References
- Al-Mamun, H. A., S. A. Clark, P. Kwan, and C. Gondro. 2015. “Genome-Wide Linkage Disequilibrium and Genetic Diversity in Five Populations of Australian Domestic Sheep.” Genetics Selection Evolution 47: 90. doi:https://doi.org/10.1186/s12711-015-0169-6.
- Berthouly, C., J. C. Maillard, L. P. Doan, T. N. Van, B. Bed’hom, G. Leroy, H. H. Thanh, et al. 2010. “Revealing Fine Scale Subpopulation Structure in the Vietnamese H’mong Cattle Breed for Conservation Purposes.” BMC Genetics 11: 45. doi:https://doi.org/10.1186/1471-2156-11-45.
- Bortoluzzi, C., R. P. M. A. Crooijmans, M. Bosse, S. J. Hiemstra, M. A. M. Groenen, and H. J. Megens. 2018. “The Effects of Recent Changes in Breeding Preferences on Maintaining Traditional Dutch Chicken Genomic Diversity.” Heredity 121: 564–578. doi:https://doi.org/10.1038/s41437-018-0072-3.
- Bosse, M., H. J. Megens, O. Madsen, Y. Paudel, L. A. F. Frantz, L. B. Schook, R. P. M. A. Crooijmans, M. A. M. Groenen, and P. M. Visscher. 2012. “Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape.” Plos Genetics 8 (11): e1003100. doi:https://doi.org/10.1371/journal.pgen.1003100.
- Broman, K. W., and J. L. Weber. 2000. “Long Homozygous Chromosomal Segments in Reference Families from the Centre D’tude Du Polymorphisme Humain.” The American Journal of Human Genetics 65 (6): 1493–1500. doi:https://doi.org/10.1086/302661.
- Browning, S. R., and B. L. Browning. 2012. “Identity by Descent between Distant Relatives: Detection and Applications.” Annual Review of Genetics 46 (1): 617–633. doi:https://doi.org/10.1146/annurev-genet-110711-155534.
- Ceballos, F. C., P. K. Joshi, D. W. Clark, M. Ramsay, and J. F. Wilson. 2018. “Runs of Homozygosity: Windows into Population History and Trait Architecture.” Nature Reviews. Genetics 19 (4): 220–234. doi:https://doi.org/10.1038/nrg.2017.109.
- Chang, C., J. L. Coville, G. Coquerelle, D. Gourichon, A. Oulmouden, and M. Tixier’boichard. 2006. “Complete Association between a Retroviral Insertion in the Tyrosinase Gene and the Recessive White Mutation in Chickens.” Bmc Genomics 7 (1): 19. doi:https://doi.org/10.1186/1471-2164-7-19.
- Chen, Q., Z. Wang, J. Sun, Y. Huang, and C. Lei. 2020. “Identification of Genomic Characteristics and Selective Signals in a Du’an Goat Flock.” Animals 10 (6): 994. doi:https://doi.org/10.3390/ani10060994.
- China National Commission of Animal Genetic Resources. 2011. Animal Genetic Resources in China: Poultry. Beijing: China Agriculture Press.
- Danecek, P., A. Auton, G. Abecasis, C. A. Albers, E. Banks, M. A. Depristo, R. E. Handsaker, et al. 2011. “The Variant Call Format and Vcftools.” bioinformatics 27 (15): 2156–2158. doi:https://doi.org/10.1093/bioinformatics/btr330.
- Dar, M., P. Mumtaz, S. Bhat, M. Nabi, Q. Taban, R. Shah, H. Khan, and S. Ahmad. 2018. “Genetics of Disease Resistance in Chicken.” In Application of Genetics and Genomics in Poultry Science, 162–174. doi:https://doi.org/10.5772/intechopen.77088.
- Dementieva, N. V., A. A. Kudinov, T. A. Larkina, O. V. Mitrofanova, A. P. Dysin, V. P. Terletsky, V. I. Tyshchenko, D. K. Griffin, and M. N. Romanov. 2020. “Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity.” Animals 10 (10): 1887. doi:https://doi.org/10.3390/ani10101887.
