Analysis Of Genetic Diversity In Six Populations Of Grass Carp (Ctenopharyngodon Idella) And Screening Of SNPs Markers Related To Growth Traits

Grass carp(Ctenopharyngodon idella) is one of the most important culturedfreshwater fishes which belongs to Cypriniformes, Cyprinida, Leuciscus, Grass carp.Because of its fast growth, good taste and low cost farming, it has been the mainbreeding species in fresh water fishery. In current, we have not yet acquired thegenetic improvement of grass carp strains. Marker assistant selection (MAS) hasbecome an important method to improve breed speed. Therefore, It is important toresearch the status of the grass carp genetic resources for genetic breeding from theinheritance structure and genetic diversity. In this research, SNPs markers of ALDOBand CPA1gene were selected from EST-SNPs database of grass carp, then weidentified the association of SNPs with growth traits in grass carp. Meanwhile, theother seven SNP mutations were identified from EST-SNP database, which wereemployed to detect the genetic diversity of six groups of grass carp populations(Ningxiang, Yuanjiang, Jianli, Shishou Nanzhuang, Honghu). The detailed contentwas as follows:1. Polymorohisms of SNPs in ALDOB and CPA1gene and association analysiswith growth traits in grass carpIn this study, genomic fragments of carboxypeptidase A1(CPA1) and ALDOBgene were amplified based on the sequences of many available contigs in theEST-SNP database of grass carp. C+687G, A117C and C+1042A mutations fromALDOB gene, C+412A and A36C mutations from CPA1gene were identified aftersequencing the PCR prodcts. Regarding the five SNPs, the genotype and genefrequency of296grass carps were further assayed with the method of SnaPshot.A general linear model was used to do the correlation analysis among the ALDOB and CPA1gene SNPs and growth traits. In ALDOB gene, the resultindicated that the three different genotypes of C+687G site showed no significantassociation at body weight. The three different genotypes of A117C andC+1042Asites showed significant association at body weight and so on (P<0.05). Threecombinations of seven, three and seven diplotypes were constructed based on threeSNPs in the experiment population. Association analysis indicated that threecombinations of diplotypes were all significant association between diplotypes andbody weight (P<0.05): the seven diplotypes of C+687G, A117C and C+687G,C+1042A showed significant association at body weight, body width and so on(P<0.05). And the three diplotypes of A117C and C+687G, C+1042A showedsignificant association at body weight and space. In CPA1gene, The three differentgenotypes of the A36C site were significantly associated with body weight and eyedistance (P<0.05) while the C+412A site showed no significant correlation with bodyweight (P<0.05). Five diplotypes constructed based on the two SNPs were different atbody weight. For example, the body weight of diplotypes D3and D5differedsignificantly (P<0.05). The diplotypes of D3and D8showed significant associationwith body weight, body length, body width and body length/head length(P<0.05)2. The Identification of SNPs Loci and Analysis of Genetic Diversity in SixPopulations of Grass CarpIn this research, Primers were designed according to ALDOB, Chymotrypsinand Elastase genes cDNA sequences from EST-SNP database of Grass Carp.Amplified and sequenced the PCR products in order to detect polymorphisms in thesegenes sequences which are expected to exist for in the EST-SNP database. SevenSNPs sites were identified: A2259G、C+468T、A+567T、 A60G、G+641C、T+507Gand C+513T.292grass carps were used to genotype the seven polymorphisms andtheir genotype and gene frequency were calculated by SnaPshot method. And sevenSNPs were employed to detect the genetic diversity of six groups(Ningxiang,Yuanjiang, Jianli, Shishou Nanzhuang, Honghu)populations were lowly differentiated.After applying Hardy-Weinberg Equilibrium(HWE) test, six populations were foundto be significantly deviated from HWE.The result of the genetic structure suggested that the average polymorphisminformation content (PIC) ranged from0.2046to0.3120, the average observedheterozygosity(Ho) was from0.2743to0.3207and the average expectedheterozygosity(He) was from1.5332to1.6835. It showed that Grass Carp population had lower genetic diversity in China. Nanzhuang had the highest average in geneticdiversity while Yuanjiang had the lowest average in genetic diversity. Fst valueindicated that the populations were lowly differentiated. After applyingHardy-Weinberg Equilibrium(HWE) test, six populations were found to besignificantly deviated from HWE. The results will lay the foundation for the futureselection of seed breeding. we can try to select the higher genetic diversity groupssuch as Nanzhuang groups, while avoiding choosing the lower genetic diversitygroups such as Yuanjiang, in order to shorten the process of grass carp breeding.