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Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus)

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Abstract

Brown-marbled grouper, Epinephelus fuscoguttatus, is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecular marker associated with growth of brown-marbled grouper is rare. Thus, we performed the first genome-wide association study (GWAS) for five growth traits in 172 brown-marbled groupers with 43,688 SNPs detected by ddRAD-seq. We identified a total of 5 significant and 18 suggestive QTLs located in multiple chromosomes associated with growth traits. In the 20 kb window of the significant SNPs and suggestive SNPs, 5 and 14 potential candidate genes affecting growth were detected, respectively. Five potential candidate genes near the significantly associated SNPs were selected for expression analysis. Among of which, bmp2k, wasf1, and acyp2 involved in bone development, maintenance of mitochondrion structure, and metabolism were differentially expressed. Interestingly, the SNP 23:29601315 located in the intron of bmp2k was significantly associated with body weight, body length, body height, and body thickness and suggestively associated with total length. We verified the locus using another new group including 123 individuals. The results showed that individuals with CC genotype have better growth traits comparing other individuals. Our findings not only contribute to understanding the molecular mechanism of growth regulation, but also promote the advance of marker-assisted selection in brown-marbled grouper.

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Acknowledgments

We thank Mr. Xiaoli Yang (Zhanjiang Hengxing aquatic science and technology co. LTD) and Dr. Haifa Zhang (Marine fisheries Development center of Guangdong Province) for providing fish samples; Jianan He (Sun Yat-sen University) for collecting the samples.

Funding

This research was funded by Agriculture Research System of China (ARS-47); Science and Technology Planning Project of Guangzhou (201804020013); National Natural Science Foundation of China (31872572); Yang Fan Innovative & Entrepreneurial Research Team Project (No.201312H10); National Natural Science Foundation of China (u1401213, 31802266); and the Program of the China-ASEAN Maritime Cooperation Fund of the Chinese government.

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  1. State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People’s Republic of China

    Yang Yang, Lina Wu, Xi Wu, Bijun Li, Wenhua Huang, Zhuoying Weng, Zixuan Lin, Leling Song, Yin Guo, Zining Meng, Xiaochun Liu & Junhong Xia

  2. Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People’s Republic of China

    Yang Yang, Lina Wu, Xi Wu, Bijun Li, Wenhua Huang, Zhuoying Weng, Leling Song, Yin Guo, Zining Meng, Xiaochun Liu & Junhong Xia

  3. Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, 510275, People’s Republic of China

    Zining Meng & Xiaochun Liu

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  1. Yang Yang
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  2. Lina Wu
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  3. Xi Wu
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Contributions

Y.Y., Z.M., and X. L. designed the study. Y.Y., L.W., L.S., and W.H. collected the samples. Y.Y. and Z.M. performed the laboratory work. Y.Y., L.W., B.L., Y.G., and Z.M. performed analyses. J.X. contributed technical assistance. Y.Y., Z.M, and X.L. drafted the paper.

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Correspondence to Zining Meng or Xiaochun Liu.

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Yang, Y., Wu, L., Wu, X. et al. Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus). Mar Biotechnol 22, 153–166 (2020). https://doi.org/10.1007/s10126-019-09940-8

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