| Channa argus,commonly known as northern Snakehead fish or black fish,b elongs to the family Channidae of the order Perciformes and is an important aquat ic genetic resource in Shandong Province,China.In order to protect,explore and creatively utilize the Snakehead fish genetic resources in Shandong,this study con ducted population genetics research on five different geographical populations.B y combining morphological markers and whole-genome resequencing technology,150 Snakehead fish samples from four wild populations in Dongping Lake,Nansi Lake,Yishui River,Yellow River,and a farmed population from the freshwater fi sheries research institute of Shandong Province were analyzed for phenotype and genetic structure.The study revealed differences in phenotypic characteristics and population genetic structure of Snakehead fish in the Shandong region,which can assist in developing effective protection measures and management strategies for the genetic conservation and breeding of Snakehead fish to maintain the health an d sustainable development of the Snakehead fish population.The main research c ontents of this paper are as follows:1.Based on morphological markers,we conducted an analysis of the morphol ogical differences among Snakehead fish populations.In this study,we measured and analyzed 33 measurable proportional traits of Snakehead fish from 5 different populations using traditional morphometric meas urements and frame measurements.The results showed that ratios of W02(body h eight/body length),W03(body width/body length),W07(head width/head height),W11(2-3/body length),W13(4-5/body length),W15(6-7/body length),W18(9-10/body length),W19(10-11/body length),and W22(1-11/body length)had signi ficant statistical differences(P<0.05)among the different populations.Principal c omponent analysis and one-way ANOVA results indicated that there were differen ces in the correlated traits of the head,body,and tail of C.argus among the five p opulations.Multivariate statistical analysis revealed that the Yellow River populat ion was the most distant from the other populations,while the Dongping Lake,Na nsihu Lake,Yishui River,and aquaculture populations were the closest to each oth er,possibly due to differences in the ecological environment and food resources in the estuary of the Yellow River compared to the other populations.2.Population genetic structure and diversity analysis of Snakehead fish base d on whole-genome resequencingIn this study,the reference genome data size was 630.39 M and the resequenc ing data size was 2100.3GB.The alignment rate of 150 samples ranged from 88.56% to 99.64%,and the coverage of the reference genome was between 96.33% an d 97.358%.A total of 11,420 genes were detected,and the average sequencing de pth ranged from 12.306 X to 39.582 X.By aligning with the Snakehead fish reference genome,the number of SNP v ariation sites was calculated for 150 Snakehead fish samples.The results showed t hat the number of SNP variation sites in the Dongping Lake population,the Yello w River population,the Yishui River population,the cultured population,and the Nansihu Lake population were 21,252,164,22,036,779,23,149,514,20,757,055,a nd 22,086,695,respectively.The distribution of insertion and deletion(In Del)site s was as follows: 4884373 in the Dongping Lake population,5,135,855 in the Yell ow River population,5,426,860 in the Yishui River population,4,690,418 in the c ultured population,and 5,054,724 in the Nansihu Lake population.The results of the systematic evolution tree analysis showed that the populati ons of Snakehead fish in Nan Si Lake and those in aquaculture first clustered toge ther,then clustered with those in Yi River,followed by those in Yellow River,and finally those in Dongping Lake.These findings indicate that the genetic relationsh ip between the populations in Dongping Lake and Nan Si Lake is the most distant,while the relationship with those in Yellow River is the closest.Analysis of the ge netic structure of the five Snakehead fish populations revealed that they are desce nded from four ancestral populations,with only Yi River and Nan Si Lake sharing a common ancestral population.The population in Nan Si Lake is a mixture of fo ur ancestral populations,with the ancestral population of Dongping Lake being th e primary source of admixture,while the population in aquaculture is a mixture of the ancestral populations of Yi River and Dongping Lake.Analysis of genetic div ersity and differentiation coefficients indicated that the five Snakehead fish popul ations are moderately polymorphic,with an intermediate level of genetic diversity.The genetic differentiation between the populations is moderate and belongs to th e inter-species level,rather than the subspecies level.The results of linkage disequ ilibrium analysis showed that the LD decay rate is fastest in the populations of Yel low River and Yi River,with an LD decay distance of 43 kb,while the LD decay r ate is slowest in the aquaculture population,at 37 kb.Gene flow analysis indicate d that gene flow has occurred from the aquaculture population to the population in Dongping Lake.The results of whole-genome resequencing analysis and morphological analy sis differed somewhat.This is likely due to the fact that the genetic polymorphism level of the five Snakehead fish populations is not high,and the genetic diversity is relatively low.With the exception of the Yellow River population,there is no si gnificant difference in the living environment and food resources among the popul ations,which may have led to significant differences in phenotypic traits between the Yellow River population and the other populations in morphological measure ments.Additionally,morphological analysis involves manual measurement of phe notypic traits,which can result in significant errors,while whole-genome reseque ncing technology focuses on the genetic molecular level of species and has a high accuracy. |
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