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Genome-Wide Association and Expression Analysis Revealed the Candidate Variants and Molecular Underpinnings of Cold-Stress Response in Large Yellow Croaker

Abstract

Large yellow croaker (Larimichthys crocea) is one of the most economically important fish in China. Recently, global climate change has caused more and more intense and extreme low temperature weathers, resulting in huge losses to the large yellow croaker industry. Therefore, it is essential to understand the mechanisms of low-temperature tolerance in large yellow croaker. Here, we conducted an integrative analysis of genome-wide association study (GWAS) and transcriptome analysis to identify candidate variants and reveal the molecular underpinning of cold-stress response in large yellow croaker. A total of 8 significant single nucleotide polymorphisms (SNPs) loci on 6 chromosomes were identified in the GWAS analysis, and 5764 (gill) and 3588 (liver) differentially expressed genes (DEGs) were detected in cold-stressed large yellow croaker, respectively. Further comparative and functional analysis of the candidate genes and DEGs highlighted the importance of pathways/genes related to immune response, cellular stress response, lipid transport, and metabolism in the cold-stress response of large yellow croaker. Our results provide insights into the cold tolerance of large yellow croaker and contribute to genomic-based selection for low-temperature-resistant large yellow croaker.

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Acknowledgements

We would like to thank Ningde Fufa Fisheries Company Limited for providing the experimental place.

Funding

This study was funded by the National Natural Science Foundation of China (U21A20264); the Local Science and Technology Development Project Guide by The Central Government (2019L3032); the Special Foundation for Major Research Program of Fujian Province (2020NZ08003); Open Research Fund Project of State Key Laboratory of Large Yellow Croaker Breeding (LYC2019RS02, LYC2019RS03); the Fundamental Research Funds for the Central Universities (20720200110); the China Agriculture Research System (CARS-47); and “Science and Technology Innovation 2025” Major Special Project of Ningbo City (2021Z002).

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PX conceived and supervised this study. YW designed the experiment. YW, HB, HL, and QK conducted the cold challenge experiment and collected samples. NS extracted the DNA and constructed the ddRAD libraries. NS and YW analyzed the data, made the charts, and drafted this manuscript. ZZ and QH helped in data analysis and DNA extraction. PX revised this manuscript. All authors have read and approved the manuscript.

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Correspondence to Peng Xu.

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Suo, N., Wu, Y., Zhou, Z. et al. Genome-Wide Association and Expression Analysis Revealed the Candidate Variants and Molecular Underpinnings of Cold-Stress Response in Large Yellow Croaker. Mar Biotechnol (2022). https://doi.org/10.1007/s10126-022-10155-7

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  • DOI: https://doi.org/10.1007/s10126-022-10155-7

Keywords

  • Large yellow croaker
  • Cold tolerance
  • Genome-wide association study
  • Transcriptome