Phylogeny, Genetic Relationships and Population Structure of Five Italian Local Chicken Breeds

References

• AllendorfF.W. LuikartG. 2007. Conservation and the genetics of populations. Blackwell Publ., Malden, MA, USA.
   Google Scholar
• AVIANDIV, 2012. Available from: http://aviandiv.tzv.fal.de/primer_table.html
   Google Scholar
• BaruchelloM. CassandroM. 2003. Avicoli veneti. Progetto CO.VA. – Interventi per la conservazione e la valorizzazione di razze avicole locali venete. Available from: http//www.venetoagricoltura.org
   Google Scholar
• BelkhirK. BorsaP. ChikhiL. RaufasteN. BonhommeF. 2004. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, Université de Montpellier II Ed., Montpellier, France. Available from: http://www.genetix.univmontp2.fr/genetix/genetix.htm
   Google Scholar
• BodzsarN. EdingH. RevayT. HidasA. WeigendS. 2009. Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markers. Anim. Genet. 4:516-523.
   Google Scholar
• DalvitC. De MarchiM. BarcacciaG. ZanonA. SabbioniA. 2005. Genetic similarities among Modenese, Romagnola and three Veneto chicken breeds. pp 106-108 in Proc. 16th Nat. Congr. ASPA, Torino, Italy. Ital. J. Anim. Sci. 4(Suppl.2):106-108.
   Google Scholar
• DalvitC. ZanettiE. CassandroM. 2009. Estimation of genetic diversity over time in an in-situ marker assisted conservation scheme of local chicken breeds. pp 63-65 in Proc. 18th Nat. Congr. ASPA, Palermo, Italy. Ital. J. Anim. Sci. 8(Suppl.2):63-65.
   Google Scholar
• EltananyM. PhilippU. WeigendS. DistlO. 2011. Genetic diversity of ten Egyptian chicken strains using 29 microsatellite markers. Anim. Genet. 42:666-669.
   PubMed Web of Science ®Google Scholar
• EvannoG. RegnautS. GoudetJ. 2005. Detecting the number of cluster of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611-2620.
   PubMed Web of Science ®Google Scholar
• ExcoffierL. LavalG. SchneiderS. 2006. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1:47-50.
   Web of Science ®Google Scholar
• FAO, 2004. Guideline for development of national management of farm animal genetic diversity. Recommended microsatellite markers. Available from: htpp://dad.fao.org/en/refer/library/guideline/marker.pdf
   Google Scholar
• FAO, 2010. Domestic animal diversity information system. Available from: http://dad.fao.org/
   Google Scholar
• FelsensteinJ. 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Available from: http://evolution.genetics.washington.edu/phylip.html
   Google Scholar
• FuY. NiuD. RuanH. 2001. Studies of genetic diversity of Zhejiang native chicken breeds. Acta Genetica Sinica 28:606-613.
   PubMedGoogle Scholar
• GranevitzeZ. HillelJ. ChenG.H. CucN.T.K. FeldmanM. EdingH. WeigendS. 2007. Genetic diversity within chicken populations from different continents and management histories. Anim. Genet. 38:576-583.
   PubMed Web of Science ®Google Scholar
• GranevitzeZ. HillelJ. FeldmanM. SixA. EdingH. WeigendS. 2009. Genetic structure of a wide-spectrum chicken gene pool. Anim. Genet. 40:686-693.
   PubMed Web of Science ®Google Scholar
• GrimalA. Viudes de CastroM.P. GómezE.A. GoyacheF. RoyoL.J. 2011. Posible origen materno común de dos poblaciones de gallinas: resultados preliminares del análisis del ADN mitocondrial. pp 482-484 in Proc. 14th Nat. Congr. AIDA on Animal Production, Zaragoza, Spain.
   Google Scholar
• GoudetJ. 2002. FSTAT 2.9.3.2, a program to estimate and test gene diversities and fixation indices. Available from: http://www.unil.ch/popgen/softwares/fstat.htm
   Google Scholar
• GualtieriM. PignatelliP. CristalliA. 2006. Pollo di razza Valdarnese bianca. Risorse genetiche animali autoctone della Toscana. ARSIA Ed., Firenze, Italy.
