Weiji Wang

Genetic parameter estimation for juvenile growth and upper thermal tolerance in turbot (Scophthalmus maximus Linnaeus)

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 mortality (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 upper 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 approximately 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.

Construction of a genetic linkage map in Fenneropenaeus chinensis using SNP markers

Genetic linkage maps of Fenneropenaeus chinensis were constructed using a “double pseudo-testcross” strategy with 200 single nucleotide polymorphisms (SNPs) markers. This study represents the first SNP genetic linkage map for F. chinensis. The parents and F1 progeny of 100 individuals were used as mapping populations. 21 genetic linkage groups in the male and female maps were identified. The male linkage map was composed of 115 loci and spanned 879.7 cM, with an average intermarker spacing of 9.4 cM, while the female map was composed of 119 loci and spanned 876.2 cM, with an average intermarker spacing of 8.9 cM. The estimated coverage of the linkage maps was 51.94% for the male and 53.77% for the female, based on two estimates of genome length. The integrated map contains 180 markers distributed in 16 linkage groups, and spans 899.3 cM with an average marker interval of 5.2 cM. This SNP genetic map lays the foundation for future shrimp genomics and genetic breeding studies, especially the discovery of gene or regions for economically important traits in Chinese shrimp.

Genetic diversity analysis of spawner and recaptured populations of Chinese shrimp (Fenneropenaeus chinensis) during stock enhancement in the Bohai Bay based on an SSR marker

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 (Na) were 8–63 and 6–60, respectively. The numbers of effective alleles (Ne) 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 (Ho) values (0.638–0.910 and 0.712–0.927) were lower than the expected heterozygosity (He) 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 Hardy-Weinberg equilibrium. Fis values were positive at seven loci and the inbreeding coefficients (F) of the two populations estimated by trioML 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. Fst 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.

Estimates of heritability and correlation for growth traits of turbot (Scophthalmus maximus L.) under low temperature conditions

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.

Estimation of genetic parameters for growth trait of turbot using Bayesian and REML approaches

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 (σa2=9 320) was highest but with the smallest residual variance, REML estimates (σa2=8 088) came second and the posterior mode estimate (σa2=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.

An estimation of genetic parameters of growth traits in juvenile turbot (Scophthalmus maximus L.) using parental molecular relatedness

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.

Genetic variation analysis across six life periods in a natural population of the Chinese shrimp “Fenneropenaeus chinensis” in Bohai bay using SSR markers

We analyzed the genetic variation across six life periods that composed 3232 samples of a natural population of the Chinese shrimp Fenneropenaeus chinensis in Bohai Bay using 4 SSR (Simple Sequence Repeats) markers. Including the observed number of alleles (Na), eight genetic variation parameters were introduced to assess the genetic diversity and trace the changing genetic variation in this natural population. The genotype number detected on each locus in each stock ranged from 27 to 503; the detected average allele number was 36.5 per locus, and the PIC values of the 4 SSR loci ranged from 0.909 to 0.954. These all reflected the high variability on these 4 SSR loci. The rates of individual number vs. genotype number (Rig) on each locus across six life periods showed an increasing tendency, the minimum and maximum change ranges were detected on EN0033 with an Rig value from 1.35 to 2.91 and on locus FCKR002 with an Rig value from 352.00 to 9.50, respectively, which suggested an increase in genotype homogenization over time in 36 the development of the natural population. The genetic differentiation coefficients (Fst), ranged from 0.00003 to 0.00206, hinted there was no significant genetic differentiation among 6 stocks. The mainly genetic differentiation contributed 83.83% of the total variation that was detected within individuals also supported the above conclusion. Regarding the genotype percentage, there were five clear instances were detected with decreasing tendency on loci EN0033 and RS0622 in six stocks, which are consistent with a previous finding that an allele on RS0622 was related to WSSV (White Spot Syndrome Virus) resistance in F. chinensis.

Cloning and characterization of a transcriptional repressor from Fenneropenaeus chinensis (Osbeck, 1765)

In this study, a transcriptional repressor was cloned and characterized from the Chinese shrimp Fenneropenaeus chinensis (Osbeck, 1765) and named FcTR. The results indicate that the full-length cDNA of 1397 bp has an open reading frame encoding a polypeptide of 354 amino acids. The calculated molecular mass of the mature protein was found to be 39.9 kDa and theoretical pI 5.59. The FcTR has four ZnF-C2H2 domains and two putative transcriptional repressor regulating G2/M transition domains (SFP1). A phylogenetic analysis of transcriptional repressor sequences shows that FcTR has a high homology with the invertebrate transcriptional repressors from Megachile rotundata (Fabricius, 1793), Apis mellifera Linnaeus, 1758, Camponotus floridanus (Buckley, 1866), Acromyrmex octospinosus echinatior (Forel, 1899) and Apis florea Fabricius, 1787 (similarity 72%). A qRT-PCR analysis indicated that FcTR was expressed in intestines, hepatopancreas, muscles and gills, and its profile was increased significantly post WSSV (white spot syndrome virus) challenge followed by a decreased trend in all examined tissues. These results indicate that FcTR might be involved in the immune defence response to WSSV in F. chinensis as a negative regulator.

Genotyping of single nucleotide polymorphisms in Fenneropenaeus chinensis (Decapoda, Penaeidae) by tetra-primer ARMA-PCR

This study introduced a kind of new SNP genotyping strategy in genetic analysis of Chinese shrimp (Fenneropenaeus chinensis). Twenty SNP tetra-primer ARMA-PCR primer sets were validated and used to investigate the genetic structure of six selected families of marine shrimp F. chinensis. The effective number of alleles ranged from 1.127 to 1.993, with an average value of 1.600. The average values of expected and observed heterozygosities of the SNPs ranged from 0.505∼0.609 and 0.373∼0.487, respectively. Polymorphism information content (PIC) values ranged from 0.145 to 0.373. Among 120 population-locus cases (six populations × twenty loci), only 8 (6.7%) showed significant deviation (P < 0.05), while the other 112 (93.3%) were in Hardy-Weinberg equilibrium (HWE) (P > 0.05). The frequencies of minor alleles ranged from 0.378 to 0.497. For the six families, the wild genotype and its allele frequency were significantly higher than that of the mutant genotype and its allele frequency. Fifty five point forty two percent of the population-locus showed heterozygosity. The results indicated that tetra-primer ARMA-PCR is a simple, rapid and efficient method for SNP genotyping which make it useful in a broad aspects of F. chinensis genetic and breeding studies.

Genetic parameters and response to selection for body weight in turbot ( Scophthalmus maximus , Linnaeus)

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, and 0.13±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.