De-novo transcriptome analysis of the banana shrimp (Fenneropenaeus merguiensis) and identification of genes associated with reproduction and development.

The banana shrimp Fenneropenaeus merguiensis is a commercially important marine crustacean for world aquaculture and fisheries. Despite this, limited genetic information is available for it and many other penaeid shrimp species. Here we present the first in-depth analysis of the transcriptional content of 8 different tissues from the banana shrimp using RNA-Seq technologies. A total of over 1 million single-end and over 49 million paired-end reads were obtained from Roche 454FLX and illumina sequencing platforms, respectively, resulting in an assembly of 124,631 transcripts with an N50 of 1,332 and mean length of 514 nt. A total of 59,179 putative protein sequences obtained from the assembled transcripts were annotated using public protein sequence databases and assigned 20,430 BLAST hits, 16,866 GO terms and 13,304 KOG categories. Further analysis revealed a rich set of transcript sequences exhibiting homology with genes associated with reproduction, sex determination and development and distinguished the tissues responsible for this expression. This report adds a substantial contribution to the sequence data currently available for F. merguiensis, providing valuable resources for further research.

Yearly, pond, lineage and family variation of hepatopancreatic parvo-like virus (HPV) copy number in banana shrimp Fenneropenaeus merguiensis.

Hepatopancreatic parvo-like virus (HPV) has been reported from a variety of shrimp species around the world, including Australia, and thought to impact negatively on production, but until now there was scant information available on variation of HPV over time, ponds and shrimp lineages or families, information that could be used to manage or reduce virus levels. Here we report HPV copy number estimated using qPCR from 1500 individual shrimp sampled over three years and encompassing 91 ponds, 21 breeding groups or lineages and 40 families. HPV copy number variation between ponds was used by farm management as a criterion to choose prospective broodstock (candidates were taken from low HPV ponds). Despite such choice, HPV levels in farmed animals were not reduced from 2011 to 2013. Accordingly, the hypothesis that HPV levels can be reduced over time simply by considering average HPV levels in ponds alone is rejected. Different lines of shrimp within the same farm had different HPV levels, but as lines were raised separately, the line differences could be due to either genetic or environmental differences, the latter including possible different rearing effects and differences in vertical transmission. There were large (up to 2-3 LOG fold) differences of HPV levels between families bred and grown together contemporaneously, and the heritability for HPV copy number was estimated to be moderate to large (0.40 ± 0.13). Apart from genetic differences, differences of vertical transmission from dams may contribute to the between family differences, in any case we postulate that selection between families could be an effective method to reduce HPV levels. HPV levels were not genetically correlated with performance traits such as body weight or length, so selection for HPV level should not adversely affect production characteristics. This is the first evidence for an aquacultured species that viral levels, as opposed to survival/resistance to viruses, may have a substantial host genetic component. The heritability reported here for virus copy number was higher that most heritabilities reported for survival to specific pathogens such as white spot, raising the general postulate that selection for virus copy number may be more effective and repeatable than selection for survival to pathogen challenge.

Heritability for body colour and its genetic association with morphometric traits in Banana shrimp (Fenneropenaeus merguiensis).

BACKGROUND: Banana shrimp Fenneropenaeus merguiensis has emerged as an important aquacultured shrimp species in South East Asia and Australia. However, the quantitative genetic basis of economically important traits in this species are currently not available, while for body colour, cooked or uncooked, there are no genetic parameter estimates for any shrimp or indeed any decapod crustacean. In this study, we report for banana shrimp genetic parameters for morphometric traits and, the first time for any shrimp, parameter estimates for body colour. Ten highly polymorphic microsatellite markers were developed from genomic sequences and used to construct a pedigree for 2000 offspring from approximately 60 female and 60 male parents that were sampled from a single routine commercial production pond. RESULTS: Restricted maximum likelihood method applied to a single trait mixed model was used to estimate heritabilities, while correlations were estimated using the multi-trait approach. The estimates of heritability for morphometric traits were moderate to high (h(2) = 0.14 - 0.50). Body colour of uncooked shrimp showed a heritable additive genetic component (h(2) = 0.03 - 0.55), and those estimates obtained for cooked shrimp were significantly different from zero. Genetic correlations among morphometric traits were all positive and very high (close to unity, rg = 0.85 - 0.99). The genetic correlations of body traits (weight, length and width) were positive with both colour after cooking (0.74 - 0.84) and body colour measured on live shrimp (0.59 to 0.70). The positive genetic correlations between the cooked body colour and uncooked body colour (0.64 ± 0.20) suggests these two traits can be simultaneously improved in practical selective breeding programs. This first ever report of genetic parameters for cooked or uncooked colour in crustacean indicates there is potential for genetic improvement of both growth and body colour through selection. CONCLUSIONS: In the present study we demonstrated for banana shrimp that genetic parameters can be estimated from commercial samples (using pedigrees based on DNA markers), that selection for shrimp colour should be successful under such commercial conditions.