Identification of genes involved in reproduction and lipid pathway metabolism in wild and domesticated shrimps

The aims of this study were to identify genes involved in reproduction and lipid pathway metabolism in Penaeus monodon and correlate their expression with reproductive performance. Samples of the hepatopancreas and ovaries were obtained from a previous study of the reproductive performance of wild and domesticated P. monodon broodstock. Total mRNA from the domesticated broodstock was used to create two next generation sequencing cDNA libraries enabling the identification of 11 orthologs of key genes in reproductive and nutritional metabolic pathways in P. monodon. These were identified from the library of de novo assembled contigs, including the description of 6 newly identified genes. Quantitative RT-PCR of these genes in the hepatopancreas prior to spawning showed that the domesticated mature females significantly showed higher expression of the Pm Elovl4, Pm COX and Pm SUMO genes. The ovaries of domesticated females had a significantly decreased expression of the Pm Elovl4 genes. In the ovaries of newly spawned females, a significant correlation was observed between hepatosomatic index and the expression of Pm FABP and also between total lipid content and the expression of Pm CYP4. Although not significant, the highest levels of correlation were found between relative fecundity and Pm CRP and Pm CYP4 expression, and between hatching rate and Pm Nvd and Pm RXR expression. This study reports the discovery of genes involved in lipid synthesis, steroid biosynthesis and reproduction in P. monodon. These results indicate that genes encoding enzymes involved in lipid metabolism pathways might be potential biomarkers to assess reproductive performance.&nbsp

Development of nutrigenomic tools to assess reproductive performance in shrimps

The Crustacean Society Summer Meeting (TCSSM) - 10th Colloquium Crustacea Decapoda Mediterranea (CCDM), 3-7 June 2012, Athens, GreecePeer Reviewe

Genetic parameters of Gill-associated virus infection and body weight under commercial conditions in black tiger shrimp, Penaeus monodon

Selective breeding to improve performance of growth and increase disease resistance is becoming commonplace within shrimp aquaculture. Whilst estimated breeding values (EBV) for growth can be evaluated easily in on-farm trials, EBVs for disease resistance are usually obtained from controlled laboratory challenges and may not be indicative of natural infection and resistance in a commercial setting. If they are not the same trait, this will result in a low genetic correlation between the traits and application of EBVs derived from the laboratory challenge will lead to overall slow genetic progress for improved disease resistance in on-farm conditions. There is a need for alternative measures of predicting disease resistance based on performance in farm environments. Two such estimates may be viral infection status (presence/absence) and load of farm reared shrimp. This study presents genetic parameter estimates of Gill-Associated Virus (GAV) infection (viral infection presence and viral loading) and body weight traits from Penaeus monodon reared under commercial farm conditions. Body weight and GAV infection traits were assessed by sampling similar to 2000 shrimp from 80 full-sib families from two replicate commercial ponds. In addition, the Pearson correlation of EBVs of pond-reared shrimp with those of siblings derived from communal laboratory GAV challenge tests (intramuscular injection of standard doses of virus) were calculated to establish if prediction of genetic merit in controlled trials would be similar to disease resistance seen on-farm. Heritability under commercial farm conditions for GAV infection status was 0.06 +/- 0.03 (percent GAV positive 45.5%) and infection load 0.21 +/- 0.10 (mean GAV infection load 3.11 +/- 1.14 log(10) GAV copies mu g(-1) TNA) and for body weight h(2) = 0.38 +/- 0.07. A high genetic correlation was observed among the two on-farm GAV infection traits (r(g) = 0.90 +/- 0.24), whereas the genetic correlation between the two GAV infection traits and body weight on-farm were positive although weak (r(g) = 0.26 +/- 0.25; 0.36 +/- 0.26). No significant correlation was found for EBVs of GAV infection (infection status and load) on-farm and GAV-induced mortality or viral load under laboratory challenge testing (R-EBV ranged from -0.06 +/- 0.14 to -0.27 +/- 0.15). Additionally, there was no correlation of EBVs between body weight of shrimp on-farm and GAV-induced disease under controlled challenge. In conclusion, measures of GAV infection from shrimp on-farm and GAV induced mortality measured under controlled challenge conditions may represent different genetic traits, at least when mortality is measured using an 'unnatural' challenge method and when no apparent disease outbreak occurs on farm

Genetic parameters for tolerance to gill-associated virus under challenge-test conditions in the black tiger shrimp (Penaeus monodon)

Diseases in shrimp aquaculture cause significant economic losses, particularly those caused by viruses. Genetic improvement of disease tolerance through selective breeding can be an important tool for managing the risk of disease in shrimp farming as long as the trait has a genetic basis (i.e. heritable) and is able to be accurately and reliably measured. This study presents the first estimates of genetic variation associated with tolerance to gill-associated virus (GAV) in Penaeus monodon using a unique controlled challenge test design. Shrimp families (n = 72) were communally spawned and reared prior to replicated communal challenge testing when they reached an average size of ~8 g. Pedigree determination was carried out using genotyping and shrimp were challenged by intramuscular injection with a weight standardised dose of GAV. Daily mortality data were collected over 15 days from 1717 individuals and GAV infection load was measured on the challenge test survivors (n = 963). Overall mortality after 15 days was 35.5% and ranged from 0 to 71% among families. Heritability estimates for mortality were 0.11 ± 0.03 using a binomial model and 0.14 (standard error not estimated) using Cox's proportional hazards model. The estimated heritability for GAV infection load was 0.21 ± 0.07. The genetic correlation between mortality and GAV infection load was not significantly different from zero, rg = 0.30 ± 0.23, suggesting that the two traits may be genetically independent, at least in the way they were measured in this study. Results from this study suggest a low but significant genetic basis for GAV tolerance in P. monodon and that selection may be a viable option to manage GAV-related disease. The study also demonstrated, for the first time in shrimp, communal-based spawning and rearing can be used for large-scale genetic analysis of disease tolerance, eliminating the need for single family rearing tanks and associated confounding environmental effects

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome

The black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally; however, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date based on nine adult tissues and eight early life-history stages (BUSCO - Complete: 98.2% [Duplicated: 51.3%], Fragmented: 0.8%, Missing: 1.0%). The assembly resulted in 236,388 contigs, which were then further segregated into 99,203 adult tissue specific and 58,678 early life-history stage specific clusters. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. Transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.status: publishe