{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T09:26:40Z","timestamp":1783416400637,"version":"3.54.6"},"reference-count":107,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T00:00:00Z","timestamp":1780876800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T00:00:00Z","timestamp":1783382400000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["BT\/PR45205\/NER\/95\/1897\/2022"],"award-info":[{"award-number":["BT\/PR45205\/NER\/95\/1897\/2022"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020703","name":"Centre for Agricultural Bioinformatics","doi-asserted-by":"publisher","award":["10006444"],"award-info":[{"award-number":["10006444"]}],"id":[{"id":"10.13039\/501100020703","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-026-56596-1","type":"journal-article","created":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T15:15:16Z","timestamp":1780931716000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Whole genome resequencing reveals the genetic basis of stature in short-statured Indian cattle"],"prefix":"10.1038","volume":"16","author":[{"given":"Sheikh Firdous","family":"Ahmad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ovais","family":"Aarif","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mir Mehroz","family":"Hassan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roshni","family":"Chand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Munish","family":"Gangwar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarath Kumar","family":"T","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,8]]},"reference":[{"key":"56596_CR1","unstructured":"dahd.gov.in\/sites\/default\/files\/2024-11\/BAHS-2024.pdf"},{"key":"56596_CR2","doi-asserted-by":"crossref","unstructured":"Srivastava, A. K. Conservation of Indigenous Cattle Breeds. JAR 9, (2019).","DOI":"10.30954\/2277-940X.01.2019.1"},{"key":"56596_CR3","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.agsy.2009.05.002","volume":"101","author":"PK Thornton","year":"2009","unstructured":"Thornton, P. K., Van De Steeg, J., Notenbaert, A. & Herrero, M. The impacts of climate change on livestock and livestock systems in developing countries: A review of what we know and what we need to know. Agric. Syst. 101, 113\u2013127 (2009).","journal-title":"Agric. Syst."},{"key":"56596_CR4","doi-asserted-by":"publisher","first-page":"1399","DOI":"10.1007\/s13258-023-01401-w","volume":"45","author":"A Chakraborty","year":"2023","unstructured":"Chakraborty, A. et al. Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds. Genes Genom. 45, 1399\u20131408 (2023).","journal-title":"Genes Genom"},{"key":"56596_CR5","doi-asserted-by":"crossref","unstructured":"Ramesha, K. P. et al. Assessment of genetic diversity among Malnad Gidda, Punganur and Vechur-dwarf cattle breeds of India using microsatellite markers. Indian J. Anim. Sci 86, 186\u2013191 (2016).","DOI":"10.56093\/ijans.v86i2.55805"},{"key":"56596_CR6","doi-asserted-by":"crossref","unstructured":"Singh, P. K. et al. Physical features, management and performance of Konkan cattle. Indian J. Anim. Sci 89(4), 413\u2013418 (2019).","DOI":"10.56093\/ijans.v89i4.89142"},{"key":"56596_CR7","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1080\/10496500802174036","volume":"9","author":"DWR Boden","year":"2008","unstructured":"Boden, D. W. R. Miniature Cattle: For Real, For Pets, For Production. J. Agricultural Food Inform. 9, 167\u2013183 (2008).","journal-title":"J. Agricultural Food Inform."},{"key":"56596_CR8","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1007\/s10482-022-01791-z","volume":"116","author":"M Deepthi","year":"2023","unstructured":"Deepthi, M. et al. Exploring variation in the fecal microbial communities of Kasaragod Dwarf and Holstein crossbred cattle. Antonie van Leeuwenhoek. 116, 53\u201365 (2023).","journal-title":"Antonie van Leeuwenhoek"},{"key":"56596_CR9","first-page":"323","volume":"77","author":"R. Pundir","year":"2007","unstructured":"Pundir, R., Pathak, B.L., Ahlawat, S.P.S. Characterization and evaluation of Kankrej Breed of cattle in its native tract. Indian J. Anim. Sci. 77, 323\u2013327 (2007).","journal-title":"Indian J. Anim. Sci."},{"key":"56596_CR10","doi-asserted-by":"publisher","first-page":"149159","DOI":"10.1016\/j.gene.2024.149159","volume":"939","author":"CS Celus","year":"2025","unstructured":"Celus, C. S., Ahmad, S. F., Gangwar, M., Kumar, S. & Kumar, A. Deciphering new insights into copy number variations as drivers of genomic diversity and adaptation in farm animal species. Gene 939, 149159 (2025).","journal-title":"Gene"},{"key":"56596_CR11","doi-asserted-by":"publisher","first-page":"e1001375","DOI":"10.1371\/journal.pgen.1001375","volume":"7","author":"AM Hancock","year":"2011","unstructured":"Hancock, A. M. et al. Adaptations to Climate-Mediated Selective Pressures in Humans. PLoS Genet. 7, e1001375 (2011).","journal-title":"PLoS Genet."},{"issue":"6","key":"56596_CR12","doi-asserted-by":"publisher","first-page":"1256","DOI":"10.3390\/genes14061256","volume":"14","author":"H Salehian-Dehkordi","year":"2023","unstructured":"Salehian-Dehkordi, H. et al. Genomic landscape of copy number variations and their associations with climatic variables in the world\u2019s sheep. Genes 14 (6), 1256 (2023).","journal-title":"Genes"},{"key":"56596_CR13","doi-asserted-by":"publisher","first-page":"100412","DOI":"10.1016\/j.cpb.2024.100412","volume":"40","author":"B Panahi","year":"2024","unstructured":"Panahi, B., Jalaly, M., Hamid, R. & H. & Using next-generation sequencing approach for discovery and characterization of plant molecular markers. Curr. Plant. Biology. 40, 100412 (2024).","journal-title":"Curr. Plant. Biology"},{"key":"56596_CR14","doi-asserted-by":"publisher","first-page":"2139","DOI":"10.1038\/s41588-023-01540-6","volume":"55","author":"ZN Choo","year":"2023","unstructured":"Choo, Z. N. et al. Most large structural variants in cancer genomes can be detected without long reads. Nat. Genet. 55, 2139\u20132148 (2023).","journal-title":"Nat. Genet."},{"key":"56596_CR15","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1016\/j.tree.2013.09.008","volume":"29","author":"H Ellegren","year":"2014","unstructured":"Ellegren, H. Genome sequencing and population genomics in non-model organisms. Trends Ecol. Evol. 29, 51\u201363 (2014).","journal-title":"Trends Ecol. Evol."},{"key":"56596_CR16","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1038\/nrg2958","volume":"12","author":"C Alkan","year":"2011","unstructured":"Alkan, C., Coe, B. P. & Eichler, E. E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363\u2013376 (2011).","journal-title":"Nat. Rev. Genet."},{"key":"56596_CR17","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/nrg2063","volume":"8","author":"GA Wray","year":"2007","unstructured":"Wray, G. A. The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8, 206\u2013216 (2007).","journal-title":"Nat. Rev. Genet."},{"key":"56596_CR18","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1186\/s12864-025-11387-2","volume":"26","author":"SF Ahmad","year":"2025","unstructured":"Ahmad, S. F. et al. Dissecting genomes of multiple yak populations: unveiling ancestry and high-altitude adaptation through whole-genome resequencing analysis. BMC Genom. 26, 214 (2025).","journal-title":"BMC Genom."},{"key":"56596_CR19","doi-asserted-by":"publisher","first-page":"e0204669","DOI":"10.1371\/journal.pone.0204669","volume":"13","author":"MG Strillacci","year":"2018","unstructured":"Strillacci, M. G. et al. A copy number variant scan in the autochthonous Valdostana Red Pied cattle breed and comparison with specialized dairy populations. PLoS ONE. 13, e0204669 (2018).","journal-title":"PLoS ONE"},{"key":"56596_CR20","doi-asserted-by":"publisher","first-page":"105430","DOI":"10.1016\/j.livsci.2024.105430","volume":"281","author":"R Ros-Freixedes","year":"2024","unstructured":"Ros-Freixedes, R. The contribution of whole-genome sequence data to genome-wide association studies in livestock: Outcomes and perspectives. Livest. Sci. 281, 105430 (2024).","journal-title":"Livest. Sci."},{"key":"56596_CR21","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1186\/s40104-024-01133-1","volume":"16","author":"S Azam","year":"2025","unstructured":"Azam, S. et al. Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus. J. Anim. Sci. Biotechnol. 16, 21 (2025).","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"56596_CR22","unstructured":"Indian Nucleotide Data Archive (INDA). Dataset accession no. INRP000053. Indian Biological Data Centre (IBDC). Available from INDA database (accessed. January (2026)."},{"key":"56596_CR23","unstructured":"Andrews, C.A. Natural selection, genetic drift, and gene flow do not act in isolation in natural populations. Nature Education Knowledge, 3(10), 5 (2010)."},{"key":"56596_CR24","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"56596_CR25","doi-asserted-by":"crossref","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).","DOI":"10.1093\/gigascience\/giab008"},{"key":"56596_CR26","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","volume":"81","author":"S Purcell","year":"2007","unstructured":"Purcell, S. et al. PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am. J. Hum. Genet. 81, 559\u2013575 (2007).","journal-title":"Am. J. Hum. Genet."