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Constructing a High-Density Genetic Linkage Map for Large Yellow Croaker (Larimichthys crocea) and Mapping Resistance Trait Against Ciliate Parasite Cryptocaryon irritans

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Abstract

The large yellow croaker (Larimichthys crocea) is the most economically important marine cage-farming fish in China in the past decade. However, the sustainable development of large yellow croaker aquaculture has been severely hampered by several diseases, of which, the white spot disease caused by ciliate protozoan parasite Cryptocaryon irritans ranks the most damaging disease in large yellow croaker cage farms. To better understand the genetic basis of parasite infection and disease resistance to C. irritans, it is vital to map the traits and localize the underlying candidate genes in L. crocea genome. Here, we constructed a high-density genetic linkage map using double-digest restriction-site associated DNA (ddRAD)-based high-throughput SNP genotyping data of a F1 mapping family, which had been challenged with C. irritans for resistant trait measure. A total of 5261 SNPs was grouped and oriented into 24 linkage groups (LGs), representing 24 chromosomes of L. crocea. The total genetic map length was 1885.67 cM with an average inter-locus distance of 0.36 cM. Quantitative trait loci (QTL) mapping identified seven significant QTLs in four LGs linked to C. irritans disease resistance. Candidate genes underlying disease resistance were identified from the reference genome, including ifnar1, ifngr2, ikbke, and CD112. Comparative genomic analysis between large yellow croaker and the four closely related species revealed high evolutionary conservation of chromosomes, though inter-chromosomal rearrangements do exist. Especially, the croaker genome structure was closer to the medaka genome than stickleback, indicating that the croaker genome might retain the teleost ancestral genome structure. The high-density genetic linkage map provides an important tool and resource for fine mapping, comparative genome analysis, and molecular selective breeding of large yellow croaker.

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Funding

We acknowledge the financial support from the State Key Laboratory of Large Yellow Croaker Breeding (Fujian Fuding Seagull Fishing Food Co., Ltd.) (LYC2017RS05 and LYC2017ZY01), the Fundamental Research Funds for the Central Universities of Xiamen University (Nos. 20720180123 and 20720160110), the Science and Technology Platform Construction of Fujian Province (No. 2018 N2005), the Local Science and Technology Development Project Guide by The Central Government (2017L3019), and the Natural Science Foundation of Fujian Province (Grant No. 2017 J06022).

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Authors and Affiliations

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

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

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

    Shengnan Kong, Qiaozhen Ke, Lin Chen, Zhixiong Zhou, Huaqiang Bai, Wenzhu Peng & Peng Xu

  3. College of Fisheries, Henan Normal University, Xinxiang, 453007, China

    Shengnan Kong

  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. Shengnan Kong
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  2. Qiaozhen Ke
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  3. Lin Chen
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  4. Zhixiong Zhou
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  9. Peng Xu
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Contributions

PX conceived of the project. PX contributed to the funding acquisition. SK wrote the manuscript. SK, LC, and WP performed the analysis and designed the charts and tables. QK, JZ, and HB conducted the C. irritans challenge experiment. ZZ and FP conducted the ddRAD libraries. All authors have validated the manuscript and appreciate to improve the quality of it.

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Correspondence to Peng Xu.

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Kong, S., Ke, Q., Chen, L. et al. Constructing a High-Density Genetic Linkage Map for Large Yellow Croaker (Larimichthys crocea) and Mapping Resistance Trait Against Ciliate Parasite Cryptocaryon irritans. Mar Biotechnol 21, 262–275 (2019). https://doi.org/10.1007/s10126-019-09878-x

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