A linkage map of transcribed single nucleotide polymorphisms in rohu (Labeo rohita) and QTL associated with resistance to Aeromonas hydrophila

Background Production of carp dominates world aquaculture. More than 1.1 million tonnes of rohu carp, Labeo rohita (Hamilton), were produced in 2010. Aeromonas hydrophila is a bacterial pathogen causing aeromoniasis in rohu, and is a major problem for carp production worldwide. There is a need to better understand the genetic mechanisms affecting resistance to this disease, and to develop tools that can be used with selective breeding to improve resistance. Here we use a 6 K SNP array to genotype 21 full-sibling families of L. rohita that were experimentally challenged intra-peritoneally with a virulent strain of A. hydrophila to scan the genome for quantitative trait loci associated with disease resistance. Results In all, 3193 SNPs were found to be informative and were used to create a linkage map and to scan for QTL affecting resistance to A. hydrophila. The linkage map consisted of 25 linkage groups, corresponding to the number of haploid chromosomes in L. rohita. Male and female linkage maps were similar in terms of order, coverage (1384 and 1393 cM, respectively) and average interval distances (1.32 and 1.35 cM, respectively). Forty-one percent of the SNPs were annotated with gene identity using BLAST (cut off E-score of 0.001). Twenty-one SNPs mapping to ten linkage groups showed significant associations with the traits hours of survival and dead or alive (P <0.05 after Bonferroni correction). Of the SNPs showing significant or suggestive associations with the traits, several were homologous to genes of known immune function or were in close linkage to such genes. Genes of interest included heat shock proteins (70, 60, 105 and “small heat shock proteins”), mucin (5b precursor and 2), lectin (receptor and CD22), tributyltin-binding protein, major histocompatibility loci (I and II), complement protein component c7-1, perforin 1, ubiquitin (ligase, factor e4b isoform 2 and conjugation enzyme e2 c), proteasome subunit, T-cell antigen receptor and lymphocyte specific protein tyrosine kinase. Conclusions A panel of markers has been identified that will be validated for use with both genomic and marker-assisted selection to improve resistance of L. rohita to A. hydrophila

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Evaluation of the New Fluorescent Internal Tag (Soft Visible Implant Alphanumeric Tag) in the Freshwater Prawn, Macrobrachium rosenbergii

The new version of the polyester visible implant alphanumeric tag (VI Alpha tag; Northwest Marine Technology Inc., Shaw Island, Washington, USA) was evaluated in the giant river prawn (Macrobrachium rosenbergii) under laboratory conditions. The new VI Alpha tag is soft and fluorescent with an alphanumeric code designed to identify individual specimens. Two tag sizes - standard (1.0 x 2.5 mm) and large (1.5 x 3.5 mm) - were tested on juve- niles (standard size), subadults (standard size), and adults (large size) for 10 weeks. Retention, readability, and effects on growth and survival were evaluated. Final mean tag retention was 71.25±3.3% in juvenile prawns, 91.3%±2.73 in subadult prawns, and 59.0%±1.65 in adult prawns. Final tag readability was 100.0% in juveniles, 88.6±5.3 in subadults, and 77.8±4.8 in adults. Average daily growth (mg/day) and SGR (%/day) of tagged juvenile prawns (22.4±0.23 and 0.81±0.02, respectively) did not significantly differ (p>0.05) from that of the untagged control (20.5±1.47 and 0.83±0.04). Similar results were observed in subadult and adult M. rosenbergii. Mean final survival did not significantly differ (p>0.05) between tagged and untagged prawns. Results indicate that tagging M. rosenbergii with VI Alpha tags has no adverse effect on survival or growth and can therefore be effec- tively used to identify individuals in selective breeding programs

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The complete mitochondrial genome of Labeo catla (Hamilton, 1822) using long read sequencing

Labeo catla is a widely cultured species in monoculture and polyculture systems of the Indian subcontinent. In this study, the complete mitochondrial genome sequence of catla was reconstructed from Oxford Nanopore sequence data. The mitochondrial genome is 16,600 bp in length (accession no. is MN830943) which is larger than the previously reported catla mitogenomes. Like other vertebrate mitochondrial genomes, it has 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a putative control region. Most of the mitogenes are encoded on H-strand. Phylogenetic analysis showed that Labeo catla is more closely related to Labeo rohita than other labeo species. The catla mtgenome reported here will facilitate population genetics, phylogenetics and molecular taxonomy of Indian major carps

Genetic parameters for growth and survival in rohu carp (Labeo rohita)

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Not Available: Although feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the fish diet, and their assimilation, are still not well understood in aquaculture species. We identified molecular events that occur due to the inclusion of high carbohydrate levels in the diets of genetically improved ‘Jayanti rohu’ Labeo rohita. To reveal transcriptional changes in the liver of rohu, a feeding experiment was conducted with three doses of gelatinized starch (20% (control), 40%, and 60%). Transcriptome sequencing revealed totals of 15,232 (4464 up- and 4343 down-regulated) and 15,360 (4478 up- and 4171 down-regulated) differentially expressed genes. Up-regulated transcripts associated with glucose metabolisms, such as hexokinase, PHK, glycogen synthase and PGK, were found in fish fed diets with high starch levels. Interestingly, a de novo lipogenesis mechanism was found to be enriched in the livers of treated fish due to up-regulated transcripts such as FAS, ACCα, and PPARγ. The insulin signaling pathways with enriched PPAR and mTOR were identified by Kyoto Encyclopedia of Genes and Genome (KEGG) as a result of high carbohydrates. This work revealed for the first time the atypical regulation transcripts associated with glucose metabolism and lipogenesis in the livers of Jayanti rohu due to the inclusion of high carbohydrate levels in the diet. This study also encourages the exploration of early nutritional programming for enhancing glucose efficiency in carp species, for sustainable and cost-effective aquaculture production.Not Availabl

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Not AvailableAlthough feed cost is the greatest concern in aquaculture, the inclusion of carbohydrates in the fish diet, and their assimilation, are still not well understood in aquaculture species. We identified molecular events that occur due to the inclusion of high carbohydrate levels in the diets of genetically improved ‘Jayanti rohu’ Labeo rohita. To reveal transcriptional changes in the liver of rohu, a feeding experiment was conducted with three doses of gelatinized starch (20% (control), 40%, and 60%). Transcriptome sequencing revealed totals of 15,232 (4464 up- and 4343 down-regulated) and 15,360 (4478 up- and 4171 down-regulated) di erentially expressed genes. Up-regulated transcripts associated with glucose metabolisms, such as hexokinase, PHK, glycogen synthase and PGK, were found in fish fed diets with high starch levels. Interestingly, a de novo lipogenesis mechanism was found to be enriched in the livers of treated fish due to up-regulated transcripts such as FAS, ACC , and PPAR . The insulin signaling pathways with enriched PPAR and mTOR were identified by Kyoto Encyclopedia of Genes and Genome (KEGG) as a result of high carbohydrates. This work revealed for the first time the atypical regulation transcripts associated with glucose metabolism and lipogenesis in the livers of Jayanti rohu due to the inclusion of high carbohydrate levels in the diet. This study also encourages the exploration of early nutritional programming for enhancing glucose e ciency in carp species, for sustainable and cost-e ective aquaculture production.Not Availabl

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Not Availablewe report here the draft genome of rohu carp and associated genomics resources. Performing phylogenetic analysis, we show that rohu forms a sister group relationship with all remaining otophysans. The draft genome of rohu and SNPs generated in the present study represent essential resource for genetic improvement of important performance traits in this species. Besides, the information generated will provide foundation for future research in evolutionary biology and comparative genomics.Not Availabl