Analysis of genetic diversity and structure of endangered Dengchuan cattle population using a single-nucleotide polymorphism chip

References

• Yang L, Su Z, Li H, Zhao T. Investigation and analysis on present situation of Dengchuan cattle breed resources. Heilongjiang Animal Sci Veterinary. 2021;58-61(67):1–13.
   Google Scholar
• Deng J, Xu W, Liu Y, Sun L. Introduction of local cattle genetic resources in Yunnan province. Yunnan Agricult. 2020;382:80–81.
   Google Scholar
• Wang J, Yang Y, Miao Y. Discussion on breeding history and present situation of Dengchuan Cattle. China Cattle Sci. 2019;45(1):39–44.
   Google Scholar
• Office of National Livestock and Poultry Genetic Resources Committee. Circular on releasing the directory of national livestock & poultry genetic resources. Gazette of the Ministry of Agriculture and Rural Affairs of the People’s Republic Of China. 2020;(06):36.
   Google Scholar
• Ellegren H, Galtier N. Determinants of genetic diversity. Nat Rev Genet. 2016;17(7):422–433.
   PubMed Web of Science ®Google Scholar
• Hulsegge B, Calus MP, Windig JJ, Hoving-Bolink AH, Maurice-van Eijndhoven MH, Hiemstra SJ. Selection of SNP from 50K and 777K arrays to predict breed of origin in cattle. J Anim Sci. 2013;91(11):5128–5134.
   PubMed Web of Science ®Google Scholar
• Shi K, Liu Y, Zhang Z, et al. Analysis of population genetic structure of six white pigs in Anqing based on SNP chip. Chinese J Anim Sci. 2022;58(8):136–140.
   Google Scholar
• Schneider AK, Niemeyer CM. DNA surface technology: from gene sensors to integrated systems for life and materials sciences. Angew Chem Int Ed Engl. 2018;57(52):16959–16967.
   PubMed Web of Science ®Google Scholar
• Marchiori CM, Pereira GL, Maiorano AM, et al. Linkage disequilibrium and population structure characterization in the cutting and racing lines of Quarter Horses bred in Brazil. Livestock Science. 2019;219:45–51.
   Web of Science ®Google Scholar
• Liu B, Shen L, Chen Y, et al. Analysis of genetic structure of conservation population in Qingyu pig based on SNP chip. Acta Veterinaria et Zootechnica Sinica. 2020;51(2):260–269.
   Google Scholar
• Deng J, Liu Y, Xu W, Sun L, Qi M. Genetic structure analysis of a conserved population of Saba pigs based on SNP chips. China Feed. 2022; (17):7–11.
   Google Scholar
• Upadhyay M, Eriksson S, Mikko S, et al. Genomic relatedness and diversity of Swedish native cattle breeds. Genet Sel Evol. 2019;51(1):1–11.
   PubMed Web of Science ®Google Scholar
• Purcell S, Neale B, Todd-Brown K, et al. PLINK:a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–575.
   PubMed Web of Science ®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.
   PubMed Web of Science ®Google Scholar
• Nei M, Chesser RK. Estimation of fixation indices and gene diversities. Ann Hum Genet. 1983;47(3):253–259.
   PubMedGoogle Scholar
• Bhuiyan MSA, Lee S-H, Hossain SMJ, et al. Unraveling the genetic diversity and population structure of Bangladeshi indigenous cattle populations using 50K SNP markers. Animals (Basel). 2021;11(8):2381.
   PubMedGoogle Scholar
• Flury C, Tapio M, Sonstegard T, et al. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. J Anim Breed Genet. 2010;127(5):339–347.
   PubMed Web of Science ®Google Scholar
• Meuwissen T. Genetic management of small populations: a review. Acta Agriculturae Scand Section A. 2009;59(2):71–79.
   Web of Science ®Google Scholar
• Taberlet P, Valentini A, Rezaei HR, et al. Are cattle sheep and goats endangered species? Mol Ecol. 2008;17(1):275–284.
   PubMed Web of Science ®Google Scholar
• Luo Y. Analysis of Lingkage Disequilibrium and Estimation of Effective Population Size in Southern Chinese Indigenous Pig Breeds MS Thesis. Department of Animal Science South China Agricultural University. Guangzhou. 2016.
   Google Scholar
• Hill WG. Estimation of linkage disequilibrium in randomly mating populations. Heredity (Edinb).). 1974;33(2):229–239.
   PubMedGoogle Scholar
• Sun H, Wang Z, Zhang Z, et al. Exploring the current situation of conservation of Meishan pigs based on genome sequencing data. J Shanghai Jiaotong University.. 2017;35(4):65–70.
   Google Scholar
• Ni G, Zhang Z, Jiang L, Ma P, Zhang Q, Ding X. Chinese Holstein Cattle effective population size estimated from whole genome linkage disequilibrium. Hereditas. 2012;34(1):52–60.
