{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:44:41Z","timestamp":1785422681396,"version":"3.56.0"},"reference-count":46,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T00:00:00Z","timestamp":1778112000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["31860629"],"award-info":[{"award-number":["31860629"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"award":["31860629"],"award-info":[{"award-number":["31860629"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Postgraduate Education Innovation Program","award":["TDGRI2024037"],"award-info":[{"award-number":["TDGRI2024037"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The Tahe red deer is derived from the wild Tarim red deer, an endemic subspecies native to the Tarim Basin in Xinjiang, China. It has recently received official approval as a locally bred deer variety, developed through artificial breeding programs. This breed retains several advantageous traits from its wild ancestors, including tolerance to coarse forage, drought resistance, and a high yield of velvet antlers. To investigate the genetic mechanisms underlying velvet antler production, phenotypic data for antler weight and blood samples were collected from 73 adult Tahe red deer. Whole-genome sequencing and genome-wide association analysis were performed to identify genetic variants associated with antler weight. Population genetic analysis revealed that the observed heterozygosity (Ho) and expected heterozygosity (He) were 0.31291 and 0.32832, respectively, while the nucleotide diversity (\u03c0) was 2.17 \u00d7 10\u22123, indicating relatively high genetic diversity within the Tahe red deer population. Using a mixed linear model (MLM), a total of 189 candidate genes and 1387 significant SNP loci associated with antler weight were identified (p &lt; 1.0 \u00d7 10\u22125). Gene Ontology (GO) enrichment analysis revealed that these candidate genes are primarily involved in intracellular calcium ion homeostasis, peptide and protein biosynthesis, extracellular matrix organization, the regulation of glycolysis, and cytoskeleton-related processes, including actin filaments and microfibrils. These biological functions are closely related to cell proliferation, differentiation, energy metabolism, and tissue remodeling. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further indicated that the candidate genes are significantly enriched in several pathways, including the Notch signaling pathway, the cGMP\u2013PKG signaling pathway, the regulation of the actin cytoskeleton, ribosome biogenesis, and mucin type O-glycan biosynthesis. These results suggest that these genes may participate in velvet antler growth and development by regulating cell proliferation and differentiation, cytoskeletal remodeling, and protein synthesis. Overall, this study identifies SNP loci and candidate genes significantly associated with antler weight in Tahe red deer, providing a theoretical basis for genetic improvement and marker-assisted selection for velvet antler production in this breed.<\/jats:p>","DOI":"10.3390\/ani16101424","type":"journal-article","created":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T12:15:07Z","timestamp":1778156107000},"page":"1424","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genome-Wide Identification of Candidate Genes Associated with Antler Weight in Tahe Red Deer"],"prefix":"10.3390","volume":"16","author":[{"given":"Zhengchuang","family":"Hou","sequence":"first","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujiao","family":"Qi","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenchen","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junjie","family":"Shao","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faling","family":"Hou","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenxi","family":"Qian","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"},{"name":"Key Laboratory of Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinghua","family":"Gao","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"},{"name":"Key Laboratory of Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, China"},{"name":"Key Laboratory of Livestock and Forage Resources Utilization Around Tarim, Ministry of Agriculture and Rural Areas, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunmei","family":"Han","sequence":"additional","affiliation":[{"name":"College of Animal Science and Technology, Tarim University, Alar 843300, China"},{"name":"Key Laboratory of Animal Husbandry Science and Technology, Xinjiang Production and Construction Corps, Alar 843300, China"},{"name":"Key Laboratory of Livestock and Forage Resources Utilization Around Tarim, Ministry of Agriculture and Rural Areas, Alar 843300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e72757","DOI":"10.1002\/ece3.72757","article-title":"Seasonal Dietary Patterns of Tarim Red Deer (Cervus hanglu yarkandensis) Revealed by the trnL Sequencing Approach in the Tarim River Basin (Xinjiang, China)","volume":"15","author":"Qi","year":"2025","journal-title":"Ecol. Evol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"16161","DOI":"10.1038\/s41598-022-20244-1","article-title":"Comprehensive transcriptome analysis of sika deer antler using PacBio and Illumina sequencing","volume":"12","author":"Zhang","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Zhao, D., Zhang, Z., Wang, Q., and Li, H. (2025). Integrated mRNA and miRNA Analysis Reveals Layer-Specific Mechanisms of Antler Yield Variation in Sika Deer. Animals, 15.","DOI":"10.3390\/ani15131964"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1101\/gr.279448.124","article-title":"High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration","volume":"35","author":"Li","year":"2025","journal-title":"Genome Res."