Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatel...Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content(PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles(Na) and effective alleles(Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity(Ho) values were lower than the expected heterozygosity(He) values(0.526–0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. Fis values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise Fst values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks(11.3%) was much lower than that within stocks(88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.展开更多
Twenty-six half-sib groups （53 full-sib families） of turbot,Scophthalmus maximus Linnaeus, were obtained by artificial insemination. We measured growth in the offspring （40-50 individuals/family） and subjected the...Twenty-six half-sib groups （53 full-sib families） of turbot,Scophthalmus maximus Linnaeus, were obtained by artificial insemination. We measured growth in the offspring （40-50 individuals/family） and subjected them to a thermal tolerance challenge over a period of 34 d. There was no significant difference in daily mor-tality （range： 0.580%-1.391%） between Days 1-13 during the thermal tolerance challenge. However, daily cumulative mortality increased rapidly between Days 14 and 29, especially on Days 15 and 16 （20.232% and 34.377%, respectively）. Mortality was highest on Day 16 （14.145%）. We estimated the genetic parameters using the average information restricted maximum likelihood method. We used a likelihood ratio test to evaluate the significance of effects in models with and without identity as an effect, and compared the final log-likelihoods （maximum log L）. Lastly, we estimated phenotypic and genetic correlation between the up-per thermal tolerance limit （UTT） and body weight （BW）. In this study, the positive phenotypic correlation was low between UTT and BW （0.093±0.029）. The genetic correlation between UTT and BW was negative （-0.044±0.239）. The heritability for upper thermal tolerance was low （0.087±0.032）, which is of approximate-ly moderate heritability. The heritability for body weight was high （0.303±0.074）. Our results suggest there is significant potential for improvement in the culture of turbot by selective breeding.展开更多
The objectives of this present research were to assess the heritability of growth traits under low temperature conditions in turbot（Scophthalmus maximus L.）, and to analyze the correlation between body weight（BW） ...The objectives of this present research were to assess the heritability of growth traits under low temperature conditions in turbot（Scophthalmus maximus L.）, and to analyze the correlation between body weight（BW） and body length（BL）. There were 536 individuals from 25 full- and half-sib families involved in this study. During the entire 90-day period, which was initiated at 233 dph（day old） and ended at 323 dph, the individuals＇ BW and BL were weighed consecutively six times every 18 days. The heritability of BW and BL and the correlation between these two traits were estimated based on an individual animal model with the derivative-free restricted maximum likelihood（DFREML） method. These results showed that the specific growth rates（SGR） of 25 families was from 0.75±0.11 to 1.05±0.14 under water temperature of 10.5–12°C. In addition, the heritability of BW and BL estimated under low-temperature were 0.32±0.04 and 0.47±0.06, respectively. The BW had a medium heritability（0.2–0.4）, and the BL had a high heritability（〉0.45）, which suggested that selection for increased weight and length was feasible. Moreover, there was potential for mass selection on growth. The genetic and phenotypic correlations between BW and BL were 0.95±0.01 and 0.91±0.01（P 〈 0.01）, respectively. A significant correlation between BW and BL showed that BL could be instead of BW for indirect selection, which could be effectively implemented in the breeding program.展开更多
Enhancement release has been proven effective in natural resources recovery of Chinese shrimp Fenneropenaeus chinensis in the last several decades in China, however, to assess the effectiveness of enhancement release,...Enhancement release has been proven effective in natural resources recovery of Chinese shrimp Fenneropenaeus chinensis in the last several decades in China, however, to assess the effectiveness of enhancement release, we still need to develop a high-efficient and easy-operational method to replace those physical-tagging release method with labor intensive, size-and number-limited. In the present study, single(with maternal known) parentage identification using eight simple sequence repeat(SSR) markers genotype fingerprint was used to trace Chinese shrimp released in Bohai Bay in 2013. A total of 884 shrimp spawners were collected from two hatcheries in Tianjin City respectively after enhancement release of shrimp larvae in May 2013. A total of 844 shrimp samples were recaptured around the release location approximately 4 months after the shrimp larvae were released into the natural sea. Genotype data of 8 SSR loci of the 1,726 samples were used for maternal-offspring parentage identification using CEervus 3.0 software. The allele number in each locus ranged from 8 to 68 with an average value of 33.25, which produced the cumulative exclusion probability with one parent known of all these sight loci up to 99%. Among the 844 recaptured shrimp samples, 448(♂:♀=212:232, gender information was lost for 4 samples) were successfully traced to their 337 maternal parents using a logarithm of odds(LOD) > 3.0 threshold. Among these 337 maternal parents, 253 had a single offspring, 62 had two offspring, 18 had three offspring, 3 had four offspring, and 1 had five offspring. For the first time, a large number of released shrimp were identified from recapture samples, and this study showed that it is possible to trace all released Chinese shrimp without using any type of physical tag in enhancement release activities. This not only means more precise recapture ratio assessment than ever expected, but also this method demonstrates an effective method for large-scale hatchery release as well as for organisms used in hatchery enhancement which are not suitable for physical tagging.展开更多
Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock ...Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.展开更多
Bayesian and restricted maximum likelihood （REML） approaches were used to estimate the genetic parameters in a cultured turbot Scophthalmus maximus stock. The data set consisted of harvest body weight from 2 462 pro...Bayesian and restricted maximum likelihood （REML） approaches were used to estimate the genetic parameters in a cultured turbot Scophthalmus maximus stock. The data set consisted of harvest body weight from 2 462 progenies （17 months old） from 28 families that were produced through artificial insemination using 39 parent fish. An animal model was applied to partition each weight value into a fixed effect, an additive genetic effect, and a residual effect. The average body weight of each family, which was measured at 110 days post-hatching, was considered as a covariate. For Bayesian analysis, heritability and breeding values were estimated using both the posterior mean and mode from the joint posterior conditional distribution. The results revealed that for additive genetic variance, the posterior mean estimate （σa^2 =9 320） was highest but with the smallest residual variance, REML estimates （σa^28 088） came second and the posterior mode estimate （σa^2=7 849） was lowest. The corresponding three heritability estimates followed the same trend as additive genetic variance and they were all high. The Pearson correlations between each pair of the three estimates of breeding values were all high, particularly that between the posterior mean and REML estimates （0.996 9）. These results reveal that the differences between Bayesian and REML methods in terms of estimation of heritability and breeding values were small. This study provides another feasible method of genetic parameter estimation in selective breeding programs of turbot.展开更多
Genetic parameters and response to selection were estimated for harvest body weight in turbot. The data consisted of 10 952 individuals of 508 full-sib families from three generations（G0, G1, and G2）. The heritabili...Genetic parameters and response to selection were estimated for harvest body weight in turbot. The data consisted of 10 952 individuals of 508 full-sib families from three generations（G0, G1, and G2）. The heritability estimates for G0, G1, and G2 were 0.11±0.08, 0.18±0.09, and 0.17±0.07, respectively. Over three generations, the heritability estimate was 0.19±0.04. Maternal and common environmental effects were 0.10±0.04, 0.14±0.04, and0.13±0.03 within each generation and 0.12±0.01 across generations. The selection differential in growth was 18.24 g in G0 and 21.19 g in G1 corresponding to an average of 19.72 g per generation. The genetic gains were also calculated, they were 22.06 g in G1 and 11.93 g in G2, corresponding to 6.36% and 3.52% body weight. The total genetic gain after two generations was 10.10% body weight, which indicated that the selective breeding program for the body weight trait in turbot was successful.展开更多
The estimation of genetic parameters has played an important role in animal selective breeding for growth traits.Recently studies show that molecular markers can be incorporated into genetic evaluations. In order to i...The estimation of genetic parameters has played an important role in animal selective breeding for growth traits.Recently studies show that molecular markers can be incorporated into genetic evaluations. In order to improve the performance of an incomplete pedigree（i.e, only parents are known） in the genetic evaluations, 12 microsatellite markers have been applied in the estimation of the genetic parameters for body weight in a farmed population（n=1 890） of juvenile turbot（Scophthalmus maximus L.）. A new relatedness called parental molecular relatedness（PMR） is estimated based on results of genotyping of 48 parents（31 males, 17 females） with microsatellites markers. The feasibility of PMR in estimation of genetic parameters is verified by comparison with pedigree related（PR） which is obtained from a complete pedigree. The results demonstrate that a high correlation（0.872） between them is found. Heritabilities are estimated using the PMR（0.52±0.13） and PR（0.55±0.22） with the same animal model. A cross-validation shows that the predictive abilities of models using the PMR and the PR are identical（0.81）. From that, a conclusion can be made that PMR and PR predicted genetic values equally well in a population of juvenile turbot. Therefore PMR can be applied as an alternative of the PR when only parents are known. However, for a better performance, more markers and more families should be included in a further study.展开更多
基金supported by the National High Technology Development Project of China under contract No. 2012AA10A404the Recommended International Advanced Agricultural Science and Technology Project of China under contract No. 2012-S5
文摘Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content(PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles(Na) and effective alleles(Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity(Ho) values were lower than the expected heterozygosity(He) values(0.526–0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. Fis values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise Fst values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks(11.3%) was much lower than that within stocks(88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.