},{"key":"56596_CR27","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1101\/gr.114876.110","volume":"21","author":"A Abyzov","year":"2011","unstructured":"Abyzov, A., Urban, A. E., Snyder, M. & Gerstein, M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974\u2013984 (2011).","journal-title":"Genome Res."},{"key":"56596_CR28","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1101\/gr.092981.109","volume":"19","author":"S Yoon","year":"2009","unstructured":"Yoon, S., Xuan, Z., Makarov, V., Ye, K. & Sebat, J. Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res. 19, 1586\u20131592 (2009).","journal-title":"Genome Res."},{"key":"56596_CR29","doi-asserted-by":"crossref","unstructured":"Hao, Z. et al. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Computer Science 6, e251 (2020).","DOI":"10.7717\/peerj-cs.251"},{"key":"56596_CR30","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"56596_CR31","doi-asserted-by":"publisher","first-page":"1880","DOI":"10.1016\/j.ajhg.2021.08.005","volume":"108","author":"BL Browning","year":"2021","unstructured":"Browning, B. L., Tian, X., Zhou, Y. & Browning, S. R. Fast two-stage phasing of large-scale sequence data. Am. J. Hum. Genet. 108, 1880\u20131890 (2021).","journal-title":"Am. J. Hum. Genet."},{"key":"56596_CR32","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1038\/hdy.2015.42","volume":"115","author":"Y Ma","year":"2015","unstructured":"Ma, Y. et al. Properties of different selection signature statistics and a new strategy for combining them. Heredity 115, 426\u2013436 (2015).","journal-title":"Heredity"},{"key":"56596_CR33","doi-asserted-by":"publisher","first-page":"1176","DOI":"10.1093\/bioinformatics\/bts115","volume":"28","author":"M Gautier","year":"2012","unstructured":"Gautier, M. & Vitalis, R. rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics 28, 1176\u20131177 (2012).","journal-title":"Bioinformatics"},{"key":"56596_CR34","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1111\/1755-0998.12634","volume":"17","author":"M Gautier","year":"2017","unstructured":"Gautier, M., Klassmann, A. & Vitalis, R. rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure. Mol. Ecol. Resour. 17, 78\u201390 (2017).","journal-title":"Mol. Ecol. Resour."},{"key":"56596_CR35","doi-asserted-by":"crossref","unstructured":"Fonseca, P. A. S., Su\u00e1rez-Vega, A., Marras, G. & C\u00e1novas, \u00c1. GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci. GigaScience 9 giaa149, 1\u20139 (2020).","DOI":"10.1093\/gigascience\/giaa149"},{"key":"56596_CR36","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1016\/j.ygeno.2020.10.012","volume":"113","author":"L Yang","year":"2021","unstructured":"Yang, L. et al. Genomic sequencing analysis reveals copy number variations and their associations with economically important traits in beef cattle. Genomics 113, 812\u2013820 (2021).","journal-title":"Genomics"},{"key":"56596_CR37","doi-asserted-by":"publisher","first-page":"30364","DOI":"10.1038\/s41598-025-14139-0","volume":"15","author":"NA Mar\u00edn-Garz\u00f3n","year":"2025","unstructured":"Mar\u00edn-Garz\u00f3n, N. A. et al. Detection and functional assessment of structural variants using whole-genome re-sequencing data in Nellore cattle. Sci. Rep. 15, 30364 (2025).","journal-title":"Sci. Rep."},{"key":"56596_CR38","doi-asserted-by":"publisher","first-page":"146510","DOI":"10.1016\/j.gene.2022.146510","volume":"830","author":"SF Ahmad","year":"2022","unstructured":"Ahmad, S. F. et al. Genome-wide elucidation of CNV regions and their association with production and reproduction traits in composite Vrindavani cattle. Gene 830, 146510 (2022).","journal-title":"Gene"},{"key":"56596_CR39","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1186\/s12864-023-09720-8","volume":"24","author":"SF Ahmad","year":"2023","unstructured":"Ahmad, S. F. et al. Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds. BMC Genom. 24, 616 (2023).","journal-title":"BMC Genom."},{"key":"56596_CR40","doi-asserted-by":"publisher","first-page":"737","DOI":"10.3389\/fgene.2019.00737","volume":"10","author":"BN Keel","year":"2019","unstructured":"Keel, B. N., Nonneman, D. J., Lindholm-Perry, A. K., Oliver, W. T. & Rohrer, G. A. A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence. Front. Genet. 10, 737 (2019).","journal-title":"Front. Genet."},{"key":"56596_CR41","doi-asserted-by":"publisher","first-page":"895","DOI":"10.1186\/s12864-018-5297-2","volume":"19","author":"the 99Lives Consortium","year":"2018","unstructured":"Genova, F., Longeri, M., Lyons, L.A., Bagnato, A. and Strillacci, M.G. First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. BMC Genom. 19, 895 (2018).","journal-title":"BMC Genom."