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Fine Mapping of the High-pH Tolerance and Growth Trait-Related Quantitative Trait Loci (QTLs) and Identification of the Candidate Genes in Pacific White Shrimp (Litopenaeus vannamei)

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Abstract

High-pH tolerance and growth are important traits for the shrimp culture industry in areas with saline-alkali water. In the present study, an F1 full-sib family of Pacific white shrimp (Litopenaeus vannamei) was generated with a new “semidirectional cross” method, and double-digest restriction site-associated DNA sequencing (ddRAD-Seq) technology was applied to genotype the 2 parents and 148 progenies. A total of 3567 high-quality markers were constructed for the genetic linkage map, and the total map length was 4161.555 centimorgans (cM), showing 48 linkage groups (LGs) with an average interlocus length of 1.167 cM. With a constrained logarithm of odds (LOD) score ≥ 2.50, 12 high-pH tolerance and 2 growth (body weight) QTLs were located. L. vannamei genomic scaffolds were used to assist with the detection of 21 stress- and 5 growth-related scaffold genes. According to the high-pH transcriptome data of our previous study, 6 candidate high-pH response genes were discovered, and 5 of these 6 genes were consistently expressed with the high-pH transcriptome data, validating the locations of the high-pH tolerance trait-related QTLs in this study. This paper is the first report of fine-mapping high-pH tolerance and growth (body weight) trait QTLs in one L. vannamei genetic map. Our results will further benefit marker-assisted selection work and might be useful for promoting genomic research on the shrimp L. vannamei.

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Acknowledgments

We thank the anonymous reviewers for comments on the manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (No. 31602135), Institution of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences (No. ISEE2018PY03), the Science & Technology Promoting Projects for Oceanic & Fishery in Guangdong Province (SDYY-2018-01), and the Guangdong Province Program (2017B030314052, 2018A030313857, 2016A030310112, 2015A030310120, 2015B020231007 and A2015230).

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Author notes

  1. Wen Huang and Chuhang Cheng contributed equally to this work.

Authors and Affiliations

  1. CAS Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB)/Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China

    Wen Huang, Chuhang Cheng, Jinshang Liu, Xin Zhang, Chunhua Ren, Xiao Jiang, Ting Chen, Kaimin Cheng, Huo Li & Chaoqun Hu

  2. Institution of South China Sea Ecology and Environmental Engineering (ISEE), Chinese Academy of Sciences, Guangzhou, 510301, China

    Wen Huang & Chaoqun Hu

  3. University of Chinese Academy of Sciences, Beijing, 100049, China

    Chuhang Cheng, Xin Zhang, Chunhua Ren & Chaoqun Hu

  4. Guangdong Jinyang Biotechnology co. LTD, Maoming, 525027, China

    Jinshang Liu & Huo Li

  5. Yuehai Feed Group co., LTD, Zhanjiang, 524017, China

    Kaimin Cheng

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  1. Wen Huang
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  9. Huo Li
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Contributions

WH and CH contributed to project conception. Experiment and data analysis was conducted by WH, CC, JL, XZ, CR, XJ, TC, KC, and HL. The manuscript was prepared by WH. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Wen Huang or Chaoqun Hu.

Ethics declarations

Statement of Human and Animal Rights

Shrimp care and experiments were carried out according to the Care and Use of Agricultural Animals in Agricultural Research and Teaching and approved by the Science and Technology Bureau of China. Approval from the Department of Wildlife Administration was not required for the experiments conducted in this paper. All experiments in this paper were performed with permits obtained from the Government of the People’s Republic of China and endorsed by the Animal Experimentation Ethics Committee of Chinese Academy of Sciences.

Conflict of Interest

The authors declare that they have no competing interests.

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Supplementary Fig. 1

Propagation characteristics of the shrimp L. vannamei. a Fertile female Pacific white shrimp, with a surgically removed eyestalk, which was usually used for stimulus-induced maturation of the shrimp, in the box, with arrows indicating the mature gonad of the female shrimp. b Fertile male Pacific white shrimp, with the spermatophore position of the male shrimp while packed with white spermatia shown in the framed area. c The thelycum position of the female shrimp, indicated by the arrow, with white spermatia adhering to the thelycum of the mated female shrimp. d The spermatophore position is framed, and the mated male parent is empty (without packed spermatium) in this position. Bars = 1 cm. (PDF 148 kb)

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Huang, W., Cheng, C., Liu, J. et al. Fine Mapping of the High-pH Tolerance and Growth Trait-Related Quantitative Trait Loci (QTLs) and Identification of the Candidate Genes in Pacific White Shrimp (Litopenaeus vannamei). Mar Biotechnol 22, 1–18 (2020). https://doi.org/10.1007/s10126-019-09932-8

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