOIUrl":"https://doi.org/10.1002/age.70159","url":null,"abstract":"<p>The belted phenotype in cattle, a distinctive white belt across the midsection observed in breeds such as the Dutch Belted and Belted Galloway, is caused by a copy number variant (CNV) upstream of <i>TWIST2</i>, a gene involved in melanocyte development. While the CNV is necessary for belt formation, the genetic basis of variation in belt width and completeness remains unclear. To refine understanding of these phenotypes, we generated a <i>de novo</i> genome assembly of Dutch Belted cattle and analysed both short- and long-read sequencing data from animals with normal-width, small-width, and incomplete belts. Standard variant calling tools failed to identify the CNV, highlighting technical challenges in detecting large insertions. Instead, coverage analysis and qPCR confirmed the CNV as a 6 kb tandem array approximately 16.5 kb upstream of <i>TWIST2</i>. Long-read evidence showed identical four-copy haplotypes for individuals with normal-width, small-width, and incomplete belts, indicating that CNV copy number does not influence belt width or completeness. Furthermore, no unique variants were detected within the CNV or <i>TWIST2</i> in a small-width belted individual, suggesting that modifiers affecting belt width likely reside elsewhere in the genome. Genome-wide scans revealed extremely low nucleotide diversity in the CNV region, consistent with a selective sweep driven by strong artificial selection unique to the Dutch Belted breed. Together, these results show that while the CNV is necessary for belt formation, additional modifier loci likely influence belt width and completeness.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/age.70159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148467438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Resequencing Reveals Genetic Diversity and Selection Signatures in Two Indigenous Goat Populations From Xizang","authors":"Tingxian Chen,&nbsp;Ting Wang,&nbsp;Wenrui Ye,&nbsp;Pan Tan,&nbsp;Quzhen Luosang,&nbsp;Hou Wen,&nbsp;Tianzeng Song,&nbsp;Zhuoga Gesang,&nbsp;Zhenzhen Zhang","doi":"10.1002/age.70162","DOIUrl":"https://doi.org/10.1002/age.70162","url":null,"abstract":"<div>\u0000 \u0000 <p>Zhangmu goats and Chentang black goats are valuable local goat genetic resources in Shigatse, Xizang. Due to long-term geographic isolation and small population size, their genetic diversity and adaptive genetic basis remain poorly understood. In this study, whole-genome resequencing was performed on 30 Zhangmu goats and 30 Chentang black goats. By calculating indicators such as observed heterozygosity (<i>H</i>_O), expected heterozygosity (<i>H</i>_E), nucleotide diversity (<i>π</i>), and inbreeding coefficient (<i>F</i>_IS), the genetic diversity of the two populations was comprehensively assessed, and their selection signatures were analyzed using both <i>F</i>_st and XP-CLR. The results showed that both Zhangmu goats and Chentang black goats exhibited relatively low but detectable levels of genetic diversity, with clear genetic differentiation from wild goats. Population structure analysis indicated that the two indigenous populations possessed relatively independent genetic backgrounds. Combined <i>F</i>_st and XP-CLR analyses identified multiple candidate genes associated with hypoxia adaptation (<i>ARNT</i>), immune response (<i>CD274</i>, <i>PTPN7</i>), growth and development (<i>FGF5</i>, <i>MYOM3</i>), and reproductive regulation (<i>GDF5</i>, <i>MEIOB</i>). Functional enrichment analysis revealed that these candidate genes were mainly enriched in GO terms such as nucleoplasm, and in pathways such as the calcium signaling pathway and propanoate metabolism. These results provide genomic insights into the genetic characteristics of Zhangmu goats and Chentang black goats, and offer a theoretical basis for the conservation and sustainable utilization of indigenous goat genetic resources in Xizang.