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1007\/s00438-021-01776-z","article-title":"Integrated analysis of miRNA and mRNA transcriptomic reveals antler growth regulatory network","volume":"296","author":"Jia","year":"2021","journal-title":"Mol. Genet. Genom."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Chen, H., Lin, C., Xiang, X., Yang, C., Han, C., and Gao, Q. (2025). The BVES Gene Regulates the Homeostasis of Deer Antler Mesenchymal Stem Cells Through Wnt Signaling. Biology, 14.","DOI":"10.3390\/biology14091210"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1038\/s42003-025-08085-w","article-title":"RXFP2-positive mesenchymal stem cells in the antlerogenic periosteum contribute to postnatal development of deer antlers","volume":"8","author":"Ba","year":"2025","journal-title":"Commun. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2535","DOI":"10.3168\/jds.2022-22277","article-title":"Longitudinal genome-wide association studies of milk production traits in Holstein cattle using whole-genome sequence data imputed from medium-density chip data","volume":"106","author":"Teng","year":"2023","journal-title":"J. Dairy. Sci."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"giaf064","DOI":"10.1093\/gigascience\/giaf064","article-title":"Identifying candidate genetic variants for egg number by analyzing over 1000 fully sequenced layers","volume":"14","author":"Ni","year":"2025","journal-title":"Gigascience"},{"key":"ref_10","first-page":"1090","article-title":"Screening weight related genes of velvet antlers by whole genome re-sequencing","volume":"39","author":"Hu","year":"2017","journal-title":"Yi Chuan"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Hu, P., Wang, Z., Li, J., Wang, D., Wang, Y., Zhao, Q., and Li, C. (2022). IGF1R and LOX Modules Are Related to Antler Growth Rate Revealed by Integrated Analyses of Genomics and Transcriptomics. Animals, 12.","DOI":"10.3390\/ani12121522"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1038\/s41597-020-0537-0","article-title":"Chromosome-level genome assembly of Tarim red deer, Cervus elaphus yarkandensis","volume":"7","author":"Ba","year":"2020","journal-title":"Sci. Data"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Alganmi, N., and Abusamra, H. (2023). Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0288371"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: Rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"Gigascience"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"3326","DOI":"10.1093\/bioinformatics\/bts606","article-title":"A high-performance computing toolset for relatedness and principal component analysis of SNP data","volume":"28","author":"Zheng","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"giaf032","DOI":"10.1093\/gigascience\/giaf032","article-title":"VCF2Dis: An ultra-fast and efficient tool to calculate pairwise genetic distance and construct population phylogeny from VCF files","volume":"14","author":"Xu","year":"2025","journal-title":"Gigascience"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1786","DOI":"10.1093\/bioinformatics\/bty875","article-title":"PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files","volume":"35","author":"Zhang","year":"2019","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/ng.2310","article-title":"Genome-wide efficient mixed-model analysis for association studies","volume":"44","author":"Zhou","year":"2012","journal-title":"Nat. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1016\/j.gpb.2020.10.007","article-title":"rMVP: A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool for Genome-wide Association Study","volume":"19","author":"Yin","year":"2021","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3704","DOI":"10.18632\/aging.102008","article-title":"Integrating genome-wide association study with regulatory SNP annotation information identified candidate genes and pathways for schizophrenia","volume":"11","author":"Liang","year":"2019","journal-title":"Aging"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1007\/s00122-016-2798-8","article-title":"Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato","volume":"130","author":"Vos","year":"2017","journal-title":"Theor. Appl. Genet. Theor. Und Angew. Genet."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1038\/ncb1757","article-title":"IQGAP3 regulates cell proliferation through the Ras\/ERK signalling cascade","volume":"10","author":"Nojima","year":"2008","journal-title":"Nat. Cell Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1038\/s41586-021-03283-y","article-title":"MAP3K2-regulated intestinal stromal cells define a distinct stem cell niche","volume":"592","author":"Wu","year":"2021","journal-title":"Nature"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1016\/j.bone.2008.06.016","article-title":"Latent TGF-beta binding proteins (LTBPs)-1 and -3 coordinate proliferation and osteogenic differentiation of human mesenchymal stem cells","volume":"43","author":"Koli","year":"2008","journal-title":"Bone"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Chen, S.H., Lu, C.H., and Tsai, M.J. (2020). TCTP is Essential for Cell Proliferation and Survival during CNS Development. Cells, 