[en] BACKGROUND: Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley. However, non-inclusion of Indian red jungle fowl (RJF), Gallus gallus murghi in previous studies has left a big gap in understanding the relationship of this major group of birds. In the present study, we addressed this issue by analyzing 76 Indian birds that included 56 G. g. murghi (RJF), 16 G. g. domesticus (domestic chicken) and 4 G. sonneratii (Grey JF) using both microsatellite markers and mitochondrial D-loop sequences. We also compared the D-loop sequences of Indian birds with those of 779 birds obtained from GenBank. RESULTS: Microsatellite marker analyses of Indian birds indicated an average FST of 0.126 within G. g. murghi, and 0.154 within G. g. domesticus while it was more than 0.2 between the two groups. The microsatellite-based phylogenetic trees showed a clear separation of G. g. domesticus from G. g. murghi, and G. sonneratii. Mitochondrial DNA based mismatch distribution analyses showed a lower Harpending's raggedness index in both G. g. murghi (0.001515) and in Indian G. g. domesticus (0.0149) birds indicating population expansion. When meta analysis of global populations of 855 birds was carried out using median joining haplotype network, 43 Indian birds of G. g. domesticus (19 haplotypes) were distributed throughout the network sharing haplotypes with the RJFs of different origins. CONCLUSION: Our results suggest that the domestication of chicken has occurred independently in different locations of Asia including India. We found evidence for domestication of Indian birds from G. g. spadiceus and G. g. gallus as well as from G. g. murghi, corroborating multiple domestication of Indian and other domestic chicken. In contrast to the commonly held view that RJF and domestic birds hybridize in nature, the present study shows that G. g. murghi is relatively pure. Further, the study also suggested that the chicken populations have undergone population expansion, especially in the Indus valley.
Disciplines :
Genetics & genetic processes
Author, co-author :
Kanginakudru, Sriramana
Metta, Muralidhar ; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Jakati, R. D.
Nagaraju, J.
Language :
English
Title :
Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken.
A History of Domesticated Animals. FE Zeuner, Harper and Row, New York 1963
Did chicken go north? New evidence for domestication. B West B-X Zhou, J Archaeol Sci 1988 15 515 533 10.1016/0305-4403(88)90080-5
Genetic and evolution of the domestic fowl. L Stevens, New York, Cambridge University Press 1991
Genetic endangerment of wild red jungle fowl (Gallus gallus)? AT Peterson IL Brisbin Jr, Bird Conservation International 1999 9 387 394
Evolutionary relationships of Red Jungle Fowl and chicken breeds. IG Moiseyeva MN Romanov AA Nikiforov AA Sevastyanova SK Semyenova, Genet Sel Evol 2003 35 4 403 423 10.1051/gse:2003031 12927074
Monophyletic origin and unique dispersal patterns of domestic fowls. A Fumihito T Miyake M Takada R Shingu T Endo T Gojobori N Kondo S Ohno, Proc Natl Acad Sci U S A 1996 93 13 6792 6795 8692897 10.1073/pnas.93.13.6792
One subspecies of the red junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds. A Fumihito T Miyake S Sumi M Takada S Ohno N Kondo, Proc Natl Acad Sci U S A 1994 91 26 12505 12509 7809067 10.1073/pnas.91.26.12505
Multiple maternal origins of chickens: out of the Asian jungles. YP Liu GS Wu YG Yao YW Miao G Luikart M Baig A Beja-Pereira ZL Ding MG Palanichamy YP Zhang, Mol Phylogenet Evol 2006 38 1 12 19 10.1016/j.ympev.2005.09.014 16275023
The origin and genetic diversity of Chinese native chicken breeds. D Niu Y Fu J Luo H Ruan XP Yu G Chen YP Zhang, Biochem Genet 2002 40 5-6 163 174 10.1023/A:1015832108669 12137331
Characterization of the genetic status of populations of red jungle fowl. IL Brisbin AT Peterson R Okimoto RG Amato, J Bombay Natural History Society 2002 99 217 223
Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. M Nishibori T Shimogiri T Hayashi H Yasue, Anim Genet 2005 36 5 367 375 10.1111/j.1365-2052.2005.01318.x 16167978
Genetic traces of ancient demography. HC Harpending MA Batzer M Gurven LB Jorde AR Rogers ST Sherry, Proc Natl Acad Sci U S A 1998 95 4 1961 1967 9465125 10.1073/pnas.95.4.1961
