Reference
Beckmann, J. & Soller, M. ( 1986 ). Restriction fragment length polymorphisms and genetic improvement of agricultural species. Euphytica 35, 111–124.
Blears, M., De Grandis, S., Lee, H. & Trevors, J. ( 1998 ). Amplified fragment length polymorphism (AFLP): a review of the procedure and its applications. Journal of Industrial Microbiology and Biotechnology 21, 99–114.
FAO (2013). Status and Trends of Animal Genetic Resources 2012. Food and Agriculture Organization, Commission on Animal Genetic Resources, Rome.
Henson, E. L. ( 1992 ). In Situ Conservation of Livestock and Poultry. Food and Agriculture
Organization of the United Nations, Rome.
Hiemstra, S. J., Drucker, A. G., Tvedt, M. W., Louwaars, N., Oldenbroek, J., Awgichew, K., Kebede, S. A., Bhat, P. & Da Silva Mariante, A.
( 2006 a). Exchange, use and Conservation of Animal Genetic Resources. Food and Agriculture Organization of the United Nations, Rome.
http://hgdownload.cse.ucsc.edu/goldenPath/galGal5/bigZips/galGal5.fa.gz.
https://ftp.ncbi.nlm.nih.gov/snp/organisms/archive/chicken_9031/VCF/.
R-Projecthttps://www.r-project.org/.
The second report on the state of the world’s animal geentic resources for food and agricultural.
Tixier-Boichard, M. ( 2014 ). Status and gaps in characterization of animal genetic
resources. In 10th World Congress on Genetics Applied to Livestock Production. August 17–22, 2014, p. 29. American Society of Animal Science, Vancouver.
Wu CX. Poultry genetic resources in China: conservation and utilization. Beijing: XXV World’s Poultry Congress; 2016. p. 88–91.
Akey, J.M., Ruhe, A.L., Akey, D.T., Wong, A.K., Connelly, C.F., Madeoy, J., Nicholas, T.J., and Neff, M.W. (2010). Tracking footprints of artificial selection in the dog genome. Proc Natl Acad Sci U S A107 , 1160-1165.
Akey, J.M., Zhang, G., Zhang, K., Jin, L., and Shriver, M.D. (2002). Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12 , 1805-1814.
Alexander, D.H., Novembre, J., and Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19 , 1655-1664.
Ali, B.A., Huang, T.-H., Qin, D.-N., and Wang, X.-M. (2004). A review of random amplified polymorphic DNA (RAPD) markers in fish research. Reviews in Fish Biology and Fisheries 14 , 443-453.
Anderson, S. (2003). Animal genetic resources and sustainable livelihoods. Ecological Economics 45 , 331-339.
Anderson, S., and Centonze, R. (2007). Property Rights and the Management of Animal Genetic Resources. World Development 35 , 1529-1541.
Andersson, L., and Georges, M. (2004). Domestic-animal genomics: deciphering the genetics of complex traits. Nature Reviews Genetics5 , 202-212.
Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A., and Saunders, N.C. (1987). INTRASPECIFIC PHYLOGEOGRAPHY: The Mitochondrial DNA Bridge Between Population Genetics and Systematics. Annual Review of Ecology and Systematics 18 , 489-522.
Avise, J.C., Ellis, D., Clarke Bryan, C., Robertson, A., and Jeffreys Alec, J. (1986). Mitochondrial DNA and the evolutionary genetics of higher animals. Philosophical Transactions of the Royal Society of London B, Biological Sciences 312 , 325-342.
Axelsson, E., Webster, M.T., Smith, N.G.C., Burt, D.W., and Ellegren, H. (2005). Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Research 15 , 120-125.
Barrett, J.C., Fry, B., Maller, J., and Daly, M.J. (2004). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics21 , 263-265.
Biscarini, F., Nicolazzi, E.L., Stella, A., Boettcher, P.J., and Gandini, G. (2015). Challenges and opportunities in genetic improvement of local livestock breeds. Front Genet 6 , 33.
Bruford, M.W., Bradley, D.G., and Luikart, G. (2003). DNA markers reveal the complexity of livestock domestication. Nature Reviews Genetics4 , 900-910.
Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E., DePristo, M.A., Handsaker, R.E., Lunter, G., Marth, G.T., Sherry, S.T., et al. (2011). The variant call format and VCFtools. Bioinformatics27 , 2156-2158.
de Cara, M.A.R., Fernأndez, J., Toro, M.A., and Villanueva, B. (2011). Using genome-wide information to minimize the loss of diversity in conservation programmes. Journal of Animal Breeding and Genetics128 , 456-464.
Do, C., Waples, R.S., Peel, D., Macbeth, G.M., Tillett, B.J., and Ovenden, J.R. (2014a). NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne ) from genetic data. Mol Ecol Resour 14 , 209-214.
Do, C., Waples, R.S., Peel, D., Macbeth, G.M., Tillett, B.J., and Ovenden, J.R. (2014b). NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Molecular Ecology Resources 14 , 209-214.
Dodgson, J.B., Cheng, H.H., and Okimoto, R. (1997). DNA marker technology: a revolution in animal genetics. Poultry Science 76 , 1108-1114.
Groeneveld, E., Westhuizen, B., Maiwashe, A., Voordewind, F., and Ferraz, J.B. (2009). POPREP: a generic report for population management. Genet Mol Res 8 , 1158-1178.
Groeneveld, L.F., Lenstra, J.A., Eding, H., Toro, M.A., Scherf, B., Pilling, D., Negrini, R., Finlay, E.K., Jianlin, H., Groeneveld, E., et al. (2010). Genetic diversity in farm animals ق€“ a review. Animal Genetics 41 , 6-31.
Harrison, R.G. (1989). Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends in Ecology & Evolution4 , 6-11.
Henson, E.L., Food, and Nations, A.O.o.t.U. (1992). In Situ Conservation of Livestock and Poultry (Food and Agriculture Organization of the United Nations).
Holsinger, K.E., and Weir, B.S. (2009). Genetics in geographically structured populations: defining, estimating and interpreting FST. Nature Reviews Genetics 10 , 639.
Hu, Z.L., Park, C.A., Wu, X.L., and Reecy, J.M. (2013). Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. Nucleic Acids Res 41 , D871-879.
Kocher, T.D., Thomas, W.K., Meyer, A., Edwards, S.V., Paabo, S., Villablanca, F.X., and Wilson, A.C. (1989). Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci U S A 86 , 6196-6200.
Koh, M.C., Lim, C.H., Chua, S.B., Chew, S.T., and Phang, S.T.W. (1998). Random amplified polymorphic DNA (RAPD) fingerprints for identification of red meat animal species. Meat Science 48 , 275-285.
Kumar, S., Stecher, G., and Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33 , 1870-1874.
Levin, I., Crittenden, L.B., and Dodgson, J.B. (1993). Genetic Map of the Chicken Z Chromosome Using Random Amplified Polymorphic DNA (RAPD) Markers. Genomics 16 , 224-230.
Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 , 1754-1760.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 , 2078-2079.
Liu, Z.J., and Cordes, J.F. (2004a). DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238 , 1-37.
Liu, Z.J., and Cordes, J.F. (2004b). Erratum to “DNA marker technologies and their applications in aquaculture genetics” [Aquaculture 238 (2004) 1–37]. Aquaculture 242 , 735-736.
McMahon, B.J., Teeling, E.C., and Hأglund, J. (2014). How and why should we implement genomics into conservation? Evolutionary Applications 7 , 999-1007.
McQuillan, R., Leutenegger, A.L., Abdel-Rahman, R., Franklin, C.S., Pericic, M., Barac-Lauc, L., Smolej-Narancic, N., Janicijevic, B., Polasek, O., Tenesa, A., et al. (2008). Runs of homozygosity in European populations. Am J Hum Genet 83 , 359-372.
Morin, P.A., Luikart, G., Wayne, R.K., and the, S.N.P.w.g. (2004). SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution19 , 208-216.
Nei, M., and Li, W.H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76 , 5269-5273.
Parsons, Y.M., and Shaw, K.L. (2001). Species boundaries and genetic diversity among Hawaiian crickets of the genus Laupala identified using amplified fragment length polymorphism. Molecular Ecology 10 , 1765-1772.
Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A., and Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38 , 904-909.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J., et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81 , 559-575.
Rambaut, A. (2018). FigTree v1. 4.4, a graphical viewer of phylogenetic trees. Available fromhttp://tree.bio.ed.ac.uk/software/figtree.
Ramstad, K.M., Woody, C.A., Sage, G.K., and Allendorf, F.W. (2004). Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska. Molecular Ecology 13 , 277-290.
Rescources, C.N.C.O.A.G. (2011). Animal Genetic Rescources In China Poultry.
Sabeti, P.C., Schaffner, S.F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A., Mikkelsen, T.S., Altshuler, D., and Lander, E.S. (2006). Positive Natural Selection in the Human Lineage. Science312 , 1614.
Sabeti, P.C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E.H., McCarroll, S.A., Gaudet, R., et al. (2007). Genome-wide detection and characterization of positive selection in human populations. Nature 449 , 913.
Saitou, N., and Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4 , 406-425.
Savelkoul, P.H.M., Aarts, H.J.M., de Haas, J., Dijkshoorn, L., Duim, B., Otsen, M., Rademaker, J.L.W., Schouls, L., and Lenstra, J.A. (1999). Amplified-Fragment Length Polymorphism Analysis: the State of an Art. Journal of Clinical Microbiology 37 , 3083.
Sun, H., Olasege, B.S., Xu, Z., Zhao, Q., Ma, P., Wang, Q., Lu, S., and Pan, Y. (2018). Genome-Wide and Trait-Specific Markers: A Perspective in Designing Conservation Programs. Front Genet 9 , 389.
Szpiech, Z.A., and Hernandez, R.D. (2014). selscan: an efficient multithreaded program to perform EHH-based scans for positive selection. Mol Biol Evol 31 , 2824-2827.
Szpiech, Z.A., Jakobsson, M., and Rosenberg, N.A. (2008). ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24 , 2498-2504.
Thurston, L.M., Siggins, K., Mileham, A.J., Watson, P.F., and Holt, W.V. (2002). Identification of Amplified Restriction Fragment Length Polymorphism Markers Linked to Genes Controlling Boar Sperm Viability Following Cryopreservation1. Biology of Reproduction 66 , 545-554.
Vignal, A., Milan, D., SanCristobal, M., and Eggen, A. (2002). A review on SNP and other types of molecular markers and their use in animal genetics. Genetics, selection, evolution : GSE 34 , 275-305.
Wang, K., Li, M., and Hakonarson, H. (2010). ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38 , e164.
Wang, M.S., Zhang, R.W., Su, L.Y., Li, Y., Peng, M.S., Liu, H.Q., Zeng, L., Irwin, D.M., Du, J.L., Yao, Y.G., et al. (2016). Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication. Cell Res 26 , 556-573.
Waples, R.S., and Do, C. (2008). ldne: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Resour 8 , 753-756.
Weir, B.S., and Cockerham, C.C. (1984). Estimating F-Statistics for the Analysis of Population Structure. Evolution 38 , 1358-1370.
WRIGHT, S. (1949). THE GENETICAL STRUCTURE OF POPULATIONS. Annals of Eugenics 15 , 323-354.
Yu, G., Wang, L.-G., Han, Y., and He, Q.-Y. (2012). clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters. OMICS: A Journal of Integrative Biology 16 , 284-287.
Zane, L., Bargelloni, L., and Patarnello, T. (2002). Strategies for microsatellite isolation: a review. Molecular Ecology 11 , 1-16.
Zeder, M.A., Emshwiller, E., Smith, B.D., and Bradley, D.G. (2006). Documenting domestication: the intersection of genetics and archaeology. Trends in Genetics 22 , 139-155.
Zhang, D.-X., and Hewitt, G.M. (1996). Nuclear integrations: challenges for mitochondrial DNA markers. Trends in Ecology & Evolution 11 , 247-251.
Zhang, M., Han, W., Tang, H., Li, G., Zhang, M., Xu, R., Liu, Y., Yang, T., Li, W., Zou, J., et al. (2018). Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs. BMC Genomics 19 , 598.