},{"key":"56596_CR42","doi-asserted-by":"publisher","first-page":"809","DOI":"10.3390\/ani9100809","volume":"9","author":"D Seol","year":"2019","unstructured":"Seol, D. et al. Identification of Copy Number Variation in Domestic Chicken Using Whole-Genome Sequencing Reveals Evidence of Selection in the Genome. Animals 9, 809 (2019).","journal-title":"Animals"},{"key":"56596_CR43","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1186\/s12864-023-09672-z","volume":"24","author":"H Shi","year":"2023","unstructured":"Shi, H. et al. Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection. BMC Genom. 24, 555 (2023).","journal-title":"BMC Genom."},{"key":"56596_CR44","doi-asserted-by":"publisher","first-page":"104892","DOI":"10.1016\/j.psj.2025.104892","volume":"104","author":"L Zhang","year":"2025","unstructured":"Zhang, L. et al. Whole-genome sequencing reveals copy number variations and their associations with body weight and size traits at slaughter in Lion-head geese. Poult. Sci. 104, 104892 (2025).","journal-title":"Poult. Sci."},{"key":"56596_CR45","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/s12863-017-0524-4","volume":"18","author":"E Gorla","year":"2017","unstructured":"Gorla, E. et al. Genomic variability in Mexican chicken population using copy number variants. BMC Genet. 18, 61 (2017).","journal-title":"BMC Genet."},{"key":"56596_CR46","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1186\/s12864-025-11536-7","volume":"26","author":"GC Ladeira","year":"2025","unstructured":"Ladeira, G. C., Pinedo, P. J., Santos, J. E. P., Thatcher, W. W. & Rezende, F. M. Detecting and characterizing copy number variation in a large commercial U.S. Holstein cattle population. BMC Genom. 26, 381 (2025).","journal-title":"BMC Genom."},{"key":"56596_CR47","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1186\/s12864-017-3636-3","volume":"18","author":"Y Gao","year":"2017","unstructured":"Gao, Y. et al. CNV discovery for milk composition traits in dairy cattle using whole genome resequencing. BMC Genom. 18, 265 (2017).","journal-title":"BMC Genom."},{"key":"56596_CR48","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1186\/s12864-023-09248-x","volume":"24","author":"T Sun","year":"2023","unstructured":"Sun, T. et al. Whole genome sequencing of simmental cattle for SNP and CNV discovery. BMC Genom. 24, 179 (2023).","journal-title":"BMC Genom."},{"key":"56596_CR49","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1186\/s12864-024-10936-5","volume":"25","author":"W Ayalew","year":"2024","unstructured":"Ayalew, W. et al. Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments. BMC Genom. 25, 1088 (2024).","journal-title":"BMC Genom."},{"key":"56596_CR50","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1186\/s12864-020-07097-6","volume":"21","author":"Y Hu","year":"2020","unstructured":"Hu, Y. et al. Comparative analyses of copy number variations between Bos taurus and Bos indicus. BMC Genom. 21, 682 (2020).","journal-title":"BMC Genom."},{"key":"56596_CR51","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1017\/S1751731116002135","volume":"11","author":"MG Strillacci","year":"2017","unstructured":"Strillacci, M. G. et al. Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers. Animal 11, 737\u2013745 (2017).","journal-title":"Animal"},{"key":"56596_CR52","doi-asserted-by":"publisher","first-page":"giz073","DOI":"10.1093\/gigascience\/giz073","volume":"8","author":"A Kommadath","year":"2019","unstructured":"Kommadath, A. et al. A large interactive visual database of copy number variants discovered in taurine cattle. GigaScience 8, giz073 (2019).","journal-title":"GigaScience"},{"key":"56596_CR53","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1186\/s12864-021-07808-7","volume":"22","author":"J Jang","year":"2021","unstructured":"Jang, J. et al. Population differentiated copy number variation of Bos taurus, Bos indicus and their African hybrids. BMC Genom. 22, 531 (2021).","journal-title":"BMC Genom."},{"key":"56596_CR54","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1186\/1471-2164-11-284","volume":"11","author":"J Fadista","year":"2010","unstructured":"Fadista, J., Thomsen, B., Holm, L. E. & Bendixen, C. Copy number variation in the bovine genome. BMC Genom. 11, 284 (2010).","journal-title":"BMC Genom."},{"key":"56596_CR55","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1111\/age.13298","volume":"54","author":"E Peripolli","year":"2023","unstructured":"Peripolli, E. et al. Assessment of copy number variants in three Brazilian locally adapted cattle breeds using whole-genome re\u2010sequencing data. Anim. Genet. 54, 254\u2013270 (2023).","journal-title":"Anim. Genet."