9.","DOI":"10.3390\/cells9010133"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1038\/ni.3122","article-title":"IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte \u03b2-selection","volume":"16","author":"Boudil","year":"2015","journal-title":"Nat. Immunol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Miao, L., Lu, Y., Nusrat, A., Abdelnasser, H.Y., Datta, S., Zhou, B., Schwartz, R.J., and Wu, M. (2021). The Spatiotemporal Expression of Notch1 and Numb and Their Functional Interaction during Cardiac Morphogenesis. Cells, 10.","DOI":"10.3390\/cells10092192"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.ydbio.2014.10.007","article-title":"Gro\/TLE enables embryonic stem cell differentiation by repressing pluripotent gene expression","volume":"397","author":"Laing","year":"2015","journal-title":"Dev. Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"4504","DOI":"10.1128\/MCB.00545-13","article-title":"Genomic and proteomic analyses of Prdm5 reveal interactions with insulator binding proteins in embryonic stem cells","volume":"33","author":"Galli","year":"2013","journal-title":"Mol. Cell Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1038\/ncomms2793","article-title":"An isoform of retinoid-related orphan receptor \u03b2 directs differentiation of retinal amacrine and horizontal interneurons","volume":"4","author":"Liu","year":"2013","journal-title":"Nat. Commun."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"107791","DOI":"10.1016\/j.jbc.2024.107791","article-title":"Histone methyltransferase KMT2A: Developmental regulation to oncogenic transformation","volume":"300","author":"Ogino","year":"2024","journal-title":"J. Biol. Chem."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"4131","DOI":"10.1242\/dev.008367","article-title":"MEF2: A central regulator of diverse developmental programs","volume":"134","author":"Potthoff","year":"2007","journal-title":"Development"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1038\/s42003-021-02717-7","article-title":"Smoc1 and Smoc2 regulate bone formation as downstream molecules of Runx2","volume":"4","author":"Takahata","year":"2021","journal-title":"Commun. Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.bone.2018.07.008","article-title":"Identification of TGF \u03b2-related genes regulated in murine osteoarthritis and chondrocyte hypertrophy by comparison of multiple microarray datasets","volume":"116","author":"Brachvogel","year":"2018","journal-title":"Bone"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Galli, G.G., de Lichtenberg, K.H., Carrara, M., Hans, W., Wuelling, M., Mentz, B., Multhaupt, H.A., Fog-Tonnesen, C.K., Jensen, K.T., and Rappsilber, J. (2012). Prdm5 regulates collagen gene transcription by association with RNA polymerase II in developing bone. PLoS Genet., 8.","DOI":"10.1371\/journal.pgen.1002711"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"18370","DOI":"10.1074\/jbc.M602469200","article-title":"Polypeptide GalNAc-transferase T3 and familial tumoral calcinosis. Secretion of fibroblast growth factor 23 requires O-glycosylation","volume":"281","author":"Kato","year":"2006","journal-title":"J. Biol. Chem."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2414","DOI":"10.1074\/jbc.M112.410043","article-title":"FGF23 suppresses chondrocyte proliferation in the presence of soluble \u03b1-Klotho both in vitro and in vivo","volume":"288","author":"Kawai","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"14211","DOI":"10.1074\/jbc.M808345200","article-title":"The orphan nuclear receptor estrogen receptor-related receptor gamma negatively regulates BMP2-induced osteoblast differentiation and bone formation","volume":"284","author":"Jeong","year":"2009","journal-title":"J. Biol. Chem."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1002\/biof.1120","article-title":"Ghrelin and bone","volume":"40","author":"Patric","year":"2014","journal-title":"Biofactors"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"557","DOI":"10.14348\/molcells.2021.0004","article-title":"BK Channel Deficiency in Osteoblasts Reduces Bone Formation via the Wnt\/\u03b2-Catenin Pathway","volume":"44","author":"Jiang","year":"2021","journal-title":"Mol. Cells"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.3390\/nu5083022","article-title":"Magnesium and osteoporosis: Current state of knowledge and future research directions","volume":"5","author":"Castiglioni","year":"2013","journal-title":"Nutrients"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"110262","DOI":"10.1016\/j.isci.2024.110262","article-title":"TGF-\u03b21 promotes osteogenesis of mesenchymal stem cells via integrin mediated mechanical positive autoregulation","volume":"27","author":"Wan","year":"2024","journal-title":"iScience"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"e5284","DOI":"10.21769\/BioProtoc.5284","article-title":"GWAS Procedures for Gene Mapping in Diverse Populations with Complex Structures","volume":"15","author":"Zuo","year":"2025","journal-title":"Bio Protoc."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/10\/1424\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T04:35:02Z","timestamp":1778301302000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/10\/1424"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,7]]},"references-count":46,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["ani16101424"],"URL":"https:\/\/doi.org\/10.3390\/ani16101424","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,7]]}}}