Mitochondrial DNA D-loop Diversity And Origins Of Chinese Dairy Goats

According to research，there is no specialized dairy goat breeds in the history in China,the existing varieties of Chinese dairy goats originated from foreign country.This researchanalyzed155complete sequences of mtDNA D-loop from4cultivars dairy goat breeds（Laoshan dairy goat, Wendeng dairy goat, Xinong Saanen dairy goat and Guanzhong dairygoat）2introduced dairy goats variety （Saannen dairy goat, Nubian dairy goat） and3nativebreeds （Jianyang big-ear goat, Lezhi black goat, Laiwu black goat）.We study the diversity andorigins of Chinese dairy goats by the population genetic structure, genetic relationship,phylogeny, population expansion. The conclusions were as follows:1. Nucleotide variation of mtDNA D-loop of China dairy goatsThe results showed the length of mtDNA D-loop in155goats was1212bp-1215bp, thepercentage of A, G, C, T were31.07%、14.17%、25.81%、28.87%G+C was39.99%.Obviously,the content of A+T was higher than that of G+C.There were97polymorphic sites, with20singleton polymorphic sites and77parsimony informative polymorphic sites. The wholesubstitution was transition in the97polymorphic sites, there is no transversion.2. Genetic diversity of dairy goats62haplotypes were defined by97polymorphic sites. Hap₂appears the highestfrequency in the shared haplotype, Hap₁follows.35of them are unique haplotypes. Themean nucleotide diversity （Pi） and haplotype diversity （Hd） were0.0098±0.0009and0.865±0.010in9goats. Among the different varieties, the highest haplotype diversity wereGuanzhong dairy goat and Laiwu black goat with0.98±0.024and1.00±0.052. Laoshandairy goat and Wendeng dairy goat have the lowest haplotype diversity with0.752±0.086and0.69±0.085. The result shows the genetic diversity of the native goats was abundant.3. The phylogenetic relationships among goat breedsThe genetic distance was calculated by MEGA4.0using Kimura2-parameter model. Theresults suggested that Nubian dairy goat had rather big distances with other goat breeds. Thecultivars dairy goat breeds Laoshan dairy goat and Wendeng dairy goat had small distances with native breeds Laiwu black goat. The native breeds Jianyang big-ear goat and Lezhi blackgoat had big distances with cultivars dairy goat breeds.4. AMOVA and median joining （MJ） networks analysedThe median-joining network of62haplotypes showed the same breeds were not gatheredin the same clusters. And many haplotypes are shared by different geographic regions. In thisanalysis a large percentage （89.34%, P=0.5572） of total mtDNA variation existed withinpopulations, and among populations within groups （FST=0.10655）. All these resultsconsistently demonstrated that1) there was no significant geographical structuring amongChinese dairy goat breed,2) the moderately differentiated is on behalf of the dairy goat.5. Dairy goat origins and phylogenetic analysisWe constructed a Neighbour Joining （NJ） tree with62haplotypes of Chinese dairy goatsby using the Kimura2-parameters model. And we searched GenBank published8sequencesbelonging to the Capra hircus mtDNA haplogroups （A, B,C） to determine their haplogroupaffiliation where identical with our data. The results indicated that Chinese dairy goats havetwo maternal origins.6. Dairy goat population expansion analysisThe neutral test and mismatch distribution analysis for the Chinese dairy goats indicatethat haplogroup A showed a unimodal distribution, but haplogroup B revealed an almostmulti-modal distribution. Fu’s Fs neural test to haplogroup A Fu’s Fs neural test to haplogroupA and B. Fu’s Fs value was24.01105; P value was0.00300for haplogroup A, whichindicated ever population expansion because of pre-dominant departure and significant fromneutrality. In haplogroup B the Fu’s Fs value was5.39616and P value was0.08500whichshowed no population expansion and relatively stable population sizes because of nosignificant difference in neutrality.