- Druml, T., K. Salajpal, M. Dikic, M. Urosevic, G. Grilz-Seger, and R. Baumung. 2012. “Genetic Diversity, Population Structure and Subdivision of Local Balkan Pig Breeds in Austria, Croatia, Serbia and Bosnia-Herzegovina and Its Practical Value in Conservation Programs.” Genetics Selection Evolution 44: 5. doi:https://doi.org/10.1186/1297-9686-44-5.
- Ferencakovic, M., E. Hamzic, B. Gredler, I. Curik, and J. Sölkner. 2011. “Runs of Homozygosity Reveal Genome-Wide Autozygosity in the Austrian Fleckvieh Cattle.” Agriculturae Conspectus Scientificus 76: 325–329.
- Fleming, D. S., S. Weigend, H. Simianer, A. Weigend, M. Rothschild, C. Schmidt, C. Ashwell, M. Persia, J. Reecy, and S. J. Lamont. 2017. “Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure.” G3: Genes, Genomes, Genetics 7 (5): 1525–1537. doi:https://doi.org/10.1534/g3.117.041228.
- Fu, S., Y. Chen, J. Wang, F. Yan, G. Sun, Z. Li, R. Han, X. Kang, and G. Li. 2018. “Tissue Expression Profile of Mir-124a-3p and Its Interaction Relationship with Acaa2 Gene in Chicken (Gallus Gallus).” Journal of Agricultural Biotechnology 26: 949–958.
- Gibson, J., N. E. Morton, and A. Collins. 2006. “Extended Tracts of Homozygosity in Outbred Human Populations.” Human Molecular Genetics 15 (5): 789–795. doi:https://doi.org/10.1093/hmg/ddi493.
- Grilz-Seger, G., M. Neuditschko, A. Ricard, B. Velie, G. Lindgren, M. Mesarič, M. Cotman, et al. 2019. “Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and near Eastern Horse Breeds.” Genes 10 (7): 491. doi:https://doi.org/10.3390/genes10070491.
- Gunnarsson, U., A. R. Hellstrom, M. Tixier’boichard, F. Minvielle, B. Bed’hom, S. I. Ito, P. Jensen, A. Rattink, A. Vereijken, and L. Andersson. 2007. “Mutations in Slc45a2 Cause Plumage Color Variation in Chicken and Japanese Quail.” Genetics 175 (2): 867–877. doi:https://doi.org/10.1534/genetics.106.063107.
- Gunnarsson, U., S. Kerje, B. Bed’hom, A. S. Sahlqvist, O. Ekwall, M. Tixier-Boichard, O. Kämpe, and L. Andersson. 2011. “The Dark Brown Plumage Color in Chickens Is Caused by an 8.3-kb Deletion Upstream of Sox10.” Pigment Cell & Melanoma Research 24 (2): 268–274. doi:https://doi.org/10.1111/j.1755-148X.2011.00825.x.
- Han, K., X. Su, L. Xu, L. Bin, J. Zhang, and H. Shu. 2004. “Mechanisms of the Trif-Induced Interferon-Stimulated Response Element and nf-κb Activation and Apoptosis Pathways.” Journal of Biological Chemistry 279 (15): 15652–15661. doi:https://doi.org/10.1074/jbc.m311629200.
- He, S., J. Di, B. Han, L. Chen, and W. Li. 2020. “Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino.” Animals 10 (3): 524. doi:https://doi.org/10.3390/ani10030524.
- Hou, Q., S. Han, L. Yang, S. Chen, J. Chen, N. Ma, C. Wang, et al. 2019. “The Interplay of Microrna-34a, Lgr4, Emt-Associated Factors, and Mmp2 in Regulating Uveal Melanoma Cells.” Investigative Ophthalmology & Visual Science 60 (13): 4503–4510. doi:https://doi.org/10.1167/iovs.18-26477.
- Huang, X., N. O. Otecko, M. Peng, Z. Weng, W. Li, J. Chen, M. Zhong, et al. 2020. “Genome-Wide Genetic Structure and Selection Signatures for Color in 10 Traditional Chinese Yellow-Feathered Chicken Breeds.” BMC Genomics 21: 316. doi:https://doi.org/10.21203/rs.2.21585/v1.
- Huang, X., Z. Weng, W. Li, J. Chen, F. Zhong, S. Tang, and Y. Zhao. 2016a. “Genetic Diversity and Breed Origin of Huanglang Chicken Inferred from Mitochondrial DNA D–loop Sequence.” Journal of Hunan Agricultural University (Natural Sciences) 42: 75–80.
