{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T09:08:37Z","timestamp":1789117717946,"version":"build-2803163510"},"reference-count":45,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2023YFD1300105"],"award-info":[{"award-number":["2023YFD1300105"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100011798","name":"National Beef Cattle and Yak Industry Technology System","doi-asserted-by":"publisher","award":["CARS-37"],"award-info":[{"award-number":["CARS-37"]}],"id":[{"id":"10.13039\/501100011798","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Modern Seed Industry Agglomeration and Attack Special Project","award":["2025JLGJ0001XM"],"award-info":[{"award-number":["2025JLGJ0001XM"]}]},{"name":"Jilin Province Modern Agricultural Industry Technology System\u2014Beef Cattle System","award":["JLARS-2026-070203"],"award-info":[{"award-number":["JLARS-2026-070203"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Intramuscular fat (IMF) deposition drives premium beef value, but phenotypic selection is costly and slow. Although genome-wide studies have linked the KIRREL3 region to meat quality, whether intronic variants directly affect carcass traits and retain predictive power across physiological stages remains unproven. We genotyped two intronic SNPs (g.29756010C&gt;T and g.29756149C&gt;T) in Woking cattle, a high-quality beef breed developed in Jilin Province, China (n = 473; 226 and 206 heifers at 36 and 48 months, respectively, plus an independent validation cohort of n = 41), assessed for fatty acid composition, meat quality, and multi-tissue gene expression. Both loci were polymorphic and in Hardy\u2013Weinberg equilibrium. At 36 months, TT individuals showed higher dressing percentage, rib thickness, and meat grade than CC at both loci. By 48 months, the 63-bp locus retained broader associations with carcass traits, whereas the 203-bp locus effects weakened. In the validation group, CC animals had higher IMF and muscle KIRREL3 expression than TT, yet received lower meat grades. Five fatty acids differed significantly among genotypes after Benjamini\u2013Hochberg correction (q &lt; 0.05), whereas the dominant fatty acids (C16:0, C18:1n9c, C18:0, C18:2n6c) showed no proportional differences. KIRREL3 was most highly expressed in the kidney among eight tissues examined. These findings identify the 63-bp site as a candidate marker for meat quality in local Chinese cattle, with potential for marker-assisted selection pending confirmation in larger cohorts and functional studies.<\/jats:p>","DOI":"10.3390\/ani16182858","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T08:17:42Z","timestamp":1789114662000},"page":"2858","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Association of KIRREL3 Intronic Polymorphisms with Carcass Traits, Meat Quality, and Muscle Fatty Acid Composition in Woking Cattle"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3022-5898","authenticated-orcid":false,"given":"Xiaotong","family":"Luo","sequence":"first","affiliation":[{"name":"Jilin Academy of Agricultural Sciences, Changchun 130033, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0599-1853","authenticated-orcid":false,"given":"Hongliang","family":"Liu","sequence":"additional","affiliation":[{"name":"Jilin Academy of Agricultural Sciences, Changchun 130033, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Xuanyu","family":"Li","sequence":"additional","affiliation":[{"name":"Jilin Academy of Agricultural Sciences, Changchun 130033, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-1066-904X","authenticated-orcid":false,"given":"Chunyu","family":"Li","sequence":"additional","affiliation":[{"name":"Jilin Academy of Agricultural Sciences, Changchun 130033, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-2503-437X","authenticated-orcid":false,"given":"Congcong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Jilin Academy of Agricultural Sciences, Changchun 130033, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-7341-0548","authenticated-orcid":false,"given":"Dong","family":"Li","sequence":"additional","affiliation":[{"name":"Changchun Haoyue Co., Ltd., Changchun 130013, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7207-0516","authenticated-orcid":false,"given":"Yongsheng","family":"Yu","sequence":"additional","affiliation":[{"name":"Jilin