Abstract
BackgroundDomestication 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.ResultsMicrosatellite 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.ConclusionOur 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.
Highlights
Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley
Genetic identity of Indian fowls In the present study, phylogenetic and demographic profiling analyses were carried out using 76 Indian birds that belong to seven populations
Since we found only one red jungle fowl (RJF) with 'A' at this site, and due to clear separation of the clades, it is unlikely that G. g. murghi and G. sonneratii hybridize in the wild contrary to the observations made by Nishibori et al [11] who suggested the possible hybridization between the RJF and GJF
Summary
Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley. 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. While some authors suggest monophyletic origin of domestic chicken [6,7], others provide evidence for multiple and independent domestication events [8]. Such inconsistent observations are attributable to the fact that the initial studies were done with relatively small set of samples. In all these reported studies the native RJFs of Indian sub-continent, G. g. murghi were not represented in the analyses due to lack of sequence or molecular marker information on this group of birds
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