{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T06:44:41Z","timestamp":1788417881391,"version":"build-2803163510"},"reference-count":92,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T00:00:00Z","timestamp":1766361600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T00:00:00Z","timestamp":1766361600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"ICAR-NBAGR","award":["7.85"],"award-info":[{"award-number":["7.85"]}]},{"name":"ICAR-NBAGR","award":["7.85"],"award-info":[{"award-number":["7.85"]}]},{"name":"ICAR-NBAGR","award":["7.85"],"award-info":[{"award-number":["7.85"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Mamm Genome"],"published-print":{"date-parts":[[2026,12]]},"DOI":"10.1007\/s00335-025-10186-0","type":"journal-article","created":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T14:59:52Z","timestamp":1766415592000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Genome-wide SNP evidence for the genetic uniqueness of indigenous cattle population"],"prefix":"10.1007","volume":"37","author":[{"given":"Kiyevi G.","family":"Chishi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjeev","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rangasai Chandra","family":"Goli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"K. K.","family":"Kanaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Indrajit","family":"Ganguly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S. V.","family":"Kuralkar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sat Pal","family":"Dixit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,22]]},"reference":[{"key":"10186_CR1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2020.00210","volume":"11","author":"N Abramovs","year":"2020","unstructured":"Abramovs N, Brass A, Tassabehji M (2020) Hardy-Weinberg equilibrium in the large scale genomic sequencing era. Front Genet 11:210","journal-title":"Front Genet"},{"issue":"9","key":"10186_CR2","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","volume":"19","author":"DH Alexander","year":"2009","unstructured":"Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19(9):1655\u20131664","journal-title":"Genome Res"},{"key":"10186_CR3","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2019.00609","author":"A Alshawi","year":"2019","unstructured":"Alshawi A, Essa A, Al-Bayatti S, Hanotte O (2019) Genome analysis reveals genetic admixture and signature of selection for productivity and environmental traits in Iraqi cattle. Front Genet. https:\/\/doi.org\/10.3389\/fgene.2019.00609","journal-title":"Front Genet"},{"key":"10186_CR4","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2015.00109","volume":"6","author":"M Barbato","year":"2015","unstructured":"Barbato M, Orozco-terWengel P, Tapio M, Bruford MW (2015) SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front Genet 6:109","journal-title":"Front Genet"},{"issue":"1","key":"10186_CR5","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1017\/S1751731117001355","volume":"12","author":"F Bertolini","year":"2018","unstructured":"Bertolini F, Galimberti G, Schiavo G, Mastrangelo S, Di Gerlando R, Strillacci MG, Bagnato A, Portolano B, Fontanesi L (2018) Preselection statistics and random forest classification identify population informative single nucleotide polymorphisms in cosmopolitan and autochthonous cattle breeds. Animal 12(1):12\u201319","journal-title":"Animal"},{"issue":"4","key":"10186_CR6","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1016\/j.ajhg.2014.08.011","volume":"95","author":"G Bhatia","year":"2014","unstructured":"Bhatia G, Tandon A, Patterson N, Aldrich MC, Ambrosone CB, Amos C, Price AL (2014) Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture. Am J Hum Genet 95(4):437\u2013444","journal-title":"Am J Hum Genet"},{"issue":"6","key":"10186_CR7","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1111\/jbg.12479","volume":"137","author":"Q Chen","year":"2020","unstructured":"Chen Q, Zhan J, Shen J, Qu K, Hanif Q, Liu J, Zhang J, Chen N, Chen H, Huang B, Lei C (2020) Whole-genome resequencing reveals diversity, global and local ancestry proportions in Yunling cattle. J Anim Breed Genet 137(6):641\u2013650","journal-title":"J Anim