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148467443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ancient Plumage Colour Genetics Reveal Goose Domestication and Hybridization","authors":"Johanna Honka,&nbsp;Suvi Olli,&nbsp;Arthur O. Askeyev,&nbsp;Igor V. Askeyev,&nbsp;Oleg V. Askeyev,&nbsp;Jouni Aspi,&nbsp;Dilyara N. Shaymuratova,&nbsp;Laura Kvist","doi":"10.1002/age.70165","DOIUrl":"10.1002/age.70165","url":null,"abstract":"<p>In archaeological assemblages, differentiating the European domestic goose and its wild progenitor, the greylag goose (<i>Anser anser</i>), has been challenging due to their similar skeletal morphologies. A short region of mitochondrial DNA (mtDNA) analysed from ancient DNA (aDNA) has been shown to distinguish wild greylags from domestic geese, but some ancient specimens display atypical haplotypes or haplotypes belonging to other wild <i>Anser</i> species. Plumage colouration could verify the domestic status of archaeological geese, as white or mottled plumage would be indicative of domestication. We analysed a SNP upstream of the <i>EDNRB2</i> gene (<i>endothelin receptor B-like</i>) linked to white spotting and a 1-bp deletion in the Z-chromosomal <i>MLANA</i> gene (<i>melan-A</i>), causative of sex-linked dilution colour (almost white male and light grey female) in European domestic geese. Together, white spotting and sex-linked dilution result in white plumage. We also analysed a Chinese domestic goose (<i>A. cygnoid</i>)-specific 14-bp insertion within the <i>EDNRB2</i> gene, which also causes white colour, and searched for possible evidence of historical interbreeding between European and Chinese domestic geese. We detected several plumage colour patterns such as solid wild type, white spotted (i.e., saddleback), nearly white with some grey spots, and white or autosexing with of ‘almost white male and saddleback female’. Further, we discovered that European domestic geese had introgression from the Chinese domestic goose at least occasionally, from the 16th-17th century Common Era, due to the presence of both European and Chinese domestic goose white alleles in a single individual.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/age.70165","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148429631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genes Associated With Fracture Risk in Thoroughbred Horses Have Novel Roles in Osteogenesis","authors":"Amy C. Ross,&nbsp;Ellison S. Lumsden,&nbsp;Caroline Flood,&nbsp;Jayesh Dudhia,&nbsp;Androniki Psifidi,&nbsp;Deborah J. Guest","doi":"10.1002/age.70166","DOIUrl":"10.1002/age.70166","url":null,"abstract":"<p>Bone fractures in Thoroughbred racehorses are a major welfare problem. Genetic factors contribute to fracture risk. Cell models have previously identified 112 differentially expressed genes in bone-forming osteoblasts derived from horses at high and low genetic risk of fracture. However, 42 of these genes have no published role in bone. In this study, we identified novel roles for a subset of these genes in bone formation. Twenty-six of the 42 genes were expressed in Saos2 cells during basal culture and/or after 21 days of osteogenic culture. Five of these genes (<i>ADSSL1</i>, <i>CABP1</i>, <i>ENO2</i>, <i>SPARCL1</i> and <i>UCP2</i>) were then stably overexpressed and knocked down, and their effect on osteogenesis was measured. Gene overexpression resulted in significant decreases in Saos2 cell viability and decreased expression of osteogenic genes under basal cell culture, but after 21 days of osteogenic culture there were few significant changes in osteogenic gene expression, collagen deposition or matrix mineralisation. Knockdown of <i>SPARCL1</i> resulted in total cell death, whereas knockdown of <i>ADSSL1</i>, <i>CABP1</i>, <i>ENO2</i> and <i>UCP2</i> resulted in decreased cell viability but limited significant changes in osteogenic gene expression under basal cell culture. However, following osteogenic culture, gene knockdown induced widespread changes in osteogenic gene expression, decreased collagen deposition and increased matrix mineralisation. <i>ADSSL1</i>, <i>CABP1</i>, <i>ENO2</i> and <i>UCP2</i> were all expressed at significantly lower levels in osteoblasts from genetically high-risk horses. Taken together, this work demonstrates novel roles for fracture-associated genes in bone formation and matrix mineralisation suggesting these processes may be altered in genetically susceptible horses.