Genome-wide association study reveals growth-related SNPs and candidate genes in mandarin fish (Siniperca chuatsi)

Zhou, Yu; Fu, Huang-Cui; Wang, Yingying; Huang, He-Zhong

doi:10.1016/j.aquaculture.2021.737879

Cited by 18 publications

(7 citation statements)

References 90 publications

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“…This cell line and the polyclonal myca ko lines generated in the present study enable testing the role that MYC TF plays for tilapia cellular osmoregulation, its contribution to the activation of the myo-inositol biosynthesis (MIB) pathway, and its contribution to other cell functions. This approach can be extended to other targets and species of interest, for example genes important for aquaculture traits other than salinity tolerance and candidate genes other than myca, including those identi ed by previous GWAS and SNP analyses in multiple aquaculture sh species (Omeka et al 2022;Zhou et al 2022;Tsai et al 2015). These ko cell lines allow for deep functional analyses that associate speci c genotypes with complex phenotypes, including systems level molecular phenotypes revealed by transcriptomics (Xie et al 2020) and proteomics (Dolgalev and Poverennaya 2021).…”

Section: Interpretation Of Gene Editing Results By Tide and Ice Analysesmentioning

confidence: 99%

Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system

Kim

Cnaani

Kültz

2022

Preprint

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MYC transcription factors have critical roles in facilitating a variety of cellular functions that have been highly conserved among species during evolution. However, despite circumstantial evidence for an involvement of MYC in animal osmoregulation, mechanistic links between MYC function and osmoregulation are missing. Mozambique tilapia (Oreochromis mossambicus) represents an excellent model system to study these links because it is highly euryhaline and highly tolerant to osmotic (salinity) stress at both the whole organism and cellular levels of biological organization. Here, we utilize an O. mossambicus brain cell line (OmB cells) and an optimized vector-based CRISPR/Cas9 system to functionally knockout MYC in the tilapia genome and to establish causal links between MYC and cell function, including cellular osmoregulation. A cell isolation and dilution strategy yielded polyclonal MYC (myca) knockout cell pools with low genetic variability and high gene editing efficiencies (as high as 98.2 %). Further isolation and dilution of cells from these pools yielded a monoclonal myca ko cell line harboring a 1-bp deletion that caused a frameshift mutation. This frameshift functionally inactivated the transcriptional regulatory and DNA-binding domains predicted by bioinformatics and structural analyses. Both the polyclonal and monoclonal myca ko cell lines were viable, propagated well in standard medium, and differed from wild-type cells in morphology. As such, they represent a new tool for causally linking myca to cellular osmoregulation and other cell functions.

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Section: Interpretation Of Gene Editing Results By Tide and Ice Analysesmentioning

confidence: 99%

Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system

Kim

Cnaani

Kültz

2022

Preprint

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“…This technology has gained widespread popularity in breeding programs because of its many advantages, such as consistent size of digested DNA fragments, streamlined library construction procedures, and high accuracy. In mandarin sh (Siniperca chuatsi), RAD-seq data were screened to identify growthassociated SNPs and candidate genes [23]. Ai et al (2023) identi ed 11 SNPs related to fast growth in orange-spotted grouper (Epinephelus coioides) using RAD-seq data.…”

Section: Introductionmentioning

confidence: 99%

Single nucleotide polymorphism SNP19140160 A>C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)

Hua,

Zhong,

Chen

et al. 2023

Preprint

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Background Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China’s freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, using restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population. Results We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, three SNPs (SNP9639603, SNP9639605, and SNP23355498) were significantly correlated with one trait, body length, in the F1 generation, and one SNP (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. Two potential genes were identified at the loci of the related markers, with fam174b being closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g). Conclusions Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection breeding of high-quality largemouth bass.

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“…To date, GWAS has been widely applied in the systematic screening of sites or genes related to economically important traits of aquatic animals such as fish, shellfish, and crustaceans (Abdelrahman et al, 2017). For example, Zhou et al (Zhou et al, 2022) obtained genome regions and candidate genes related to various growth traits of mandarinfish through GWAS. In addition, Yang et al (Yang et al, 2020) identified candidate SNPs and genes related to growth traits of Epinephelus fuscoguttatus using GWAS.…”

Section: Introductionmentioning

confidence: 99%

Revealing Selection in Breeding and Genetic Characteristics of Economically Important Traits of New Species of Apostichopus Japonicas Based on Genome Resequencing and GWAS Analysis

et al. 2022

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Apostichopus japonicas is an economically important species with high nutritional value. However, our knowledge of its genetic diversity and the genetic changes that occurred during its domestication or trait selection is quite limited. In this study, the whole genomes of 254 A. japonicas samples were resequenced. Analyses of the population genetic structure revealed that the genetic diversity of A. japonicas in the north of China is generally high, there was no difference in the population structure among the six cultured populations, and they were divided into two subpopulations together with AY-1 (new species). The results also showed that the genetic diversity of the AY-1 population was relatively low, the degree of linkage of alleles was high, and this population had been subjected to more positive selection. Based on Tajima’s D, FST analysis, and ROD analysis, the selected intervals and genes of the AY-1 population were identified, with some of the candidate intervals being related to an economically important trait and breeding target, namely, the number of parapodia. Gene Ontology analysis of the candidate genes revealed that the two subpopulations differed in their immune function, protein synthesis, decomposition, and transport, among others. Using GWAS, we identified 39 candidate genes for four economically important traits of A. japonicas, and we verified that those genes contained non-synonymous SNPs. Through this verification, BSL78_00022 and BSL78_00023 were found to be key genes for the number of parapodia in A. japonicas. Of these two genes, BSL78_00022 encodes a protein related to cell differentiation and proliferation, so it was assumed that three non-synonymous substitutions (Ser-Phe, Glu-Asp, and Ala-Val) in this gene are related to the changes in the number of parapodia. Meanwhile, the pleiotropic gene BSL78_04631, which is related to body weight and body wall weight, and promotes protein synthesis and cell growth, has a non-synonymous substitution (IlE-Val), which is assumed to be the reason for the difference in body weight and body wall weight of A. japonicas. These results provide a new perspective for explaining the genetic structure characteristics of A. japonicas and analyzing the selection and economically important traits in the breeding of new species.

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Genome-wide association study reveals growth-related SNPs and candidate genes in mandarin fish (Siniperca chuatsi)

Cited by 18 publications

References 90 publications

Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system

Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system

Single nucleotide polymorphism SNP19140160 A>C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)

Revealing Selection in Breeding and Genetic Characteristics of Economically Important Traits of New Species of Apostichopus Japonicas Based on Genome Resequencing and GWAS Analysis

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Genome-wide association study reveals growth-related SNPs and candidate genes in mandarin fish (Siniperca chuatsi)

Cited by 18 publications

References 90 publications

Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system

Removal of evolutionarily conserved functional MYC domains in a tilapia cell line using a vector-based CRISPR/Cas9 system

Single nucleotide polymorphism SNP19140160 A&gt;C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)

Revealing Selection in Breeding and Genetic Characteristics of Economically Important Traits of New Species of Apostichopus Japonicas Based on Genome Resequencing and GWAS Analysis

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Single nucleotide polymorphism SNP19140160 A>C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides)