| Hypophthalmichthys molitrix belongs to Actinopterygii,Cypriniformes,Cypri nidae,Hypophthalmichthyinae,Hypophthalmichthys.H.molitrix is one of the fo ur domestic fishes and has the characteristics of fast growth,high economic va lue,and water purification.In order to understand the distribution characteristic s and regulations of microsatellites in the genome,we developed polymorphic markers to evaluate the status of germplasm resources in Hubei Province.In th is study,the distribution characteristics and regulations of microsatellites were a nalyzed based on the genome level of H.molitrix,and 21 pairs of polymorphi c microsatellite markers were developed.Then,the genetic diversity and geneti c structure of 8 cultured populations of Hubei Shishou(SS),Jianli(JL),Yaowa n(YW),Xishui(XS),Hongan(HA),Suizhou(SZ),Xiaochang(XC)and Huan gpi(HP)were studied by using microsatellite with high polymorphism and mit ochondrial COI markers.In order to provide a theoretical basis for the protecti on of H.molitrix germplasm resources.The main results are as follows:(1)A total of 368,572 microsatellite repeat sequences were screened in the842.01 Mb H.molitrix genome using MISA software.The total length of the identified microsatellite sequence was 6,492,076 bp,accounting for 0.77 % of the total genome length.The average length was 84.66 bp,the frequency was 437.73loci/Mb,and the density was 7,713.16 bp/Mb.According to the statistical results of repeat types,the number of dinucleotide repeats(204,873)accounted for 55.59 % of the total number of microsatellites,followed by tetranucleotide(70,012,19 %),pentanucleotide(44,921,12.19 %),trinucleotide(38,048,10.32 %),and hexanucleotide(10,718,2.91 %).In the whole H.molitrix genome,the top ten dominant microsatellites were AC,AT,AG,AAT,AAAT,AGAT,AAAAT,AAC,AAAAAT,and ATC.The number of microsatellites on each chromosome was positively correlated with length.Twenty-one SSR markers with stable amplification and polymorphism were screened.A total of 94 alleles were detected at 21 microsatellite markers.The allele(Na)ranged from 2 to 7(mean 4.476),the effective allele(Ne)ranged from 1.052 to 4.765(mean 2.757),the observed heterozygosity(Ho)ranged from 0.017 to 0.875(mean 0.517),and the expected heterozygosity(He)ranged from 0.049 to 0.800(mean 0.553).The polymorphism information content(PIC)was 0.048～0.768(mean 0.512).(2)The genetic diversity and genetic structure of 11 pairs of microsatellite markers with high polymorphism were analyzed in 8 populations.It was found that the genetic diversity of these populations was abundant.The allele range of the 8populations was 4～8,with an average of 6.125.The observed heterozygosity range was 0.580～0.712,with an average of 0.632.The expected heterozygosity was0.567～0.722,with an average of 0.658.The polymorphism information content was0.516～0.689,with an average of 0.618.The genetic diversity of the JL population was the highest,and that of the YW population was relatively low.The genetic differentiation among populations was at a moderate level(Fst = 0.10147).AMOVA analysis showed that 89.43 % of the genetic variation came from within the population,and the genetic variation between populations was 10.57 %.Based on genetic distance and cluster analysis,the eight populations were divided into two significantly differentiated lineages.(3)The genetic diversity and genetic structure of 8 silver carp populations in Hubei Province were analyzed using the mitochondrial COI gene.The results showed that a total of 18 haplotypes were detected in 8 populations,and there were 76 mutation sites in 659 effective gene sequences,including 21 single point mutations and 55 parsimony informative sites.The average contents of T,C,A,and G bases in 8populations were 29.99 %,26.62 %,26.08 % and 17.32 %,respectively.The haplotype diversity and nucleotide diversity were 0.604 and 0.00325,respectively.The genetic diversity of the JL population(Hd: 0.883,π: 0.00699)was the highest,and the genetic diversity of the YW population(Hd: 0.186,π: 0.00085)was the lowest.The genetic differentiation between populations was at the lower-middle level(Fst:0.05924).The genetic distance between populations and within populations was small— 0.00353 and 0.00329,respectively.The molecular variance analysis(AMOVA)showed that the genetic variation mainly occurred within populations(93.42 %).There was less variation among populations(6.58 %).The results of UPGMA clustering tree showed that the Jianli population was the first to cluster into one group,and then the HP,SZ,XS,HA,XC,YW and SS populations were clustered into one group,and no significant geographical population was formed.The NJ phylogenetic tree based on 18 haplotypes had a low support rate(< 50 %)for each node branch,which was consistent with the results of the haplotype network map,and did not form a clear systematic geographical group. |
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