- Huang, X., J. Zhang, D. He, X. Zhang, F. Zhong, W. Li, Q. Zheng, J. Chen, and B. Du. 2016b. “Genetic Diversity and Population Structure of Indigenous Chicken Breeds in South China.” Frontiers of Agricultural Science and Engineering 3 (2): 97–101. doi:https://doi.org/10.15302/J-FASE-2016102.
- Jiang, E., Y. Zhang, Y. Guo, Y. Jia, Z. Han, X. Song, J. Zhao, and C. Xu. 2019. “Progress in the Research of the Effect of the Kit Gene on the Formation of White Coat in Mammals.” Animal Husbandry & Veterinary Medicine 51: 147–150. doi:https://doi.org/10.1016/s0378-1119(97)00600-8.
- Kaiser, P., H. M. Wain, and L. Rothwell. 1998. “Structure of the Chicken interferon-γ Gene, and Comparison to Mammalian Homologues.” Gene 207 (1): 25–32. doi:https://doi.org/10.1016/s0378-1119(97)00600-8.
- Keller, M. C., P. M. Visscher, and M. E. Goddard. 2011. “Quantification of Inbreeding Due to Distant Ancestors and Its Detection Using Dense Single Nucleotide Polymorphism Data.” Genetics 189 (1): 237–249. doi:https://doi.org/10.1534/genetics.111.130922.
- Kerje, S., J. Lind, K. Schütz, P. Jensen, and L. Andersson. 2003. “Melanocortin 1-Receptor (Mc1r) Mutations are Associated with Plumage Colour in Chicken.” Animal Genetics 34 (4): 241–248. doi:https://doi.org/10.1534/genetics.104.027995.
- Kerje, S., P. Sharma, U. Gunnarsson, H. Kim, S. Bagchi, R. Fredriksson, K. Schütz, P. Jensen, H. G. Von, and R. Okimoto. 2004. “The Dominant White, Dun and Smoky Color Variants in Chicken are Associated with Insertion/deletion Polymorphisms in the Pmel 7 Gene.” Genetics 168 (3): 1507–15018. doi:https://doi.org/10.1534/genetics.104.027995.
- Lencz, T., C. Lambert, P. Derosse, K. Burdick, T. Morgan, J. M. Kane, R. Kucherlapati, and A. Malhotra. 2007. “Runs of Homozygosity Reveal Highly Penetrant Recessive Loci in Schizophrenia.” Proceedings of the National Academy of Sciences of the United States of America 104 (50): 19942–19947. doi:https://doi.org/10.1073/pnas.0710021104.
- Li, D., T. Che, B. Chen, S. Tian, X. Zhou, G. Zhang, M. Li, et al. 2017. “Genomic Data for 78 Chickens from 14 Populations.” GigaScience 6 (6): gix026. doi:https://doi.org/10.1093/gigascience/gix026.
- Li, X., M. Gao, J. Li, K. Xing, X. Qi, X. Wang, L. Xiao, Y. Guo, H. Ni, and X. Sheng. 2020. “Research Advances on Candidate Genes Affecting Chicken Quality.” China Poultry 42 (5): 79–84.
- Liu, G., F. Sun, F. Zhu, H. Feng, and X. Han. 2019. “Runs of Homozygosity and Its Application on Livestock Genome Study.” Yi Chuan 41 (4): 304–317. doi:https://doi.org/10.16288/j.yczz.18-287.
- Liu, X. 2008. “Focus on Disease Resistance and Disease Resistance Breeding in Poultry.” China Poultry 30 (2): 25–30.
- Loog, L., M. G. Thomas, R. Barnett, R. Allen, N. Sykes, P. D. Paxinos, O. Lebrasseur, et al. 2017. “Inferring Allele Frequency Trajectories from Ancient DNA Indicates that Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices.” Molecular Biology and Evolution 34 (8): 1981–1990. doi:https://doi.org/10.1093/molbev/msx142.
- Mao, H., X. Wang, Y. Fan, D. Cheng, K. Chen, S. Liu, S. Xi, L. Wan, X. Li, and J. Ren. 2019. “Whole-Genome Snp Data Unravel Population Structure and Signatures of Selection for Black Plumage of Indigenous Chicken Breeds from Jiangxi Province, China.” Animal Genetics 50 (5): 475–483. doi:https://doi.org/10.1111/age.12827.
