Transcriptome sequencing using Illumina RNA-seq was performed on populations of black tiger shrimp from India. Samples were collected from (i) four landing centres around the east coastline (EC) of India, (ii) survivors of a severe WSSV infection during pond culture (SUR) and (iii) the Andaman Islands (AI) in the Bay of Bengal. Equal quantities of purified total RNA from homogenates of hepatopancreas, muscle, nervous tissue, intestinal tract, heart, gonad, gills, pleopod and lymphoid organs were combined to create AI, EC and SUR pools for RNA sequencing. De novo transcriptome assembly resulted in 136,223 contigs (minimum size 100 base pairs, bp) with a total length 61 Mb, an average length of 446 bp and an average coverage of 163× across all pools. Approximately 16% of contigs were annotated with BLAST hit information and gene ontology annotations. A total of 473,620 putative SNPs/indels were identified. An Illumina iSelect genotyping array containing 6,000 SNPs was developed and used to genotype 1024 offspring belonging to seven full-sibling families. A total of 3959 SNPs were mapped to 44 linkage groups. The linkage groups consisted of between 16–129 and 13–130 markers, of length between 139–10.8 and 109.1–10.5 cM and with intervals averaging between 1.2 and 0.9 cM for the female and male maps respectively. The female map was 28% longer than the male map (4060 and 2917 cM respectively) with a 1.6 higher recombination rate observed for female compared to male meioses. This approach has substantially increased expressed sequence and DNA marker resources for tiger shrimp and is a useful resource for QTL mapping and association studies for evolutionarily and commercially important traits.

A 16-week indoor culture trial was conducted to evaluate the effect of varying C:N ratio on growth performance, physico-chemical parameters, microbial dynamics, feed utilization, and immunological parameters. The experiment comprised of five biofloc treatment groups (with varying C:N ratio 5:1, 10:1, 15:1, 20:1) and a control with three replicates each, having 100 nos/m 3 as stocking density in 500 L tanks with constant aeration. The C:N ratios of the treatments were manipulated using molasses as an organic carbon source whereas there was no carbon source added in control. The water quality parameters monitored throughout the experiment were found to be within permissible limits in shrimp culture. At the end of the experiment, it was observed that there were significant differences between the treatment groups and the control regarding absolute growth, SGR, FCR, PER, and FER.Furthermore, a considerable difference in immunological parameters, namely, THC, phagocytosis, and PO activity (17.5 × 10 6 cells per ml, 43.5%, 0.112 Units min −1 mg min −1 ), was recorded among the treatments compared to that of the control groups (6.2 × 10 6 cells per ml, 31.5%, 0.051 Units min −1 mg min −1 ) respectively. Enhanced growth and survival with substantial disease resistance were recorded in C15 treatment. The results indicate that the CN15 ratio coupled with minimal water exchange is optimal for improved survival, growth, and immune activity. K E Y W O R D S C:N ratio, molasses, water quality, zero-water exchange 1 | INTRODUCTION Availability of specific pathogen-free shrimp has resulted in increased shrimp farming in terms of culture as well as production. The choice of Litopenaeus vannamei over Penaeus monodon is primarily due to enhanced production, SPF availability, higher yield after processing, and higher market demand. Of late, biofloc technology (BFT) has gained momentum and positive response in shrimp and tilapia farming. In India, farmed shrimp production increased from <1 lakh tonnes in 2009 to 3.5 lakh tonnes in 2014. In 2016-2017, the production was over 5 lakh tonnes, accounting for 38% in quantity and 64.5% in value (Rs. 24,426 crores) of the total Indian seafood export worth 5.78 billion dollars (Rs. 37,870 crores) (MPEDA, 2017). The expanding culture system influences water quality and environmental factors. Due to intensification with higher stocking densities, there isHighlights Growth, physico-chemical, and microbiological parameters were substantially higher in carbon and nitrogen (CN) ratio treatments compared to control. Optimization of C:N ratio in L. vannamei culture revealed an optimum ratio of 15 to be ideal for a biofloc-based system. Challenge study revealed higher mortality in control compared to CN-treated groups when challenged with the pathogen Vibrio parahaemolyticus (MTCC 451). Carbon supplementation appears to influence heterotrophic bacteria and provides immunity and protective response under BFT-based rearing. Immune responses like THC, phagocytic activity, and proPhenoloxidase activity we...

BackgroundShrimp culture is a fast growing aquaculture sector, but in recent years there has been a shift away from tiger shrimp Penaeus monodon to other species. This is largely due to the susceptibility of P. monodon to white spot syndrome virus disease (Whispovirus sp.) which has impacted production around the world. As female penaeid shrimp grow more rapidly than males, mono-sex production would be advantageous, however little is known about genes controlling or markers associated with sex determination in shrimp. In this study, a mapped set of 3959 transcribed single nucleotide polymorphisms were used to scan the P. monodon genome for loci associated with resistance to white-spot syndrome virus and sex in seven full-sibling tiger shrimp families challenged with white spot syndrome virus.ResultsLinkage groups 2, 3, 5, 6, 17, 18, 19, 22, 27 and 43 were found to contain quantitative trait loci significantly associated with hours of survival after white spot syndrome virus infection (P < 0.05 after Bonferroni correction). Nine QTL were significantly associated with hours of survival. Of the SNPs mapping to these and other regions with suggestive associations, many were found to occur in transcripts showing homology to genes with putative immune functions of interest, including genes affecting the action of the ubiquitin-proteasome pathway, lymphocyte-cell function, heat shock proteins, the TOLL pathway, protein kinase signal transduction pathways, mRNA binding proteins, lectins and genes affecting the development and differentiation of the immune system (eg. RUNT protein 1A). Several SNPs significantly associated with sex were mapped to linkage group 30, the strongest associations (P < 0.001 after Bonferroni correction) for 3 SNPs located in a 0.8 cM stretch between positions 43.5 and 44.3 cM where the feminisation gene (FEM-1, affecting sexual differentiation in Caenorhabditis elegans) mapped.ConclusionsThe markers for disease resistance and sexual differentiation identified by this study could be useful for marker assisted selection to improve resistance to WSSV and for identifying homogametic female individuals for mono-sex (all female) production. The genes with putative functions affecting immunity and sexual differentiation that were found to closely map to these loci provide leads about the mechanisms affecting these important economic traits in shrimp.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-731) contains supplementary material, which is available to authorized users.