Research On Characteristics Of Germplasm Resources And Adaptation To High Altitude Of Local Chicken In Eastern Pamir Plateau

Local chickens in south Xinjiang live on the eastern slope of the Pamir Plateau,which has a natural altitude gradient,and local chickens at different altitudes show differences in macroscopic traits and microscopic traits.In order to better conserve and breed local chickens in South Xinjiang,this study explored the genetic diversity and plateau adaptation of local chickens in three regions of South Xinjiang at different altitudes: Tashikurgan County（TX,average of 3200 m）,Wuqia County（WQ,average of 2200 m）,Shule County and Shufu County（SL,average of 1100 m）: Firstly,differences were analysed in terms of quality traits,quantitative traits and plumage;secondly,the CO Ⅰ gene and D-loop region were amplified to explore their genetic diversity,and an evolutionary tree was drawn up by combining the sequences of other breeds of chickens on Gen Bank;finally,full-length transcriptome analysis was used to screen for plateau adaptation-related genes.The main studies and results are as follows:（1）Statistics,correlation analysis and principal component analysis were performed on a total of 84 local chickens from three regions at different altitudes for qualitative and quantitative traits.The results showed that the qualitative traits（crown shape,coat colour,tail feathers,bill,tibiae,iris）of the local chickens living in the three altitude gradients were diverse;while the differences in quantitative traits were closely related to the altitude factor,where the body slope length and tibia length of the local chickens in the three areas were inversely proportional to the altitude,and the body weight and body size data of the male chickens were significantly greater than the female chickens.Correlation analysis found that live weight was significantly（P<0.05）positively correlated with breast width,tibia length,tibia circumference,body slope length,keel length and breast depth;and negatively correlated with pelvic bone width.Principal component analysis found that the most determinant of body weight was breast width.（2）The breast feather structure of 84 free-range local chickens from three different altitudes was assessed,measured and subjected to ANOVA statistical analysis.The results showed that: the total feather length increased significantly with increasing altitude;the density of plumulaceous feather branches decreased with increasing altitude,but the absolute and relative length of the plumulaceous feather part increased significantly with increasing altitude,indicating that the thermal insulation performance of local chickens adapting to extreme low temperatures gradually improved;while the density of the pennaceous feather branches increased slightly with decreasing altitude.This indicates that the difference in feather structure is not only affected by altitude,but also depends on the feeding environment,feeding management mode and nutritional conditions.（3）The SNP analysis and phylogenetic analysis of CO Ⅰ gene and D-loop region of mt DNA full-length sequence were performed on 23 local chickens from high,middle and low altitudes in South Xinjiang,and a phylogenetic tree was constructed based on the comparison of CO Ⅰ gene and D-loop region with other breeds on NCBI.The results showed that there were two mutation sites and three haplotypes in the CO Ⅰ gene,of which Hap3 was unique to SL.24 mutation sites and 11 haplotypes were found in the D-loop region,of which Hap2 was unique to TX,Hap6,Hap7 and Hap8 were unique to WQ,and Hap9,Hap10 and Hap11 were unique to WQ,Hap9,Hap10 and Hap11 are haplotypes unique to SL.The results indicate that CO Ⅰ genes are stably inherited in the three regions,and the D-loop region has a higher degree of variation;there is some gene exchange between SL and WQ and TX;the geographical and genetic distances of local chickens in South Xinjiang show some correlation.（4）Full-length transcriptome sequencing was performed on the genomes of three southern Xinjiang local chickens from high,middle and low altitudes,and the fulllength transcripts were analysed for differential expression and functional annotation.The numbers of differentially expressed genes（DGPs）in the three regions were 266 in SL and TX,of which 110 were up-regulated and 156 were down-regulated;227 in SL and WQ,of which 82 were up-regulated and 145 were down-regulated;and 172 in TX and WQ,of which 96 were up-regulated and 76 were down-regulated.Seven genes were found to be significantly differentially expressed in the local chickens of the three regions together.Two of the genes with significantly different expression,S100A12 and CTRP9,were plateau adaptation-related genes.