| The large yellow croaker occupies important status in seawater aquaculture in China.Genetic improvement for quality has been the main target of genetic breeding.In this study,we have located some phenotypic traits in the LG family and random group of large yellow croaker by linkage analysis and association analysis.The major results are listed as follows: 1.Phenotypic traits data analysisStatistical analysis for twelve phenotypic traits(body weight,total length,body length,body height,body thickness,head length,snout length,eye diameter,caudal fin length,caudal peduncle length,caudal peduncle height,trunk length)in LG family group of large yellow croaker indicates that all traits are subject to normal distribution,and showing the characteristics of continuous variation.In random population of large yellow croaker,all phenotypic traits reached extremely significant(P <0.01)by correlation analysis,and also subject to normal distributed too.2.The Quantitative trait loci for morphological traits of LG family in large yellow croakerThe locations and effects of quantitative trait loci(QTL)were estimated using MapQTL6.0 software based on the genetic map.In 19 month-age,seventeen QTLs were detected and distributed in 2,3,5,9,18,20,22 and 23 linkage groups,the phenotypic variation explained by a single QTL from 22.2% to 36.8%,but we did not locate the QTL for snout length and caudal peduncle height.In 24 month-age,twenty-five QTLs were detected,and distributed on linkage groups of 1,13,14 and 24,the phenotypic variation explained by a single QTL from 13.2% to 37.1%,and we did not locate the QTL for eye diameter and caudal fin length.As the same time,it is interesting to note that quantitative trait loci for many morphological traits were mapped on the same positions that control the different morphological characters.This phenomenon implies that multiple phenotypic traits may be controlled by a same QTL and shared the common genetic elements.In addition,the QTL that control the same traits will migrate in different periods.3.GWAS analysis of LG family phenotypic traits in large yellow croakerThe locations of quantitative trait loci were estimated for LG morphological traits in the large yellow croaker using single marker association analysis.In 19 month-age,16 SNPs were detected and distributed on linkage groups of 2,3,9,13,18,21,22 and 23.31 SNPs were detected and distributed on linkage groups of 1,5,7,13,14,18 and 24 in 24month-age.Among them,the number of SNP of the body weight,total length,body length,body height,body thickness,head length,snout length,eye diameter,caudal peduncle length,caudal fin length,caudal peduncle height and trunk length were 1(5),1(4),1(4),1(2),1(4),3(a),1(a),2(a),1(3),1(1),1(3),2(2)in 19 month-age and 24 month-age,respectively.The numbers of SNP of 24 month-age are shown in brackets.4.GWAS analysis of phenotypic traits in large yellow croakerUsing GBS(Genotyping-by-Sequencing)and SNP genotyping,a total of 500 individuals of large yellow croaker and 24,645 SNPs were fitted using the Plink program with a mixed linear model.The results showed that 68 genome-wide significant SNP were identified that were significantly associated with seven growth-related traits,including nine for carcass weight,six for total-length,seven for body thickness,nine for caudal peduncle length,12 for caudal peduncle height,2 for fatness and 23 for net weight rate.We found that control different characters sites are located at the same location on the same chromosome.For example,the SNP located at 24.4Mb or 19.9Mb on chromosome 1 that were associated with the carcass weight,length of caudal peduncle length and caudal peduncle height,simultaneously.Indicating that this SNPs may be possible to control the 4 traits,and the SGCZ,XPNPEP1 and PNPLA6 genes may be closely linked to affect the growth-related traits of large yellow croaker that were found near the SNPs.The phenomenon is similar to the results of MAPQTL,and suggests to reliable of the results in both methods. |
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