   Google Scholar
• GuoS.W. ThompsonE.A. 1992. A Monte Carlo method for combined segregation and linkage analysis. Am. J. Hum. Genet. 51:1111-1126.
   PubMed Web of Science ®Google Scholar
• HartmannW. 1997. Evaluation of major genes affecting resistance to disease in poultry. World. Poultry Sci. J. 53: 231-251.
   Web of Science ®Google Scholar
• HensonE.L. 1992. In situ conservation of livestock and poultry. Available from: http://www.fao.org/docrep/004/T0559E/T0559E00.htm#TOC>
   Google Scholar
• HillelJ. GroenenM.A.M. Tixier-BoichardM. KorolA.B. DavidL. KirzhnerV.M. BurkeT. Barre-DirieA. CrooijmansR.P.M.A EloK. FeldmanM.W. FreidlinP.J. Mäki-TanilaA. OortwijnM. ThomsoneP. VignalA. WimmersK. WeigendS. 2003. Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet. Sel. Evol. 35:533-557.
   PubMed Web of Science ®Google Scholar
• JakobssonM. RosenbergN.A. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801-1806.
   PubMed Web of Science ®Google Scholar
• JakobssonM. ScholzS. W. ScheetP. GibbsJ.R. VanLiereJ.M. FungH-C. SzpiechZ.A. DegnanJ.H. WangK. GuerreiroR. BrasJ.M. SchymickJ.C. HernandezD.G. TraynorB. J. Simon-SanchezJ. MatarinM. BrittonA. van de LeemputJ. RaffertyI. BucanM. CannH.M. HardyJ.A. RosenbergN.A. SingletonA.B. 2008. Genotype, haplotype and copy-number variation in worldwide human population. Nature 451:998-1003.
   PubMed Web of Science ®Google Scholar
• LandeR. 1988. Genetics and demography in biological conservation. Science 241:1455-1460.
   PubMed Web of Science ®Google Scholar
• LibradoP. RozasJ. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
   PubMed Web of Science ®Google Scholar
• LiuY.P. WuG.S. YaoY.G. MiaoY.W. LuikartG. BaigM. Beja-PereiraA. DingZ.L. PalanichamyM.G. ZhangY.P. 2006. multiple maternal origins of chickens: Out of the Asian jungles. Mol. Phylogenet. Evol. 38:12-19.
   PubMed Web of Science ®Google Scholar
• MarelliS.P. StrillacciM.G. FerranteV. PignatelliP. GualtieriM. Guidobono CavalchiniL. 2006. Genetic variability in Valdarnese Bianca chicken breed using microsatellite markers. World. Poultry Sci. J. 6:207-208.
   Google Scholar
• MazzonI. 1932. Pollicoltura Padovana. Soc. Coop.Tipografica Ed., Padova, Italy.
   Google Scholar
• MazzorinJ.D.G. 2000. Introduzione e diffusione del pollame in Italia ed evoluzione delle sue forme di allevamento fino al Medioevo. pp 351-361 in Proc. 3rd Nat. Congr. of Archaeozoology, Siracusa, Italy.
   Google Scholar
• MtileniB.J. MuchadeyiF.C. MaiwasheA. GroeneveldE. GroeneveldL.F. DzamaK. WeigendS. 2011. Genetic diversity and conservation of South African indigenous chicken populations. J. Anim. Breed Genet. 128:209-218.
   PubMed Web of Science ®Google Scholar
• MuchadeyiF.C. EdingH. SimianerH. WollnyC.B.A. GroeneveldE. WeigendS. 2008. Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens. Anim. Genet. 39:615-622.
   PubMed Web of Science ®Google Scholar
• MuchadeyiF.C. EdingH. WollnyC.B.A. GroeneveldE. MakukaS.M. ShamseldinR. SimianerH. WeigendS. 2007. Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. Anim. Genet. 38:332-339.
   PubMed Web of Science ®Google Scholar
• MugnaiC. Dal BoscoA. CastelliniC. 2009. Effect of rearing system and season on the performance and egg characteristics of Ancona laying hens. Ital. J. Anim. Sci. 8:175-188.
   Web of Science ®Google Scholar
• MwacharoJ.M. BjørnstadG. MobegiV. NomuraK. HanadaH. AmanoT. JianlinH. HanotteO. 2011. Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. Mol. Phylogenet. Evol. 58:374-382.