Breed Genet"},{"issue":"2","key":"10186_CR8","doi-asserted-by":"publisher","first-page":"1726","DOI":"10.1016\/j.ygeno.2019.10.008","volume":"112","author":"S Chhotaray","year":"2020","unstructured":"Chhotaray S, Panigrahi M, Pal D, Ahmad SF, Bhushan B, Gaur GK, Singh RK (2020) Ancestry informative markers derived from discriminant analysis of principal components provide important insights into the composition of crossbred cattle. Genomics 112(2):1726\u20131733","journal-title":"Genomics"},{"issue":"6","key":"10186_CR11","doi-asserted-by":"publisher","first-page":"e0198419","DOI":"10.1371\/journal.pone.0198419","volume":"13","author":"B Czech","year":"2018","unstructured":"Czech B, Fr\u0105szczak M, Mielczarek M, Szyda J (2018) Identification and annotation of breed-specific single nucleotide polymorphisms in Bos taurus genomes. PLoS One 13(6):e0198419. https:\/\/doi.org\/10.1371\/journal.pone.0198419","journal-title":"PLoS One"},{"key":"10186_CR74","unstructured":"DAHD. Breed-wise report of livestock and poultry. Based on 20th livestock census (2022) https:\/\/dahd.nic.in\/sites\/default\/filess\/Breed%20Report%20Full%20Book.pdf)"},{"issue":"1","key":"10186_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-021-01144-2","volume":"11","author":"SP Dixit","year":"2021","unstructured":"Dixit SP, Bhatia AK, Ganguly I, Singh S, Dash S, Sharma A, Anandkumar N, Dang AK, Jayakumar S (2021) Genome analyses revealed genetic admixture and selection signatures in Bos indicus. Sci Rep 11(1):1\u201311","journal-title":"Sci Rep"},{"key":"10186_CR12","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2020.00092","volume":"11","author":"SP Dixit","year":"2020","unstructured":"Dixit SP, Ganguly I, Bhatia AK, Kumar NA, Jayakumar S (2020) Genome-wide runs of homozygosity revealed selection signatures in Bos indicus. Front Genet 11:476081","journal-title":"Front Genet"},{"key":"10186_CR14","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/s12863-014-0092-9","volume":"15","author":"KG Dodds","year":"2014","unstructured":"Dodds KG, Auvray B, Newman SAN, McEwan JC (2014) Genomic breed prediction in New Zealand sheep. BMC Genet 15:92. https:\/\/doi.org\/10.1186\/s12863-014-0092-9","journal-title":"BMC Genet"},{"key":"10186_CR78","doi-asserted-by":"publisher","unstructured":"Edea Z, Bhuiyan MSA, Dessie T, Rothschild MF, Dadi H, Kim KS (2015) Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds. Animal 9:218\u2013226. https:\/\/doi.org\/10.1017\/S1751731114002560","DOI":"10.1017\/S1751731114002560"},{"key":"10186_CR15","unstructured":"Falconer DS (1996) Introduction to quantitative genetics. Pearson Education India"},{"key":"10186_CR23","unstructured":"FAO (2007) Global plan of action and the interlaken declaration commission on genetic resources for food and agriculture. Food and agriculture organization of the United Nations, Rome"},{"key":"10186_CR51","unstructured":"FAO (2012) Phenotypic characterization of animal genetic resources. FAO Animal Production and Health Guidelines Rome No. 11"},{"key":"10186_CR69","unstructured":"FAO (2015) The second report on the state of the world\u2019s FAO commission on genetic resources for food and agriculture assessments \u2022 2015"},{"key":"10186_CR80","doi-asserted-by":"publisher","unstructured":"Fonseca PAS, Su\u00e1rez-Vega A, Marras G, C\u00e1novas \u00c1 (2020) GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci. GigaScience 9:giaa149. https:\/\/doi.org\/10.1093\/gigascience\/giaa149","DOI":"10.1093\/gigascience\/giaa149"},{"key":"10186_CR81","doi-asserted-by":"crossref","unstructured":"Frkonja A, Gredler B, Schnyder U, Curik I, S\u00f6lkner J (2012) Prediction of breed composition in an admixed cattle population. Anim Genet 43:696\u2013703","DOI":"10.1111\/j.1365-2052.2012.02345.x"},{"issue":"1\u20133","key":"10186_CR16","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1016\/j.smallrumres.2011.03.031","volume":"98","author":"LT Gama","year":"2011","unstructured":"Gama LT, Bressan MC (2011) Biotechnology applications for the sustainable management of goat genetic resources. Small Ruminant Res 98(1\u20133):133\u2013146","journal-title":"Small Ruminant