Decoding the fish genome opens a new era in important trait research and molecular breeding in China

Aquaculture represents the fastest-growing global food production sector,as it has become an essential component of the global food supply.China has the world's largest aquaculture industry in terms of production volume.However,the sustainable development of fish culture is hindered by several concerns,including germplasm degradation and disease outbreaks.The practice of genomic breeding,which relies heavily on genome information and genotypephenotype relationships,has significant potential for increasing the efficiency of aquaculture production.In 2014,the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China.Since then,domestic researchers have made dramatic progress in functional genomic studies.To date,the genomes of more than 60 species of fish in China have been assembled and annotated.Based on these reference genomes,evolutionary,comparative,and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes,including growth and development,sex determination,disease resistance,metamorphosis,and pigmentation.Furthermore,genomic tools and breeding techniques such as SNP arrays,genomic selection,and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities.This review aims to summarize the current status,advances,and perspectives of the genome resources,genomic study of important traits,and genomic breeding techniques of fish in China.The review will provide aquaculture researchers,fish breeders,and farmers with updated information concerning fish genomic research and breeding technology.The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.

Perspectives:Gene expression in fisheries management

Functional genes and gene expression have been connected to physiological traits linked to effective production and broodstock selection in aquaculture, selective implications of commercial fish harvest, and adaptive changes reflected in non-commercial fish populations subject to human disturbance and climate change. Gene mapping using single nucleotide polymorphisms （SNPs） to identify functional genes, gene expression （analogue microarrays and real-time PCR）, and digital sequencing technologies looking at RNA transcripts present new concepts and opportunities in support of effective and sustainable fisheries. Genomic tools have been rapidly growing in aquaculture research addressing aspects of fish health, toxicology, and early development. Genomic technologies linking effects in functional genes involved in growth, maturation and life history development have been tied to selection resulting from harvest practices. Incorporating new and ever-increasing knowledge of fish gehomes is opening a different perspective on local adaptation that will prove invaluable in wild fish conservation and management. Conservation of fish stocks is rapidly incorporating research on critical adaptive responses directed at the effects of human dis- turbance and climate change through gene expression studies. Genomic studies of fish populations can be generally grouped into three broad categories： l） evolutionary genomics and biodiversity; 2） adaptive physiological responses to a changing environment; and 3） adaptive behavioral genomics and life history diversity. We review current genomic research in fisheries focusing on those that use microarrays to explore differences in gene expression among phenotypes and within or across populations, information that is critically important to the conservation of fish and their relationship to humans [Current Zoology 56 （1）： 157-174, 2010].

Genomes of major fishes in world fisheries and aquaculture: Status, application and perspective

Capture fisheries and aquaculture provide a significant amount of high-quality protein to human beings and thus play an essential role in ending global hunger and malnutrition.The availability of tens of hundreds of fish genomes and the advances of genomics have allowed addressing many challenging issues such as overfishing and germplasm degradation faced by fisheries and aquaculture.In this review,we describe the current status of genomics in fisheries and aquaculture,with an emphasis on 14 species of fish that are considerably important to global fisheries and aquaculture,in the context of genome sequencing and assembly,annotation,GC contents,and repeats.The majority of these genomes are assembled at the chromosome level and annotated with proteins and pathways,with functional relevance to fisheries and aquaculture,such as environmental adaptation and phenotypic variation.We summarize potential genomic applications in fisheries and aquaculture that are related to assessment and use of genetic resources,disease resistance,growth and development,sexual determination,and fisheries management.Although much progress has been achieved in genomic application to fisheries and aquaculture,the full potential remains to be explored and reaped.We discuss the challenges and perspectives of genomics in translational aquaculture and fisheries,which include genome assembly and annotation,genomic selection and breeding,genomics in fisheries management,and integrated artificial intelligence systems.In the coming decades,we anticipate the applications of genomic techniques such as genome editing and genomic selection,along with the use of emerging intelligence systems,in aquaculture and fisheries will contribute significantly to genetic improvements of farmed fish and sustainable exploitation of fishery resources,which consequently lead to eradicating global poverty by 2030,an ambitious goal set by the United Nations.