Ajmone-Marsan P, Colli L, Ginja C, Kantanen J, Lenstra JA, eds. Genomic characterization of animal genetic resources. FAO Animal Production and Health Guidelines No. 32. Rome: FAO; 2023. https://doi.org/10.4060/cc3079en

Baes C, Makanjuola B, Miglior F, Marras G, Howard J, Fleming A, et al. Symposium review: the genomic architecture of inbreeding: how homozygosity affects health and performance. J Dairy Sci. 2019;102:2807–17. https://doi.org/10.3168/jds.2018-15520.

Article  CAS  PubMed  Google Scholar 

Ballou JD. Ancestral inbreeding only minimally affects inbreeding depression in mammalian populations. J Hered. 1997;88(3):169–78. https://doi.org/10.1093/oxfordjournals.jhered.a023085.

Article  CAS  PubMed  Google Scholar 

Barbato M, Orozco-terWengel P, Tapio M, Bruford MW. SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front Genet. 2015;6:109. https://doi.org/10.3389/fgene.2015.00109.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Basic Animal Husbandry Statistics. Production statistics report, Department of Animal Husbandry, Dairying and Fisheries, Ministry of Fisheries, Animal Husbandry and Dairying, Government of India. 2024. https://dahd.gov.in/schemes/programmes/animal-husbandry-statistics (Accessed on 05 August 2025)

Baumung R, Farkas J, Boichard D, Mészáros G, Sölkner J, Curik I. GRAIN: a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach. J Anim Breed Genet. 2015;132(2):100–8. https://doi.org/10.1111/jbg.12145.

Article  CAS  PubMed  Google Scholar 

Bem RD, Benfica LF, Silva DA, Carrara ER, Brito LF, Mulim HA, et al. Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population. BMC Genomics. 2024;25(1):738. https://doi.org/10.1186/s12864-024-10641-3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Beribe MJ, Carignano HA, Poli MA, Lopez-Villalobos N. Effects of breed and genomic inbreeding on milk, fat and protein lactation yields and fertility traits in pasture-based dairy cows in Argentina. J Agric Sci. 2024;162(2):181–9. https://doi.org/10.1017/S0021859624000273.

Article  CAS  Google Scholar 

Biscarini F, Mastrangelo S, Catillo G, Senczuk G, Ciampolini R. Insights into genetic diversity, runs of homozygosity and heterozygosity-rich regions in Maremmana semi-feral cattle using pedigree and genomic data. Animals. 2020;10(12):2285. https://doi.org/10.3390/ani10122285.

Article  PubMed  PubMed Central  Google Scholar 

Bjelland DW, Weigel KA, Vukasinovic N, Nkrumah JD. Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. J Dairy Sci. 2013;96(7):4697–706. https://doi.org/10.3168/jds.2012-6435.

Article  CAS  PubMed  Google Scholar 

Caballero A, Fernández A, Villanueva B, Toro MA. A comparison of marker-based estimators of inbreeding and inbreeding depression. Genet Sel Evol. 2022;54:82. https://doi.org/10.1186/s12711-022-00772-0.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cañas-Álvarez JJ, Ossa-Saraz GA, Garcés-Blanquiceth JL, Burgos-Paz WO. Genealogical structure of the Colombian romosinuano creole cattle. Trop Anim Health Prod. 2023;55(5):292. https://doi.org/10.1007/s11250-023-03694-1.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carrier A, Gilbert I, Leclerc P, Duchesne M, Robert C. Characterization of the genetic pool of the Canadienne dairy cattle breed. Genet Sel Evol. 2023;55(1):32. https://doi.org/10.1186/s12711-023-00793-3.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Corbin LJ, Liu AYH, Bishop SC, Woolliams JA. Estimation of historical effective population size using linkage disequilibria with marker data. J Anim Breed Genet. 2012;129:257–70. https://doi.org/10.1111/j.1439-0388.2012.01003.x.

Article  CAS  PubMed  Google Scholar 

da Rosa MS, De Andrade FM, Machado JD, Cobuci JA. Population structure of Girolando cattle using pedigree analysis. Available at SSRN. 2023. https://doi.org/10.2139/ssrn.4356066.