Res"},{"issue":"1","key":"10186_CR17","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-024-10924-9","volume":"25","author":"M Gangwar","year":"2024","unstructured":"Gangwar M, Ahmad SF, Ali AB, Kumar A, Kumar A, Gaur GK, Dutt T (2024) Identifying low-density, ancestry-informative SNP markers through whole genome resequencing in Indian, Chinese, and wild yak. BMC Genomics 25(1):1043","journal-title":"BMC Genomics"},{"issue":"2","key":"10186_CR19","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.1534\/genetics.107.075804","volume":"177","author":"M Gautier","year":"2007","unstructured":"Gautier M, Faraut T, Moazami-Goudarzi K, Navratil V, Foglio M, Grohs C, Eggen A (2007) Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics 177(2):1059\u20131070","journal-title":"Genetics"},{"issue":"15","key":"10186_CR18","doi-asserted-by":"publisher","first-page":"3128","DOI":"10.1111\/j.1365-294X.2011.05163.x","volume":"20","author":"M Gautier","year":"2011","unstructured":"Gautier M, Naves M (2011) Footprints of selection in the ancestral admixture of a new world Creole cattle breed. Mol Ecol 20(15):3128\u20133143","journal-title":"Mol Ecol"},{"key":"10186_CR75","unstructured":"Gazetteer of the Bombay Presidency: Vol. A. Amraoti District. Government of Maharashtra, Gazetteers Department, Executive, Editor, Secretary (1911) Gazetteers Department. (www.gazetteers.maharashtra.gov.in\/cultural.maharashtra.gov.in\/english\/gazetteer\/Amravati%20District\/agriculture_live_stock.html)"},{"issue":"5","key":"10186_CR22","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1093\/hmg\/ddi493","volume":"15","author":"J Gibson","year":"2006","unstructured":"Gibson J, Morton NE, Collins A (2006) Extended tracts of homozygosity in outbred human populations. Hum Mol Genet 15(5):789\u2013795","journal-title":"Hum Mol Genet"},{"issue":"4","key":"10186_CR24","doi-asserted-by":"publisher","first-page":"237","DOI":"10.2174\/0113892029298909240426094055","volume":"25","author":"RC Goli","year":"2024","unstructured":"Goli RC, Chishi KG, Ganguly I, Singh S, Dixit SP, Rathi P, Diwakar Vikas, C Chandana Sree, Limbalkar Omkar Maharudra, Sukhija Nidhi, Kanaka KK (2024b) Global and local ancestry and its importance: a review. Curr Genomics 25(4):237\u2013260","journal-title":"Curr Genomics"},{"issue":"1","key":"10186_CR26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-025-01971-7","volume":"15","author":"RC Goli","year":"2025","unstructured":"Goli RC, Chishi KG, Mahar K, Ganguly I, Singh S, Dixit SP, Sruthi OS, Choudhary S, Diwakar V, Rathi P, Chinnareddyvari CS (2025b) Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India. Sci Rep 15(1):1\u201315","journal-title":"Sci Rep"},{"issue":"5","key":"10186_CR25","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1089\/omi.2024.0206","volume":"29","author":"RC Goli","year":"2025","unstructured":"Goli RC, Chishi KG, Mahar K, Gunturu T, Metta M, Diwakar V, Purohit P, Kumar A, Channabasappa NK, Aderao GN, Sukhija N (2025a) Rethinking River buffalo domestication through the lens of population genetics tools: mehsana buffalo is a unique population. OMICS: A Journal of Integrative Biology 29(5):206\u2013220","journal-title":"OMICS: A Journal of Integrative Biology"},{"key":"10186_CR27","doi-asserted-by":"publisher","DOI":"10.1016\/j.smallrumres.2025.107492","volume":"247","author":"RC Goli","year":"2025","unstructured":"Goli RC, Mahar K, Chishi KG, Koloi S, Gunturu T, Diwakar V, Metta M, Kumar A, Aderao GN, Nikhil KC, Sarkar S (2025c) X-linked signatures of positive selection and adaptive genetic plasticity shaping high-altitude resilience in Indian Changthangi sheep. Small Ruminant Res 247:107492","journal-title":"Small Ruminant Res"},{"key":"10186_CR28","doi-asserted-by":"publisher","first-page":"1778","DOI":"10.1017\/S1751731116000914","volume":"10","author":"SJG Hall","year":"2016","unstructured":"Hall SJG (2016) Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data. Anim 10:1778\u20131785","journal-title":"Anim"},{"issue":"1","key":"10186_CR30","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"DW Huang","year":"2009","unstructured":"Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44\u201357","journal-title":"Nat