Academy of Agricultural Sciences, Changchun 130033, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-0992-7994","authenticated-orcid":false,"given":"Jian","family":"Wu","sequence":"additional","affiliation":[{"name":"Jilin Academy of Agricultural Sciences, Changchun 130033, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1016\/j.meatsci.2007.07.019","article-title":"Fat Deposition, Fatty Acid Composition and Meat Quality: A Review","volume":"78","author":"Wood","year":"2008","journal-title":"Meat Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.5713\/ab.20.0672","article-title":"Associations between Gene Polymorphisms and Selected Meat Traits in Cattle\u2014A Review","volume":"34","author":"Zalewska","year":"2021","journal-title":"Anim. Biosci."},{"key":"ref_3","first-page":"E313","article-title":"Commercial Application of Marker- and Gene-Assisted Selection in Livestock: Strategies and Lessons","volume":"82","author":"Dekkers","year":"2004","journal-title":"J. Anim. Sci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"6","DOI":"10.3168\/jds.2024-24953","article-title":"Invited Review: Phenotyping Strategies and Genetic Background of Dairy Cattle Behavior in Intensive Production Systems\u2014From Trait Definition to Genomic Selection","volume":"108","author":"Pacheco","year":"2025","journal-title":"J. Dairy Sci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Ueda, S., Sasaki, R., Nakabayashi, R., Yamanoue, M., Sirai, Y., and Iwamoto, E. (2021). Exploring the Lipids Involved in the Formation of Characteristic Lactones in Japanese Black Cattle. Metabolites, 11.","DOI":"10.3390\/metabo11040203"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Yu, J., Naseem, S., Park, S., Hur, S., Choi, Y., Lee, T., Li, X., and Choi, S. (2025). FASN, SCD, and PLAG1 Gene Polymorphism and Association with Carcass Traits and Fatty Acid Profile in Hanwoo Cattle. Animals, 15.","DOI":"10.3390\/ani15060897"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e12516","DOI":"10.1111\/gbb.12516","article-title":"Neph2\/Kirrel3 Regulates Sensory Input, Motor Coordination, and Home-Cage Activity in Rodents","volume":"17","author":"Volker","year":"2018","journal-title":"Genes Brain Behav."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e09395","DOI":"10.7554\/eLife.09395","article-title":"The Intellectual Disability Gene Kirrel3 Regulates Target-Specific Mossy Fiber Synapse Development in the Hippocampus","volume":"4","author":"Martin","year":"2015","journal-title":"Elife"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1016\/j.neuroscience.2007.10.013","article-title":"Expression of mKirre in the Developing Sensory Pathways: Its Close Apposition to Nephrin-Expressing Cells","volume":"150","author":"Morikawa","year":"2007","journal-title":"Neuroscience"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"5376","DOI":"10.1523\/JNEUROSCI.3058-19.2020","article-title":"Kirrel3-Mediated Synapse Formation Is Attenuated by Disease-Associated Missense Variants","volume":"40","author":"Taylor","year":"2020","journal-title":"J. Neurosci."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/nature13772","article-title":"Synaptic, Transcriptional and Chromatin Genes Disrupted in Autism","volume":"515","author":"He","year":"2014","journal-title":"Nature"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1186\/s13052-023-01488-7","article-title":"KIRREL3-Related Disorders: A Case Report Confirming the Radiological Features and Expanding the Clinical Spectrum to a Less Severe Phenotype","volume":"49","author":"Querzani","year":"2023","journal-title":"Ital. J. Pediatr."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"154025","DOI":"10.1016\/j.prp.2022.154025","article-title":"Preliminary Study on the Role and Mechanism of KIRREL3 in the Development of Esophageal Squamous Cell Carcinoma","volume":"237","author":"Yang","year":"2022","journal-title":"Pathol. Res. Pract."