[1] Strucken E M, Gebrehiwot N Z, Swaminathan M, et al. Genetic diversity and effective population sizes of thirteen Indian cattle breeds[J]. Genet Sel Evol, 2021, 53(1):47.
[2] Notter D R. The importance of genetic diversity in livestock populations of the future [J]. J Anim Sci, 1999, 77(1):61-69.
[3] Amaya A, Martínez R, Cerón-Mu?oz M. Population structure and genetic diversity in Colombian Simmental cattle[J]. Trop Anim Health Prod, 2020, 52(3):1133-1139..
[4] MA j, GAO x, Li J, et al. Assessing the genetic background and selection signatures of Huaxi Cattle using High-Density SNP array [J]. Animals (Basel), 2021, 11(12):3469.
[5] Liu Z, Sun H, Lai W, et al. Genome-wide re-sequencing reveals population structure and genetic diversity of Bohai Black cattle[J]. Anim Genet, 2022, 53(1):133-136.
[6] Chang C C, Chow C C, Tellier l C, et al. Second-generation PLINK: rising to the challenge of larger and richer datasets[J]. Gigascience, 2015, 4:7.
[7] Gómez-Rubio V. ggplot2-elegant graphics for data analysis[J]. Journal of Statistical Software, 2017, 77:1-3.
[8] Bryant D, Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks[J]. Mol Biol Evol, 2004, 21(2): 255-265.
[9] Navas A, Albar J P. Application of proteomics in phylogenetic and evolutionary studies[J]. Proteomics, 2004, 4(2):299-302.
[10] Alexander D H, Lange K. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation[J]. BMC Bioinformatics, 2011, 12:246.
[11] Zhang C, Dong S S, Xu J Y, et al. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files[J]. Bioinformatics, 2019, 35(10):1786-1788.
[12] Toro M A, Caballero A. Characterization and conservation of genetic diversity in subdivided populations [J]. Philos Trans R Soc Lond B Biol Sci, 2005, 360(1459):1367-1378.
[13] Zhang S, Yao Z, Li X, et al. Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data [J]. BMC Genomics, 2022, 23(1):460.
[14] Mészáros G, Boison S A, Pérez O'brien A M, et al. Genomic analysis for managing small and endangered populations: a case study in Tyrol Grey cattle[J]. Front Genet, 2015, 6:173.
[15] Kuang W, Hu J, Wu H, et al. Genetic diversity, inbreeding level, and genetic load in endangered snub-nosed monkeys (rhinopithecus)[J]. Front Genet, 2020, 11:615926.
[16] Eding H, Crooijmans R P, Groenen M A, et al. Assessing the contribution of breeds to genetic diversity in conservation schemes[J]. Genet Sel Evol, 2002, 34(5):613-33.
[17] King F J M, Banga C B, Visser C. Genetic diversity and population structure of three native cattle populations in Mozambique[J]. Trop Anim Health Prod, 2021, 53(1):117.
[18] Van Der Nest M A, Hlongwane N, Hadebe K, et al. breed ancestry, divergence, admixture, and selection patterns of the simbra crossbreed [J]. Front Genet, 2020, 11:608650.
[19] Zhang Q, Calus M P, Guldbrandtsen B, et al. Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds[J]. BMC Genet, 2015, 16:88.
[20] Maiorano A M, Lourenco D L, Tsuruta S, et al. Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information[J]. PLoS One, 2018, 13(8):e0200694.
[21] Macciotta N P, Gaspa G, Steri R, et al. Using eigenvalues as variance priors in the prediction of genomic breeding values by principal component analysis[J]. J Dairy Sci, 2010, 93(6): 2765-2774.
[22] Boschiero C, Moreira G C M, Gheyas A A, et al. Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines[J]. BMC Genomics, 2018, 19(1):83.
[23] Tauber E, Kyriacou C P. Molecular evolution and population genetics of circadian clock genes [J]. Methods Enzymol, 2005, 393: 797-817.
[24] Gobena M, Elzo M A, Mateescu R G. Population Structure and Genomic Breed Composition in an Angus-Brahman Crossbred Cattle Population[J]. Front Genet, 2018, 9:90.
[25] Kopelman N M, Mayzel J, Jakobsson M, et al. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K[J]. Mol Ecol Resour, 2015, 15(5):1179-1191.
[26] Ocampo R J, Martínez J F, Martínez R. Assessment of genetic diversity and population structure of Colombian Creole cattle using microsatellites [J]. Trop Anim Health Prod, 2021, 53(1):122.
[27] Ma H, Wang S, Zeng G, et al. The origin of a coastal indigenous Horse Breed in China revealed by genome-wide SNP data[J]. Genes (Basel), 2019, 10(3):241.
[28] Kim E S, Kirkpatrick B W. Linkage disequilibrium in the North American Holstein population[J]. Anim Genet, 2009, 40(3):279-88.
[29] Pérez O'brien A M, Utsunomiya Y T, Mészáros G, et al. Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle[J]. Genet Sel Evol, 2014, 46(1):19.
[30] Zhao P, Yu Y, Feng W, et al. Evidence of evolutionary history and selective sweeps in the genome of Meishan pig reveals its genetic and phenotypic characterization[J]. Gigascience, 2018, 7(5):giy058.
[31] Biegelmeyer P, Gulias-gomes C C, Caetano A R, et al. Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle[J]. BMC Genet, 2016, 17:32.
[32] Lan D, Xiong X, Mipam T D, et al. Genetic Diversity, Molecular Phylogeny, and Selection Evidence of Jinchuan Yak Revealed by Whole-Genome Resequencing[J]. G3 (Bethesda), 2018, 8(3):945-52. |