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Genomic Selection Using Extreme Phenotypes and Pre-Selection of SNPs in Large Yellow Croaker (Larimichthys crocea)

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Abstract

Genomic selection (GS) is an effective method to improve predictive accuracies of genetic values. However, high cost in genotyping will limit the application of this technology in some species. Therefore, it is necessary to find some methods to reduce the genotyping costs in genomic selection. Large yellow croaker is one of the most commercially important marine fish species in southeast China and Eastern Asia. In this study, genotyping-by-sequencing was used to construct the libraries for the NGS sequencing and find 29,748 SNPs in the genome. Two traits, eviscerated weight (EW) and the ratio between eviscerated weight and whole body weight (REW), were chosen to study. Two strategies to reduce the costs were proposed as follows: selecting extreme phenotypes (EP) for genotyping in reference population or pre-selecting SNPs to construct low-density marker panels in candidates. Three methods of pre-selection of SNPs, i.e., pre-selecting SNPs by absolute effects (SE), by single marker analysis (SMA), and by fixed intervals of sequence number (EL), were studied. The results showed that using EP was a feasible method to save the genotyping costs in reference population. Heritability did not seem to have obvious influences on the predictive abilities estimated by EP. Using SMA was the most feasible method to save the genotyping costs in candidates. In addition, the combination of EP and SMA in genomic selection also showed good results, especially for trait of REW. We also described how to apply the new methods in genomic selection and compared the genotyping costs before and after using the new methods. Our study may not only offer a reference for aquatic genomic breeding but also offer a reference for genomic prediction in other species including livestock and plants, etc.

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Acknowledgments

Kun Ye, Qingkai Chen, Yang Liu, and other colleagues in the laboratory participated in fish sampling and the trait measurement. We thank two reviewers for providing many helpful suggestions.

Authors’ Contributions

ZW conceived and designed the study and revised manuscript; LD analyzed the data and drafted the manuscript; SX discovered SNPs and revised the manuscript; JC participated in the trait measurement and DNA extraction. LW participated in the genotyping costs estimation. All authors read and approved the final manuscript.

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Authors and Affiliations

  1. Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Jimei University, Xiamen, Fujian, People’s Republic of China

    Linsong Dong, Shijun Xiao, Junwei Chen & Zhiyong Wang

  2. Academy of Animal Science and Technology, Collaborative Innovation Center for Aquatic Efficient Health Production of Fisheries, Hunan Agricultural University, Changsha, Hunan, People’s Republic of China

    Liang Wan

Authors
  1. Linsong Dong
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  2. Shijun Xiao
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  3. Junwei Chen
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  4. Liang Wan
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  5. Zhiyong Wang
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Corresponding author

Correspondence to Zhiyong Wang.

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Ethics Statement

All fish were reared in a nucleus farm named “Jinling Aquaculture Science and Technology Co. Ltd.” in Ningde City, Fujian Province, P.R. China. The trail was carried out in the Key Laboratory of Healthy Mariculture for the East China Sea. This study was approved by the Animal Care and Use Committee of Fisheries College of Jimei University. All participants consented to publish the paper.

Availability of Data

Raw DNA sequencing reads were deposited in NCBI with the project accession of PRJNA309464 and SRA accession of SRR3114179.

Competing Interests

The authors declare that they have no competing interests.

Fundings

This work was supported by the National Natural Science Foundation of China (U1205122), Key projects of the Xiamen Southern Ocean Research Center (14GZY70NF34), the National ‘863’ Project of China (2012AA10A403), the Natural Science Foundation of Fujian Province (2016J05081) and the Foundation for Innovation Research Team of Jimei University (2010A02).

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Dong, L., Xiao, S., Chen, J. et al. Genomic Selection Using Extreme Phenotypes and Pre-Selection of SNPs in Large Yellow Croaker (Larimichthys crocea). Mar Biotechnol 18, 575–583 (2016). https://doi.org/10.1007/s10126-016-9718-4

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  • DOI: https://doi.org/10.1007/s10126-016-9718-4

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