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/age.70166","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148403380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization and Validation of A-to-I RNA Editing Events Reveal Their Potential Regulatory Role in Bovine Adipogenesis","authors":"Chenglong Li,&nbsp;Xiaonan Zhou,&nbsp;Yanling Ding,&nbsp;Junjie Xu,&nbsp;Jiahao Liang,&nbsp;Li’e Hou,&nbsp;Xiaolong Kang","doi":"10.1002/age.70163","DOIUrl":"10.1002/age.70163","url":null,"abstract":"<div>\u0000 \u0000 <p>Intramuscular fat (IMF) content is a critical determinant of meat quality, directly influencing flavor and palatability. RNA editing, a prevalent posttranscriptional modification in mammals, has been extensively investigated in cattle; however, its role in bovine intramuscular fat deposition remains poorly understood. Here, we performed a comprehensive analysis of RNA editing differences in the longissimus dorsi muscle between cattle groups with divergent IMF content to identify editing sites potentially associated with IMF deposition. A total of 283 581 RNA editing sites (RESs) were identified from transcriptomic data of cattle with contrasting IMF phenotypes. Among the differential A-to-I editing sites located in coding sequences, 14 led to amino acid alterations, including an editing event in <i>MYBPH</i>, a gene with important functions in muscle and adipose tissues. Differential A-to-I editing sites in the 3′ UTR resulted in altered miRNA binding patterns: 30 sites led to loss of miRNA binding, whereas 16 sites gained novel miRNA binding capacity. Dual-luciferase reporter assays confirmed that the editing site chr2:106787199 in the 3′ UTR of <i>PRKAG3</i> affects binding by bta-miR-23b-5p. Functional validation experiments demonstrated that bta-miR-23b-5p promotes <i>PRKAG3</i> expression, and overexpression of <i>PRKAG3</i> suppresses preadipocyte differentiation and lipid droplet formation. Collectively, these findings uncover a regulatory role for RESs in IMF deposition and provide new insights into the functional significance of RNA editing in bovine intramuscular fat accumulation.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148395675","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ISAG 2024/2025 Forensic Comparison Test: A Curated Pilot Dataset for Domestic Animal Forensic Genetics","authors":"Guillermo Giovambattista,&nbsp;Angelika Mąsior,&nbsp;Sree Kanthaswamy,&nbsp;Leslie A. Lyons,&nbsp;Chesleigh Winfree,&nbsp;Rosina Fossati,&nbsp;Virginia Filipello,&nbsp;Manuel Murillo-Alcedo,&nbsp;Pier Luigi Acutis,&nbsp;Bertram Brenig,&nbsp;Carmen Cons,&nbsp;Ahmad Ebrahimi,&nbsp;Michelle Fremaux,&nbsp;Maria Elena Turba,&nbsp;George Sofronidis","doi":"10.1002/age.70164","DOIUrl":"10.1002/age.70164","url":null,"abstract":"","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148395663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sex-Linked Dilution Colour in the European Domestic Goose Indicated To Be a 1-Bp Deletion in the Melan-A Gene","authors":"Suvi Olli,&nbsp;Vikke Ahola,&nbsp;Marja E. Heikkinen,&nbsp;Johanna Honka","doi":"10.1002/age.70161","DOIUrl":"10.1002/age.70161","url":null,"abstract":"<p>Plumage colour in domestic geese is an important economic trait and a selection target since the early days of domestication. In European domestic geese of greylag goose (<i>Anser anser</i>) origin, white plumage is known to be determined by two independent loci, one causing white spotting and another sex-linked dilution, together producing white plumage. Strong candidate genetic variants have been identified upstream of the <i>EDNRB2</i>, that is, <i>LOC106047519</i> gene (<i>endothelin receptor B-like</i>) and within the sex-linked <i>MLANA</i> gene (<i>melan-A</i>). To confirm these candidate variants, we genotyped differently coloured European domestic goose breeds, wild greylag geese, Chinese domestic geese (derived from swan goose <i>A. cygnoid</i>) and European and Chinese domestic geese