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Genome-Wide Association Study Identifies Genomic Loci of Sex Determination and Gonadosomatic Index Traits in Large Yellow Croaker (Larimichthys crocea)

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Abstract

Larimichthys crocea is one of the traditional marine culture fishes in China, widely distributed in South China Sea, East Sea, and southern Yellow Sea. Sex dimorphism is evident in this species that females present a substantial growth strength than males, suggesting breeding females could obtain more economic benefits in L. crocea aquaculture industry. With the continuous expansion of aquaculture industry, both identifying sex-associated genome region and understanding the genetic basis underlying gonad differentiation and development matter to not only sex control aquaculture but also breeding industry. Thus, genome-wide association analysis (GWAS) of sex determination was conducted with a random breeding population of 905 individuals (including 463 females and 442 males) by ddRAD sequencing. For sex determination, 21 significant single nucleotide polymorphisms (SNPs) in chromosome (Chr) 22 were identified. Surrounding these SNPs, we founded 14 candidate genes, including dmrt1, dmrt3, and piwil2, fam102a, and odf2. The sex-associated region was narrowed down further to 2.4 Mb on Chr22 through Fst scanning and insertion-deletion (InDel) analysis. Besides, 3 SNPs in the supposed sex-determining region on Chr22 were identified as highly associated with gonad differentiation through GWAS on gonadosomatic index (GSI) in 350 males and 231 females. Because of the significant difference of GSI between females and males of L. crocea, GWAS on GSI of different genders was also conducted independently. Finally, we identified a SNP in Chr18 showing genome-wide significant association with male GSI (MGSI) and three genes axl, cyp2a10, and cyp2g1 involved in the gonadal development regulation process of aromatase. Overall, this study explored the genetic basis of sex determination mechanism and provided novel insights into gonad differentiation and development, offering solid genetic support for sex control breeding, marker-assisted selection, and marine resources conservation.

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Abbreviations

Chr:

chromosome

BW:

body weight

ddRAD:

double-digest restriction site-associated DNA

Fst :

fixation index

GSI:

gonadosomatic index

GW:

gonad weight

GWAS:

genome-wide association study

InDel:

insertion-deletion

MLM:

mixed linear model

MAF:

minor allele frequency

SNP:

significant single nucleotide polymorphism

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Acknowledgments

We acknowledge financial support from the Industry-University-Research Collaboration Project in Fujian Province (2019 N51010081), the Fundamental Research Funds for the Central Universities, Xiamen University (No. 20720180123 & 20720160110), the Science and Technology Platform Construction of Fujian Province (No. 2018 N2005) and Industry-University-Research Cooperation Project of Xiamen University and Ningde (2019C002), and Open Research Fund Project of State Key Laboratory of Large Yellow Croaker Breeding (LYC2017RS05, LYC2019RS02, and LYC2019RS03).

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Authors and Affiliations

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

    Huanling Lin, Zhixiong Zhou, Ji Zhao, Tao Zhou, Huaqiang Bai, Qiaozhen Ke, Fei Pu & Peng Xu

  2. State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China

    Huanling Lin & Peng Xu

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

    Qiaozhen Ke, Weiqiang Zheng & Peng Xu

Authors
  1. Huanling Lin
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  2. Zhixiong Zhou
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  3. Ji Zhao
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  4. Tao Zhou
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  5. Huaqiang Bai
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  6. Qiaozhen Ke
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  7. Fei Pu
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  8. Weiqiang Zheng
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  9. Peng Xu
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Contributions

PX conceived and supervised the study. HL wrote the manuscript. HL and ZZ analyzed the data and designed the charts and tables. ZZ and JZ constructed the ddRAD libraries. JZ and HB worked on breeding. QK and FP collected the samples. PX and TZ revised the manuscript. All authors read and approved the manuscript.

Corresponding author

Correspondence to Peng Xu.

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The authors declare that they have no conflict of interest.

Ethical Approval

All experiments were in accordance with the approved guidelines of IACUC (Institutional Animal Care and Use Committee) of the College of Ocean and Earth Sciences, Xiamen University.

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Supplementary Information

Fig. S1

Histograms of original and normalized phenotypic data of L. crocea. FGSI, MGSI, NFGSI, and NMGSI were acronyms for female gonadosomatic index, male gonadosomatic index, normalized female gonadosomatic index, and normalized male gonadosomatic index, respectively. (PNG 295 kb)

High resolution image (TIF 1133 kb)

Fig. S2

Correlation graph of phenotypic statistics, in which the upper part indicates correlation coefficient and corresponding p value, the lower part displays the scatter plots with fitting curve, and the diagonal shows names of phenotypic traits. (PNG 1020 kb)

High resolution image (TIF 1333 kb)

Fig. S3

Description of genotyping statistics. Minor allele frequency and genotyping missing rate of raw SNPs were displayed on the violin plot with red and green dotted lines representing thresholds of MAF and missing rate, respectively (a). The sequence depth and genome coverage of filtered SNPs were presented in scatter plot (b) and the histogram showed a general distribution of MAF (c) and call rate (d) in filtered SNPs. (PNG 338 kb)

High resolution image (TIF 1062 kb)

Fig. S4

Manhattan and QQ plots displaying InDel markers’ association with sex. (PNG 427 kb)

High resolution image (TIF 709 kb)

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Lin, H., Zhou, Z., Zhao, J. et al. Genome-Wide Association Study Identifies Genomic Loci of Sex Determination and Gonadosomatic Index Traits in Large Yellow Croaker (Larimichthys crocea). Mar Biotechnol 23, 127–139 (2021). https://doi.org/10.1007/s10126-020-10007-2

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