Protoc"},{"issue":"11","key":"10186_CR31","doi-asserted-by":"publisher","first-page":"5128","DOI":"10.2527\/jas.2013-6678","volume":"91","author":"B Hulsegge","year":"2013","unstructured":"Hulsegge B, Calus MPL, Windig JJ, Hoving-Bolink AH, Maurice-van Eijndhoven MHT, Hiemstra SJ (2013) Selection of SNP from 50K and 777K arrays to predict breed of origin in cattle. J Anim Sci 91(11):5128\u20135134. https:\/\/doi.org\/10.2527\/jas.2013-6678","journal-title":"J Anim Sci"},{"key":"10186_CR76","unstructured":"ICAR-NBAGR (2016) Guidelines for Management of Animal GeneticResources of India. National Bureau of Animal Genetic Resources(Indian Council of Agricultural Research), Karnal (Haryana), India, 163 p. (PDF) Guidelines for Management of Animal Genetic Resources of India. Available from: https:\/\/www.researchgate.net\/publication\/315836080_Guidelines_for_Management_of_Animal_Genetic_Resources_of_India [accessed Jun 18 2025]"},{"key":"10186_CR55","doi-asserted-by":"crossref","unstructured":"Kanaka KK, Ganguly I, Singh S, Kuralkar SV, Dixit S, Sukhija N, Goli RC (2025) RASEL: An ensemble model for selection of core SNPs and its application for identification and classification of cattle breeds","DOI":"10.1007\/s10528-025-11230-z"},{"key":"10186_CR32","doi-asserted-by":"publisher","first-page":"100278","DOI":"10.1016\/j.cpb.2023.100278","volume":"33","author":"KK Kanaka","year":"2023","unstructured":"Kanaka KK, Sukhija N, Goli RC, Singh S, Ganguly I, Dixit SP, Malik AA (2023) On the concepts and measures of diversity in the genomics era. Curr Plant Biol 33:100278","journal-title":"Curr Plant Biol"},{"issue":"5","key":"10186_CR33","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1093\/jhered\/esv044","volume":"106","author":"I Kavakiotis","year":"2015","unstructured":"Kavakiotis I, Triantafyllidis A, Ntelidou D, Alexandri P, Megens HJ, Crooijmans RP, Vlahavas I (2015) TRES: identification of discriminatory and informative SNPs from population genomic data. J Hered 106(5):672\u2013676","journal-title":"J Hered"},{"key":"10186_CR41","unstructured":"Ketkar SV (ed) (1929) Maharashtriya Dyankosh. Maharashtra Rajya Sahitya ani Sanskriti Mandal"},{"issue":"1","key":"10186_CR34","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-187","volume":"9","author":"MS Khatkar","year":"2008","unstructured":"Khatkar MS, Nicholas FW, Collins AR, Zenger KR, Cavanagh JA, Barris W, Raadsma HW (2008) Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 9(1):187","journal-title":"BMC Genomics"},{"key":"10186_CR82","doi-asserted-by":"publisher","unstructured":"Kijas JW, Lenstra JA, Hayes B et al (2012) Genome-wide analysis of the world\u2019s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol 10:e1001258. https:\/\/doi.org\/10.1371\/journal.pbio.1001258","DOI":"10.1371\/journal.pbio.1001258"},{"key":"10186_CR35","doi-asserted-by":"publisher","first-page":"148957","DOI":"10.1016\/j.gene.2024.148957","volume":"933","author":"S Koloi","year":"2025","unstructured":"Koloi S, Ganguly I, Singh S, Dixit S (2025) Whole genome re-sequencing reveals high altitude adaptation signatures and admixture in Ladakhi cattle. Gene 933:148957","journal-title":"Gene"},{"key":"10186_CR77","doi-asserted-by":"crossref","unstructured":"Kumar H, Panigrahi M, Chhotaray S, Pal D, Bhanuprakash V, Saravanan KA, Bhushan B (2019) Identification of breed-specific SNP panel in nine different cattle genomes. Biomed Res, 30(1)","DOI":"10.35841\/biomedicalresearch.30-18-1195"},{"key":"10186_CR36","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2024.149096","volume":"936","author":"TS Kumar","year":"2025","unstructured":"Kumar TS, Singh S, Ganguly I, Dixit SP (2025) Mitogenome diversity and evolution of Bos indicus cattle in India. Gene 936:149096","journal-title":"Gene"},{"issue":"9","key":"10186_CR37","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1002\/bies.201300014","volume":"35","author":"J Lachance","year":"2013","unstructured":"Lachance J, Tishkoff SA (2013) Snp ascertainment bias in population genetic analyses: why it is important, and how to correct it. Bioessays 35(9):780\u2013786","journal-title":"Bioessays"},{"key":"10186_CR83","doi-asserted-by":"publisher","unstructured":"Laird NM, Lange C (2011) The fundamentals of modern statistical genetics. Springer, New