| Forest musk deer(Moschus berezovskii)is an economic species restricted to the East Asia.It is famous for the musk secreted by the musk gland of males,which is a precious traditional Chinese medicine and premium spice.However,affected by over-exploitation and habitat fragmentation,wild musk deer populations declined sharply.The captive breeding of forest musk deer captive breeding is an effective way to protect wild population resourses,and it is also the best way to acquire musk.In recent years,breeders have accumulated rich experiences in forest musk deer captive breeding.Nonetheless,some genetic problems have been prominently with the population increment.Currently,there are limited informations available for forest musk deer genetic mangament,and full exploitation and utilization of existing genetic resources require us master the genetic variation comprehensively.In present study,ear tissue samples of 274 forest musk deer were collected form 3captive farms and RAD sequence were employed to evaluate the genetic variations and population structure.The three populations were originally from Ta-pa Mountains(Tp),the middle part of Qinling Mountains(Ql),and Western Sichuan Plateau(WS),respestively.It almost included all the core origin areas of forest musk deer captive populations,and were the epitome of musk deer breeding industry in China.Moreover,we also evaluated wherther there was a difference in musk secretion quantity among the three populations and performed an association analysis for the trait of musk secretion quantity.The main results as follows:1.A total of 3,155,404,082 high quality clean reads were generated through RAD sequence,and a number of 188,761,630 stacks were yielded by cluster.The average sequence depth achieved was 5.32 × per individual.A total of 4,371,985 high quality SNPs were identified through varation calling.2.The result showed that Ql population displayed the highest level of genetic diversity.The value of Tajima’s D revealed that a recent population bottleneck occurrened in Tp and WS populations.Postive values of inbreeding coefficient were found in three populations,ranging from 0.34 to 0.56,indicated that inbreeding existed within these populations.3.Phylogenetic and population structure analysis showed that three populations had evolved independently,and WS was differentiation from Ql population and formed a separate group.There was a closer relationship between WS and Ql than either population with the Tp population,and there was a low frequency gene flow across Tp and Ql populations.The FST between three populations ranged from 0.065 to 0.088,indicated that a moderate genetic divergence has developed in these populations.4.Statistical analysis of musk secretion quantity were performed,the result showed that Tp and WS population had higher proportion individuals with unqualified srcretion compared with Ql population.The average musk quantity of three populations were as follows: Tp(12.82 ± 4.76 g)> WS(12.51 ± 4.79 g)> Ql(10.99 ± 4.79 g),and the weight in both Tp and WS populations were significantly higher than Ql population(P < 0.05)5.A total of 11 SNPs linkage to musk secretion were screened through association analysis,and four SNP loci exbibited a significant association with musk secretion.These four loci explained 16.28% of the musk secretion trait.Furthermore,two of SNPs were annotated as ubiquitin-related protein and calcium-binding protein.In brief,the present research evaluated the genetic structure of captive forest musk deer in a larger scale,and found that there are low level of genetic diversity in captive forest musk deer and a moderate genetic divergence has developed in these populations.The present study provided a data for the conservation of genetic resource and genetic improvement in forest musk deer breeding,and could help breeders to to develop a healthy genetic management strategy. |
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