Identification of candidate SNPs and genes associated with anti-RGNNV using GWAS in the red-spotted grouper, Epinephelus akaara

Yang, Min; Wang, Qing; Chen, Jinpeng; Wang, Yuxin; Zhang, Yong; Qin, Qiwei

doi:10.1016/j.fsi.2021.02.010

Cited by 13 publications

(1 citation statement)

References 53 publications

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“…33 Three known successful examples of MAS application for disease resistance in aquaculture species are found for Japanese flounder (Paralichthys olivaceus), 34 Atlantic salmon 35 and rainbow trout. 36 GWAS has been used to elucidate the associations between genetic markers and disease resistance to specific pathogens in some fish, such as channel catfish backcross progenies [♂ F 1 hybrid catfish (channel catfish ♀ Â blue catfish ♂) Â ♀ channel catfish], [37][38][39] Atlantic salmon, [40][41][42] European sea bass (Dicentrarchus labrax), 43 rainbow trout, 44,45 orangespotted grouper (Epinephelus coioides), 46 red-spotted grouper (Epinephelus akaara), 47 Cynoglossus semilaevis, 48 pacu (Piaractus mesopotamicus), 49 yellow drum (Nibea albiflora) 50 and others (Figure 2). Compared to MAS, the effects of all significant markers (SNPs) are estimated simultaneously, leading to more accurate breeding values in genomic selection (GS).…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide identification of catfish antimicrobial peptides: A new perspective to enhance fish disease resistance

Wang

Dunham

2022

Reviews in Aquaculture

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Antimicrobial peptides (AMPs), also known as host defence peptides, are evolutionarily ancient defensive weapons that can combat infections caused by pathogens. Fish‐derived AMPs have shown microbicidal properties, host immunomodulatory responses, and are induced by a variety of factors, especially pathogenic infection and abiotic stress, which may activate downstream signalling pathways to initiate the expression of antimicrobial peptide genes. Large‐scale genome sequencing has been applied in many aquatic animals, providing databases for the systematic identification of putative AMPs in these species. Recently, the whole genome and the proteome of channel catfish (Ictalurus punctatus) were released; by taking advantage of the antimicrobial peptide database and combining the proteome of catfish, we established a bioinformatic analysis pipeline to identify catfish AMP repertoire. This review introduces an effective method for the identification and development of putative AMPs based on protein datasets, and summarizes the structural properties, immunomodulation and molecular responses in vivo of catfish AMPs. In addition, the evaluation of the antibacterial activity of synthetic or isolated AMPs in vitro, and the applications of AMPs in fish via genetic engineering and clustered regularly interspaced short palindromic repeats associated proteins system (CRISPR/Cas9) were presented, which supports antimicrobial research and aquaculture therapy. The summary and comparison of these AMPs will enhance our understanding and their cross‐species applications. Combined with current genetic engineering and genome editing techniques, it is possible to promote the development of immune processes to protect valuable aquatic animals from infectious diseases.

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Section: Introductionmentioning

confidence: 99%

Genome‐wide identification of catfish antimicrobial peptides: A new perspective to enhance fish disease resistance

Wang

Dunham

2022

Reviews in Aquaculture

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Genome‐wide association study and genomic prediction for growth traits in spotted sea bass (Lateolabrax maculatus) using insertion and deletion markers

Zhang,

Liu

et al. 2024

Animal Research and One Health

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Spotted sea bass (Lateolabrax maculatus) is a species of significant economic importance in aquaculture. However, genetic degeneration, such as declining growth performance, has severely impeded industry development, necessitating urgent genetic improvement. Here, we conducted a genome‐wide association study (GWAS) and genomic prediction for growth traits using insertion and deletion (InDel) markers, and systematically compared the results with our previous studies using single nucleotide polymorphism (SNP) markers. A total of 97 significant InDels including a 6 bp insertion in an exon region were identified. It is worth noting that only 5 and 1 candidate genes for DY and TS populations were also detected in previous GWAS using SNPs, and numerous novel genes including c4b, fgf4, and dnajb9 were identified as vital candidate genes. Moreover, several novel growth‐related procedures, such as the growth and development of the bone and muscle, were also detected. These findings indicated that InDel‐based GWAS can provide valuable complement to SNP‐based studies. The comparison of genomic predictive performance for total length trait under different marker selection strategies and genomic selection models indicated that GWAS selection strategy exhibits more stable predictive performance compared to the evenly selection strategy. Additionally, support vector machine model demonstrated better predictive accuracy and efficiency than traditional best linear unbiased prediction and Bayes models. Furthermore, the superior predictive performance using InDel markers compared to SNP markers highlighted the potential of InDels to enhance genomic predictive accuracy and efficiency. Our results carry significant implications for dissecting genetic mechanisms and contributing genetic improvement of growth traits in spotted sea bass through genomic resources.

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The Application of Molecular Markers in Fish Breeding and Aquaculture

Rodrigues

Biun

Yong

et al. 2023

Marine Biotechnology: Applications in Food, Drugs and Energy

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Identification of candidate SNPs and genes associated with anti-RGNNV using GWAS in the red-spotted grouper, Epinephelus akaara

Cited by 13 publications

References 53 publications

Genome‐wide identification of catfish antimicrobial peptides: A new perspective to enhance fish disease resistance

Genome‐wide identification of catfish antimicrobial peptides: A new perspective to enhance fish disease resistance

Genome‐wide association study and genomic prediction for growth traits in spotted sea bass (Lateolabrax maculatus) using insertion and deletion markers

The Application of Molecular Markers in Fish Breeding and Aquaculture

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