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Genome-Wide Association Study of Body Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea)

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Abstract

Large yellow croaker (Larimichthys crocea) is one of the most important cultured marine fish on the southeast coast of China. Its body shape is important for the aquaculture industry since it affects the behavior such as swimming, ingesting, and evading, as well as customer preference. Due to the greater consumer demand of small head, slender body large yellow croaker, selecting and breeding of slender individuals with the assistance of genetic markers will benefit the industry quickly. In this study, several traits were employed to represent body shape, including body depth/body length (BD/BL), body thickness/body length (BT/BL), caudal peduncle depth/caudal peduncle length (CPDLR), tail length/body length (TL/BL), and body area/head area (BA/HA). Genome-wide association study was conducted with a panmictic population of 280 individuals to identify SNP and genes potentially associated with body shape. A set of 20 SNPs on 12 chromosomes were identified to be significantly associated with body shape-related traits. Besides, 5 SNPs were identified to be suggestive associated with CPDLR and BT/BL. Surrounding these SNPs, we found some body shape-related candidate genes, including fabp1, acrv1, bcor, mstn, bambi, and neo1, which involved in lipid metabolism, TGF-β signaling, and BMP pathway and other important regulatory pathways. These results will be useful for the understanding of the genetic basis of body shape formation and helpful for body shape controlling of large yellow croaker by using marker-assisted selection.

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Funding

We acknowledge financial support from State Key Laboratory of Large Yellow Croaker Breeding (Fujian Fuding Seagull Fishing Food Co., Ltd) (LYC2017RS05 & LYC2017ZY01), the Industry-University-Research Collaboration Project in Fujian Province (2019N51010081), the Fundamental Research Funds for the Central Universities, Xiamen University (Nos. 20720180123 & 20720160110), the Science and Technology Platform Construction of Fujian Province (No. 2018N2005), the Local Science and Technology Development Project Guide by The Central Government (2017L3019), and Industry-University-Research Cooperation Project of Xiamen University in Ningde (2018C003).

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Author notes

  1. Shengnan Kong and Zhixiong Zhou contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352103, China

    Shengnan Kong, Ji Zhao, Fei Pu, Qiaozhen Ke & Peng Xu

  2. Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China

    Shengnan Kong, Zhixiong Zhou, Tao Zhou, Ji Zhao, Lin Chen, Huanling Lin, Qiaozhen Ke, Huaqiang Bai & Peng Xu

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  1. Shengnan Kong
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Contributions

PX conceived the project. PX contributed to the funding acquisition. SK and ZZ wrote the manuscript. TZ and HL revised the manuscript. SK, ZZ, and LC performed the analysis and designed the charts and tables. QK, JZ, and HB conducted the random mating population of large yellow croaker. ZZ and FP conducted the ddRAD libraries. All authors have validated and approved the manuscript.

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Correspondence to Peng Xu.

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Fig. S1

Schematic diagram of body-shape-related traits of large yellow croaker. (a). Phenotypic measurement of large yellow croaker (b). The modularization of the body shape with simple geometric shape. HD: Head Depth; BD: Body Depth; TL: Tail Length; BL: Body Length; HL: Head Length; Trl: Trunk Length; CPL: Caudal Peduncle Length; CFL: Caudal Fin Length; CPD: Caudal Peduncle Depth. (PDF 397 kb)

Fig. S2

Phenotypic correlation of the body-shape-related traits in large yellow croaker. The scatterplots between different traits are on lower diagonal elements and correlation values are on the upper diagonal elements. *** represents the significant level of 0.01, ** represent the significant level of 0.05. The histogram of each traits was represented in the diagonal line. (PDF 5371 kb)

Fig. S3

The statistics of genotyping. (a) Heatmap of SNPs density on each chromosome (b) the distribution of minimum allele frequency (c) the distribution of quality score of SNPs. (PDF 3243 kb)

Fig. S4

The correlation of P value between UML and MLMM models. (a) BD/BL (b) BT/BL (c) BA/HA (d) CPDLR (e) TL/BL. (PDF 2760 kb)

Fig. S5

The QQ-plot of GWAS. (a) GWAS of BD/BL by UML (b) GWAS of BD/BL by MLMM (c) GWAS of BT/BL by UML (d) GWAS of BT/BL by MLMM (e) GWAS of BA/HA by UML (f) GWAS of BA/HA by MLMM (g) GWAS of CPDLR by UML (h) GWAS of CPDLR by MLMM (i) GWAS of TL/BL by UML (j) GWAS of TL/BL by MLMM. (PDF 2924 kb)

Fig. S6

Genome-wide association study on (a) Body Depth/Body Length (b) Body Thickness/Body Length in large yellow croaker using MLMM model. Genome significance levels are shown by the dotted line. (PDF 3255 kb)

Fig. S7

Genome-wide association study on (a) Body Area/Head Area (b) Caudal Peduncle Depth/Caudal Peduncle Length (c) Tail Length/Body Length in large yellow croaker using UML model. Genome significance levels are shown by the dotted line. (PDF 5026 kb)

Fig. S8

The TGF-β signaling pathway in L. crocea. Gene neo1, bambi, acrv1 and acrv1c were marker by red block. (PDF 178 kb)

Fig. S9

The PPAR signaling pathway in L. crocea. Gene ppara and fabp1 were marker by red block. (PDF 169 kb)

ESM 10

Table S1. Phenotypic data of large yellow croaker. Table S2 Statistics of genotyping of large yellow croaker. Table S3. The significant and suggestive threshold of body-shape-related traits of UML and MLMM. “\” represent that there is no significant or suggestive was identified in GWAS. Table S4. P values for suggestive associated SNPs of body-shape-related traits. The Beta P value was calculated by Beta estimates, which represent the phenotypic variance explained (PVE). (XLSX 71 kb)

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Kong, S., Zhou, Z., Zhou, T. et al. Genome-Wide Association Study of Body Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea). Mar Biotechnol 22, 631–643 (2020). https://doi.org/10.1007/s10126-020-09983-2

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