Molecular Characteristics And Phylogenetic Analysis Of Chinese Domestic Bactrian Camel From Maternal And Paternal Lineages

To clarify the maternal origin and phylogenetic relationships of Chinese domesticbactrian camel,as well as mtDNA distribution and introgression in China,we studied thephylogenetic relationship of Southern Xinjiang domestic bactrian camel, Nouthern Xinjiangdomestic bactrian camel, Eastern Xinjiang domestic bactrian camel,Hexi domestic bactriancamel,Qinghai domestic bactrian camel,Alashan domestic bactrian camel and Sunite domesticbactrian camel by sequencing the complete mitochondrial Cyt b gene of183individuals andpart of D-loop region of172individuals. We studied the Y-specific gene polymorphisms of100male domestic bactrian camels for the first time, we tried to design the single nucleotidepolymorphism primer of Y chromosome (Y-SNP) by PCR, cloning sequencing andbioinformatics technology. Furthermore, we revealed the paternal origion and phylogeneticrelationships of Chinese domestic bactrian camel by analysing the polymorphisms of the Y-SNPs. The main results are as follows:1. mtDNA cyt b gene diersity and the phylogenetic evolution of Chinese domestic bactriancamelThe Cyt b gene in183individuals of7domestic bactrian camel populations all spanned1140bp, stared with the ATG codon and ended with the AGA codon, there was noinsertion/deletion in these sequences. the average nucleotide composition of A, T, C, G is29.01%,27.81%,28.17%,15.01%, respectivly. And the average composition of A+T (56.82%)is much higher than that of C+G (43.18%). The second codon position of Cyt b gene is rich inT (41.82%) and the third position is rich in A (38.66%) and C (34.54%), but lower in G(8.41%). It indicated that there is a strong composition bias in the second and the third codonposition, especially in the third codon position.We observed25polymorphic sites in Cyt b gene of183individuals, representing2.19%of the Cyt b gene1140bp sequences. The average number of nucleotide differences andnucleotide diversity is2.07122and0.00182. Among the25polymorphic sites,23aretransitions (representing92%) and2are transversions (representing8%), thetransition/transversion ratio (R) is7.663. All the183sequences belong to22haplotypesdefined by the25polymorfic sites, the haplotype diversity is0.846. It showes that the genetic diversity of Chinese domestic bactrian camel is rich.The NJ and UPGMA phylogenetic tree and NETWORK analyse based on the haplotypesof Cyt b gene showes all the183individuals are clustered into one lineage.2. mtDNA D-loop region diersity and the phylogenetic evolution of Chinese domesticbactrian camelThe D-loop region in172individuals of7domestic bactrian camel populations allspanned1225～1247bp, in this research we only analised670bp sequences, the averagenucleotide composition of A, T, C, G is27.67%,26.68%,26.97%,18.68%, respectivly. Andthe average composition of A+T (54.35%) is much higher than that of C+G (45.65%). Weobserved18polymorphic sites in D-loop region of172individuals, representing2.69%of theD-loop region670bp sequences. The average number of nucleotide differences andnucleotide diversity is1.935and0.00291. Among the18polymorphic sites,14are transitions(representing72.22%) and4are transversions (representing27.78%), thetransition/transversion ratio (R) is2.669. All the172sequences belong to22haplotypesdefined by the25polymorfic sites, the haplotype diversity is0.803. Tajima’s D is-1.02880，P>0.10,no significant differences, it indicated that the evolution of Chinese domesticbactrian camel meet the neutral choice.The NJ and UPGMA phylogenetic tree and NETWORK analyse based on the haplotypesof D-loop region showes all the172individuals are clustered into one lineage.3. The Screening of Y-SNPs and the paternal origion and phylogenetic relationships ofChinese domestic bactrian camelWe designed DBY1, DBY7, UTY11and USP9Y9Y-SNP primers, and analyzed a lotDBY1and USP9Y9sequence using direct DNA sequencing, but did not find polymorphicsites. We analyzed DBY7using PCR-SSCP and TA cloning sequencing also did not findpolymorphic sites. The TA cloning sequencing of UTY11also showed no polymorphic sites.So we infer that Chinese domestic bactrian camel have limited Y chromosomal geneticvariation and single paternal origin.