Genetic Diversity Of Cultured Population Of Cobia(Rachycentron Canadum)and Preliminary Screening Of Microsatellite Markers Based On Genomic Information

Cobia?Rachycentron canadum?,is a warm-water pelagic migratory fish,which belonging to the Perciformes and Rachycentridae.Because of tender meat,delicious taste,fast growth and other advantages,has become an important aquaculture fish in South China.The number of molecular markers of cobia that was limited,and there are relatively few studies on the genetic diversity of cultured population in China.This study analyzed the genetic diversity of 174 individuals in five culturd populations of cobia from Beihai?BH?,Lingshui?LS?,Naozhou?NZ?,Xuwen?XW?and Sanya?SY?,searched and screened of microsatellite sequences based on the sequencing results of the whole genome of cobia in order to further improve the breeding of cobia.The main results are as follows:1.129 alleles were detected by 12 polymorphic microsatellite loci in five cultured populations of cobia from BH,LS,NZ,XW,and SY.The mean number of alleles was between 3.833 and 6.750,the mean number of effective alleles ranged from 2.284 to 3.645,the mean of observed heterozygosity and expected heterozygosity was between 0.481 and0.635,and 0.533 and 0.681,respectively,and the mean polymorphism information content ranged from 0.463 to 0.630.The population deviated significantly from a Hardy-Weinberg equilibrium at multiple microsatellite loci?P<0.05?.Analysis of genetic differentiation indicated that the F_st range was from 0.055 to 0.150 and the genetic distance?D?range was from 0.240 to 0.635.BH and NZ had the highest F_st?0.150?and the highest D?0.635?.The results of an analysis of molecular variance showed that 84%of the genetic variations were within cultured populations.A phylogenetic analysis using the unweighted pair group method with arithmetic mean showed that one cluster comprising BH and SY,and the other cluster comprising LS and XW formed a branch,which was then clustered with NZ.2.Amplified fragment length polymorphism?AFLP?was used to investigate and assess the level of genetic diversity of four cultured population of cobia from BH,NZ,XW and LS.Respectively in the BH,NZ,XW and LS cultured population,the number and percentage of polymorphic loci were 90?50%?,19?10.56%?,28?15.56%?and 115?63.89%?;the Nei's genetic diversity index?h?were 0.0659,0.0227,0.0292 and 0.0832;and Shannon's information index?I?were 0.1141,0.0364,0.0481 and 0.1441.The results of AMOVA analysis showed that 65%of the genetic variations were among populations.The UPGMA phylogenetic analysis based on Nei's genetic distance showed that NZ,XW and BH were firstly clustered together,and then clustered with LS.3.170 mitochondrial cytochrome b gene sequences with length of 1070 bp were obtained from 5 cultured populations of BH,LS,NZ,XW and SY.The average contents of A,T,C,and G were 27.2%,29.6%,29.2%,and 14.0%;A total of 6 haplotypes were defined in five populations,and the average haplotype diversity and nucleotide diversity were 0.5160 and 0.00675,respectively.AMOVA analysis showed that 94.3%of the genetic variation came from within population.The phylogenetic analysis based on Nei's genetic distance showed that NZ and XW were firstly clustered together,which was clustered with BH,then clustered with LS,last clustered with SY.4.424827 microsatellite repeats were found from the genome data of cobia,including344820 microsatellites with 1?6 nucleotide repeat type,accounting for 81.167%;Among the six repeat unit of SSRs,mono-nucleotide,di-nucleotide,tri-nucleotide,tetra-nucleotide,penta-nucleotide and hexa-nucleotide were 174146?50.49%?,104242?30.23%?,48358?14.02%?,12792?3.71%?,4403?1.28%?and 879?0.25%?,respectively;A/T,AC/GT,AAT/ATT,AAAN,AGAGN and ACCAGG were the main repeat units of mono-nucleotide,di-nucleotide,tri-nucleotide,tetra-nucleotide,penta-nucleotide and hexa-nucleotide repeat types,respectively 159774?91.75%?,75190?72.13%?,13133?27.16%?,4990?39%?,1165?26.46%?and 92?10.47%?.120 microsatellite sequences with high polymorphism potential were screened among the 2?5 nucleotide repeat types,then primer were designed at both ends of the core sequence.The present study obtained the genetic data of 5 cultured populations of cobia,analyzed the distribution characteristics of microsatellite sequences in the genome of cobia,and selected 120 microsatellite sequences with high polymorphism potential,which will provide scientific data for the selection of SSR marker and the evaluation of genetic diversity of progeny.