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.

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A 75-day 2 9 3 factorial experiment was conducted to evaluate the effect of two levels of dietary protein (32 and 40%) and two different carbon sources (rice flour-R and molasses-M), and without carbohydrate (control-C) in black tiger shrimp Penaeus monodon juveniles (3.37 AE 0.04 g) at 100 nos. m À3 in 100 L fibre reinforced plastic tanks. Biofloc volume and total suspended solid were higher in molasses added groups (32 + M and 40 + M) followed by rice flour (32 + R and 40 + R) and controls (32C and 40C). Molasses and rice flour addition significantly reduced (P < 0.01) the total ammonia-N compared to controls. The highest Vibrio, Bacillus and Lactobacillus counts were recorded in 40 + M, 32 + M and 32 + R respectively. Among the treatments, significantly higher (P < 0.01) final body weight was recorded in 40 + R (8.5 AE 0.3 g), 40 + M (7.8 AE 0.3 g) and 32 + R (7.5 AE 0.4 g) compared to control groups, 32C (6.1 AE 0.3 g), 40C (6.4 AE 0.3 g) and molasses added group, 32 + M (5.7 AE 0.4 g). Rice flour supplementation significantly increased (P < 0.01) the total haemocyte count (910 6 cells mL À1 ) in 32 + R (45.7 AE 3.7) and 40 + R (44.3 AE 3.1) compared to controls, 32C (27.3 AE 3.4) and 40C (25.8 AE 0.9). Similarly, higher superoxide dismutase, catalase, serum protein and glucose were recorded in the rice flour added groups, 40 + R followed by 32 + R. Among the treatments, the highest level of prophenoloxidase (OD 490 nm, 0.3 AE 0.0) and survival after challenge with Vibrio harveyi (55.6%) was observed in 32 + R. The study elucidates that rice flour addition produces optimum level of biofloc with better growth and immune responses compared to molasses and control. Furthermore, rice flour addition at 32% protein level could replace 40% protein feed.

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.

To compare the production and economic performance of two polyculture systems with different species combinations in brackishwater tide-fed ponds, a 180-day trial was carried out. In the first combination (T1), mullets (Mugil cephalus, Liza tade and L. parsia at 3 : 1 : 1.3 ratio) and tiger shrimp (Penaeus monodon) and in the second (T2), milkfish (Chanos chanos) and tiger shrimp were stocked keeping the fishes and shrimp at 8000 and 20 000 numbers ha )1 , respectively, in both treatments with duplicate ponds. Since shrimp was an important component of these two systems with open water exchange, the dynamics of heterotrophic bacteria (THB) including Vibrio spp. (TVC) and the occurrence of viral infection agents were studied to understand the disease risks. Among the fishes in T1, M. cephalus attained the highest final weight of 92.29 ± 4.36 g followed by L. tade and L. parsia with 80.40 ± 4.02 and 54.02 ± 2.11 g, respectively. C. chanos in T2 had the highest net weight gain (127.85 g) and daily weight gain (0.71 g day )1 ), while M. cephalus in T1 attained the highest specific growth rate (1.60% day )1 ). Growth parameters of tiger shrimp were almost similar in both treatments, with no significant differences (P > 0.05). Though total production of fishes and shrimp was lower in T1 (689 kg ha )1 180 day )1 ), it was not significantly different (P > 0.05) from T2 (721 kg ha )1 180 day )1 ). Monthly THB and TVC were not alarming and the absence of viral infections in shrimp indicated no disease risk. Total income from T1 was significantly higher (P < 0.05) than that of T2, but net income and benefit-cost ratio were insignificantly different between the treatments (P > 0.05). The present findings indicate that upon availability of stocking materials, both polyculture systems would be suitable farming options.

Pacific white shrimp, Litopenaeus vannamei has been introduced recently for culture practice in India. Though SPF stocks are imported for larval production and thereafter culture practice, these are prone to infection with the existing viruses in the environment. Here we report mortality of L.vannamei in several farms in India with minimum biosecurity. The shrimp were harvested early within 50-72 days of culture due to the onset of disease and consequent mortality. As per the analysis carried out, the shrimp were infected with two virus, white spot syndrome virus (WSSV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV). About 80 % of the samples collected had either or both of the viruses. A majority of these samples (60 %) had dual infection with WSSV and IHHNV. Infection of shrimp with WSSV and IHHNV could be detected both by PCR and histopathology. Some of the samples had either exclusively WSSV infection or IHHNV infection and were also harvested before the completion of the required culture period. All the samples analyzed were negative for taura syndrome virus, yellow head virus and infectious myonecrosis virus. While it is difficult to point out the exact etiological agent as the cause of mortality, strict biosecurity measures are advisable for the continuity of L. vannamei culture in India.

Asian seabass or barramundi (Lates calcarifer) is an important food fish with commercial value and a wide geographic distribution. Though some reports based on molecular and/or morphological data exist, a comprehensive effort to establish species identity across its range is lacking. In order to address this issue and especially to ascertain whether the widespread distribution has resulted in bifurcation of the species, we collected Asian seabass samples from various locations representing the Western and Eastern Coastline of India, Andaman and Nicobar Islands, Bangladesh and Australia. Samples from Malaysia, Indonesia, Thailand and Singapore were collected as part of a previous study. DNA sequence variations, including cytochrome c oxidase subunit 1 (COI), 16S rDNA and the highly variable D-loop (or control region), were examined to establish species delineation. Data from all the sequences analyzed concordantly point to the existence of at least two distinct species-one representing the Indian subcontinent plus Myanmar, and a second, representing Southeast Asia (Singapore, Malaysia, Thailand and Indonesia) plus Northern Australia. These data are useful for conservation ecology, aquaculture management, for establishing the extent of genetic diversity in the Asian seabass and implementing selective breeding programs for members of this species complex.

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