Research advances and future perspectives of genomics and genetic improvement in allotetraploid common carp

Abstract

Aquatic species have become an integral part of human culture. As an internationally important food fish species, the common carp Cyprinus carpio accounted for over 7% of global aquaculture production in 2020. In addition to serving as a food source, common carp varieties are used as ornamental fish and valued in recreational fisheries. The continuously updated reference genome of common carp has recently served as a foundation for both basic genetic studies and evolutionary studies. With the recent emphasis on the allotetraploid signature of common carp, researchers have begun to focus on how hybridization and polyploidization affect the successful speciation and advantageous behaviour of common carp. In this review, we survey current and emerging research topics on common carp, including genomic and genetic tools, germplasm resources, genetic diversity, genetic mechanism and improvement of economic traits, as well as multiple breeding technologies employed in common carp. We also provide an overview of recent trends in genetic studies and improvements in common carp and encourage researchers to monitor the allotetraploid signature of common carp. Understanding the genetic basis of economically important traits and the mechanisms of allopolyploidization in common carp will be important for genetic improvement and germplasm innovation in agronomically important fish species, although the road ahead will be challenging for this widely domesticated allotetraploid species.

Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture

“…However, these highly produced species remain amongst the least advanced in terms of the application of genetic technologies, and associated genetic tools and research, typically at Level 1 or Level 2 (Table 1). The common carp is arguably the most advanced of these species in terms of application of genetic technologies, extent of genetic research, and the genomic toolbox [reviewed in (Chen et al, 2021)]. European and Asian common carp strains have been farmed in both continents for over two thousand years, with the development of a wealth of strains or varieties (Chen et al, 2021).…”

Isolation, Identification, and Investigation of Pathogenic Bacteria From Common Carp (Cyprinus carpio) Naturally Infected With Plesiomonas shigelloides

“…Cyprinus carpio is a valuable and unique fish resource that belongs to the order Cypriniformes and family Cyprinidae ( 1 ). As a dominant cyprinid species, C. carpio has been reported to account for almost 10% of the annual freshwater aquaculture production ( 1 , 2 ).…”

“…Cyprinus carpio is a valuable and unique fish resource that belongs to the order Cypriniformes and family Cyprinidae ( 1 ). As a dominant cyprinid species, C. carpio has been reported to account for almost 10% of the annual freshwater aquaculture production ( 1 , 2 ). However, with the deterioration of the natural environment and the increase in breeding density, the breeding environment of C. carpio has been destroyed.…”

Mapping Growth-Related Quantitative Trait Locus (QTL) in Commercial Yellow River Carp (Cyprinus carpio haematopterus) during Overwintering

“…Among the methods used in breeding research, such as selective breeding and crossbreeding, quantitative trait locus (QTL) mapping is important, as it helps screen trait-related markers and assists breeding; studies on growth, feed conversion rate, disease resistance, sex, and muscle quality have been carried out using QTL [7]. Completion of the mapping of the carp genome resulted in the determination of the QTL location with increased accuracy [8,9].…”