York. https:\/\/doi.org\/10.1007\/978-1-4419-7338-2","DOI":"10.1007\/978-1-4419-7338-2"},{"key":"10186_CR38","doi-asserted-by":"publisher","unstructured":"Li R, Chen S, Li C, Xiao H, Costa V, Bhuiyan MSA, Baig M, Beja-Pereira A (2022) Whole-genome analysis deciphers population structure and genetic introgression among bovine species. Front Genet 13:847492. https:\/\/doi.org\/10.3389\/fgene.2022.847492","DOI":"10.3389\/fgene.2022.847492"},{"key":"10186_CR39","doi-asserted-by":"crossref","unstructured":"Mahar K, Goli RC, Chishi KG, Ganguly I, Dixit SP, Singh S, Choudhary S, Rathi P, Chinnareddyvari CS, Diwakar V, Metta M (2024) Runs of homozygosity decipher genetic diversity in cattle breed dwelling in the colder regions of the world. Cytogenet Genome Res 164(3\u20134):154\u2013164","DOI":"10.1159\/000541723"},{"key":"10186_CR40","doi-asserted-by":"crossref","unstructured":"Mahar K, Goli RC, Chishi KG, Ganguly I, Dixit SP, Singh S, Kareningappa KK (2024b) Runs of homozygosity Decipher genetic diversity in cattle breed dwelling in the colder regions of the world. Cytogenet Genome Res 164(3\u20134):154\u2013164","DOI":"10.1159\/000541723"},{"issue":"5","key":"10186_CR42","doi-asserted-by":"publisher","first-page":"e0246497","DOI":"10.1371\/journal.pone.0246497","volume":"16","author":"V Manomohan","year":"2021","unstructured":"Manomohan V, Saravanan R, Pichler R, Murali N, Sivakumar K, Sudhakar K, Nachiappan RK, Periasamy K (2021) Legacy of draught cattle breeds of South India: insights into population structure, genetic admixture and maternal origin. PLoS One 16(5):e0246497","journal-title":"PLoS One"},{"issue":"2","key":"10186_CR43","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1111\/age.12259","volume":"46","author":"G Marras","year":"2015","unstructured":"Marras G, Gaspa G, Sorbolini S et al (2015) Analysis of runs of homozygosity and their relationship with inbreeding in five cattle breeds farmed in Italy. Anim Genet 46(2):110\u2013121","journal-title":"Anim Genet"},{"issue":"1","key":"10186_CR44","doi-asserted-by":"publisher","first-page":"9379","DOI":"10.1038\/s41598-023-32418-6","volume":"13","author":"N Masharing","year":"2023","unstructured":"Masharing N, Sodhi M, Chanda D, Singh I, Vivek P, Tiwari M, Mukesh M (2023) DdRAD sequencing based genotyping of six Indigenous dairy cattle breeds of India to infer existing genetic diversity and population structure. Sci Rep 13(1):9379","journal-title":"Sci Rep"},{"key":"10186_CR45","doi-asserted-by":"crossref","unstructured":"Mokry FB, Buzanskas ME, de Alvarenga Mudadu M, do, Amaral Grossi D, Higa RH, Ventura RV, de Almeida Regitano LC (2014) Linkage disequilibrium and haplotype block structure in a composite beef cattle breed. BMC genomics, 15(7), 1\u20139","DOI":"10.1186\/1471-2164-15-S7-S6"},{"issue":"6","key":"10186_CR47","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1111\/jbg.12356","volume":"135","author":"N Nayee","year":"2018","unstructured":"Nayee N, Sahana G, Gajjar S, Sudhakar A, Trivedi K, Lund MS, Guldbrandtsen B (2018) Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses. J Anim Breed Genet 135(6):432\u2013441","journal-title":"J Anim Breed Genet"},{"issue":"949","key":"10186_CR48","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1086\/282771","volume":"106","author":"M Nei","year":"1972","unstructured":"Nei M (1972) Genetic distance between populations. Am Nat 106(949):283\u2013292","journal-title":"Am Nat"},{"key":"10186_CR84","unstructured":"Neogen Corporation (2021) GGP Indicus technical specifications. Neogen Corporation, Lincoln, NE"},{"issue":"1","key":"10186_CR49","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1046\/j.1523-1739.1994.08010175.x","volume":"8","author":"L Nunney","year":"1994","unstructured":"Nunney L, Elam DR (1994) Estimating the effective population size of conserved populations. Conserv Biol 8(1):175\u2013184","journal-title":"Conserv Biol"},{"key":"10186_CR85","unstructured":"Ojango JM, Marete A, Mujibi FDN, Rao EJO, Poole EJ, Rege JEO, Chagunda MGG, Kahi AK, Gibson J (2014) A novel use of high-density SNP assays to optimize choice of different crossbred dairy cattle genotypes in smallholder systems in East Africa. In: Proc 10th World