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Durcan, P.J., Conradie, J.D., Van DeVyver, M., and Myburgh, K.H. (2014). Identification of novel Kirrel3 gene splice variants in adult human skeletal muscle. BMC Physiol., 14.","DOI":"10.1186\/s12899-014-0011-3"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Deng, S., Qiu, Y., Zhuang, Z., Wu, J., Li, X., Ruan, D., Xu, C., Zheng, E., Yang, M., and Cai, G. (2023). Genome-Wide Association Study of Body Conformation Traits in a Three-Way Crossbred Commercial Pig Population. Animals, 13.","DOI":"10.3390\/ani13152414"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1002\/cne.25234","article-title":"Comparative Description of the mRNA Expression Profile of Na+\/K+-ATPase Isoforms in Adult Mouse Nervous System","volume":"530","author":"Jiao","year":"2022","journal-title":"J. Comp. Neurol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"33815","DOI":"10.1038\/s41598-025-04205-y","article-title":"Decoding the Beef Cattle Genome through Whole-Genome Sequencing Reveals the Genetic Basis of Carcass and Meat Quality Traits","volume":"15","author":"Nanaie","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1111\/age.13364","article-title":"Detection of Genomic Variations and Selection Signatures in Wagyu Using Whole-Genome Sequencing Data","volume":"54","author":"Shi","year":"2023","journal-title":"Anim. Genet."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1740-0929.2010.00845.x","article-title":"Identification and Utilization of Genes Associated with Beef Qualities","volume":"82","author":"Mannen","year":"2011","journal-title":"Anim. Sci. J."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Basson, A., Strydom, P.E., van Marle-Koster, E., Webb, E.C., and Frylinck, L. (2022). Sustained Effects of Muscle Calpain System Genotypes on Tenderness Phenotypes of South African Beef Bulls during Ageing up to 20 Days. Animals, 12.","DOI":"10.3390\/ani12060686"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1222794","article-title":"Systematic Localization of Common Disease-Associated Variation in Regulatory DNA","volume":"337","author":"Maurano","year":"2012","journal-title":"Science"},{"key":"ref_22","unstructured":"(2016). Determination of Fat in Foods (Standard No. GB 5009.6-2016)."},{"key":"ref_23","unstructured":"(2016). Determination of Moisture in Foods (Standard No. GB 5009.3-2016)."},{"key":"ref_24","unstructured":"(2016). Determination of Protein in Foods (Standard No. GB 5009.5-2016)."},{"key":"ref_25","unstructured":"(2016). Determination of Fatty Acids in Foods (Standard No. GB 5009.168-2016)."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Yuan, J.S., Reed, A., Chen, F., and Stewart, C.N. (2006). Statistical analysis of real-time PCR data. BMC Bioinform., 7.","DOI":"10.1186\/1471-2105-7-85"},{"key":"ref_27","unstructured":"Hartl, D.L., and Clark, A.G. (2007). Principles of Population Genetics, Sinauer Associates. [4th ed.]. Available online: https:\/\/global.oup.com\/ushe\/product\/principles-of-population-genetics-9780197778739?q=Principles%20of%20Population%20Genetics,%204th%20ed&cc=us&lang=en."},{"key":"ref_28","unstructured":"McDonald, J.H. (2014). Fisher\u2019s exact test of independence. Handbook of Biological Statistics, Sparky House Publishing. [3rd ed.]. Available online: https:\/\/www.biostathandbook.com\/fishers.html."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1111\/age.12523","article-title":"Genetic Association of PLAG1, SCD, CYP7B1 and FASN SNPs and Their Effects on Carcass Weight, Intramuscular Fat and Fatty Acid Composition in Hanwoo Steers (Korean Cattle)","volume":"48","author":"Kim","year":"2017","journal-title":"Anim. Genet."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Traenkner, D., Shennib, O., Johnson, A., Weinbrom, A., Taylor, M.R., and Williams, M.E. (2023). Modular Splicing Is Linked to Evolution in the Synapse-Specificity Molecule Kirrel3. eNeuro, 10.","DOI":"10.1101\/2023.07.25.550563"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Chen, Y., Wang, Z., Qu, X., Song, B., Tang, Y., Li, B., Cao, G., and Yi, G. (2024). An Intronic SNP Affects Skeletal Muscle Development by Regulating the Expression of TP63. Front. Vet. Sci., 11.","DOI":"10.3389\/fvets.2024.1396766"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Sakowski, T., Grodkowski, G., Golebiewski, M., Slosarz, J., Kostusiak, P., Solarczyk, P., and Puppel, K. (2022). Genetic and Environmental Determinants of Beef Quality\u2014A Review. Front. Vet. Sci., 9.","DOI":"10.3389\/fvets.2022.819605"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"4083","DOI":"10.1007\/s11033-011-1190-7","article-title":"Fatty Acid Composition of Beef Is Associated with Exonic Nucleotide Variants of the Gene Encoding FASN","volume":"39","author":"Oh","year":"2012","journal-title":"Mol. Biol. Rep."