Science in China Series C: Life Sciences © 2008 SCIENCE IN CHINA PRESS Springer Sci China Ser C-Life Sci | Jun. 2008 | vol. 51 | no. 6 | 560-568 www.scichina.com life.scichina.com www.springerlink.com Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls BAO WenBin 1 , CHEN GuoHong 1† , LI BiChun 1 , WU XinSheng 1 , SHU JingTing 1 , WU ShengLong 1 , XU Qi 1 & Steffen WEIGEND 2 1 College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; 2 Institute for Animal Breeding, Federal Agricultural Research Centre, Mariensee 31535, Germany Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspe- cies (Gallus gallus spadiceus in China and Gallus gallus gallus in Thailand) and 14 Chinese domestic chicken breeds were evaluated with 29 microstaellite loci, the genetic variability within population and genetic differentiation among population were estimated, and then genetic diversity and phylogenetic relationships were analyzed among red jungle fowls and Chinese domestic fowls. A total of 286 alleles were detected in 16 population with 29 microsatellite markers and the average number of the alleles observed in 29 microsatellite loci was 9.86±6.36. The overall expected heterozygosity of all population was 0.6708±0.0251, and the number of population deviated from Hardy-Weinberg equilibrium per locus ranged from 0 to 7. In the whole population, the average of genetic differentiation among population, measured as FST value, was 16.7% (P<0.001), and all loci contributed significantly (P<0.001) to this differentiation. It can also be seen that the deficit of heterozygotes was very high (0.015) (P<0.01). Reynolds’ distance values varied between 0.036 (Xiaoshan chicken-Luyuan chicken pair) and 0.330 (G. gallus gallus-Gushi chicken pair). The Nm value ranged from 0.533 (between G. gallus gallus and Gushi chicken) to 5.833 (between Xiaoshan chicken and Luyuan chicken). An unrooted consensus tree was constructed using the neighbour-joining method and the Reynolds’ genetic distance. The heavy-body sized chicken breeds, Luyuan chicken, Xiaoshan chicken, Beijing Fatty chicken, Henan Game chicken, Huainan Partridge and Langshan chicken formed one branch, and it had a close genetic relationship between Xiaoshan chicken-Luyuan chicken pair and Chahua chicken-Tibetan chicken pair. Chahua chicken and Tibetan chicken had closer genetic relationship with these two subspecies of red jungle fowl than other domestic chicken breeds. G. gallus spadiceus showed closer phylogenetic relationship with Chinese domestic chicken breeds than G. gallus gallus. All 29 microstaellite loci in this study showed high levels of polymorphism and significant genetic differentiation was observed among two subspecies of red jungle fowl and 14 Chinese domestic chicken breeds. The evolutional dendrogram is as follows: evolutional breeds primitive breeds (Chahua chicken and Tibetan) red jungle fowl in China (G. gallus spadiceus) red jungle fowl in Thailand (G. gallus gallus). The results supported the theory that the domestic fowls might originate from different subspecies of red jungle fowl and Chinese domestic fowls had independent origin. red jungle fowl, domestic fowl, microsatellite, genetic diversity, phylogenetic relationship Received September 5, 2006; accepted April 15, 2008 doi: 10.1007/s11427-008-0076-y † Corresponding author (email: ghchen@yzu.edu.cn) Supported by 863 Program of Ministry of Science and Technology of China (Grant No. 2006AA10Z1E7), and National Natural Science Foundation of China (Grant No. 30170673)