},{"key":"56596_CR56","doi-asserted-by":"publisher","first-page":"568","DOI":"10.3390\/genes16050568","volume":"16","author":"D Dang","year":"2025","unstructured":"Dang, D. et al. Genome-Wide Analysis of Copy Number Variations in Three Populations of Nanyang Cattle Using Whole-Genome Resequencing. Genes 16, 568 (2025).","journal-title":"Genes"},{"key":"56596_CR57","doi-asserted-by":"publisher","first-page":"11919","DOI":"10.3390\/ijms252211919","volume":"25","author":"Z Zhong","year":"2024","unstructured":"Zhong, Z. et al. Insights into Adaption and Growth Evolution: Genome\u2013Wide Copy Number Variation Analysis in Chinese Hainan Yellow Cattle Using Whole\u2013Genome Re\u2013Sequencing Data. IJMS 25, 11919 (2024).","journal-title":"IJMS"},{"key":"56596_CR58","doi-asserted-by":"publisher","first-page":"8044","DOI":"10.1038\/s41598-020-64680-3","volume":"10","author":"AM Butty","year":"2020","unstructured":"Butty, A. M. et al. High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data. Sci. Rep. 10, 8044 (2020).","journal-title":"Sci. Rep."},{"key":"56596_CR59","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1186\/s12864-016-2754-7","volume":"17","author":"GM Jenkins","year":"2016","unstructured":"Jenkins, G. M. et al. Copy number variants in the sheep genome detected using multiple approaches. BMC Genom. 17, 441 (2016).","journal-title":"BMC Genom."},{"key":"56596_CR60","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1186\/s12864-019-5687-0","volume":"20","author":"NB Stafuzza","year":"2019","unstructured":"Stafuzza, N. B. et al. A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive. BMC Genom. 20, 321 (2019).","journal-title":"BMC Genom."},{"key":"56596_CR61","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1111\/age.12247","volume":"46","author":"K Dong","year":"2015","unstructured":"Dong, K. et al. Copy number variation detection using SNP genotyping arrays in three Chinese pig breeds. Anim. Genet. 46, 101\u2013109 (2015).","journal-title":"Anim. Genet."},{"key":"56596_CR62","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/s12864-021-07387-7","volume":"22","author":"C Yuan","year":"2021","unstructured":"Yuan, C. et al. A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing. BMC Genom. 22, 78 (2021).","journal-title":"BMC Genom."},{"key":"56596_CR63","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1186\/1471-2164-11-232","volume":"11","author":"JS Bae","year":"2010","unstructured":"Bae, J. S. et al. Identification of copy number variations and common deletion polymorphisms in cattle. BMC Genom. 11, 232 (2010).","journal-title":"BMC Genom."},{"key":"56596_CR64","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1186\/s12864-018-4699-5","volume":"19","author":"Y Zhou","year":"2018","unstructured":"Zhou, Y. et al. Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle. BMC Genom. 19, 314 (2018).","journal-title":"BMC Genom."},{"key":"56596_CR65","doi-asserted-by":"publisher","first-page":"874","DOI":"10.1016\/j.omtn.2020.07.002","volume":"21","author":"C Song","year":"2020","unstructured":"Song, C. et al. lncRNA IGF2 AS Regulates Bovine Myogenesis through Different Pathways. Mol. Therapy Nucleic Acids. 21, 874\u2013884 (2020).","journal-title":"Mol. Therapy Nucleic Acids"},{"key":"56596_CR66","doi-asserted-by":"publisher","first-page":"856","DOI":"10.3390\/genes13050856","volume":"13","author":"W Str\u00f3\u017cewska","year":"2022","unstructured":"Str\u00f3\u017cewska, W., Durda-Masny, M. & Szwed, A. Mutations in GHR and IGF1R Genes as a Potential Reason for the Lack of Catch-Up Growth in SGA Children. Genes 13, 856 (2022).","journal-title":"Genes"},{"key":"56596_CR67","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1016\/j.bone.2015.10.007","volume":"83","author":"J Heilig","year":"2016","unstructured":"Heilig, J., Paulsson, M. & Zaucke, F. Insulin-like growth factor 1 receptor (IGF1R) signaling regulates osterix expression and cartilage matrix mineralization during endochondral ossification. Bone 83, 48\u201357 (2016).","journal-title":"Bone"},{"key":"56596_CR68","doi-asserted-by":"publisher","first-page":"111416","DOI":"10.1016\/j.mce.2021.111416","volume":"536","author":"RC Scalco","year":"2021","unstructured":"Scalco, R. C., Correa, F. A., Dantas, N. C. B., Vasques, G. A. & Jorge, A. A. L. Hormone resistance and short stature: A journey through the pathways of hormone signaling. Mol. Cell. Endocrinol. 536, 111416 (2021).","journal-title":"Mol. Cell. Endocrinol."},{"key":"56596_CR69","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/2049-1891-3-39","volume":"3","author":"LB Smith","year":"2012","unstructured":"Smith, L. B., Belanger, J. M. & Oberbauer, A. M. Fibroblast growth factor receptor 3 effects on proliferation and telomerase activity in sheep growth plate chondrocytes. J. Anim. Sci. Biotechnol. 3, 39 (2012).","journal-title":"J. Anim. Sci. Biotechnol."