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1111\/j.1365-2052.2007.01681.x","article-title":"DNA Polymorphisms in Bovine Fatty Acid Synthase Are Associated with Beef Fatty Acid Composition","volume":"39","author":"Zhang","year":"2008","journal-title":"Anim. Genet."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1111\/asj.12357","article-title":"The g.841G>C SNP of FASN Gene Is Associated with Fatty Acid Composition in Beef Cattle","volume":"86","author":"Hayakawa","year":"2015","journal-title":"Anim. Sci. J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1111\/j.1365-2052.2009.01913.x","article-title":"A Splice Site Single Nucleotide Polymorphism of the Fatty Acid Binding Protein 4 Gene Appears to Be Associated with Intramuscular Fat Deposition in Longissimus Muscle in Australian Cattle","volume":"40","author":"Barendse","year":"2009","journal-title":"Anim. Genet."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"4571","DOI":"10.2527\/jas.2013-6402","article-title":"Associations between DGAT1, FABP4, LEP, RORC, and SCD1 Gene Polymorphisms and Fat Deposition in Spanish Commercial Beef","volume":"91","author":"Aviles","year":"2013","journal-title":"J. Anim. Sci."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1017\/S1751731109991091","article-title":"Intramuscular Fat Content in Meat-Producing Animals: Development, Genetic and Nutritional Control, and Identification of Putative Markers","volume":"4","author":"Hocquette","year":"2010","journal-title":"Animal"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"119","DOI":"10.2527\/jas.2008-1082","article-title":"Gene Expression Patterns during Intramuscular Fat Development in Cattle","volume":"87","author":"Wang","year":"2009","journal-title":"J. Anim. Sci."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Baek, J., Yan, C.L., Gao, Q., Son, S., Lee, H.K., Shin, D., and Yan, C.G. (2025). Genomic Insights into Yanbian Cattle: Breed-Specific Selective Sweeps Identified by Whole-Genome Sequencing. PLoS ONE, 20.","DOI":"10.1371\/journal.pone.0331448"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Yu, H., Zhang, K., Cheng, G., Mei, C., Wang, H., and Zan, L. (2024). Genome-Wide Analysis Reveals Genomic Diversity and Signatures of Selection in Qinchuan Beef Cattle. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10482-0"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1080\/10495398.2022.2033252","article-title":"Selection Signatures of Qinchuan Cattle Based on Whole-Genome Sequences","volume":"34","author":"Wang","year":"2023","journal-title":"Anim. Biotechnol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"research0034","DOI":"10.1186\/gb-2002-3-7-research0034","article-title":"Accurate Normalization of Real-Time Quantitative RT-PCR Data by Geometric Averaging of Multiple Internal Control Genes","volume":"3","author":"Vandesompele","year":"2002","journal-title":"Genome Biol."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Song, Y., Zhang, J., Jiang, C., Song, X., Chen, X., Raza, S.H.A., Pant, S.D., Ma, Y., Zan, L., and Wei, D. (2025). Vitamin A Mediates FABP4 to Regulate Intramuscular Fat Production: A New Target and Strategy for Optimizing Beef Quality. BMC Genom., 26.","DOI":"10.1186\/s12864-025-11544-7"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"44793","DOI":"10.1038\/srep44793","article-title":"Functional Confirmation of PLAG1 as the Candidate Causative Gene Underlying Major Pleiotropic Effects on Body Weight and Milk Characteristics","volume":"7","author":"Fink","year":"2017","journal-title":"Sci. Rep."}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/18\/2858\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T08:41:19Z","timestamp":1789116079000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/18\/2858"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,11]]},"references-count":45,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["ani16182858"],"URL":"https:\/\/doi.org\/10.3390\/ani16182858","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,11]]}}}