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Advancements in the DNA sequencing technologies and computational biology have revolutionized genome/transcriptome sequencing of non-model fishes at an affordable cost. This has led to a paradigm shift with regard to our heightened understandings of structure-functional relationships of genes at a global level, from model animals/fishes to non-model large animals/fishes. Whole genome/transcriptome sequencing technologies were supplemented with the series of discoveries in gene editing tools, which are being used to modify genes at pre-determined positions using programmable nucleases to explore their respective in vivo functions. For a long time, targeted gene disruption experiments were mostly restricted to embryonic stem cells, advances in gene editing technologies such as zinc finger nuclease, transcriptional activator-like effector nucleases and CRISPR (clustered regulatory interspaced short palindromic repeats)/CRISPR-associated nucleases have facilitated targeted genetic modifications beyond stem cells to a wide range of somatic cell lines across species from laboratory animals to farmed animals/fishes. In this review, we discuss use of different gene editing tools and the strategic implications in fish species for basic and applied biology research.

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Farmed rohu, Labeo rohita, is an economically important freshwater aquaculture species in south Asia. Consumer preference for this species has driven researchers to develop genetically improved rohu (Jayanti) for important traits such as growth and disease resistance. The feeding and breeding biology of rohu is well‐studied, but the physiological responses to stress or climate change at the molecular level are less understood. We summarized the genetic and advanced molecular tools used for biological insights into farmed rohu. Recently, next‐generation sequencing technology (NGS) and genome informatics have helped to identify biological questions in fish using genome, transcriptome, metagenome, proteome and epigenome sequencing. We briefly reviewed past rohu research using traditional selective breeding methods for genetic improvement, as well as the other molecular tools that have been utilized to understand the fish’s physiology, health, nutrition, stress and reproduction. We discuss the molecular techniques used in rohu, such as gene cloning and expression profiling, DNA markers, NGS, metagenomics, epigenomics, proteomics, cell culture/cell line development and transgenics. Finally, we address the future perspectives of rohu research, which may be driven by NGS and other advanced techniques like genome editing to improve rohu aquaculture production. The comprehensive information presented here will provide insights for the carp aquaculture research community.