crossbreeds. One base pair deletion in the <i>MLANA</i> gene (NW_013185876.1: g.950868 C&gt;−) was confirmed to cause sex-linked dilution, and thus autosexing (almost white gander and diluted grey goose). However, a genetic variant upstream of <i>EDNRB2</i> (NW_013185915.1: g.775151 G&gt;T) was not causative of saddleback pattern but strongly linked to it in European domestic geese. We sequenced the <i>EDNRB2</i> gene and coding sequence of a neighbouring <i>VAMP7</i> gene (<i>vesicle-associated membrane protein 7</i>) but found no genetic variation linked to colour. Additionally, we sequenced the coding sequence of <i>TYRP1</i> (<i>tyrosinase related protein 1</i>), a candidate gene for buff colouration, but no variation linked to colour was found. Further, we genotyped a 14-bp insertion in exon 3 of the <i>EDNRB2</i> gene, known to be causative of the white phenotype in the Chinese domestic goose, and identified it in one European domestic goose.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/age.70161","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148389868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Indicators of Performance Resilience in Barrel Racing Quarter Horses","authors":"Mário Luiz Santana,&nbsp;Annaiza Braga Bignardi","doi":"10.1002/age.70158","DOIUrl":"10.1002/age.70158","url":null,"abstract":"<p>Resilience, defined as the capacity to maintain consistent performance under variable conditions, has emerged as a relevant breeding objective in livestock systems, yet remains largely unexplored in equine populations. The objectives of this study were to (1) derive indicators of resilience from longitudinal barrel racing time (BRT) records in Brazilian Quarter Horses, (2) estimate genetic parameters for these indicators, and (3) quantify their genetic relationships with BRT and accumulated career earnings (ACE). The dataset comprised BRT records from barrel racing events held between 2010 and 2024, involving 10 665 horses. Resilience indicators were derived from short-term deviations around an expected performance trajectory after removing systematic effects and persistent horse- and rider-specific performance levels. Three indicators were evaluated: median absolute deviation (MAD), logarithm of the variance of deviations (LNVAR), and proportion of positive deviations (PPOS). Posterior mean heritability estimates for the resilience indicators were low (0.06 to 0.09), but still indicated exploitable additive genetic variation. Genetic correlations revealed a near-complete overlap between MAD and LNVAR (0.987), while PPOS captured partially distinct genetic information. All resilience indicators showed favorable genetic associations with ACE (mean −0.59) and positive associations with BRT (mean 0.44), indicating that genetically more resilient horses tended to perform faster and achieve higher economic returns. Therefore, resilience indicators derived from longitudinal performance records captured genetically meaningful variation related to performance consistency and economic success. These indicators complemented traditional performance traits and provided a scalable framework for incorporating resilience and long-term regularity into genetic evaluations of sport horses.</p>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/age.70158","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148395620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-Wide Association Study and Genomic Prediction for Maximum Litter Size in Sows","authors":"Changyi Chen,&nbsp;Hao Sun,&nbsp;Xiaoran Zhang,&nbsp;Juan Ke,&nbsp;Jing Li,&nbsp;Jiayi Ning,&nbsp;Fengyi Dong,&nbsp;Long Jin,&nbsp;Wuyang Liu,&nbsp;Huimin Yu,&nbsp;Chengyue Feng,&nbsp;Chunyan Bai,&nbsp;Boxing Sun","doi":"10.1002/age.70155","DOIUrl":"10.1002/age.70155","url":null,"abstract":"<div>\u0000 \u0000 <p>Total born number (TBN) and number born alive (NBA) are primary selection targets for improving reproduction performance in pigs; however, genetic progress is constrained by the low heritability of single-parity records. To better capture the genetic potential underlying litter size, we evaluated maximum (maxTBN and