- Marchesi, J. A. P., M. E. Buzanskas, M. E. Cantão, A. M. G. Ibelli, J. O. Peixoto, L. B. Joaquim, G. C. M. Moreira, et al. 2018. “Relationship of Runs of Homozygosity with Adaptive and Production Traits in a Paternal Broiler Line.” Animal 12 (6): 1126–1134. doi:https://doi.org/10.1017/S1751731117002671.
- Marras, G., G. Gaspa, S. Sorbolini, C. Dimauro, P. Ajmone-Marsan, A. Valentini, J. L. Williams, and N. P. P. Macciotta. 2015. “Analysis of Runs of Homozygosity and Their Relationship with Inbreeding in Five Cattle Breeds Farmed in Italy.” Animal Genetics 46 (2): 110–121. doi:https://doi.org/10.1111/age.12259.
- Mastrangelo, S., M. Tolone, R. Di Gerlando, L. Fontanesi, M. T. Sardina, and B. Portolano. 2016. “Genomic Inbreeding Estimation in Small Populations: Evaluation of Runs of Homozygosity in Three Local Dairy Cattle Breeds.” Animal 10 (5): 746–754. doi:https://doi.org/10.1017/S1751731115002943.
- Mcquillan, R., A. L. Leutenegger, R. Abdelrahman, C. S. Franklin, M. Pericic, L. Baraclauc, N. Smolejnarancic, B. Janicijevic, O. Polasek, and A. Tenesa. 2008. “Runs of Homozygosity in European Populations.” The American Journal of Human Genetics 83 (5): 359–372. doi:https://doi.org/10.1016/j.ajhg.2008.08.007.
- Meng, X., T. Xu, B. Du, and X. Teng. 2017. Chicken Art – Ancient Chinese Wisdom on Chicken-Raising with an Appendix of the Chinese Art of Calligraphy. Beijing: China Agriculture Press.
- Mo, G., Y. Huang, Q. Wu, X. Zhang, F. Wei, and Y. Liao. 2020. “Analysis on Genetic Diversity and Conservation Effect of Guangxi Three Yellow Chicken.” Genomics and Applied Biology 39: 2021–2027.
- Nei, M., and W. H. Li. 1979. “Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonucleases.” Proceedings of the National Academy of Sciences 76 (10): 5269–5273. doi:https://doi.org/10.1073/pnas.76.10.5269.
- Paião, F. G., L. M. Ferracin, M. Pedrão, T. Kato, and M. Shimokomaki. 2013. “Skeletal Muscle Calcium Channel Ryanodine and the Development of Pale, Soft, and Exudative Meat in Poultry.” Genetics & Molecular Research 12 (3): 3017–3027. doi:https://doi.org/10.4238/2013.August.20.3.
- Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. Ferreira, D. Bender, J. Maller, et al. 2007. “Plink: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses.” American Journal of Human Genetics 81 (3): 559–575. doi:https://doi.org/10.1086/519795.
- Purfield, D. C., D. P. Berry, M. P. Sinead, and D. G. Bradley. 2012. “Runs of Homozygosity and Population History in Cattle.” BMC Genetics 13: 70. doi:https://doi.org/10.1186/1471-2156-13-70.
- Purfield, D. C., S. Mcparland, E. Wall, and D. P. Berry. 2017. “The Distribution of Runs of Homozygosity and Selection Signatures in Six Commercial Meat Sheep Breeds.” Plos One 12 (5): e0176780. doi:https://doi.org/10.1371/journal.pone.0176780.
- Randall, R. E., and S. Goodbourn. 2008. “Interferons and Viruses: An Interplay between Induction, Signalling, Antiviral Responses and Virus Countermeasures.” Journal of General Virology 89: 1–47. doi:https://doi.org/10.1099/vir.0.83391-0.
- Ren, X., W. Xia, P. Xu, H. Shen, X. Dai, M. Liu, Y. Shi, X. Ye, and Y. Dang. 2020. “Lgr4 Deletion Delays the Hair Cycle and Inhibits the Activation of Hair Follicle Stem Cells.” Journal of Integrative Dermatology 140 (9): 1706–1712. doi:https://doi.org/10.1016/j.jid.2019.12.034.