   Google Scholar
• Wang H. Evaluating Beijing You Chickens Conservation Status by Genome Information MS Thesis. Institute of Animal Science Graduate School Chinese Academy of Agricultural Sciences. Beijing. 2021.
   Google Scholar
• Cao ZF, Zhang Y, Zhang Y, Chen GH, Xu Q. Analysis of genetic diversity of 9 duck population via microsatellite markers. China Poultry. 2021;43(02):15–20.
   Google Scholar
• Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980;32(3):314–331.
   PubMed Web of Science ®Google Scholar
• Schmidt TL, Jasper ME, Weeks AR, Hoffmann AA. Unbiased population heterozygosity estimates from genome‐wide sequence data. Methods Ecol Evol. 2021;12(10):1888–1898.
   Web of Science ®Google Scholar
• Liu C, Lu D, Zhou Q, et al. Analysis of population genetic structure of Hang Pigs by high density SNP chip. Acta Veterinaria et ZootechnicaSinica. 2022;53(8):2502–2513.
   Google Scholar
• Senczuk G, Mastrangelo S, Ciani E, et al. The genetic heritage of Alpine local cattle breeds using genomic SNP data. Genet Sel Evol. 2020;52(1):40. 11-020-00559-1.
   PubMed Web of Science ®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 (Basel). 2020;10(12):2285.
   PubMedGoogle Scholar
• Molina Flores B, Camacho Vallejo ME, Delgado Bermejo JV, Navas González FJ, Martínez MDA. Do Pharaohs’ cattle still graze the Nile valley? Genetic characterization of the Egyptian Baladi cattle breed. Anim Biotechnol. 2021;34(3):645–657.
   PubMedGoogle Scholar
• Xu L, Zhang WG, Shen HX, et al. Genome-wide scanning reveals genetic diversity and signatures of selection in Chinese indigenous cattle breeds. Livestock Sci. 2018;216:100–108.
   Web of Science ®Google Scholar
• Jin L, Qu K, Hanif Q, et al. Whole-genome sequencing of endangered Dengchuan cattle reveals its genomic diversity and selection signatures. Front Genet. 2022;13(13):833475.
   PubMedGoogle Scholar
• Ling X, Zhang WG, Li JY, et al. Genetic background analysis and breed evaluation of Yiling yellow cattle. J Integ Agricult. 2017;16(10):2246–2256.
   Web of Science ®Google Scholar
• Quan J, Li Y, Yang Y, et al. Population genetic diversity and genetic evaluation models reveal the maternal genetic structure and conservation priority characteristics of indigenous cattle in China. Global Ecol Conserv. 2021;32:e01903.
   Web of Science ®Google Scholar
• Kawaguchi F, Nakamura M, Kobayashi E, Yonezawa T, Sasazaki S, Mannen H. Comprehensive assessment of genetic diversity structure and relationship in four Japanese cattle breeds by Illumina 50 K SNP array analysis. Anim Sci J. 2022;93(1):e13770.
   PubMed Web of Science ®Google Scholar
• Purfield DC, Berry DP, McParland S, Bradley DG. Runs of homozygosity and population history in cattle. BMC Genet. 2012;13(1):70.
   PubMedGoogle Scholar
• Zhao G, Zhang T, Liu Y, et al. Genome-wide assessment of runs of homozygosity in Chinese Wagyu beef cattle. Animals (Basel). 2020;10(8):1425.
   PubMedGoogle Scholar
• Keller MC, Visscher PM, Goddard ME. Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics. 2011;189(1):237–249.
   PubMed Web of Science ®Google Scholar
• Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF. Genomic runs of homozygosity record population history and consanguinity. PLoS One. 2010;5(11):e13996.
   PubMed Web of Science ®Google Scholar
• Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet. 2006;15(5):789–795.
   PubMed Web of Science ®Google Scholar
• Xu L, Zhao G, Yang L, et al. Genomic patterns of homozygosity in Chinese local cattle. Sci Rep. 2019;9(1):16977.
   PubMedGoogle Scholar
• Liu S, Ma X, Hassan FU, Gao T, Deng T. Genome-wide analysis of runs of homozygosity in Italian Mediterranean buffalo. J Dairy Sci. 2022;105(5):4324–4334.
   PubMed Web of Science ®Google Scholar
• Addo S, Klingel S, Hinrichs D, Thaller G. Runs of homozygosity and NetView analyses provide new insight into the genome-wide diversity and admixture of three German cattle breeds. PLoS One. 2019;14(12):e0225847.
   PubMed Web of Science ®Google Scholar
• Szmatoła T, Gurgul A, Jasielczuk I, et al. Comprehensive analysis of runs of homozygosity of eleven cattle breeds representing different production types. Animals (Basel). 2019;9(12):1024.
   PubMedGoogle Scholar
• Zhao G, Liu Y, Niu Q, et al. Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle. BMC Genomics. 2021;22(1):678.
   PubMed Web of Science ®Google Scholar