Congr Genet Appl Livest Prod, Vancouver, Canada"},{"issue":"3","key":"10186_CR50","doi-asserted-by":"publisher","first-page":"1065","DOI":"10.1534\/genetics.112.145037","volume":"192","author":"N Patterson","year":"2012","unstructured":"Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, Zhan Y, Reich D (2012) Ancient admixture in human history. Genetics 192(3):1065\u20131093","journal-title":"Genetics"},{"key":"10186_CR86","doi-asserted-by":"crossref","unstructured":"Peripolli E, Stafuzza NB, Munari DP et al (2018) Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. BMC Genomics 19:34","DOI":"10.1186\/s12864-017-4365-3"},{"key":"10186_CR87","doi-asserted-by":"publisher","unstructured":"Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8:e1002967. https:\/\/doi.org\/10.1371\/journal.pgen.1002967","DOI":"10.1371\/journal.pgen.1002967"},{"key":"10186_CR9","volume-title":"Agro-climatic Regional Planning: An Overview","author":"Planning Commission","year":"1989","unstructured":"Planning Commission (1989) Agro-climatic Regional Planning: An Overview. Government of India, New Delhi"},{"issue":"3","key":"10186_CR52","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","volume":"81","author":"S Purcell","year":"2007","unstructured":"Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559\u2013575","journal-title":"Am J Hum Genet"},{"key":"10186_CR53","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2156-13-70","volume":"13","author":"DC Purfield","year":"2012","unstructured":"Purfield DC, Berry DP, McParland S, Bradley DG (2012) Runs of homozygosity and population history in cattle. BMC Genet 13:1\u201311","journal-title":"BMC Genet"},{"issue":"4","key":"10186_CR54","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1111\/j.1365-2052.2009.02016.x","volume":"41","author":"S Qanbari","year":"2010","unstructured":"Qanbari S, Pimentel ECG, Tetens J, Thaller G, Lichtner P, Sharifi AR, Simianer H (2010) A genome-wide scan for signatures of recent selection in Holstein cattle. Anim Genet 41(4):377\u2013389","journal-title":"Anim Genet"},{"issue":"5602","key":"10186_CR56","doi-asserted-by":"publisher","first-page":"2381","DOI":"10.1126\/science.1078311","volume":"298","author":"NA Rosenberg","year":"2002","unstructured":"Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298(5602):2381\u20132385","journal-title":"Science"},{"issue":"1","key":"10186_CR57","doi-asserted-by":"publisher","first-page":"pdb-prot4455","DOI":"10.1101\/pdb.prot4455","volume":"2006","author":"J Sambrook","year":"2006","unstructured":"Sambrook J, Russell DW (2006) Purification of nucleic acids by extraction with phenol: chloroform. Cold Spring Harb Protoc 2006(1):pdb-prot4455","journal-title":"Cold Spring Harb Protoc"},{"issue":"2","key":"10186_CR58","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1016\/j.ajhg.2007.09.022","volume":"82","author":"S Sankararaman","year":"2008","unstructured":"Sankararaman S, Sridhar S, Kimmel G, Halperin E (2008) Estimating local ancestry in admixed populations. Am J Hum Genet 82(2):290\u2013303","journal-title":"Am J Hum Genet"},{"issue":"3","key":"10186_CR59","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1080\/09291016.2019.1642650","volume":"53","author":"KA Saravanan","year":"2022","unstructured":"Saravanan KA, Panigrahi M, Kumar H, Bhushan B (2022b) Advanced software programs for the analysis of genetic diversity in livestock genomics: a mini review. Biol Rhythm Res 53(3):358\u2013368","journal-title":"Biol Rhythm Res"},{"key":"10186_CR88","doi-asserted-by":"publisher","unstructured":"Schmidt TL, Jasper M, Weeks AR, Hoffmann AA (2021) Unbiased population heterozygosity estimates from genome-wide sequence data. Methods Ecol Evol 12:1888\u20131898. https:\/\/doi.org\/10.1111\/2041-210X.13659","DOI":"10.1111\/2041-210X.13659"},{"key":"10186_CR89","doi-asserted-by":"crossref","unstructured":"Scraggs E, Zanella R, Wojtowicz A et al (2014) Estimation of inbreeding and effective population size of full-blood Wagyu cattle registered with the American Wagyu Cattle Association. J Anim Breed Genet 131:3\u201310","DOI":"10.1111\/jbg.12066"},{"key":"10186_CR61","doi-asserted-by":"publisher","first-page":"6429","DOI":"10.1007\/s11033-020-05639-5","volume":"47","author":"R