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First Genome-wide Association Analysis for Growth Traits in the Largest Coral Reef-Dwelling Bony Fishes, the Giant Grouper (Epinephelus lanceolatus)

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Abstract

The giant grouper, Epinephelus lanceolatus, is the largest coral reef-dwelling bony fish species. However, despite extremely fast growth performance and the considerable economic importance in this species, its genetic regulation of growth remains unknown. Here, we performed the first genome-wide association study (GWAS) for five growth traits in 289 giant groupers using 42,323 single nucleotide polymorphisms (SNPs) obtained by genotyping-by-sequencing (GBS). We identified a total of 36 growth-related SNPs, of which 11 SNPs reached a genome-wide significance level. The phenotypic variance explained by these SNPs varied from 7.09% for body height to 18.42% for body length. Moreover, 22 quantitative trait loci (QTLs) for growth traits, including nine significant QTLs and 13 suggestive QTLs, were found on multiple chromosomes. Interestingly, the QTL (LG17: 6934451) was shared between body weight and body height, while two significant QTLs (LG7: 22596399 and LG15: 11877836) for body length were consistent with the associated regions of total length at the genome-wide suggestive level. Eight potential candidate genes close to the associated SNPs were selected for expression analysis, of which four genes (phosphatidylinositol transfer protein cytoplasmic 1, protein tyrosine phosphatase receptor type E, alpha/beta hydrolase domain-containing protein 17C, and vascular endothelial growth factor A-A) were differentially expressed and involved in metabolism, development, response stress, etc. This study improves our understanding of the complex genetic architecture of growth in the giant grouper. The results contribute to the selective breeding of grouper species and the conservation of coral reef fishes.

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Acknowledgments

We would like to thank the referees and editor for their valuable comments and suggestions, as well as careful corrections of our manuscript. We thank Dr. Leyun Zheng (Fisheries Research Institute of Fujian) for providing fish samples.

Sequence Data Accession

The sequencing data have been deposited into the DDBJ sequence read archive (DRA) with BioProject no. PRJDB8251.

Funding

This research was funded by the Science and Technology Planning Project of Guangzhou (201804020013), the Special Fund for Agro-scientific Research in the Public Interest (201403008), the National Natural Science Foundation of China (31872572), and the Modern Agriculture Talents Support Program (2016–2020).

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Authors and Affiliations

  1. State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, 510275, China

    Lina Wu, Yang Yang, Bijun Li, Wenhua Huang, Xi Wang, Xiaochun Liu, Zining Meng & Junhong Xia

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  1. Lina Wu
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  2. Yang Yang
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  5. Xi Wang
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Contributions

L.W. and Z.M. designed the study. X.W. and W.H. collected the samples. L.W. and Z.M. performed the laboratory work. L.W., Y.Y., and B.L. performed the analyses. J.X. contributed technical assistance. L.W. and Z.M. drafted the paper. X.L. and Z.M. contributed reagents/materials/analysis tools.

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Correspondence to Zining Meng.

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All experiments in the present study were approved by the Animal Care and Use Committee in the Life Sciences School of Sun Yet-Sen University.

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Fig. S1

Frequency of SNPs in different structural attributes of genic and intergenic regions (PNG 130 kb)

High Resolution Image (TIF 212 kb)

Fig. S2

Frequency distribution of different traits in giant grouper (PNG 90 kb)

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Fig. S3

Correlation heatmap between different characteristics (PNG 170 kb)

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Fig. S4

Population genetic relatedness among the 289 fishes. The genetic relatedness showed that most of the values are distributed at the levels of 0~0.5 (blue region) (PNG 558 kb)

High Resolution Image (TIF 2001 kb)

Fig. S5

QQ plots of the p values in GWAS analysis using GLM and MLM models for (a) total length (TL), (b) body length (BL), (c) body height (BH), (d) body thickness (BT), (e) body weight (BW) (PNG 204 kb)

High Resolution Image (TIF 1343 kb)

Fig. S6

QQ plots of the p values in GWAS analysis using the MLM model for (a) total length (TL), (b) body length (BL), (c) body height (BH), (d) body thickness (BT), (e) body weight (BW) (TIF 1127 kb) (PNG 159 kb)

High Resolution Image (TIF 1127 kb)

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Wu, L., Yang, Y., Li, B. et al. First Genome-wide Association Analysis for Growth Traits in the Largest Coral Reef-Dwelling Bony Fishes, the Giant Grouper (Epinephelus lanceolatus). Mar Biotechnol 21, 707–717 (2019). https://doi.org/10.1007/s10126-019-09916-8

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