Article  Google Scholar 

Dadousis C, Ablondi M, Cipolat-Gotet C, Van Kaam JT, Marusi M, Cassandro M, et al. Genomic inbreeding coefficients using imputed genotypes: assessing different estimators in Holstein-Friesian dairy cows. J Dairy Sci. 2022;105(7):5926–45. https://doi.org/10.3168/jds.2021-21125.

Article  CAS  PubMed  Google Scholar 

Dash S, Singh A, Bhatia AK, Jayakumar S, Sharma A, Singh S, et al. Evaluation of bovine high-density SNP genotyping array in indigenous dairy cattle breeds. Anim Biotechnol. 2018;29(2):129–35. https://doi.org/10.1080/10495398.2017.1329150.

Article  CAS  PubMed  Google Scholar 

Dezetter C, Leclerc H, Mattalia S, Barbat A, Boichard D, Ducrocq V. Inbreeding and crossbreeding parameters for production and fertility traits in Holstein, Montbéliarde, and Normande cows. J Dairy Sci. 2015;98:4904–13. https://doi.org/10.3168/jds.2014-8386.

Article  CAS  PubMed  Google Scholar 

Doekes HP, Bijma P, Windig JJ. How depressing is inbreeding? A meta-analysis of 30 years of research on the effects of inbreeding in livestock. Genes. 2021;12:926. https://doi.org/10.3390/genes12060926.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doekes HP, Curik I, Nagy I, Farkas J, Kövér G, Windig JJ. Revised calculation of Kalinowski’s ancestral and new inbreeding coefficients. Diversity. 2020;12:155. https://doi.org/10.3390/d12040155.

Article  Google Scholar 

Doekes HP, Veerkamp RF, Bijma P, de Jong G, Hiemstra SJ, Windig JJ. Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle. Genet Sel Evol. 2019;51(1):54. https://doi.org/10.1186/s12711-019-0497-z.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fabbri MC, Gonçalves de Rezende MP, Dadousis C, Biffani S, Negrini R, Souza Carneiro PL, et al. Population structure and genetic diversity of Italian beef breeds as a tool for planning conservation and selection strategies. Animals. 2019;9(11):880. https://doi.org/10.3390/ani9110880.

Article  PubMed  PubMed Central  Google Scholar 

Falconer DS, MacKay TFC. Introduction to quantitative genetics. 4th ed. Harlow, UK: Longmans Green; 1996.

Ferenčaković M, Sölkner J, Curik I. Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors. Genet Sel Evol. 2013;45(1):42. https://doi.org/10.1186/1297-9686-45-42.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fioretti M, Negrini R, Biffani S, Quaglia A, Valentini A, Nardone A. Demographic structure and population dynamics of Maremmana cattle local breed after 35 years of traditional selection. Livest Sci. 2020;232:103903. https://doi.org/10.1016/j.livsci.2019.103903.

Article  Google Scholar 

Flury C, Tapio M, Sonstegard T, Drögemüller C, Leeb T, Simianer H, et al. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. J Anim Breed Genet. 2010;127(5):339–47. https://doi.org/10.1111/j.1439-0388.2010.00862.x.

Article  CAS  PubMed  Google Scholar 

Forutan M, Ansari Mahyari S, Baes C, Melzer N, Schenkel FS, Sargolzaei M. Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle. BMC Genomics. 2018;19:98. https://doi.org/10.1186/s12864-018-4453-z.

Article  PubMed  PubMed Central  Google Scholar 

Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, et al. Genetic diversity and signatures of selection for thermal stress in cattle and other two Bos species adapted to divergent climatic conditions. Front Genet. 2021;12:604823. https://doi.org/10.3389/fgene.2021.604823.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Garcia AO, Otto PI, Glatzl Junior LA, Rocha RDFB, Dos Santos MG, De Oliveira DA, et al. Pedigree reconstruction and population structure using SNP markers in Gir cattle. J Appl Genet. 2023;64(2):329–40. https://doi.org/10.1007/s13353-023-00747-x.

Article  CAS  PubMed