Sharma","year":"2020","unstructured":"Sharma R, Ahlawat S, Sharma H, Bhagat RL, Singh PK, Tantia MS (2020) Identification of a new potential native Indian cattle breed by population differentiation based on microsatellite markers. Mol Biol Rep 47:6429\u20136434","journal-title":"Mol Biol Rep"},{"key":"10186_CR60","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.mgene.2016.01.002","volume":"8","author":"R Sharma","year":"2016","unstructured":"Sharma R, Kumar B, Arora R, Ahlawat S, Mishra AK, Tantia MS (2016) Genetic diversity estimates point to immediate efforts for conserving the endangered Tibetan sheep of India. Meta Gene 8:14\u201320","journal-title":"Meta Gene"},{"key":"10186_CR62","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1007\/s11032-012-9774-z","volume":"31","author":"K Shirasawa","year":"2012","unstructured":"Shirasawa K, Ishii K, Kim C, Ban T, Suzuki M, Ito T et al (2012) Development of Capsicum EST\u2013SSR markers for species identification and in silico mapping onto the tomato genome sequence. Mol Breed 31:101\u2013110. https:\/\/doi.org\/10.1007\/s11032-012-9774-z","journal-title":"Mol Breed"},{"key":"10186_CR63","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1007\/s00439-002-0896-y","volume":"112","author":"MD Shriver","year":"2003","unstructured":"Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, Jovel C, Pfaff C, Jones C, Massac A, Cameron N, Baron A (2003) Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet 112:387\u2013399","journal-title":"Hum Genet"},{"key":"10186_CR10","unstructured":"Singh CV (2016) Cross-breeding in cattle for milk production: Achievements, challenges and opportunities in India-A review. Adv Dairy Res, 1\u201314"},{"issue":"4","key":"10186_CR64","first-page":"44","volume":"38","author":"S Singh","year":"2014","unstructured":"Singh S, Singh RS, Singh SP (2014) Farm power availability on Indian farms. Agric Eng Today 38(4):44\u201352","journal-title":"Agric Eng Today"},{"key":"10186_CR90","doi-asserted-by":"publisher","unstructured":"Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science 236:787\u2013792. https:\/\/doi.org\/10.1126\/science.3576198","DOI":"10.1126\/science.3576198"},{"key":"10186_CR20","unstructured":"Strucken EM, Swaminathan M, Joshi S, Gibson JP (2019) Genetic characterization of Indian indigenous cattle breeds. In Proc. Assoc. Advmt. Anim. Breed. Genet (Vol. 23, pp. 187\u2013190)"},{"issue":"6","key":"10186_CR65","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1007\/s11250-023-03798-8","volume":"55","author":"A Sudhakar","year":"2023","unstructured":"Sudhakar A, Nayee N, Saha S, Donthula SK, Poojara HV, Gohil T, Patel AC, Maurya BK (2023) Role of genetic introgression in introducing mutant alleles in Bos indicus cattle and prevalence of lethal genetic disorders in Bos taurus\u00d7 Bos indicus and Bos indicus cattle in India. Trop Anim Health Prod 55(6):399","journal-title":"Trop Anim Health Prod"},{"issue":"1","key":"10186_CR66","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1007\/s12686-023-01339-x","volume":"16","author":"N Sukhija","year":"2024","unstructured":"Sukhija N, Goli RC, Sukhija M, Rathi P, Jaglan K, Dash A, Nandhini PB, Kanaka KK (2024) Evolutionary stamps for adaptation traced in cervus Nippon genome using reduced representation sequencing. Conserv Genet Resour 16(1):135\u2013146","journal-title":"Conserv Genet Resour"},{"issue":"2","key":"10186_CR67","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1007\/s00335-025-10122-2","volume":"36","author":"N Sukhija","year":"2025","unstructured":"Sukhija N, Kanaka KK, Ganguly I, Dixit S, Singh S, Goli RC, Rathi P, Nandini PB, Koloi S (2025) Cataloging copy number variation regions and allied diversity in goat breeds spanning Pan India. Mamm Genome 36(2):523\u2013540","journal-title":"Mamm Genome"},{"issue":"3","key":"10186_CR68","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1086\/520769","volume":"81","author":"H Tang","year":"2007","unstructured":"Tang H, Choudhry S, Mei R, Morgan M, Rodriguez-Cintron W, Burchard EG, Risch NJ (2007) Recent genetic selection in the ancestral admixture of Puerto Ricans. Am J Hum Genet 81(3):626\u2013633","journal-title":"Am