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 w...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.展开更多
Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to br...Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools Mix P and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop(Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction(GBLUP) method which has been applied widely. Our results showed that both Mix P and gsbay could accurately estimate single-nucleotide polymorphism(SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values(GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by Mix P; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by Mix P and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with Mix P the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by Mix P and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.展开更多
基金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)the Fundamental Research Funds for the Central Universities(No.201564009)
文摘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.
基金supported by the National High-Tech R&D Program (863 Program No. 2012AA10A405)the earmarked fund for Modern Agro-industry Technology Research Systemthe National Natural Science Foundation of China (No. 31302182)
文摘Genomic selection is more and more popular in animal and plant breeding industries all around the world, as it can be applied early in life without impacting selection candidates. The objective of this study was to bring the advantages of genomic selection to scallop breeding. Two different genomic selection tools Mix P and gsbay were applied on genomic evaluation of simulated data and Zhikong scallop(Chlamys farreri) field data. The data were compared with genomic best linear unbiased prediction(GBLUP) method which has been applied widely. Our results showed that both Mix P and gsbay could accurately estimate single-nucleotide polymorphism(SNP) marker effects, and thereby could be applied for the analysis of genomic estimated breeding values(GEBV). In simulated data from different scenarios, the accuracy of GEBV acquired was ranged from 0.20 to 0.78 by Mix P; it was ranged from 0.21 to 0.67 by gsbay; and it was ranged from 0.21 to 0.61 by GBLUP. Estimations made by Mix P and gsbay were expected to be more reliable than those estimated by GBLUP. Predictions made by gsbay were more robust, while with Mix P the computation is much faster, especially in dealing with large-scale data. These results suggested that both algorithms implemented by Mix P and gsbay are feasible to carry out genomic selection in scallop breeding, and more genotype data will be necessary to produce genomic estimated breeding values with a higher accuracy for the industry.