maxNBA) and mean (meanTBN and meanNBA) litter size traits derived from multiple parities as alternative selection criteria. Using data from a Dongliao Black (DL) pig population, heritability estimates for maxTBN (<i>h</i>² = 0.19), meanTBN (<i>h</i>² = 0.16), maxNBA (<i>h</i>² = 0.24) and meanNBA (<i>h</i>² = 0.17) were substantially higher than those for single-parity TBN (<i>h</i>² = 0.06) and NBA (<i>h</i>² = 0.07). Genome-wide association analyses (GWAS) based on estimated breeding values of maximum and mean traits identified 158 significant single-nucleotide polymorphisms, implicating several candidate genes, including <i>BPI</i>, <i>KCNC2</i>, <i>ELMO1</i>, <i>CHD6</i>, <i>OPCML,</i> and <i>MND1</i>. Validation in an independent Large White population with high litter size (TBN &gt; 16) showed that favorable alleles at representative loci were close to fixation, supporting their effects on reproduction performance. Furthermore, genomic prediction models based on maxTBN and maxNBA exhibited higher cross-validation variance than those using conventional litter size traits, reflecting greater prediction instability. Collectively, these results demonstrate that mean litter size traits constitute robust phenotypes for genetic evaluation of sow fertility, while maximum traits may serve as supplementary indicators for identifying elite individuals, and provide functionally relevant markers that can be exploited to inform balanced selection strategies for reproduction in pig breeding programs.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148359080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic Analysis Reveals Multilayer Regulation Underlying Development and Pregnancy in the Malayan Pangolin","authors":"Xianghui Liang,&nbsp;Miaomiao Jia,&nbsp;Zhiguang Wang,&nbsp;YuShan Ding,&nbsp;Fanghui Hou,&nbsp;Chengwei Xiang,&nbsp;Wanhe Huang,&nbsp;He Wang,&nbsp;Xuelin Xu,&nbsp;Yingjin Mao,&nbsp;Luman Chen,&nbsp;Guangda Yang,&nbsp;Yongyi Shen,&nbsp;Wu Chen,&nbsp;Xuejuan Shen","doi":"10.1002/age.70153","DOIUrl":"10.1002/age.70153","url":null,"abstract":"<div>\u0000 \u0000 <p>The critically endangered Malayan pangolin (<i>Manis javanica</i>) exhibits distinctive physiological adaptations; nevertheless, its molecular mechanisms underlying development and reproduction remain inadequately characterized, thereby impeding effective conservation initiatives. In this study, we conducted a comprehensive transcriptomic analysis of six tissues (intestine, kidney, liver, lung, muscle, and spleen) derived from adult, fetal, and pregnant individuals. The fetal stage demonstrated the greatest abundance of stage-specific genes, which were predominantly enriched in developmental pathways such as epithelial organization and transmembrane signaling. Differential gene expression (DGE) analysis revealed that genes upregulated in adults were primarily associated with metabolic and immune functions, whereas those upregulated in fetuses were linked to developmental processes and cell cycle regulation. Co-expression network analysis identified critical hub genes, including <i>GLDC</i> in adults and <i>NCAM1</i> in fetuses, that are implicated in stage-specific regulatory mechanisms. Additionally, extensive differential alternative splicing (DAS) events were observed, with exon skipping (SE) representing the most frequent splicing pattern. Integrative analyses suggested that DGE and DAS largely constitute independent regulatory layers; however, a subset of hub genes, such as <i>OBSL1</i> and <i>TNIP1</i>, exhibited concurrent differential expression and splicing, indicating their potential central roles in coordinating developmental processes. This study presents a detailed transcriptomic atlas of Malayan pangolin development and pregnancy, providing candidate biomarker genes for evaluating reproductive health and developmental status, thereby informing future conservation strategies.</p>\u0000 </div>","PeriodicalId":7905,"journal":{"name":"Animal genetics","volume":"57 4","pages":""},"PeriodicalIF":2.2,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148350237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}