Research advances in the genomics and applications for molecular breeding of aquaculture animals

We have sequenced the genome of the largest freshwater fish species of the world, the arapaima. Analysis of gene family dynamics and signatures of positive selection identified genes involved in the specific adaptations and unique features of this iconic species, in particular it’s large size and fast growth. Genome sequences from both sexes combined with RAD-tag analyses from other males and females led to the isolation of male-specific scaffolds and supports an XY sex determination system in arapaima. Whole transcriptome sequencing showed that the product of the gland-like secretory organ on the head surface of males and females may not only provide nutritional fluid for sex-unbiased parental care, but that the organ itself has a more specific function in males, which engage more in parental care.

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The genome of the arapaima (Arapaima gigas) provides insights into gigantism, fast growth and chromosomal sex determination system.

Fish biology has been developed for more than 100 years, but some important breakthroughs have been made in the last decade. Early studies commonly concentrated on morphology, phylogenetics, development, growth, reproduction manipulation, and disease control. Recent studies have mostly focused on genetics, molecular biology, genomics, and genome biotechnologies, which have provided a solid foundation for enhancing aquaculture to ensure food security and improving aquatic environments to sustain ecosystem health. Here, we review research advances in five major areas: (1) biological innovations and genomic evolution of four significant fish lineages including non-teleost ray-finned fishes, northern hemisphere sticklebacks, East African cichlid fishes, and East Asian cyprinid fishes; (2) evolutionary fates and consequences of natural polyploid fishes; (3) biological consequences of fish domestication and selection; (4) development and innovation of fish breeding biotechnologies; and (5) applicable approaches and potential of fish genetic breeding biotechnologies. Moreover, five precision breeding biotechniques are examined and discussed in detail including gene editing for the introgression or removal of beneficial or detrimental alleles, use of sex-specific markers for the production of mono-sex populations, controllable primordial germ cell on-off strategy for producing sterile offspring, surrogate broodstock-based strategies to accelerate breeding, and genome incorporation and sexual reproduction regain-based approach to create synthetic polyploids. Based on these scientific and technological advances, we propose a blueprint for genetic improvement and new breed creation for aquaculture species and analyze the potential of these new breeding strategies for improving aquaculture seed industry and strengthening food security.

Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

Fish biology has been developed for more than 100 years, but some important breakthroughs have been made in the last decade. Early studies commonly concentrated on morphology, phylogenetics, development, growth, reproduction manipulation, and disease control. Recent studies have mostly focused on genetics, molecular biology, genomics, and genome biotechnologies, which have provided a solid foundation for enhancing aquaculture to ensure food security and improving aquatic environments to sustain ecosystem health. Here, we review research advances in five major areas: (1) biological innovations and genomic evolution of four significant fish lineages including non-teleost ray-finned fishes, northern hemisphere sticklebacks, East African cichlid fishes, and East Asian cyprinid fishes; (2) evolutionary fates and consequences of natural polyploid fishes; (3) biological consequences of fish domestication and selection; (4) development and innovation of fish breeding biotechnologies; and (5) applicable approaches and potential of fish genetic breeding biotechnologies. Moreover, five precision breeding biotechniques are examined and discussed in detail including gene editing for the introgression or removal of beneficial or detrimental alleles, use of sex-specific markers for the production of mono-sex populations, controllable primordial germ cell on-off strategy for producing sterile offspring, surrogate broodstock-based strategies to accelerate breeding, and genome incorporation and sexual reproduction regain-based approach to create synthetic polyploids. Based on these scientific and technological advances, we propose a blueprint for genetic improvement and new breed creation for aquaculture species and analyze the potential of these new breeding strategies for improving aquaculture seed industry and strengthening food security. 

Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7% (784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 protein-coding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper. Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes (DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.

Whole-genome sequencing of leopard coral grouper ( Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution.

The blunt snout bream Megalobrama amblycephala is the economically most important cyprinid fish species As an herbivore, it can be grown by eco-friendly and resource-conserving aquaculture However, the large number of intermuscular bones in the trunk musculature is adverse to fish meat processing and consumption As a first towards optimizing this aquatic livestock, we present a 1116-Gb draft genome of M amblycephala, with 77954 Mb anchored on 24 linkage groups Integrating spatiotemporal transcriptome analyses, we show that intermuscular bone is formed in the more basal teleosts by intramembranous ossification and may be involved in muscle contractibility and coordinating cellular events Comparative analysis revealed that olfactory receptor genes, especially of the beta type, underwent an extensive expansion in herbivorous cyprinids, whereas the gene for the umami receptor T1R1 was specifically lost in M amblycephala The composition of gut microflora, which contributes to the herbivorous adaptation of M amblycephala, was found to be similar to that of other herbivores As a valuable resource for the improvement of M amblycephala livestock, the draft genome sequence offers new insights into the development of intermuscular bone and herbivorous adaptation

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The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet.

