Genetic Diversity Estimation And Phylogenetic Analyses Of Five Chongqing Indigenous Chicken Populations

The genetic diversity of local chicken populations was higher than that of commercial chicken populations.High genetic diversity means that populations are more adaptable to harsh environments and more resistant to disease.However,since the 20th century,commercial chicken populations have become popular because of their fast growth and high egg-laying performance.This situation has resulted in the reduction in the populations of low-performing native populations.Moreover,native domestic chicken populations are at risk of extinction.Local chicken populations contain important information that is the building block of subsequent breeding work of livestock and poultry.Investigating the genetic diversity and phylogeny of livestock and poultry breeds is of great significance for the protection and utilisation of genetic resources of local livestock and poultry breeds.In this study,we analysed the genetic diversity and genetic structure of five local chicken populations（Chengkou mountain chicken[CK],Nanchuan chicken[NC],Daninghe chicken[DN],Xiushan native chicken[XS]and Zengfu native chicken[ZF]）from Chongqing by using 24 autosomal microsatellite markers and the D＿Loop region of mt DNA.The purpose of this study was to fully understand the current survival status of five local chicken populations of Chongqing and provide theoretical basis for population protection and resource development and utilisation in the future.The main results of this study are as follows:1.The genetic diversity of five chicken populations in Chongqing area was studied by using mitochondrial DNA D＿Loop sequence.A total of 41 polymorphic makers（8.1%）were found in the 506 bp length range of mt DNA D＿Loop sequence of all samples.The overall haplotype diversity（Hd）and nucleotide diversity（Pi）of the five chicken populations were 0.91646 and 0.01273,respectively.The genetic diversity of CK was higher amongst the five populations（Hd=0.91694;Pi=0.01181）,whilst the genetic diversity of DN populations was low（Hd=0.53654;Pi=0.00841）.This finding suggested that the maternal genetic diversity of the five local chicken populations in Chongqing was rich,especially the CK population.Thirty-five haplotypes were found in five Chongqing native chickens.phylogenetic tree with reference sequence showed that these 35 haplotypes were distributed in six haplogroups（A,B,C,E,G,Y）.Haplogroup A had the highest frequency（about 54.3%）,and haplogroups G and Y had the lowest frequency（about2.9%）.At the same time,all populations had private haplotypes,suggesting that the genetic background of each group is relatively independent.In addition,the NETWORK relationship showed that these five local chicken populations in Chongqing were mainly distributed in haplogroups A,B,C and E,which is consistent with the general characteristics of local chicken breeds in China.At the same time,each breed had private haplotypes,which indicated that the local chicken breeds in Chongqing had better conservation value.The inter-population difference(F_ST)ranged from 0.00167（ZF vs CK）to 0.29117（XS vs DN）,and the F_S value of DN was higher than that of the other four Chongqing local populations,indicating significant genetic divergence between DN and other populations.Mismatch distribution analysis showed that the distribution of each population was multimodal,suggesting that no population expansion event occurred in the history of the five populations.The results were further confirmed by Tajima’s neutral test.2.A total of 296 alleles were obtained from 242 samples with 24 microsatellite markers.The number of alleles of each locus ranged from 4（MCWO22）to 37（LEI0234）.The polymorphic information content distribution ranged from 0.4936（MCW0216）to 0.9092（LEI0234）.The average number of alleles（N_A）ranged from7.08（DN）to 8.46（NC）.The average expected heterozygosity（H_E）and observed heterozygosity（H_O）of each point were 0.7390 and 0.6441,respectively.These results indicated that the 24 microsatellite markers were rich in genetic diversity in the five local chicken breeds in Chongqing and could represent the real level of population genetic diversity to a certain extent.At the population level,N_A ranged from 7.08±3.23（DN）to 8.46±4.38（NC）.HE ranged from 0.67±0.03（XS）to 0.74±0.02（DN,ZF）.H_O ranged from 0.59±0.02（XS）to 0.73±0.02（DN）.All populations showed rich genetic diversity.H_E was higher than HO in all five populations,suggesting that the heterozygosity of all five populations decreased to different degrees.The Hardy–Weinberg equilibrium（HWE）test showed that CK had the most points of deviation from HWE（16）followed by XS（13）,NC and ZF had the same points of deviation from HWE（11）,and DN had the least points of deviation from HWE（10）.The population inbreeding number(F_IS)ranged from 0.022（DN）to 0.123（NC）,and CK,NC,XS and ZF showed significant inbreeding level（P<0.005）.These results suggested that although the genetic diversity of these five populations was relatively rich,there was still a risk in the species conservation status.The results of population genetic differentiation analysis showed that the F_STvalue of XS was the highest,indicating that the difference between XS and the other four populations was significant（P<0.05）.According to the gene flow（Nm）calculated by F_ST,the Nm value amongst all breeds was less than 1,indicating that the interspecific gene flow of five local chickens in Chongqing was low.In addition,according to the results of phylogenetic tree and structure analysis,the genetic background of the five local chicken breeds in Chongqing is not only independent,but also has the possibility of interpenetration.In particular,the results of principal component analysis further suggested the possibility of genetic material exchange amongst these five populations due to human activities.This is also reflected by the fact that the genetic results of their populations are not completely consistent with the characteristics of habitat distribution.In conclusion,this study used mitochondrial DNA and microsatellite markers to analyse the genetic diversity and population genetic structure of five indigenous chicken breeds in Chongqing.The overall results suggest that the genetic diversity of the five indigenous chicken populations is rich,but there is still a risk.Thus,the existing conservation strategies need to be changed or adjusted.In addition,the obvious genetic differentiation among populations indicated that the genetic background of each population was relatively independent...