SNPs Identification Of Growth-related Genes And Correlation Analysis On Growth Traits In Sinipercid Species

With the application and development of DNA marker technology, thecombination between traditional breeding method and molecular-marker assistedselection (MAS) breeding have promoted the process of new variety breeding infishes. Founding the major genes or markers which are closely connected with thesignificant grwoth traits is the basis of MAS. The most important growth anddevelopment traits in fishes are body weight (BWT), body length (BL), body depth(BD) and body width (BWH). So in this research, three genes were chosen as thecandidate genes for sinipercid species growth traits and were studied on. The resultsare as follows:1.(1) The full genomic sequences of IGF-I and IGF-II gene from Sinipercachuatsi, Siniperca kneri, Siniperca scherzeri were isolated.(2) The sequence structure,amino acid sequence encoding by DNA, difference between sequences were analyzed,the phylogenetic trees were constructed as well.(3) By sequence alignment,125and86potential SNPs were identified in IGF-I and IGF-II gene respectivley, thereinto,there are5and4SNPs in exons respectively.2. In the different eleven sinipercide populations, the5potential SNPs in IGF-Iexons were detected using HRM. The result showed only2mutations have polymorphism.(1) About SNP1(A321G), in all those population, the frequency ofallele A was higher than that of allele G. especially in S. chuatsi S. kneri (SCSK)and Hunan S. chuatsi×Hunan S. chuatsi F2(HuSCSC F2), the frequency of allele Awas1, but that of allele G was0. χ2fitness test showed that the Jiangsu S.chuatsi Hunan S. chuatsi (JiangSCHuSC), S. chuatsi S. scherzeri (SCSS), S.kneri S. chuatsi (SKSC), Hunan S. chuatsi (S. chuatsi S. scherzeri)(HuSC*SCSS), S. chuatsi S. scherzeri F2(SCSS F2) population were in the stateof Hardy-Weinberg equilibrium. As for polymorphism information content (PIC),SCSS, HuSC*SCSS, SCSS F2were all moderate polymorphism(0.25<PIC<0.5).Association analysis of markers and growth traits found that the relation betweenSNP1and BWT, BL, BWH in SCSS F2was highly significant. The individuals withgenotype AA and AG had a significantly faster growing rate than that with genotypeGG (P<0.05).(2) About SNP2(A537G), GG genotype was not found in all thesepopulation except SCSS F2. Allele A was the dominant allele in all population. χ2fitness test showed that SKSC, HuSC*SCSS, SCSS F2were in the state ofHardy-Weinberg equilibrium, while in all the other population deviated from ofHardy-Weinberg equilibrium. As for PIC, four SCSS population were intermediatepolymorphism (PIC<0.25), and all the other population were moderate polymorphism(0.25<PIC<0.5). Association analysis of markers and growth traits found that betweenSNP2and BWT, BD, BWH in SCSS F2was highly significant. The individuals withgenotype AG had a higher growth rate than that with genotype GG. The individualswith genotype AG had a higher BWH compared with GG genotype in HuSCSC F2.(3)Statistical results showed that8diplotypes for SNP1and SNP2were observed inSCSS F2. H1H1diplotype were the significantly lower in BWT, BL, BD, BWH thanthose of four diplotypes (P <0.05).3. The4potential SNPs in IGF-II exons were detected using HRM, and the resultshowed only2mutations have polymorphism.(1) At locus SNP3(C307T), in thedifferent eleven sinipercide populations, the frequency of allele T in SCSK and SKSCwas higher than that of allele C, while in all the other population the allele C was thedominant allele. χ2fitness test showed that HuSCSC, SCSK, SKSC and SKSC F2 were in the state of Hardy-Weinberg equilibrium. Genetic diversity showed that thepopulation of SCSK and SKSC had low homozygosity and moderate PIC.Association analysis of markers and growth traits found that the relation betweenSNP3and BWT, BL, BD and BWH in SKSC F2was highly significant. Theindividuals with genotype CT had a significantly higher than that with genotype TT inthe four growth traits (P <0.05).(2) At locus SNP4(C618T), in all eleven sinipercidepopulation, the frequency of allele C was higher than that of allele T. especially inSCSK, HuSCSC F2, SKSC F2, the frequency of allele C amounted to1while that ofallele T was0. χ2fitness test showed that JiangSCHuSC and SKSC were in the stateof Hardy-Weinberg equilibrium. Genetic diversity showed that the population ofSCSS, HuSC*SCSS and SCSS F2had high heterozygosity and moderate PIC.Association analysis of markers and growth traits found that between SNP4and BWT,BL, BD in SCSS F2was highly significant. The individuals with genotype CC andCT had a higher growth rate than that with genotype TT.(3) Statistical results showedthat8diplotypes for SNP3and SNP4were observed in SCSS F2. H1H2and H3H3diplotypes were significantly higher in BWT, BL, BD, BWH than those elsediplotypes (P <0.05).4. There were, SNP5(T491C、C501A) in exon5, SNP6(T75G) in intron5andSNP7(A720G、T739C) in3’-UTR,7mutations to be detected in GH gene by HRM.The mutation C501A being missense mutation was found in only SCSS. The A720Gand T739C mutations were in complete linkage.(1) At locus SNP5(T491C), in thedifferent eleven sinipercide population, CC genotype was not found. Allele T wasdominant allele in all population. χ2fitness test showed that HuSCSC, JiangSCSC,SKSC, HuSC*SCSS and SCSS F2were in the state of Hardy-Weinberg equilibrium.Genetic diversity showed that all population had moderate PIC except JiangSCSC andSCSS F2population. Association analysis of markers and growth traits found thatbetween SNP5and BWH in HuSCSC F2was highly significant. Individuals withgenotype TT were higher than that with genotype TT in BWH (P <0.05).(2) At locusSNP6(T75G), genotype TG was dominant genotype in all population exceptJiangSCSC population which only had TT genotype. χ2fitness test showed that SCSS, SCSK and SKSC F2deviated from the Hardy-Weinberg equilibrium. Geneticdiversity showed that all population had moderate PIC. Statistical results showed thatindividuals with TG genotype had a significantly faster growing rate than those ofgenotype GG on BWT, BL in the SCSS F2population. Association between SNP6and BWT, BL, BD, BWH in HuSCSC F2was highly significant. Fishes with GGgenotype had fastest growth rate, while fishes with TT genotype had lowest growingrate. The difference between GG and TT genotype was highly significant (P <0.01),and the difference between TG and TT genotype was significant (P <0.05).(3) For thetwo mutation in SNP7were in complete linkage, only the mutation A720G wasanalyzed in this study. There was only one genotype AA to be found in eightsinipercide population except SCSS, HuSC*SCSS and SCSS F2. χ2fitness testshowed that only SCSS highly significantly deviated from the Hardy-Weinbergequilibrium. Genetic diversity showed that SCSS, HuSC*SCSS and SCSS F2hadmoderate PIC. Statistical results showed that there were no significant associationbetween SNP7and four growth traits in SCSS F2.(4) Statistical results showed that6haplotypes and8diplotypes for SNP5, SNP6and SNP7were observed in SCSS F2.Diplotype H2H4had a significant difference in BWT, BL, BD and BWH comparedwith the other five diplotypes (P <0.05). There were5diplotypes for SNP5andSNP6in HuSCSC F2, thereinto, H2H4diplotype was significantly higher in BWT,BL and BD than else diplotypes (P <0.05). There were5diplotypes for SNP5andSNP6in SKSC F2, thereinto, H1H1diplotype was significantly lower in BWH thanelse diplotypes (P <0.05).