The invention discloses a descendant determining method for the development of yellow catfishes, snakehead super male fishes and all male fishes. The method comprises the following steps: (1) controlling the sex by the hormone of the yellow catfishes and the snakehead super male fishes; (2) testcrossing and screening pseudo males; (3) obtaining all female groups and pseudo female groups; (4) testcrossing by the pseudo males and screening the pseudo females; (5) testcrossing by the all female groups and screening YY males and YY females to form super male lines. Compared with the prior art, the descendant determining method for the development of the yellow catfishes, the snakehead super male fishes and the all male fishes has the advantages of easiness in operation, high efficiency, low risk in breeding and high testcross efficiency, overcomes the problem of the uncertainty for traditionally developing the all male offspring seeds of XX-XY genotype farmed animals, and reduces the counting difficult.

Descendant determining method for the development of yellow catfishes, snakehead super male fishes and all male fishes

The utility model discloses an oxygenation device with a buried pipe at the bottom of a seedling growing pool, which aims to solve the problems that conventional flexible pipes and air stone aerating and oxygenation devices for fish and shrimp seedling growing pools are not easy in installation, the production operation is hampered and pathogenic bacteria are provided with a breeding environment in the prior art. By utilizing the oxygenation device of the utility model, the survival rate of the seedling in the pool is increased and the water space of the seedling growing pool is saved. Meanwhile, the environment is concise and clean. The oxygenation device comprises a bottom-buried air pipe, air holes, an inverted U-shaped air conduit, a valve, a main air duct and an air blower. Compressed air provided by the air blower escapes from the bottom of the seedling growing pool via the main air duct, the inverted U-shaped air conduit, the valve, the bottom-buried air pipe and the air holes to provide oxygen and aeration for the seedling growing pool. The bottom-buried air pipe is a PVC hard water supply pipe buried at the bottom of the seedling growing pool when the seedling growing pool is built or reconstructed. The upper edge of the bottom-buried air pipe is flush with or slightly lower than the bottom of the seedling growing pool. The inverted U-shaped air conduit is connected with the main air duct and the bottom-buried air pipe. The highest position of the U-shaped air conduit is higher than the highest water level in the seedling growing pool.

Oxygenation device with buried pipe at bottom of seedling growing pool

The utility model discloses an air curtain type fish-exercise aerator for settling the defects of high labor intensity in net hauling for fish exercise, easy scratch of the fry and fish seed, survival rate reduction caused by impact damage, etc. Simultaneously the water quality at the tank bottom is improved through supplying oxygen to the bottom. The generation of large amount of pathogens caused by net hauling is prevented, and the physique of the fry is improved integrally. The aerator is simultaneously suitable for exercise and oxygen enrichment of marketable fish and ripe fish in a marketable fish tank and a ripe fish tank. The aerator comprises the following components: an air compressor (7), an air guiding pipe (6), an air curtain generation pipe (10), a joint (9), a steel wire (1), a connection wire (2), a sinker (5) and an air compressor moving device (8). The air compressor (7) is mainly used for supplying the air with a certain pressure. The air guiding pipe (6) is a flexible pipe which is made of rubber or other material, is mainly used for connecting the air compressor (7) with the air curtain generation pipe (10), and has a length that is determined according to a height and a gradient of the pond bank. The air curtain generation pipe (10) is made of material such as rubber and plastic for forming a uniform air curtain. The air curtain is generated by the compressed air through the air holes (3) which are arranged in one line or two lines on the air curtain generation pipe. The hole diameter and hole distance are particularly set with a principle of forming the uniform air curtain.

Air curtain type fish-exercise aerator

The utility model discloses an improved fish full-filter hatching loop, which consists of an embedded inflating device, a filter screen device, a base, a wall, a water inlet system, a drainage blow-off system, an egg feeding and fry discharging system, an inner ring access passage and the like. The hatching loop is characterized in that: based on the original fish full-filter hatching loop, the embedded inflating device capable of increasing the dissolved oxygen of water for hatching is increased; the embedded inflating device comprises an air controlled valve, an inverse U-shaped connecting pipe, a main air guide pipe, an air compressor and an embedded air pipe, wherein the inverse U-shaped connecting pipe is connected with the embedded air pipe; and the full-filter filter screen device is improved. Compared with the original device, 10 to 15 percent of dissolved oxygen can be improved under the same hatching quantity condition; and under the condition of ensuring the same dissolved oxygen, 20 to 30 percent of hatching quantity can be increased. Meanwhile, egg escape and fry leakage easily caused in the hatching process of the original device are effectively avoided by improving a fixing device at the bottom of a filter screen, moreover, the labor intensity of the assembly and disassembly processes of the filter screen is effectively reduced, and the hatching efficiency is comprehensively improved.

Xiewu Jiang

Papers

The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet.

Descendant determining method for the development of yellow catfishes, snakehead super male fishes and all male fishes

Oxygenation device with buried pipe at bottom of seedling growing pool

Air curtain type fish-exercise aerator

Improved fish full-filter hatching loop