- Reuter, A., S. Soubies, S. Härtle, B. Schusser, B. Kaspers, P. Staeheli, and D. Rubbenstroth. 2014. “Antiviral Activity of Interferon-Lambda in Chickens.” Journal of Virology 88 (5): 2835–2843. doi:https://doi.org/10.1128/JVI.02764-13.
- Rudan, I. 1999. “Inbreeding and Cancer Incidence in Human Isolates.” Human Biology 71: 173–187.55.
- Szmatoła, T., A. Gurgul, K. Ropka-Molik, I. Jasielczuk, T. Ząbek, and M. Bugno-Poniewierska. 2016. “Characteristics of Runs of Homozygosity in Selected Cattle Breeds Maintained in Poland.” Livestock Science 188: 72–80. doi:https://doi.org/10.1016/j.livsci.2016.04.006.
- Szmatoła, T., I. Jasielczuk, E. Semik-Gurgul, M. Szyndler-Nędza, T. Blicharski, K. Szulc, E. Skrzypczak, and A. Gurgul. 2020. “Detection of Runs of Homozygosity in Conserved and Commercial Pig Breeds in Poland.” Journal of Animal Breeding and Genetics 137 (6): 571–580. doi:https://doi.org/10.1111/jbg.12482.
- Szpiech, Z. A., M. Jakobsson, and N. A. Rosenberg. 2008. “Adze: A Rarefaction Approach for Counting Alleles Private to Combinations of Populations.” Bioinformatics 24 (21): 2498–2504. doi:https://doi.org/10.1093/bioinformatics/btn478.
- Talebi, R., T. Szmatoła, G. Mészáros, and S. Qanbari. 2020. “Runs of Homozygosity in Modern Chicken Revealed by Sequence Data.” G3: Genes, Genomes, Genetics 10 (12): 4615–4623. doi:https://doi.org/10.1534/g3.120.401860.
- Weng, Z., X. Huang, M. Zhong, J. Chen, Y. Tang, F. Zhong, and B. Zhang. 2018. “Growth Curve Fitting and the Optimal Marketing Time for Wuhua Yellow Chickens.” Journal of Economic Animal 22: 181–186.
- Weng, Z., Y. Xu, W. Li, J. Chen, M. Zhong, F. Zhong, B. Du, B. Zhang, and H. Xunhe. 2020. “Genomic Variations and Signatures of Selection in Wuhua Yellow Chicken.” Plos One 15 (10): e0241137. doi:https://doi.org/10.1371/journal.pone.0241137.
- Xie, R., L. Shi, J. Liu, T. Deng, L. Wang, Y. Liu, and F. Zhao. 2019. “Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes in Three Pig Breeds.” Animals 9 (8): 518. doi:https://doi.org/10.3390/ani9080518.
- Xu, Z., H. Sun, Z. Zhang, Q. Zhao, S. B. Olasege, Q. Li, Y. Yue, et al. 2019. “Assessment of Autozygosity Derived from Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data.” Frontiers in Genetics 10: 274. doi:https://doi.org/10.3389/fgene.2019.00274.
- Zhang, C., D. Lin, Y. Wang, D. Peng, H. Li, J. Fei, K. Chen, N. Yang, X. Hu, and Y. Zhao. 2019. “Widespread Introgression in Chinese Indigenous Chicken Breeds from Commercial Broiler.” Evolutionary Applications 12 (3): 610–621. doi:https://doi.org/10.1111/eva.12742.
- Zhang, M., W. Han, H. Tang, G. Li, M. Zhang, R. Xu, Y. Liu, et al. 2018. “Genomic Diversity Dynamics in Conserved Chicken Populations are Revealed by Genome-Wide Snps.” Bmc Genomics 19 (1): 598. doi:https://doi.org/10.1186/s12864-018-4973-6.
- Zhong, F., W. Li, W. Lin, X. Huang, and C. Zhou. 2014. “Growth and Development Characteristics and Carcass Traits of Wuhua Three-Yellow Chicken.” Journal of Hunan Agricultural University (Natural Sciences) 40: 56–59.
- Zhou, Y., W. Tian, M. Zhang, T. Ren, and G. Sun. 2019. “Transcriptom Analysis Revealed Regulation of Dexamethasone Induced Micrornas in Chicken Thymus.” Journal of Cellular Biochemistry 120: 6570–6579. doi:https://doi.org/10.1002/jcb.27950.