Evolutionary genetics. Clonal inheritance of avian mitochondrial DNA. S Berlin H Ellegren, Nature 2001 413 6851 37 38 10.1038/35092623 11544517
Genetic evidence for an East Asian origin of domestic dogs. P Savolainen YP Zhang J Luo J Lundeberg T Leitner, Science 2002 298 5598 1610 1613 10.1126/science.1073906 12446907
Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile. AA Storey JM Ramirez D Quiroz DV Burley DJ Addison R Walter AJ Anderson TL Hunt JS Athens L Huynen EA Matisoo-Smith, Proc Natl Acad Sci U S A 2007 104 25 10335 10339 17556540 10.1073/pnas.0703993104
The evolution of molecular markers - just a matter of fashion? C Schlotterer, Nat Rev Genet 2004 5 1 63 69 10.1038/nrg1249 14666112
Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. J Hillel MA Groenen M Tixier-Boichard AB Korol L David VM Kirzhner T Burke A Barre-Dirie RP Crooijmans K Elo MW Feldman PJ Freidlin A Maki-Tanila M Oortwijn P Thomson A Vignal K Wimmers S Weigend, Genet Sel Evol 2003 35 5 533 557 10.1051/gse:2003038 12939204
Highly polymorphic microsatellite markers in poultry. RP Crooijmans AJ van Kampen JJ van der Poel MA Groenen, Anim Genet 1993 24 6 441 443 8273919
The genetic link between the Chinese bamboo partridge (Bambusicola thoracica) and the chicken and junglefowls of the genus Gallus. A Fumihito T Miyake M Takada S Ohno N Kondo, Proc Natl Acad Sci U S A 1995 92 24 11053 11056 7479935 10.1073/pnas.92.24.11053
Estimation of levels of gene flow from DNA sequence data. RR Hudson M Slatkin WP Maddison, Genetics 1992 132 2 583 589 1427045
Using mitochondrial and nuclear DNA markers to reconstruct human evolution. LB Jorde M Bamshad AR Rogers, Bioessays 1998 20 2 126 136 10.1002/(SICI)1521-1878(199802)20:2<126::AID-BIES5>3.0.CO;2-R 9631658
Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. T Oka Y Ino K Nomura S Kawashima T Kuwayama H Hanada T Amano M Takada N Takahata Y Hayashi F Akishinonomiya, Anim Genet 2007 38 3 287 293 10.1111/j.1365-2052.2007.01604.x 17539973
Evidence for two independent domestications of cattle. RT Loftus DE MacHugh DG Bradley PM Sharp P Cunningham, Proc Natl Acad Sci U S A 1994 91 7 2757 2761 8146187 10.1073/pnas.91.7.2757
The origin of the domestic pig: independent domestication and subsequent introgression. E Giuffra JM Kijas V Amarger O Carlborg JT Jeon L Andersson, Genetics 2000 154 4 1785 1791 10747069
Molecular Cloning, A laboratory manual. J Sambrook RD W., New York., Cold Spring Harbor Laboratory Press. 2001
GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. R Peakall PE Smouse, Molecular Ecology Notes 2006 6 288 295 10.1111/j.1471-8286.2005.01155.x
Arlequin: A software for population genetics data analysis. S Schneider D. Roessli, L. Excoffier., Geneva, Genetics and Biometry Lab, Dept. of Anthropology, University of Geneva Ver. 2.000. 2000
GenBank. http://www.ncbi.nlm.nih.gov
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. JD Thompson TJ Gibson F Plewniak F Jeanmougin DG Higgins, Nucleic Acids Res 1997 25 24 4876 4882 9396791 10.1093/nar/25.24.4876
Genedoc, a Tool for Editing and Annotating Multiple Sequence Alignments. KB Nicholas HBJ Nicholas, Distributed by the author 1997
DnaSP, DNA polymorphism analyses by the coalescent and other methods. J Rozas JC Sanchez-DelBarrio X Messeguer R Rozas, Bioinformatics 2003 19 18 2496 2497 10.1093/bioinformatics/btg359 14668244
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. F Tajima, Genetics 1989 123 3 585 595 2513255
Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. YX Fu, Genetics 1997 147 2 915 925 9335623
Population growth makes waves in the distribution of pairwise genetic differences. AR Rogers H Harpending, Mol Biol Evol 1992 9 3 552 569 1316531
Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. HC Harpending, Hum Biol 1994 66 4 591 600 8088750
Development of a genetic map of the chicken with markers of high utility. HH Cheng I Levin RL Vallejo H Khatib JB Dodgson LB Crittenden J Hillel, Poult Sci 1995 74 11 1855 1874 8614694
Functional genes mapped on the chicken genome. RP Crooijmans JJ van der Poel MA Groenen, Anim Genet 1995 26 2 73 78 7733510
New microsatellite markers in chicken optimized for automated fluorescent genotyping. RP Crooijmans RJ Dijkhof JJ van der Poel MA Groenen, Anim Genet 1997 28 6 427 437 10.1111/j.1365-2052.1997.00205.x 9589584