基金The Special Scientific Research Funds for Central Non-profit Institutes,Yellow Sea Fisheries Research Institutes under contract No.20603022012002the National High Technology Research and Development Program of China(863 Program) under contract No.2012AA10A408-7
文摘Twenty-six half-sib groups （53 full-sib families） of turbot,Scophthalmus maximus Linnaeus, were obtained by artificial insemination. We measured growth in the offspring （40-50 individuals/family） and subjected them to a thermal tolerance challenge over a period of 34 d. There was no significant difference in daily mor-tality （range： 0.580%-1.391%） between Days 1-13 during the thermal tolerance challenge. However, daily cumulative mortality increased rapidly between Days 14 and 29, especially on Days 15 and 16 （20.232% and 34.377%, respectively）. Mortality was highest on Day 16 （14.145%）. We estimated the genetic parameters using the average information restricted maximum likelihood method. We used a likelihood ratio test to evaluate the significance of effects in models with and without identity as an effect, and compared the final log-likelihoods （maximum log L）. Lastly, we estimated phenotypic and genetic correlation between the up-per thermal tolerance limit （UTT） and body weight （BW）. In this study, the positive phenotypic correlation was low between UTT and BW （0.093±0.029）. The genetic correlation between UTT and BW was negative （-0.044±0.239）. The heritability for upper thermal tolerance was low （0.087±0.032）, which is of approximate-ly moderate heritability. The heritability for body weight was high （0.303±0.074）. Our results suggest there is significant potential for improvement in the culture of turbot by selective breeding.
基金The National High Technology Research and Development Program of China under contract No.2012AA10A408-7the Special Funding for Basic Scientific Research of Yellow Sea Fisheries Research Institute under contract No.2010-cb-04
文摘The objectives of this present research were to assess the heritability of growth traits under low temperature conditions in turbot（Scophthalmus maximus L.）, and to analyze the correlation between body weight（BW） and body length（BL）. There were 536 individuals from 25 full- and half-sib families involved in this study. During the entire 90-day period, which was initiated at 233 dph（day old） and ended at 323 dph, the individuals＇ BW and BL were weighed consecutively six times every 18 days. The heritability of BW and BL and the correlation between these two traits were estimated based on an individual animal model with the derivative-free restricted maximum likelihood（DFREML） method. These results showed that the specific growth rates（SGR） of 25 families was from 0.75±0.11 to 1.05±0.14 under water temperature of 10.5–12°C. In addition, the heritability of BW and BL estimated under low-temperature were 0.32±0.04 and 0.47±0.06, respectively. The BW had a medium heritability（0.2–0.4）, and the BL had a high heritability（〉0.45）, which suggested that selection for increased weight and length was feasible. Moreover, there was potential for mass selection on growth. The genetic and phenotypic correlations between BW and BL were 0.95±0.01 and 0.91±0.01（P 〈 0.01）, respectively. A significant correlation between BW and BL showed that BL could be instead of BW for indirect selection, which could be effectively implemented in the breeding program.
基金This work was supported by National Basic Research Program of China(973 Program)(2015CB453303)and International Science and Technology Cooperation Program of China(2013DFA31410)
文摘Enhancement release has been proven effective in natural resources recovery of Chinese shrimp Fenneropenaeus chinensis in the last several decades in China, however, to assess the effectiveness of enhancement release, we still need to develop a high-efficient and easy-operational method to replace those physical-tagging release method with labor intensive, size-and number-limited. In the present study, single(with maternal known) parentage identification using eight simple sequence repeat(SSR) markers genotype fingerprint was used to trace Chinese shrimp released in Bohai Bay in 2013. A total of 884 shrimp spawners were collected from two hatcheries in Tianjin City respectively after enhancement release of shrimp larvae in May 2013. A total of 844 shrimp samples were recaptured around the release location approximately 4 months after the shrimp larvae were released into the natural sea. Genotype data of 8 SSR loci of the 1,726 samples were used for maternal-offspring parentage identification using CEervus 3.0 software. The allele number in each locus ranged from 8 to 68 with an average value of 33.25, which produced the cumulative exclusion probability with one parent known of all these sight loci up to 99%. Among the 844 recaptured shrimp samples, 448(♂:♀=212:232, gender information was lost for 4 samples) were successfully traced to their 337 maternal parents using a logarithm of odds(LOD) > 3.0 threshold. Among these 337 maternal parents, 253 had a single offspring, 62 had two offspring, 18 had three offspring, 3 had four offspring, and 1 had five offspring. For the first time, a large number of released shrimp were identified from recapture samples, and this study showed that it is possible to trace all released Chinese shrimp without using any type of physical tag in enhancement release activities. This not only means more precise recapture ratio assessment than ever expected, but also this method demonstrates an effective method for large-scale hatchery release as well as for organisms used in hatchery enhancement which are not suitable for physical tagging.
