Liver-Specific microRNA Identification in Farmed Carp, Labeo bata (Hamilton, 1822), Fed with Starch Diet Using High-Throughput Sequencing

Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production

Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.

Insights Into miRNA-mRNA Regulatory Mechanisms of Cold Adaptation in Gymnocypris eckloni: Ubiquitin-Mediated Proteolysis Is Pivotal for Adaptive Energy Metabolism

This study aimed to understand cold stress adaptations mechanism in fish. Thus, the transcriptional response to cold conditions in Gymnocypris eckloni was evaluated using RNA-seq and microRNA (miRNA)-seq analyses. Low-temperature (LT) group G. eckloni was cultivated outdoors in waters cooled to 2–4°C for 3 weeks, while individuals in the control temperature (CT) group were exposed to 14–16°C. Significantly different responses were observed in both mRNA and miRNA expression profiles, with more mRNAs (1,833 and 1,869 mRNAs were up- and downregulated, respectively) and fewer miRNAs (15 and 6 were up- and downregulated, respectively) observed in the LT group individuals relative to the CT group individuals. A miRNA-mRNA network involved in the regulation of G. eckloni responses to cold stress was constructed; this network included ubiquitin-mediated proteolysis, protein processing, and oxidative phosphorylation. These results provided new insights into mechanisms of cold tolerance by fish, including decreased metabolic activity in addition to proteolysis.

Aquaculture omics: An update on the current status of research and data analysis

Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing technology has revolutionized the biological sciences and provided necessary tools. Application of 'omics' in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.

Starch in aquafeeds: the benefits of a high amylose to amylopectin ratio and resistant starch content in diets for the carnivorous fish, largemouth bass (Micropterus salmoides)

Aquafeeds for carnivorous species face a nutritional-technological conundrum: containing sufficient starch to meet specific manufacturing requirements for binding, extrusion and expansion, but ideally containing as little starch as possible owing to their limited ability to utilise carbohydrates. The present study evaluated the effects of dietary starch with different amylose to amylopectin ratios and resistant starch contents on growth performance, hepatic glycogen accumulation and glucose metabolism of an important cultured carnivorous finfish, largemouth bass (Micropterus salmoides). A common starch source (α-cassava starch (CS)) was tested as is or after being enzymatically de-branched at three different inclusion levels in diets for largemouth bass. Results showed that the increased dietary starch levels compromised performance and high dietary α-CS content led to obvious liver damage. However, the growth performances of fish fed the diets with de-branched starch (DS) were improved, and no manifest liver damages were observed even at the higher inclusion level. The increasing dietary starch contents significantly increased hepatic glycogen accumulation, but not when DS was used. High dietary starch content, without regard to starch sources, had no effect on the expression of glucose metabolism-related genes, except for down-regulation of insulin receptor expression. However, the use of dietary DS promoted the expression of genes involved in the insulin pathway and glycolysis. In conclusion, this study showed that the use of starch sources with a high amylose to amylopectin ratio and resistant starch in the feed for cultured carnivorous finfish could alleviate the hepatic glycogen deposition through regulating the insulin pathway and glycolysis.