J Hum Genet"},{"key":"10186_CR46","unstructured":"Teneva A (2009) Molecular markers in animal genome analysis. Biotechnol Anim Husb 25:1267\u20131284"},{"key":"10186_CR91","doi-asserted-by":"publisher","unstructured":"Tittensor DP, Walpole M, Hill SLL et al (2014) A mid-term analysis of progress toward international biodiversity targets. Science 346:241\u2013244. https:\/\/doi.org\/10.1126\/science.1257484","DOI":"10.1126\/science.1257484"},{"issue":"1","key":"10186_CR70","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/1471-2156-10-19","volume":"10","author":"R Villa-Angulo","year":"2009","unstructured":"Villa-Angulo R, Matukumalli LK, Gill CA, Choi J, Van Tassell CP, Grefenstette JJ (2009) High-resolution haplotype block structure in the cattle genome. BMC Genet 10(1):19","journal-title":"BMC Genet"},{"key":"10186_CR21","doi-asserted-by":"crossref","unstructured":"Ward JA, McHugo GP, Dover MJ, Hall TJ, Ismael Ng\u2019ang\u2019a, Sonstegard S, Bradley TS, Frantz DG, Salter-Townshend LA, M. and, MacHugh DE (2022) Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations. Iscience, 25(7)","DOI":"10.1016\/j.isci.2022.104672"},{"key":"10186_CR92","doi-asserted-by":"crossref","unstructured":"Wickham H (2016) ggplot2: elegant graphics for data analysis, 2nd edn. Springer, New York","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"10186_CR71","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1111\/j.1469-1809.1949.tb02451.x","volume":"15","author":"S Wright","year":"1951","unstructured":"Wright S (1951) The genetical structure of populations. Ann Eugen 15:323\u2013354","journal-title":"Ann Eugen"},{"issue":"10","key":"10186_CR72","doi-asserted-by":"publisher","first-page":"1786","DOI":"10.1093\/bioinformatics\/bty875","volume":"35","author":"C Zhang","year":"2019","unstructured":"Zhang C, Dong SS, Xu JY, He WM, Yang TL (2019) PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics 35(10):1786\u20131788","journal-title":"Bioinformatics"},{"issue":"19","key":"10186_CR73","doi-asserted-by":"publisher","DOI":"10.3390\/ijms251910557","volume":"25","author":"M Zhang","year":"2024","unstructured":"Zhang M, Wang Y, Chen Q, Wang D, Zhang X, Huang X, Xu L (2024) Genome-wide association study on body conformation traits in Xinjiang Brown Cattle. Int J Mol Sci 25(19):10557","journal-title":"Int J Mol Sci"},{"key":"10186_CR93","doi-asserted-by":"publisher","unstructured":"Zhang Q, Calus MPL, Guldbrandtsen B, Lund MS, Sahana G (2017) Contribution of rare and low-frequency whole-genome sequence variants to complex traits variation in dairy cattle. Genet Sel Evol 49:60. https:\/\/doi.org\/10.1186\/s12711-017-0336-z","DOI":"10.1186\/s12711-017-0336-z"},{"key":"10186_CR29","doi-asserted-by":"crossref","unstructured":"Zhu X, Zhang S, Kan D, Cooper R (2003) Haplotype block definition and its application. In Biocomputing 2004 (pp. 152\u2013163)","DOI":"10.1142\/9789812704856_0015"}],"container-title":["Mammalian Genome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00335-025-10186-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00335-025-10186-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00335-025-10186-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,22]],"date-time":"2025-12-22T16:01:50Z","timestamp":1766419310000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s00335-025-10186-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,22]]},"references-count":92,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["10186"],"URL":"https:\/\/doi.org\/10.1007\/s00335-025-10186-0","relation":{},"ISSN":["0938-8990","1432-1777"],"issn-type":[{"value":"0938-8990","type":"print"},{"value":"1432-1777","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,22]]},"assertion":[{"value":"22 August 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 December 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 December 2025","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.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"The procedures for blood sampling were performed as per general guidelines and approval of Institute Animal Ethical Committee (IAEC).","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}}],"article-number":"18"}}