   PubMed Web of Science ®Google Scholar
• NishiboriM. ShimogiriT. HayashiT. YasueH. 2005. Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Anim. Genet. 36:367-375.
   PubMed Web of Science ®Google Scholar
• ParkS.D.E. 2001. Trypanotolerance in West African cattle and the population genetic effects of selection. Degree Diss., University of Dublin, Ireland.
   Google Scholar
• PritchardJ.K. StephensM. DonnellyP. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
   PubMed Web of Science ®Google Scholar
• RaymondM. RoussetF. 1995. An exact test for population differentiation. Evolution 49:1280-1283.
   PubMed Web of Science ®Google Scholar
• RevayT. BodzarN. MobegiV.E. HanotteO. HidasA. 2010. Origin of Hungarian indigenous chicken breeds inferred from mitochondrial DNA D-loop sequences. Anim. Genet. 41:548-550.
   PubMed Web of Science ®Google Scholar
• ReynoldsJ. WeirB.S. CockerhamC.C. 1983. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105:767-779.
   PubMed Web of Science ®Google Scholar
• RosenbergN.A. 2004. Distruct: a program for the graphical display of population structure. Mol. Ecol. Notes 4:137-138.
   Web of Science ®Google Scholar
• RosenbergN.A. PritchardJ.K. WeberJ.L. CannH.M. KiddK.K. ZhivotovskyL.A. FeldmanM.W. 2002. Genetic structure of human populations. Science 298:2381-2385.
   PubMed Web of Science ®Google Scholar
• SabbioniA. ZanonA. BerettiV. SuperchiP. ZambiniE.M. 2006. Carcass yield and meat quality parameters of two Italian autochthonous chicken breeds reared outdoor: Modenese and Romagnola. Paper n. 204 in Proc. 12th Eur. Poultry Conf., Verona, Italy.
   Google Scholar
• SacchiR. 1960. Il pollo Valdarno ha un avvenire. Avicoltura 11:41-45.
   Google Scholar
• SerjeantsonD. 2009. Birds. Cambridge University Press, New York, NY, USA.
   Google Scholar
• StoreyA.A. AthensJ.S. BryantD. CarsonM. EmeryK. deFranceS. HighamC. HuynenL. IntohM. JonesS. KirchP.V. LadefogedT. McCoyP. Morales-MuñizA. QuirozD. ReitzE. RobinsJ. WalterR. Matisoo-SmithE. 2012. Investigating the Global Dispersal of Chickens in Prehistory using ancient mitochondrial DNA signatures. Plos One 7:e39171.
   PubMed Web of Science ®Google Scholar
• WeigendS. GroenenM.A.M. Tixier-BoichardM. VignalA. HillelJ. WimmersK. BurkeT. Mäki-TanilaA. 1998. Development of strategy and application of molecular tools to asses biodiversity in chicken genetic resources. Available from: http://aviandiv.tzv.fal.de/
   Google Scholar
• WeirB.S. CockerhamC.C. 1984. Estimating Fstatistics for the analysis of population structure. Evolution 38:1358-1370.
   PubMed Web of Science ®Google Scholar
• WrightS. 1978. Evolution and the genetics of populations, variability within and among natural populations. University of Chicago Press, Chicago, IL, USA.
   Google Scholar
• YehF.C. YangR.C. BoyleT. 1999. Popgene version 1.31. Microsoft window-based freeware for population genetic analysis. Department of Renewable Resources, University of Alberta Ed., Edmonton, Canada.
   Google Scholar
• ZanettiE. De MarchiM. DalvitC. CassandroM. 2010. Genetic characterisation of Italian chickens undergoing in situ conservation. Poultry Sci. 89:420-427.
   PubMed Web of Science ®Google Scholar
• ZanonA. SabbioniA. 2001. Identificazione e salvaguardia genetica delle razze avicole italiane. Ann. Facoltà Medicina Veterinaria di Parma 21:117-134.
   Google Scholar
• ZanonA. BerettiV. SuperchiP. ZambiniE.M. SabbioniA. 2006. Psico-chemical characteristics of eggs from two Italian autochthonous chicken breeds: Modenese and Romagnola. Paper n. 203 in Proc. 12th Eur. Poultry Conf., Verona, Italy.
   Google Scholar