| The green peafowl(Pavo muticus)is a Class I key protected wild bird in China,listed as a globally endangered(EN)species by the IUCN,and is also an important flagship species.Affected by poaching,human disturbance and habitat fragmentation,the global green peafowl population has plummeted,according to the survey results of the Kunming Institute of Zoology of the Chinese Academy of Sciences,the number of green peafowl in the wild may be less than500.China has carried out the artificial breeding of green peafowl in the 90 s of last century,and has preserved important pure sources for the restoration of green peafowl populations,but due to the lack of scientific pedigree management and systematic genetic management,the early artificial breeding population has hybridization situations between blue peafowl and green peafowl.After combining mitochondrial gene and microsatellite sequence identification strategy,some pure breeding populations were preliminarily identified,and the identification results also showed that the genetic diversity of these breeding green peafowl populations was low and accompanied by significant heterozygous loss,indicating that these populations had obvious inbreeding.To better evaluate the genetic diversity of the green peafowl population and explore the conservation strategy of the green peafowl from the perspective of conservation genetics,this study combined multiple sequencing methods to assemble first chromosome-level green peafowl genome,then resequenced the genomes of small populations for green peafowl and blue peafowl respectively.From the perspective of comparative genomics,the genomic differences between the two peacocks and other birds were analyzed.Then,by comparing the resequencing of the small populations of the two peafowl,the historical effective population dynamics of the two peafowl were reconstructed,the divergence time of them were estimated,the genetic structure between the samples was determined and the genetic diversity was evaluated,the effects of inbreeding on the genomes of the two peafowl were revealed,the types,species and quantities of genetic loads were counted,and the direction and strategy of green peafowl conservation were preliminarily discussed according to the above results.The main results obtained are as follows:1.In this study,a high-quality reference genome of green peafowl was constructed firstly in the chromosome level,and the results showed that compared with the previously published green peafowl genome,our version of genome has been significantly improved both in terms of continuity,completeness and annotation results.2.The comparative genomics analysis showed that the genome of the green peafowl expanded significantly in genes related to metabolism,immunity,especially amoebic infectious diseases,while the blue peacock only expanded genes related to immunity,which indicates that the green peafowl is similar to most chicken birds,susceptible to exogenous infections and relatively special metabolic conditions and nutritional needs.3.Blue peafowl and green peafowl completely separated at about ～11kya,and both have experienced a decline in effective populations,and the decline process of green peafowl is significantly faster than that of blue peafowl and this decline process is still obvious.4.According to the analysis results of the green peafowl population structure,the samples from Yunnan can be clearly divided into two subgroups,indicating there are at least two subpopulations of wild green peafowl populations in Yunnan.5.The statistical genetic load showed that the number of harmful non-synonymous mutations and functional loss mutations and the number of affected genes in green peacock were significantly higher than that in blue peacock,but the proportion of harmful genes in homozygous state was lower than that in blue peacock,indicating that although there were more harmful genes in green peacock’s genome,mild clearance took place.6.According to the results of the analysis of continuous homozygous ROH and ancestor homologous fragment IBD on the autosomal of the green peafowl population,the phenomenon of inbreeding decline has occurred within the green peafowl population,specifically manifested as that the distribution and number of ROH of long segments of green peafowl are much higher than that of blue peafowl,and the longest IBD segment on the green peafowl chromosome covers 625 genes,which will eventually lead to the inheritance of a large number of homozygous ancestor fragments in descendants,making the probability of homozygous harmful alleles higher,resulting in a gradual decrease in the evolutionary potential of the green peafowl population and the adaption to new environments.Through the above investigation on the genetic background of captive green peacocks,it is necessary to find out the genetic background of green peacocks among different geographical populations in Yunnan and other green peacocks distribution areas in the future when developing the conservation and management strategy of wild green peacocks.Secondly,the information of genome ROH,IBD and heterozygosities should be included into the genetic management unit to improve the management accuracy.Finally,suitable provenances were screened according to the genetic management criteria,and scientific and reasonable genealogy management was established to carry out provenance exchange as soon as possibleThis study provides insights for the formulation of scientific and effective genetic management of green peafowl,and also provides fundamental evidence to create effective and feasible rescue strategy for other rare birds distributed in the same area through the conservation research of flagship species similar to green peafowl. |
