Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers.

China is rich in chicken genetic resources, and many indigenous breeds can be found throughout the country. Due to poor productive ability, some of them are threatened by the commercial varieties from domestic and foreign breeding companies. In a large-scale investigation into the current status of Chinese poultry genetic resources, 78 indigenous chicken breeds were surveyed and their blood samples collected. The genomes of these chickens were screened using microsatellite analysis. A total of 2740 individuals were genotyped for 27 microsatellite markers on 13 chromosomes. The number of alleles of the 27 markers ranged from 6 to 51 per locus with a mean of 18.74. Heterozygosity (H) values of the 78 chicken breeds were all more than 0.5. The average H value (0.622) and polymorphism information content (PIC, 0.573) of these breeds suggested that the Chinese indigenous chickens possessed more genetic diversity than that reported in many other countries. The fixation coefficients of subpopulations within the total population (F(ST)) for the 27 loci varied from 0.065 (LEI0166) to 0.209 (MCW0078), with a mean of 0.106. For all detected microsatellite loci, only one (LEI0194) deviated from Hardy-Weinberg equilibrium (HWE) across all the populations. As genetic drift or non-random mating can occur in small populations, breeds kept on conservation farms such a Langshan chicken generally had lower H values, while those kept on large populations within conservation regions possessed higher polymorphisms. The high genetic diversity in Chinese indigenous breeds is in agreement with great phenotypic variation of these breeds. Using Nei's genetic distance and the Neighbor-Joining method, the indigenous Chinese chickens were classified into six categories that were generally consistent with their geographic distributions. The molecular information of genetic diversity will play an important role in conservation, supervision, and utilization of the chicken resources.

Qu L ，Li X ，Xu G ，Chen K ，Yang H ，Zhang L ，Wu G ，Hou Z ，Xu G ，Yang N ... -  《science in china series c-life sciences》

Genetic diversity of local Yunnan chicken breeds and their relationships with Red Junglefowl.

Yunnan is situated in the Southwest China and encompasses regions having high biodiversity, including habitats for several ancestral species of domestic animals such as chicken. Domestic chickens in Yunnan were kept by peoples of varied ethnic and economic backgrounds living in highly varied geographic environments. To identify the genetic background of Yunnan domestic chickens and their relationships with Red Junglefowl, we applied 28 widely used microsatellite DNA markers to genotype 340 birds from 7 chicken breeds and Red Junglefowl indigenous to Yunnan. Among a total of 342 alleles identified, 121 (35.4%) were breed specific, with Red Junglefowl harboring most microsatellite alleles (23). High levels of heterozygosity were observed within populations indicated by a mean unbiased HE value of 0.663, which was higher than the reported for most populations elsewhere. The FIS value of domestic populations ranged from -0.098-0.005, indicating a lack of inbreeding among these populations. A high proportion of significant departures (89) from the 224 HWE tests for each locus in each population reflected an excess of heterozygosity and population substructure. Individual assignment tests, high FST values (0.1757-0.3015), and Nei's DA genetic distances (0.4232-0.6950) indicated clear differentiation among these populations. These observations, along with the close genetic distance between indigenous domestic populations and Red Junglefowl, were consistent with the primitive and ancestral state of Yunnan indigenous chickens. Protecting the unique variants of these indigenous poultry varieties from contamination with commercial breeds might provide values for improving modern agricultural livestock and breeding programs. Thus, the current study may benefit breeding management and conservation efforts.

Huo JL ，Wu GS ，Chen T ，Huo HL ，Yuan F ，Liu LX ，Ge CR ，Miao YW ... -  《Genetics and Molecular Research》

[Conservation efficiency of local chicken breeds in different farms as revealed by microsatellite markers].

Twenty-eight microsatellite markers were used to analyze the conservation efficiency of two local chicken breeds (Dagu Chicken and Beijing Fatty Chicken) in different farms. Genotypes were detected in 125 samples. The genetic variations among and within the populations were calculated by the number of alleles, gene frequency, genetic heterozygosity (H), PIC, F-statistics, Nei's genetic distance and UPGMA. High polymorphism was found in the four populations, and H and PIC values of each population were more than 0. 5. All loci detected in the study showed polymorphism and the number of alleles ranged from 2 to 22 in total population. Most of these loci were at Hardy-Weinberg equilibrium except two loci (LE110194, MCW0032). The four conservation farms for the two breeds were shown to have retained substantial biodiversity, indicating that the conservation programs are efficient. However, differences between the farms of the same breeds were observed.

Qu LJ ，Wu GQ ，Li XY ，Yang N ... -  《-》

[Analysis of genetic diversity of Shandong indigenous chicken breeds using microsatellite marker].

Microsatellite marker is one of the frequently used molecular markers. It has been used in the genotype identification, pedigree analysis and estimation of genetic distance. In this paper, five microsatellite markers with high polymorphisms were selected to detect the genetic diversity of seven chicken breeds. The alleles frequencies, polymorphism information content (PIC) and average heterozygosity within each population, and DA genetic distance among breeds were analyzed. The application of microsatellite polymorphisms to the detection of genetic variability and relationship among populations was discussed. Altogether, forty alleles were found in this experiment, and among them the most alleles (10) were detected by ADL0136 and the least (5) were detected by ADL0146. The distribution of alleles was not balanced, each locus having one or more dominant alleles. The average heterozygosity in the Shouguang chicken was the lowest (0.3327), and that in other breeds was also less than 0.4. It can be seen then that microsatellite polymorphisms can be used to reveal the variability within population through calculation of average heterozygosity. The PIC values ranged from 0.6169 (Shouguang chicken) to 0.7027 (Laiwu Black chicken). UPGMA tree was completed through analysis of DA genetic distance. In the tree, the Rizhao Pockmarked and the Jining Hundred chicken were first grouped together with a bootstrap value of 92%, before they were grouped with the Laiwu Black and the Shouguang chickens. The Anoka Yellow and the Guangxi Yellow chicken were grouped together with a bootstrap value of 80%, but the Luxi Fighting chicken had its own branch. In summary, the UPGMA tree well reflected the evolutionary and breeding history of the seven breeds.

Cheng HJ ，Yue YS ，Fan XZ ，Zhang CS ，Du LX ... -  《-》

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》