| The ridgetail white prawn, Exopalaemon carinicauda, belongs to Palaemonidae(Crustacea: Decapoda). It is one of the unique marine economy shrimp in our country. In our study, we made a simple analysise for the characteristics of microsatellite sequences, these all based on transcriptome sequencing information of E. carinicauda. Then we used SSR markers to research the genetic diversity on E. carinicauda inbred lines. The results were as follows:1. E. carinicauda’s SSR analysis of transcriptome sequencingWe found 8172 microsatellite sequences in the E. carinicauda transcriptome through splicing and selection. According to the number of its core repeat sequences, we classified seven types of microsatellite sequence. Among them, dinucleotide were the highest number of microsatellite sequences, which accounts for about 44.82%. Trinucleotide and hexanucleotide microsatellite sequences came in second and third, respectively. Among the dinucleotide repeat type, AC motif was at most for 90%. We divided microsatellite sequences into three types according to the degree of perfection, there were perfect type, imperfect type and compound type. The perfect type is the main type in E. carinicauda, which is the same with other scholars.2. Rapid development of SSR markers from E. carinicauda based on transcriptome sequencingIn this paper, we isolated microsatellite markers from transcriptome information. We designed primers using microsatellite flanking sequence from transcriptome. 33 pairs of SSR primers were founded from 241 pairs of SSR primers. The averge allele number was 6.69(3~11), the mean observed heterozygosity was 0.661(0.067~0.967), the average expected heterozygosity was 0.716(0.188~0.906), with the polymorphism information contents 0.668(0.177~0.883). 11 loci(less than one third) deviated from Hardy-Weinberg(p<0.05), 27 SSR loci were with high polymorphism(PIC﹥0.5). Besides, core repeat sequences of the polymorphism was analyzed, the number of repetitions and polymorphism were positively correlated.3. Genetic diversity analysis on E. carinicauda inbred linesWe chosen 33 microsatellite loci make genetic detection of E. carinicauda inbred lines which were breeded in laboratory conditions. It turned out that we got 72 allele from all three inbreed lines of four generations, with which inbred A、B and H respectively with 40、53、56 alleles,, including 32 alleles for each department. Most of the 33 microsatellite locis were moderate polymorphism or low-grade polymorphism. The results of total groups in inbred lines which with an average allele of 2.758, mean heterozygosity of 0.294, average polymorphism information content 0.272 were far less than the data of Jiangsu wild tail ridge white shrimp. Genetic differentiation coefficient of 3 inbred lines is 0.118, which shows three families has been a trend of differeftiation to be an independengt family. We defined some locis perfored of singularity only in one line special gene loci for genetic inspection. 7 loci would be used as this: A, 2(EC16、EC18); B, 4(EC11、EC12、EC21、EC30); H,1(EC19). We can use them to distinguish between different inbred lines. Homozygous genes rate were inspected. It showed a trend of rapid rise with a sight decline in the middle. And it got 77.59% when F9. The data shows that E. carinicauda inbred lines has resched to a certain degree of inbreeding. Of 3 inbred lines, genetic distance between A and B is the nearest(0.178) with A and H is the furthest(0.352). Cluster analysis showed that A and B were gathered first, and then with H together. The conclusions indicated the pattern of genetic variation at 33 SSR loci in the inbred lines of E. carinicauda; evaluated inbreeding families had reached to a certain degree of inbreeding; found some loci would be used as special gene loci for genetic inspection; speculated each lineage had been different groups with individual genes. |
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