},{"key":"56596_CR70","doi-asserted-by":"publisher","first-page":"3651","DOI":"10.3390\/ani13233651","volume":"13","author":"K Wang","year":"2023","unstructured":"Wang, K. et al. Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats. Animals 13, 3651 (2023).","journal-title":"Animals"},{"key":"56596_CR71","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1002\/dvdy.24479","volume":"246","author":"DM Ornitz","year":"2017","unstructured":"Ornitz, D. M., Legeai-Mallet, L. & Achondroplasia Development, pathogenesis, and therapy. Dev. Dyn. 246, 291\u2013309 (2017).","journal-title":"Dev. Dyn."},{"key":"56596_CR72","doi-asserted-by":"publisher","first-page":"2815","DOI":"10.1038\/s41467-020-16485-1","volume":"11","author":"X Li","year":"2020","unstructured":"Li, X. et al. Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits. Nat. Commun. 11, 2815 (2020).","journal-title":"Nat. Commun."},{"key":"56596_CR73","doi-asserted-by":"publisher","first-page":"3074","DOI":"10.3390\/ani12223074","volume":"12","author":"X Li","year":"2022","unstructured":"Li, X. et al. Copy Number Variation of the SOX6 Gene and Its Associations with Growth Traits in Ashidan Yak. Animals 12, 3074 (2022).","journal-title":"Animals"},{"key":"56596_CR74","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1186\/s13052-015-0162-2","volume":"41","author":"M Bozzola","year":"2015","unstructured":"Bozzola, M. et al. Hereditary multiple exostoses and solitary osteochondroma associated with growth hormone deficiency: to treat or not to treat? Ital. J. Pediatr. 41, 53 (2015).","journal-title":"Ital. J. Pediatr."},{"key":"56596_CR75","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1210\/endrev\/bnad003","volume":"44","author":"N Zhang","year":"2023","unstructured":"Zhang, N., Yuan, M. & Wang, J. LGR4: A New Receptor Member in Endocrine and Metabolic Diseases. Endocr. Rev. 44, 647\u2013667 (2023).","journal-title":"Endocr. Rev."},{"key":"56596_CR76","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1093\/biolreprod\/87.s1.211","volume":"87","author":"AD Ealy","year":"2012","unstructured":"Ealy, A. D., Yang, Q. E., Ozawa, M. & Johnson, S. E. Expression Profiling and Potential Functions of Protein Kinase C Delta During Early Bovine Embryo Development. Biol. Reprod. 87, 211\u2013211 (2012).","journal-title":"Biol. Reprod."},{"key":"56596_CR77","doi-asserted-by":"publisher","first-page":"32107","DOI":"10.1074\/jbc.M504432200","volume":"280","author":"AE Santiago-Walker","year":"2005","unstructured":"Santiago-Walker, A. E. et al. Protein Kinase C \u03b4 Stimulates Apoptosis by Initiating G1 Phase Cell Cycle Progression and S Phase Arrest. J. Biol. Chem. 280, 32107\u201332114 (2005).","journal-title":"J. Biol. Chem."},{"key":"56596_CR78","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.matbio.2019.02.001","volume":"82","author":"D Hubmacher","year":"2019","unstructured":"Hubmacher, D. et al. Limb- and tendon-specific Adamtsl2 deletion identifies a role for ADAMTSL2 in tendon growth in a mouse model for geleophysic dysplasia. Matrix Biol. 82, 38\u201353 (2019).","journal-title":"Matrix Biol."},{"key":"56596_CR79","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.174417","author":"V Camarena","year":"2024","unstructured":"Camarena, V. et al. ADAMTSL2 mutations determine the phenotypic severity in Geleophysic Dysplasia. JCI Insight. https:\/\/doi.org\/10.1172\/jci.insight.174417 (2024).","journal-title":"JCI Insight"},{"key":"56596_CR80","doi-asserted-by":"publisher","first-page":"3137","DOI":"10.1007\/s00018-011-0780-9","volume":"68","author":"D Hubmacher","year":"2011","unstructured":"Hubmacher, D. & Apte, S. S. Genetic and functional linkage between ADAMTS superfamily proteins and fibrillin-1: a novel mechanism influencing microfibril assembly and function. Cell. Mol. Life Sci. 68, 3137\u20133148 (2011).","journal-title":"Cell. Mol. Life Sci."},{"key":"56596_CR81","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1186\/s12967-025-06976-4","volume":"23","author":"M Anselme","year":"2025","unstructured":"Anselme, M., He, H., Lai, C., Luo, W. & Zhong, S. Targeting mitochondrial transporters and metabolic reprogramming for disease treatment. J. Transl Med. 23, 1111 (2025).","journal-title":"J. Transl Med."},{"key":"56596_CR82","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.3389\/fgene.2019.01337","volume":"10","author":"H Li","year":"2020","unstructured":"Li, H. et al. Runting and Stunting Syndrome Is Associated With Mitochondrial Dysfunction in Sex-Linked Dwarf Chicken. Front. Genet. 10, 1337 (2020).","journal-title":"Front. Genet."},{"key":"56596_CR83","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1080\/10495398.2021.1942029","volume":"34","author":"H Liu","year":"2023","unstructured":"Liu, H., Xu, H., Lan, X., Cao, X. & Pan, C. The InDel variants of sheep IGF2BP1 gene are associated with growth traits. Animal Biotechnol. 