Development Of SNP Markers And Population Genetics Analysis Of Gymnocypris Przewalskii

Gymnocypris przewalskii,the naked carp is one of the unique and rare species in Lake Qinghai.It is essential to scientifically conserve its existing populations.Systematic investigation of the status of germplasm resources,the genetic structure and adaptive characteristics of G.przewalskii can provide a reference basis for the development of conservation measures for this species.In this study,we identified single-nucleotide polymorphism markers for six geographic populations of G.przewalskii using GBS library construction and pair-end sequencing.The genetic diversity level,population genetic structure and local adaptation of the populations were analyzed based on the available SNP markers.The main results are as follows:1.The GBS technology was used to sequence 72 individuals from six populations of G.przewalskii,and 192.29 Gb of high-quality data（Clean data）were obtained,with an average data volume of 2.67 Gb per sample,high sequencing quality（Q20≥96.75%,Q30≥91.16%）and stable GC content（38.17%～39.92%）.After filtering（filter criteria were DP≥5,miss≤0.2,MAF≥0.05）,a total of 45266 high-quality SNP sites were obtained.2.Genetic diversity analysis showed that the observed heterozygosity（H_o）of the six populations ranged from 0.4594 to 0.4823,the expected heterozygosity（H_e）from0.3367 to 0.3444,and the nucleotide diversity（P_i）from 0.3170 to 0.3274.Among them,H_o,H_e,and P_iwere the largest in the Quanji River population,while the smallest in the Yi langjian population,indicating that the genetic diversity level was the highest in the QJH population and the lowest in the YLJ population.In addition,H_oindexes were higher than H_eindexes in all six populations,showing an excess of heterozygotes,indicating a high level of genetic diversity in G.przewalskii.3.The genetic distance（D）was 0.0184～0.0233 and the genetic differentiation index(F_st)were not significant（P>0.05）.AMOVA analysis showed that the genetic variation was 102.37%within populations.Furthermore,both population structure and phylogenetic tree analysis showed that the six populations clustered into one glade with similar genetic structure.In contrast,the genetic structure obtained from DAPC analysis was relatively clearer,showing that the Haergai,Heima and Shaliu river populations cross-clustered with each other,while the remaining three populations clustered into three other branches.4.The 1566 highly variable adaptive outliers were detected by F_stvalue-based outliers detection.Contigs containing the outliers were used for matched and functional annotation,the functions of 391,26 and 96 contigs were annotated in NR,GO and KEGG databases,respectively.NR annotation showed that the top two species with the highest proportion of similar sequences were Anabarilius graham and Cyprinus carpio,respectively.GO annotation analysis revealed that more contigs were annotated to cellular process metabolic process and binding.KEGG annotation analysis showed that the most contigs were annotated to metabolic pathways and neuroactive ligand-receptor interaction pathways.Among them genes annotated to metabolic pathways included ctu1,cps1,gba2,fasn,plcg1,etc.,which may be associated with the local adaptation of G.przewalskii.Moreover,adaptive genetic structure analysis based on 1566 outliers indicated that all samples could be divided into five adaptive units,among which the genetic characteristics of the QJH population were relatively unique.Together,the results revealed the level of genetic diversity,population genetic structure and adaptive differentiation patterns of G.przewalskii,which were of great significance for scientific conservation and management of fishery resources.To obtain a more accurate and comprehensive understanding of the genetic characteristics of the G.przewalskii,whole genome re-sequencing could be carried out in the future.