基金The National Basic Research Program of China(973 Program)Adaptive Response of Fishery Species to Environmental Changes and Their Effects on Population Dynamics under contract No.2015CB453303the International Science&Technology Cooperation Program of China under contract No.2013DFA31410
文摘Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.
基金The Taishan Scholar Program for Seed Industry under contract No.ZR2014CQ001the National High Technology Research and Development Program of China under contract No.2012AA10A408-7
文摘Bayesian and restricted maximum likelihood （REML） approaches were used to estimate the genetic parameters in a cultured turbot Scophthalmus maximus stock. The data set consisted of harvest body weight from 2 462 progenies （17 months old） from 28 families that were produced through artificial insemination using 39 parent fish. An animal model was applied to partition each weight value into a fixed effect, an additive genetic effect, and a residual effect. The average body weight of each family, which was measured at 110 days post-hatching, was considered as a covariate. For Bayesian analysis, heritability and breeding values were estimated using both the posterior mean and mode from the joint posterior conditional distribution. The results revealed that for additive genetic variance, the posterior mean estimate （σa^2 =9 320） was highest but with the smallest residual variance, REML estimates （σa^28 088） came second and the posterior mode estimate （σa^2=7 849） was lowest. The corresponding three heritability estimates followed the same trend as additive genetic variance and they were all high. The Pearson correlations between each pair of the three estimates of breeding values were all high, particularly that between the posterior mean and REML estimates （0.996 9）. These results reveal that the differences between Bayesian and REML methods in terms of estimation of heritability and breeding values were small. This study provides another feasible method of genetic parameter estimation in selective breeding programs of turbot.
基金The Taishan Scholar Program for Seed Industry under contract No.ZR2014CQ001the Accurate Identification and Selection Breeding Creative Utilization of Turbot Germplasm Resources under contract No.2016LZGC031-2
文摘Genetic parameters and response to selection were estimated for harvest body weight in turbot. The data consisted of 10 952 individuals of 508 full-sib families from three generations（G0, G1, and G2）. The heritability estimates for G0, G1, and G2 were 0.11±0.08, 0.18±0.09, and 0.17±0.07, respectively. Over three generations, the heritability estimate was 0.19±0.04. Maternal and common environmental effects were 0.10±0.04, 0.14±0.04, and0.13±0.03 within each generation and 0.12±0.01 across generations. The selection differential in growth was 18.24 g in G0 and 21.19 g in G1 corresponding to an average of 19.72 g per generation. The genetic gains were also calculated, they were 22.06 g in G1 and 11.93 g in G2, corresponding to 6.36% and 3.52% body weight. The total genetic gain after two generations was 10.10% body weight, which indicated that the selective breeding program for the body weight trait in turbot was successful.
基金The National High Technology Research and Development Program of China under contract No.2012AA10A408-7Special Scientific Research Funds for Central Non-profit Institute,Yellow Sea Fisheries Research Institute,Chinese Academy of Fishery Sciences+2 种基金the Compare of Genome-wide Association Study Models in Turbot under contract 20603022013026Shandong Provincial Department of Agriculture,the Taishan scholar program for seed industryMinistry of Agriculture of the People’s Republic of China,Agricultural Science and Technology Achievements Transformation Fund "Propagation and promotion of seawater breeding new varieties of turbot ‘Danfa turbot’ "under contract No.2013GB2A200036
文摘The estimation of genetic parameters has played an important role in animal selective breeding for growth traits.Recently studies show that molecular markers can be incorporated into genetic evaluations. In order to improve the performance of an incomplete pedigree（i.e, only parents are known） in the genetic evaluations, 12 microsatellite markers have been applied in the estimation of the genetic parameters for body weight in a farmed population（n=1 890） of juvenile turbot（Scophthalmus maximus L.）. A new relatedness called parental molecular relatedness（PMR） is estimated based on results of genotyping of 48 parents（31 males, 17 females） with microsatellites markers. The feasibility of PMR in estimation of genetic parameters is verified by comparison with pedigree related（PR） which is obtained from a complete pedigree. The results demonstrate that a high correlation（0.872） between them is found. Heritabilities are estimated using the PMR（0.52±0.13） and PR（0.55±0.22） with the same animal model. A cross-validation shows that the predictive abilities of models using the PMR and the PR are identical（0.81）. From that, a conclusion can be made that PMR and PR predicted genetic values equally well in a population of juvenile turbot. Therefore PMR can be applied as an alternative of the PR when only parents are known. However, for a better performance, more markers and more families should be included in a further study.
