Using The Y Chromosome Gene Analysis The Paternal Type Of Cervus Nippon

Sika deer(Cervus Nippon) belongs to mammals(Mammalia), Artiodactyla(Artiodactyla), cervidae(Cerridae), deer(Cervus). They were widely distributed in northeast Asia, from Siberia ussuri river to northern Vietnam, including the Korean peninsula, China, Japan, Vietnam and Russia. The fossil record shows that sika deer originated in northeast Asia. Sika deer differentiated from recent common ancestor with the red deer in late pliocene and early pleistocene. The research about the origin of sika deer on archaeology and molecular genetics was rarely. Mitochondrial DNA studies could only provide molecular evidence of the origins of maternal sika deer. The male Y chromosome specific area diversity research was necessary to provide evidence of sika deer paternal origin. The 4794 bp through the Y chromosome AMELY1, AMELY2, DBY, SRY, USP9 Y gene in six varieties grown sika deer(Aodong, Dongfeng sika deer, Siping sika deer, Shuangyang sika deer, Xifeng sika deer, Xingkaihu sika deer), a breeding strains(Changbai sika deer), a group of sika deer(Dongda sika deer) a total of 690 individuals, are measured in this study. Haploid type diversity of 8 sika deer groups on Y chromosome was analyzed. System evolutionary tree was built. Population genetic diversity and paternal origin of domestic sika deer were discussed. We provide an important theoretical basis for Chinese sika deer genetic resources protection, germplasm innovation and breeding. We also provide data support for the sustainable and standardized development of domestic sika deer industry in China.The length of amplification fragment constituted of AMELY1, AMELY2, DBY, USP9 Y, SRY genes on Y chromosome in 8 sika deer goups is 4794 bp. Sequence analysis of base composition is similar. Content of A + T base is 66.065% ~ 66.065%, and content of G + C base is 33.930% ~ 33.940%. Nucleic acid diversity between Aodong sika deer and Shuangyang sika deer is maximum(Dxy=0.00036). Nucleic acid diversity between Dongda sika deer and Xifeng sika deer is minimum(Dxy=0.00017). Nucleotide diversity of Aodong sika deer and Dongfeng sika deer is highest(π=0.00035), and Changbaishan sika deer is lower(π=0.00027). Genetic distance between Aodong sika deer and Shuangyang sika deer is farthest(D=0.000357), and genetic distance between Xifeng sika deer and Dongda sika deer is nearer(D=0.000174). 8 variation sites were found, of which emerged in 65, 623, 65 location C- T conversion, emerged in 135 location T- G transversion, appeared in the 811, 3243 location A- T transversion, appeared in the 1273, 1941, location A- G,.10 haploid type is defined and frequency of haploid type are 62.90%, 13.33%, 10.72%, 13.33%, 0.87%, 1.01%, 1.01%, 1.74%, 0.86%, 5.80%.H2, H4, H1, H3 is advantage of haploid types, and the frequency ranges between 6.96% and 62.90%. There are 5 haploid types in Aodong sika deer(H2、H4、H1、H3、H5), and 4 haploid types in Changbaishan sika deer(H2、H4、H1、H3),4 haploid types in Dongda sika deer(H2、H4、H1、H3),3 haploid types in Dongfeng sika deer(H2、H1、H3),6 haploid types in Siping sika deer(H2、H4、H1、H3、H6、H7),6 haploid types in Shuangyang sika deer(H1、H2、H4、H5、H8、H9),4 haploid types in Xifeng sika deer(H2、H4、H1、H3),6 haploid types in Xingkaihu sika deer(H1、H2、H3、H4、H8、H10). Haploid type H6 and H7 exists only in Siping sika deer, and its frequency is 1.01%. Haploid type H8 exists only in Shuangyang sika deer, its frequency is 1.74%. Haploid type H10 exists only in Xingkaihu sika deer, its frequency is 0.58%.Mega 6.0 software was used to analysis the sequence of AMELY1, AMELY2, DBY, SRY, USP9 Y gene. 3 gene mutation sites are found in AMELY1 gene, in which diversity of haploid type is most abundant. Only one mutation loci was found in DBY, SRY, USP9 Y genes. it was illustrated that the genetic background of 8 sika deer was similiar and conformed to the idea that domestic groups of sika deer derived from the northeast subspecies. AMELY1 and AMELY2 gene both showed a single type of haploid in Siping sika deer. In order to further improve the analysis of sika deer population genetic diversity, the 5 Y chromosome gene sequences were integrated together. A total of eight mutation sites were found, there were 10 haploid type defined. Siping sika deer and Shuangyang sika deer both have 6 haploid type, in addition, Shuangyang sika deer and Xingkai lake sika deer both have their own unique haploid type.The AMELY1, AMELY2, DBY and SRY were integrated with USP9 Y gene sequences. Using the method of Mega 6.0 software in the adjacency NJ(Neighbor Joining) and Maximum likelihood ML(Maximum Likeihood) of eight sika deer groups and haploid type were adopt to build molecular phylogenetic tree, respectively. NJ method and ML method to construct the system of evolutionary tree topology shape is consistent, and have a high degree of confidence. Analysis shows that the sika deer originated from two paternity, H3, H5, H9 uniparental I formation, H1, H2, H4, H6, H7, H8, H10 uniparentalⅡformation. Combined with the minimum span network diagram, presumably, H3, H5, H9 type is the original list times, other haploid type evolved from the three haploid type.The different segments of the Y chromosome were used to analysis population genetic diversity of sika deer, respectively. the results showed that the AMELY1, AMELY2, DBY genes are consistent, the genetic distance between Dongfeng sika deer, Aodong sika deer and other groups is relatively far, genetic distance between Dongda sika deer and Siping sika deer, Shuangyang sika deer, Xifeng sika deer, Xingkaihu sika deer is relatively close, and the nucleotide diversity of Dongfeng sika deer is highest, whereas the results of SRY, USP9 Y gene showed that the genetic distance between Shuangyang sika deer and other groups is relatively far, and the nucleotide diversity of Shuangyang sika deer is the highest. To get a more accurate genetic relationship of eight sika deer populations, we put integrated 5 Y chromosome gene sequence into entirety, the results showed that the genetic distance between Shuangyang sika deer and Dongfeng sika deer, Aodong sika deer was relatively far, and that between other groups was close. Nucleotide diversity of Dongfeng sika deer and Aodong sika deer is highest, followed by Changbai sika deer, Shuangyang sika deer. As the results was based on the analysis of single gene synthesis, we believed that the result of comprehensive analysis is more accurate.