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Genome-Wide Association Study of Growth and Body-Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea) Using ddRAD Sequencing

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Abstract

Large yellow croaker (Larimichthys crocea) is an economically important marine fish species of China. Due to overfishing and marine pollution, the wild stocks of this croaker have collapsed in the past decades. Meanwhile, the cultured croaker is facing the difficulties of reduced genetic diversity and low growth rate. To explore the molecular markers related to the growth traits of croaker and providing the related SNPs for the marker-assisted selection, we used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic bases of growth traits in a cultured population and identify the SNPs that associated with important growth traits by GWAS. A total of 220 individuals were genotyped by ddRAD sequencing. After quality control, 27,227 SNPs were identified in 220 samples and used for GWAS analysis. We identified 13 genome-wide significant associated SNPs of growth traits on 8 chromosomes, and the beta P of these SNPs ranged from 0.01 to 0.86. Through the definition of candidate regions and gene annotation, candidate genes related to growth were identified, including important regulators such as fgf18, fgf1, nr3c1, cyp8b1, fabp2, cyp2r1, ppara, and ccm2l. We also identified SNPs and candidate genes that significantly associated with body shape, including bmp7, col1a1, col11a2, and col18a1, which are also economically important traits for large yellow croaker aquaculture. The results provided insights into the genetic basis of growth and body shape in large yellow croaker population and would provide reliable genetic markers for molecular marker-assisted selection in the future. Meanwhile, the result established a basis for our subsequent fine mapping and related gene study.

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Funding

We acknowledge financial support from the State Key Laboratory of Large Yellow Croaker Breeding (Fujian Fuding Seagull Fishing Food Co., Ltd) (Nos. LYC2017ZY01, LYC2017RS05, and LYC2016RS02), the Fundamental Research Funds for the Central Universities (Nos. 20720180123 and 20720160110), the Science and Technology Platform Construction of Fujian Province (No. 2018N2005), the Natural Science Foundation of Fujian Province, China (Nos. 2015J06019 and 2017J06022), the Local Science and Technology Development Project Guide by The Central Government (No. 2017L3019), the National Key Research and Development Program of China (No. 2018YFC1406305), China Agriculture Research System (No. CARS-47), and the Major Special Projects of Fujian Province (No. 2016NZ0001).

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  1. Zhixiong Zhou and Kunhuang Han contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China

    Zhixiong Zhou, Kunhuang Han, Qiaozhen Ke, Fei Pu, Yilei Wang & Peng Xu

  2. State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China

    Zhixiong Zhou, Yidi Wu, Huaqiang Bai, Qiaozhen Ke, Fei Pu & Peng Xu

  3. Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Jimei University, Xiamen, 361021, China

    Kunhuang Han & Yilei Wang

  4. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China

    Peng Xu

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  1. Zhixiong Zhou
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Contributions

PX and YLW conceived and supervised the study. ZZ construct the ddRAD library, analyzed the data, and drafted the manuscript. HB helped on data analysis. FP, KH, and QK helped with croaker breeding and sample collection. PX and YDW revised the manuscript. All authors have read and approved the manuscript.

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Correspondence to Yilei Wang or Peng Xu.

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The authors declare that they have no conflict of interest.

Ethical Approval

This study was approved by the Animal Care and Use committee of State Key Laboratory of Large Yellow Croaker Breeding. All the methods used in this study were carried out in accordance with approved guidelines.

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Figure S1

Distribution histogram of the number of SNPs on each chromosome. Un represents scaffolds that are unassembled onto chromosome. (PNG 43 kb)

High Resolution Image (TIF 234 kb)

Figure S2

Frequency distribution histogram and frequency estimation curve of r2 in 13,417 SNPs located on different loci. Red and blue dotted line represents 99% and 95% of r2 distribution. (PNG 53 kb)

High Resolution Image (TIF 155 kb)

ESM 1

(XLSX 66 kb)

Supplementary sequence

The Sequence of significance SNPs in this analysis. (DOCX 19 kb)

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Zhou, Z., Han, K., Wu, Y. et al. Genome-Wide Association Study of Growth and Body-Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea) Using ddRAD Sequencing. Mar Biotechnol 21, 655–670 (2019). https://doi.org/10.1007/s10126-019-09910-0

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