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Applications of Next-Generation Sequencing in Aquaculture and Fisheries

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Advances in Fisheries Biotechnology

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Abstract

The aquaculture industry supplies a substantial portion to meet the demand for protein rich food. It also serves as a means of livelihood for the farmers by providing employment opportunities to them. Despite increased demand for fish meat, the aquaculture industry faces several challenges that hamper the adequate supply of fishes. Some of those challenges, faced worldwide, are overfishing, anthropogenic disturbances, obstruction of migration, inconsistency in growth rate, weakened immunity, problem of diseases, dysbiosis of the microbiome, and toxicity due to xenobiotics. One of the setbacks in the attempts to tackle these issues has been the lack of genetic information such as whole-genome and transcriptome. With the advancements in the next-generation sequencing technologies (NGS), such genetic information can be obtained rapidly at an affordable cost. This has led to the application of whole genome and whole transcriptome in aquaculture to understand the molecular mechanisms during infections, migration, sexual development, and response to toxicants. It has also led to the application of metagenomics to explore the symbiotic relationship between the fish and its microbiome. Such studies have brought forth understanding of the genes and SNPs that are involved in gonadal development, sex determination, colonization resistance, migration, dissemination of genetic diversity and rapid growth. The cumulative knowledge of these studies can help in selective breeding of the desired line, sustain the supply of fish meat, and also greatly help in the conservation of wildlife in its natural habitat. In this chapter, we report the current challenges and recent advances in the aquaculture industry through the application of next-generation sequencing.

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Acknowledgment

The authors are thankful to Director, ICAR—Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha for the facilitation of the work. The authors are grateful to CABIN project on Centre of Agricultural Bioinformatics (CABin) of ICAR-IASRI, New Delhi for the financial support as a fellowship to first author.

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Authors and Affiliations

  1. Division of Fish Genetics and Biotechnology, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India

    Pragyan Paramita Swain, Lakshman Sahoo, Rajesh Kumar & Jitendra Kumar Sundaray

  2. Division of Aquaculture Production and Environment, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India

    Rajesh Kumar

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  1. Pragyan Paramita Swain
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  2. Lakshman Sahoo
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  3. Rajesh Kumar
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  4. Jitendra Kumar Sundaray
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Editors and Affiliations

  1. ICAR-Directorate of Coldwater Fisheries Resources, Bhimtal, Uttarakhand, India

    Pramod Kumar Pandey

  2. Fish Genetics and Reproduction, College of Fisheries, CAU (I), Lembucherra, Tripura, India

    Janmejay Parhi

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Swain, P.P., Sahoo, L., Kumar, R., Sundaray, J.K. (2021). Applications of Next-Generation Sequencing in Aquaculture and Fisheries. In: Pandey, P.K., Parhi, J. (eds) Advances in Fisheries Biotechnology. Springer, Singapore. https://doi.org/10.1007/978-981-16-3215-0_3

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