A Population Genetic Analysis of Continuously Selected Chlamys farreri Populations
This study applied an optimized one-step 2b-RAD library construction strategy and performed simplified genome sequencing of 539 individuals from three continuously selected Chlamys farreri populations. SNP screening was performed using RAD typing software and population genetic parameters for the continuously selected populations from three generations (G1, G2, G3) were determined. The results showed that the optimized one-step 2b-RAD library construction strategy greatly simplified the experimental process, making it suitable for efficiently constructing a large number of libraries. A total of 18450 SNP markers were identified, which evenly distributed throughout the genome. Population genetic analysis of these three generations showed that the mean value of observed heterozygosity was 0.275 ± 0.177, 0.272 ± 0.181 and 0.275 ± 0.166, respectively. Meanwhile, the mean value of expected heterozygosity was 0.275 ± 0.141, 0.274 ± 0.145 and 0.280 ± 0.133, respectively. The Wright’s fixation index (F) was 0.04291, 0.04976 and 0.06685, respectively. Markers deviated from Hardy–Weinberg equilibrium accounted for 10.34%, 12.64%, and 23.11%, and the Shannon diversity index was 0.0999 ± 0.0404, 0.0921 ± 0.0388 and 0.0733 ± 0.0308. FIS (also known as the inbreeding coefficient) of the three populations was 0.0256, 0.0323 and 0.0468, respectively. We suggested that the 2b-RAD method is well suited to population genetic studies of aquacultured organisms. Moreover, our results indicated that the continuous selection affected the population genetic structure of the cultured Penglai-Red scallop, but the change was not significant; therefore, population selection should continue.
Key words2b-RAD population genetic Chlamys farreri SNP
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We acknowledge the supports from the National Natural Science Foundation of China (Nos. 31130054 and 31472258), the AoShan Talents Program of Qingdao National Laboratory for Marine Science and Technology (No. 2015ASTP-ES02), and the Fundamental Research Funds for the Central Universities (No. 201564009).
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