34, 134\u2013142 (2023).","journal-title":"Animal Biotechnol."},{"key":"56596_CR84","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/j.jcmgh.2023.12.001","volume":"17","author":"LR Parham","year":"2024","unstructured":"Parham, L. R. et al. IGF2BP1\/IMP1 Deletion Enhances a Facultative Stem Cell State via Regulation of MAP1LC3B. Cell. Mol. Gastroenterol. Hepatol. 17, 439\u2013451 (2024).","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"56596_CR85","doi-asserted-by":"publisher","first-page":"1637","DOI":"10.3390\/genes15121637","volume":"15","author":"T Li","year":"2024","unstructured":"Li, T. et al. Genome-Wide Association Analysis of Growth Traits in Hu Sheep. Genes 15, 1637 (2024).","journal-title":"Genes"},{"key":"56596_CR86","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.3389\/fgene.2019.01157","volume":"10","author":"X Zhang","year":"2019","unstructured":"Zhang, X. et al. Interdigital Hyperplasia in Holstein Cattle Is Associated With a Missense Mutation in the Signal Peptide Region of the Tyrosine-Protein Kinase Transmembrane Receptor Gene. Front. Genet. 10, 1157 (2019).","journal-title":"Front. Genet."},{"key":"56596_CR87","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/j.gene.2014.01.044","volume":"540","author":"Y Liu","year":"2014","unstructured":"Liu, Y. et al. Genetic variations in insulin-like growth factor binding protein acid labile subunit gene associated with growth traits in beef cattle (Bos taurus) in China. Gene 540, 246\u2013250 (2014).","journal-title":"Gene"},{"key":"56596_CR88","doi-asserted-by":"publisher","first-page":"9945","DOI":"10.3390\/ijms25189945","volume":"25","author":"XF Yu","year":"2024","unstructured":"Yu, X. F. et al. Novel Function of Osteocalcin in Chondrocyte Differentiation and Endochondral Ossification Revealed on a CRISPR\/Cas9 bglap\u2013bglap2 Deficiency Mouse Model. IJMS 25, 9945 (2024).","journal-title":"IJMS"},{"key":"56596_CR89","doi-asserted-by":"publisher","first-page":"5839","DOI":"10.3390\/ijms25115839","volume":"25","author":"V Reyes Alcaraz","year":"2024","unstructured":"Alcaraz, V.R., Pattappa, G., Miura, S., Angele, P., Blunk, T., Rudert, M., Hiraki, Y., Shukunami, C. and Docheva, D. A Narrative Review of the Roles of Chondromodulin-I (Cnmd) in Adult Cartilage Tissue. IJMS 25, 5839 (2024).","journal-title":"IJMS"},{"key":"56596_CR90","doi-asserted-by":"publisher","first-page":"S91","DOI":"10.1053\/joca.2001.0450","volume":"9","author":"C Shukunami","year":"2001","unstructured":"Shukunami, C. & Hiraki, Y. Role of cartilage-derived anti-angiogenic factor, chondromodulin-I, during endochondral bone formation. Osteoarthr. Cartil. 9, S91\u2013S101 (2001).","journal-title":"Osteoarthr. Cartil."},{"key":"56596_CR91","doi-asserted-by":"publisher","first-page":"45156","DOI":"10.1038\/srep45156","volume":"7","author":"X Chen","year":"2017","unstructured":"Chen, X. et al. Akirin2 regulates proliferation and differentiation of porcine skeletal muscle satellite cells via ERK1\/2 and NFATc1 signaling pathways. Sci. Rep. 7, 45156 (2017).","journal-title":"Sci. Rep."},{"key":"56596_CR92","doi-asserted-by":"publisher","first-page":"835","DOI":"10.3390\/ani11030835","volume":"11","author":"M Mohammadabadi","year":"2021","unstructured":"Mohammadabadi, M., Bordbar, F., Jensen, J., Du, M. & Guo, W. Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals. Animals 11, 835 (2021).","journal-title":"Animals"},{"key":"56596_CR93","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s12929-023-00925-3","volume":"30","author":"YC Lin","year":"2023","unstructured":"Lin, Y. C., Sahoo, B. K., Gau, S. S. & Yang, R. B. The biology of SCUBE. J. Biomed. Sci. 30, 33 (2023).","journal-title":"J. Biomed. Sci."},{"key":"56596_CR94","doi-asserted-by":"publisher","first-page":"3356","DOI":"10.1016\/j.celrep.2019.11.015","volume":"29","author":"J Ferent","year":"2019","unstructured":"Ferent, J. et al. The Ciliary Protein Arl13b Functions Outside of the Primary Cilium in Shh-Mediated Axon Guidance. Cell. Rep. 29, 3356\u20133366e3 (2019).","journal-title":"Cell. Rep."},{"key":"56596_CR95","doi-asserted-by":"publisher","first-page":"102088","DOI":"10.1016\/j.tice.2023.102088","volume":"82","author":"T Lin","year":"2023","unstructured":"Lin, T. & Sun, Y. Arl13b promotes the proliferation, migration, osteogenesis, and mechanosensation of osteoblasts. Tissue Cell. 82, 102088 (2023).","journal-title":"Tissue Cell."