Genome‐wide identification of the <i>traf</i> gene family in yellow catfish (<i>Pelteobagrus fulvidraco</i>) and analysis of their expression in response to bacterial challenge

Nie, Zhiwei; Wang, Bo; Zhang, Zhixuan; Jia, Zeming; Xu, Runjie; Wang, Heyu; Zhou, Wei; Yifu, Gong

doi:10.1111/jfb.15126

Cited by 2 publications

(1 citation statement)

References 49 publications

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“…Genes located near these peaks are traf2a, tnc, zfr on chr5, and uqcc1, gdf5 on chr6. Gene traf2a, is from traf gene family, which has been shown to participate in the immune system and apoptotic process (Nie et al, 2022). Tenascin-C has been shown to regulate the activity of growth factors, such as epidermal growth factor (EGF)-dependent cell growth (Bradshaw, 2014).…”

Section: Discussionmentioning

confidence: 99%

Genomic architecture of selection for adaptation to challenging environments in aquaculture

Yu¹

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Yu, X. (2022). Genomic architecture of selection for adaptation to challenging environments in Aquaculture. PhD thesis, Wageningen University and Research, the Netherlands.Aquaculture, including freshwater and marine farming, has been important for global fish production during the past few decades. However, climate change presents a major risk threatening both quality and quantity of aquaculture production. The environmental stressors in aquaculture resulting from climate change, are temperature rise, salinity changes, sea level rise, acidification and changes of other chemical properties and changes of oxygen levels. Although a reasonable genetic gain can be achieved by selective breeding, this genetic response may not be enough to adapt fish species to the effects of climate change. Markerassisted selection focusing on specific genes or alleles that allow fish to cope with these changes would allow more rapid adaptation of fish to these new environments. In this thesis, I focused on three essential environmental stressorsdissolved oxygen, salinity and temperature as primarily determined in aquaculture production. The main objective is to provide insight in the genomic architecture underlying the mechanism of adaptation to challenging environments of aquaculture species under farming conditions. First, I determined candidate QTL associated with phenotypic variation during adaptation to hypoxia or normoxia. I identified overrepresented pathways that could explain the genetic regulation of hypoxia on growth. To identify fish with better hypoxia tolerance and growth under a hypoxic environment, I quantified the genetic correlations between an indicator trait for hypoxia tolerance (critical swimming performance) and growth. Moreover, the genomic architecture associated with swimming performance was demonstrated, while the effect of significant QTLs on growth was estimated. Beyond applying genome-wide association studies, I used selection signatures to identify QTLs and genes contributing to salinity tolerance. In addition, I also compared the genome of the saline-tolerant and highly productive tilapia "Sukamandi", that was developed by the aquaculture research institute in Indonesia, to that of blue tilapia and Nile tilapia, to identify the QTLs contributing to salinity tolerance. Finally, I investigated QTLs associated with growth-related traits and organ weights at two distinct commercial Mediterranean product sites differing in temperature (farms in Spain and Greece). Overall, this thesis considerably adds to insight into how fish adapt to challenging environments, which will aid marker-assisted selection for improved resilience of aquaculture species under climate change. ContentsChapter 1 General introductionChapter 2 Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus) Chapter 3Quantitative trait loci controlling swimming performance and their effect on growth in Nile tilapia (Oreochromis niloticus)Chapter 4 Genomic analysis of a Nile tilapia strain selected...

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Section: Discussionmentioning

confidence: 99%

Genomic architecture of selection for adaptation to challenging environments in aquaculture

Yu¹

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The TRAF gene family in turbot (Scophthalmus maximus): Identification, characterization, molecular evolution and expression patterns analysis

Zhou¹,

Wang²,

Li³

et al. 2023

Fish & Shellfish Immunology

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Genome‐wide identification of the traf gene family in yellow catfish (Pelteobagrus fulvidraco) and analysis of their expression in response to bacterial challenge

Cited by 2 publications

References 49 publications

Genomic architecture of selection for adaptation to challenging environments in aquaculture

Genomic architecture of selection for adaptation to challenging environments in aquaculture

The TRAF gene family in turbot (Scophthalmus maximus): Identification, characterization, molecular evolution and expression patterns analysis

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