MtDNA D-loop Polymorphism And Phylogenetic Study Of Symptric Goat Populations In The Lower Region Of Yellow River

Shandong province lies in the lower region of the Yellow River and in the farmland of the Yellow River,Huai River and Hai River.Indigenous breeds such as Laoshan milk goat and Yimeng black goat,together with new-finding Laiwu black goat,Yashan black goat and imported Boer goat as well as its hybridized descendent comprised the goat resource of the area.The genetic diversity of 6 indigenous and 1 imported goat populations(Laiwu black goat(LBG),Jining blue goat(JBG),Laoshan milk goat(LMG),Yashan black goat(YBG),Lubei white goat(LWG),Beor goat(BG) and hybridized goat(HG)) was evaluated by sequencing partial sequence of mtDNA D-loop,and defined different haplotypes. The haplotype diversity,nucleotide diversity,average nucleotide substitution per site between population,net genetic distance between population,average nucleotide difference within population were computed to evaluate the genetic structure and level of genetic diversity;meanwhile,the genetic variance was analyzed through AMOVA;dendrogram was constructed to evaluate the origin of the goat.Mismatch analysis was dealed in the resulted lineages. The results were as follows:1. Among all the 59 sequences,a 5 bp fragment deletion was detected in one sequence from LMG,while the other sequences were 533bp long. All the sequences defined 59 polymorphic sites, among which singleton polymorphic sites are 22, parsimony informative sites are 37, account for 4.13%,6.97% of the whole sequence, respectively. Their were 1 transversion(site 100) and 1 coexistent site of transition and transversion(site 42),the others were all transition, which showed high ratio of transition to transversion.2.59 polymorphic sites defined 37 haplotypes, population shared haplotypes were H16,H21,H24 and H33, the others were private haplotype within population, whole haplotype diversity was 0.9540.Mismatch analysis showed that 10 nucleotides differences between haplotypes was the highest.3. Haplotype diversity and nucleotide diversity of the populations were 0.7857~0.9697 and 0.12716~0.17170 respectively, which suggested high genetic diversity. AMOVA analysis shows variation percentage within population was 94.87 % ,and among population was 5.13 % ,population differentiation was not clear. Net genetic distance between population was from 0.015%~0.665%,while the nucleotide divergence was form1.336% to 1.951%.By constructing NJ tree with Da we find that HG,JBG,LBG,and LWG clustered together, they might have close relative relationship, YBG and LMG clustered together, which shows close relationship, too. Thus LBG and YBG should be divided to two different breeds, and emergent protection is needed to YBG..4. Dendrogram divided 37 haplotypes into two major clusters(lineage A and B), capra aegagrus clustered into lineage A, while capra falconeri clustered into other lineage. Lineage A is the predominance lineage of the 7 goat populations, while lineage B has a relatively small proportion.5. Mismatch analysis of lineage A and B showed that lineage A experienced population expansion, and the expansion time was relatively early, while lineage B didn't experience population expansion.