Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls.

Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspecies (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.

Bao W ，Chen G ，Li B ，Wu X ，Shu J ，Wu S ，Xu Q ，Weigend S ... -  《science in china series c-life sciences》

[Genetic diversity of red jungle fowl in China (Gallus gallus spadiceus) and red jungle fowl (Gallus gallus gallus) in Thailand].

Genetic diversity of red jungle fowl in China (Gallus gallus spadiceus) and red jungle fowl in Thailand (Gallus gallus gallus) was evaluated with 29 microstaellite loci, the genetic variability within subspecies and genetic differentiation between subspecies were estimated. The results showed that the 168 alleles were amplified with the number of alleles per locus from 2 to 13. The average expected heterozygosity and polymorphism information content (PIC) of all loci were 0.5780 and 0.53, respectively. The mean numbers of effective alleles of red jungle fowl in China and red jungle fowl in Thailand were 5.55 and 6.38. The heterozygosity and the genetic diversity of the two subspecies were high. Genetic differentiation index (FST) of these populations was 0.194 (P<0.01). Reynolds' genetic distance and gene flow between the two populations were 0.157 and 1.040, respectively. Based on these results, genetic structure and significant genetic differentiation of red jungle fowl in China were different from red jungle fowl in Thailand. The results of this study did not support to identify these red jungle fowl subspecies as the same subspecies, but supported the theory that Chinese domestic fowls have independent origin.

Bao WB ，Chen GH ，Wu XS ，Xu Q ，Wu SL ，Shu JT ，Weigend S ... -  《-》

[Correlation between adenylosuccinate lyase (ADSL) gene polymorphism and inosine monophosphate acid (IMP) content in domestic fowl and genetic relationship between red jungle fowl and domestic fowl].

This study investigates single nucleotide polymorphism (SNP) of the adenylosuccinate lyase(ADSL) gene in variety chicken breeds, including Recessive White chickens, Silkies chickens, Baier chickens, Tibetan chickens and two red jungle fowls. Primers for exon 2 in ADSL gene were designed based on the chicken genomic sequence and a SNP(C/T at 3484) was detected by PCR-SSCP and DNA sequencing. Three genotypes within all breeds were found and least square analysis showed that TT genotype birds had a significant higher inosine monophosphate acid (IMP) content than TC (P < 0.01) and CC (P < 0.05) genotype birds, TC genotype birds had a little higher IMP content than CC genotype birds, but the difference was not significant. We proposed this SNP site correlated with IMP content in chickens. A neighbour-joining dendrogram was constructed based on the Nei's genentic distance. The genetic relationship between Chinese red jungle fowl and Tibetan chickens was the nearest, whereas Baier chickens were more closer to Silkies chickens. The Chinese red jungle fowls were relatively closer to the domestic fowls, whereas Thailand red jungle fowls were relatively diverging to the Chinese native breeds. These results supported the theory concerning the independent origins of Chinese native fowl breeds.

Shu JT ，Bao WB ，Zhang HX ，Zhang XY ，Ji CL ，Chen GH ... -  《-》

[Analysis of genetic relationship among Chinese native chicken breeds using microsatellites marker].

The allele frequencies, heterozygosity (H), mean heterozygosity, polymorphism information content (PIC) and genetic relationships were studied in Luyuan chicken, Gushi chicken, Tibetan chicken, Baier chicken, Xianju chicken, Chahua chicken, Dagu chicken,Beijing Fatty chicken, Langshan chicken, Henan Game chicken,Taihe Silkies chicken and Xiaoshan chicken using seven microsatellite DNA markers. The results showed that there were differences among allele fequencies of seven microsatellite loci in 12 Chinese native chicken breeds. Among the 12 Chinese native chicken breeds, mean heterozygosity of Luyuan chicken was the highest (0.5929), and that of Chahua chicken was the lowest (0.3514). There were similar results in PIC. By fuzzy cluster analysis was found that the genetic relationship between Taihe Silkies chicken and Henan Game chicken was the nearest, and that between Gushi chicken and the other chicken breeds was the most distant. The 12 Chinese native chicken breeds were divided into three group by fuzzy cluster analysis. The first group included Taihe Silkies chicken, Henan Game chicken, Langshan chicken, Xiaoshan chicken, Dagu chicken, Beijing Fatty chicken and Luyuan chicken, the second group included Chahua chicken, Tibetan chicken, Xianju chicken and Baier chicken, and the third group included Gushi chicken.

Wu XS ，Chen GH ，Wang DQ ，Zhang XY ，Wang KH ，Cheng R ，Liu B ，Xu Q ，Zhou QL ... -  《-》

[Analysis of genetic diversity of preserved population of native chicken breeds by microsatellites and file foundation of markers].

The genetic diversity (allele frequency, mean heterozygosity, mean polymorphic information content(PIC), and Nei genetic distances) of preserved population of 11 native chicken breeds was analyzed by 20 microsatellite markers with high polymorphism. The clustering dendrogram was obtained eventually based on Nei genetic distances of 20 microsatellite. The results showed that 176 alleles were detected of 20 microsatellite loci in 11 native chicken breeds, the average number of alleles of each loci was 8.8 and the range of allele frequencies was 0.013-0.838, and 11 native chicken breeds shared 45 alleles. The average heterozygosity of 20 microsatellite loci was 0.6800-0.7432, the heterozygosity of Zang chicken was the highest (0.7432), and that of Langshang chicken was the lowest (0.6800). The range of PIC of 20 microsatellite loci were 0.6329-0.7023, which is higher than 0.5 and highly polymorphic. By the results of UPGMA tree, four groups were formed from 11 chicken breeds, the first group was Silky, Chahua, Xianju, Zang and Xiaoshan chicken; the second group was Luyuan and Langshan chicken; the third group was Gushi, Fatty and Dagu chicken; and the fourth group was Henan game chicken. The effect of preserved breeds and the differences among generations can be tested by the file foundation of molecular markers, which contained allele frequency, mean heterozygosity, and mean PIC of 20 microsatellite loci in different generation populations.

Gao YS ，Yang N ，Li HF ，Wang KH ，Tong HB ... -  《-》