},{"key":"56596_CR96","doi-asserted-by":"publisher","first-page":"3566","DOI":"10.1242\/jcs.051904","volume":"122","author":"Y Yan","year":"2009","unstructured":"Yan, Y. et al. Axin2 controls bone remodeling through the \u03b2-catenin\u2013BMP signaling pathway in adult mice. J. Cell Sci. 122, 3566\u20133578 (2009).","journal-title":"J. Cell Sci."},{"key":"56596_CR97","doi-asserted-by":"publisher","first-page":"2571","DOI":"10.3390\/ani12192571","volume":"12","author":"D Zhou","year":"2022","unstructured":"Zhou, D. et al. The MyoD1 Promoted Muscle Differentiation and Generation by Activating CCND2 in Guanling Cattle. Animals 12, 2571 (2022).","journal-title":"Animals"},{"key":"56596_CR98","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1186\/s12861-021-00241-9","volume":"21","author":"MT Langhans","year":"2021","unstructured":"Langhans, M. T. et al. Wdpcp regulates cellular proliferation and differentiation in the developing limb via hedgehog signaling. BMC Dev. Biol. 21, 10 (2021).","journal-title":"BMC Dev. Biol."},{"key":"56596_CR99","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1186\/s12864-022-08527-3","volume":"23","author":"T Zhang","year":"2022","unstructured":"Zhang, T. et al. Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts. BMC Genom. 23, 387 (2022).","journal-title":"BMC Genom."},{"key":"56596_CR100","doi-asserted-by":"publisher","unstructured":"Feng, L. et al. Tnnt1 Gene Expression and its Polymorphism Association with Growth Traits and Feed Intake in Sheep. Preprint at (2025). https:\/\/doi.org\/10.2139\/ssrn.5167748","DOI":"10.2139\/ssrn.5167748"},{"key":"56596_CR101","doi-asserted-by":"publisher","first-page":"7964","DOI":"10.1074\/jbc.M109.063586","volume":"285","author":"W Hu","year":"2010","unstructured":"Hu, W. et al. Alkaline Ceramidase 3 (ACER3) Hydrolyzes Unsaturated Long-chain Ceramides, and Its Down-regulation Inhibits Both Cell Proliferation and Apoptosis. J. Biol. Chem. 285, 7964\u20137976 (2010).","journal-title":"J. Biol. Chem."},{"key":"56596_CR102","doi-asserted-by":"publisher","first-page":"e135355","DOI":"10.1172\/jci.insight.135355","volume":"5","author":"N Schall","year":"2020","unstructured":"Schall, N. et al. Protein kinase G1 regulates bone regeneration and rescues diabetic fracture healing. JCI Insight. 5, e135355 (2020).","journal-title":"JCI Insight"},{"key":"56596_CR103","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1186\/s13059-024-03288-6","volume":"25","author":"J Yang","year":"2024","unstructured":"Yang, J. et al. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol. 25, 148 (2024).","journal-title":"Genome Biol."},{"key":"56596_CR104","doi-asserted-by":"publisher","unstructured":"Farhan, H., Zahoor, M., Tauer, J. T. & H\u00f6gler, W. The endoplasmic reticulum proteostasis network and bone disease. Trends Mol. Med. S1471491425001455 https:\/\/doi.org\/10.1016\/j.molmed.2025.06.005 (2025).","DOI":"10.1016\/j.molmed.2025.06.005"},{"key":"56596_CR105","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/s40575-024-00138-3","volume":"11","author":"DD Cayabyab","year":"2024","unstructured":"Cayabyab, D. D., Belanger, J. M., Xu, C., Maga, E. A. & Oberbauer, A. M. Cellular localization of a variant RAPGEF5 protein associated with idiopathic epilepsy risk in the Belgian shepherd. Canine Med. Genet. 11, 4 (2024).","journal-title":"Canine Med. Genet."},{"key":"56596_CR106","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1016\/j.devcel.2017.12.001","volume":"44","author":"JN Griffin","year":"2018","unstructured":"Griffin, J. N. et al. RAPGEF5 Regulates Nuclear Translocation of \u03b2-Catenin. Dev. Cell. 44, 248\u2013260e4 (2018).","journal-title":"Dev. Cell"},{"key":"56596_CR107","doi-asserted-by":"publisher","first-page":"2353","DOI":"10.1074\/jbc.M705986200","volume":"283","author":"SN Freeman","year":"2008","unstructured":"Freeman, S. N., Ma, Y. & Cress, W. D. RhoBTB2 (DBC2) Is a Mitotic E2F1 Target Gene with a Novel Role in Apoptosis. J. Biol. Chem. 283, 2353\u20132362 (2008).","journal-title":"J. Biol. Chem."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-56596-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-56596-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-56596-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T09:07:20Z","timestamp":1783415240000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-56596-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,8]]},"references-count":107,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["56596"],"URL":"https:\/\/doi.org\/10.1038\/s41598-026-56596-1","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,8]]},"assertion":[{"value":"11 March 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"8 June 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests pertaining to the research published in this manuscript.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"20985"}}