Current status of genome sequencing and its applications in aquaculture

Yue, Gen Hua; Wang, L.

doi:10.1016/j.aquaculture.2016.10.036

Cited by 83 publications

(44 citation statements)

References 92 publications

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“…Re-sequencing of genomes of several individuals belonging to the same species gives the possibility to obtain from dozens of thousands to dozens of millions SNPs (Abdelrahman et al, 2017;Yue and Wang, 2017). However, this approach is still expensive and time-consuming.…”

Section: Discussionmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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-An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

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Section: Discussionmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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“…Genome sequences allow genetic markers to be mapped to a specific location in the genome, and when genetic markers associated with particular traits are identified, a genome sequence provides the opportunity to investigate nearby genes or genetic elements to potentially identify causative mutations. As of 2017, there were 22 published, scaffold-level genome sequences for finfish (Yue and Wang, 2017 ) and at the time of writing only six for molluscs: Pacific oyster (Zhang et al, 2012 ), pearl oyster (Takeuchi et al, 2012 , 2016 ), Yesso scallop (Wang et al, 2017 ), Zhikong scallop (Li et al, 2017 ), Manila clam (Mun et al, 2017 ), and Eastern oyster (NCBI accession GCA_002022765.4) with a seventh species, blue mussel, (Nguyen et al, 2014 ; Murgarella et al, 2016 ) currently at contig level (Supplemental File 2 ). While at the time of writing it is currently unpublished, the most complete molluscan genome assembled to date is that of the Eastern oyster (NCBI accession GCA_002022765.4).…”

Section: Whole Genome Sequencesmentioning

confidence: 99%

Genomic Tools and Selective Breeding in Molluscs

Hollenbeck

Johnston

2018

Front. Genet.

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The production of most farmed molluscs, including mussels, oysters, scallops, abalone, and clams, is heavily dependent on natural seed from the plankton. Closing the lifecycle of species in hatcheries can secure independence from wild stocks and enables long-term genetic improvement of broodstock through selective breeding. Genomic techniques have the potential to revolutionize hatchery-based selective breeding by improving our understanding of the characteristics of mollusc genetics that can pose a challenge for intensive aquaculture and by providing a new suite of tools for genetic improvement. Here we review characteristics of the life history and genetics of molluscs including high fecundity, self-fertilization, high genetic diversity, genetic load, high incidence of deleterious mutations and segregation distortion, and critically assess their impact on the design and effectiveness of selective breeding strategies. A survey of the results of current breeding programs in the literature show that selective breeding with inbreeding control is likely the best strategy for genetic improvement of most molluscs, and on average growth rate can be improved by 10% per generation and disease resistance by 15% per generation across the major farmed species by implementing individual or family-based selection. Rapid advances in sequencing technology have resulted in a wealth of genomic resources for key species with the potential to greatly improve hatchery-based selective breeding of molluscs. In this review, we catalog the range of genomic resources currently available for molluscs of aquaculture interest and discuss the bottlenecks, including lack of high-quality reference genomes and the relatively high cost of genotyping, as well as opportunities for applying genomics-based selection.

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“…In the recent decades, evolutionary biologists have mainly focused on positive and negative selection due to their intuitive importance in adaptation (Nielsen, 2005;e.g., Gerrard & Meyer, 2007;Salzburger et al, 2007;Salzburger, 2009;Diepeveen & Salzburger, 2011;Fan et al, 2011;Diepeveen et al, 2013;Keller et al, 2013;Brawand et al, 2014;Henning & Meyer, 2014;Xia et al, 2015;Pavlova et al, 2017). In contrast, balancing selection has not been widely studied, especially in fish (reviewed in López et al, 2015;Bernatchez, 2016;Kumar & Kocour, 2017;Yue & Wang, 2017). Nonetheless, balancing selection can have major influences on evolutionary processes, particularly in adaptation.…”

Section: Background: Balancing Selection and Its Importance In Adaptamentioning

confidence: 99%

A comprehensive overview of the developmental basis and adaptive significance of a textbook polymorphism: head asymmetry in the cichlid fish Perissodus microlepis

Raffini

Meyer

2018

Hydrobiologia

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Identifying the evolutionary and developmental bases of adaptive phenotypes is of central interest in evolutionary biology. Cichlid fishes have been a useful research model due to their extraordinary phenotypic diversity reflecting adaptations to often very narrow niches. Among them, the scale-eating Perissodus microlepis is considered to be a textbook example for balanced polymorphism: its asymmetric head and handed behavior is thought to be maintained by negative frequency-dependent selection via prey-predator interactions. However, several contradictory findings and open questions have emerged in recent years, challenging our understanding of this model. Here, we review existing evidence for both genetic and non-genetic effects influencing head asymmetry, the association between morphological asymmetry and behavioral laterality, and the identification of signatures of balancing selection. Recent technological and theoretical developments have opened new exciting research avenues that can help identifying the drivers of adaptive traits in P. microlepis and other nonmodel organisms, and we discuss promising directions worth exploring. We highlight the importance of using integrative approaches that analyze genetic, environmental, and epigenetic variation in natural populations to aid a comprehensive understanding of why cichlids are so diverse and how Hydrobiologia (2019) 832:65-84 https://doi.org/10.1007/s10750-018-3800-z( 0123456789().,-volV) (0123456789().,-volV) evolution has produced and continues to generate such a vibrant and often complex phenotypic diversity.

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Current status of genome sequencing and its applications in aquaculture

Cited by 83 publications

References 92 publications

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Genomic Tools and Selective Breeding in Molluscs

A comprehensive overview of the developmental basis and adaptive significance of a textbook polymorphism: head asymmetry in the cichlid fish Perissodus microlepis

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