Volume 18 Issue 5
Oct.  2022
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SAN Lize, LIU Baosuo, ZHANG Nan, GUO Liang, GUO Huayang, ZHU Kecheng, ZHANG Dianchang. Mining of InDel marker and association analysis of hypoxia tolerance traits in Trachinotus ovatus based on resequencing[J]. South China Fisheries Science, 2022, 18(5): 100-109. DOI: 10.12131/20210347
Citation: SAN Lize, LIU Baosuo, ZHANG Nan, GUO Liang, GUO Huayang, ZHU Kecheng, ZHANG Dianchang. Mining of InDel marker and association analysis of hypoxia tolerance traits in Trachinotus ovatus based on resequencing[J]. South China Fisheries Science, 2022, 18(5): 100-109. DOI: 10.12131/20210347
shu

Mining of InDel marker and association analysis of hypoxia tolerance traits in Trachinotus ovatus based on resequencing

  • 1.

    Ocean College, Hebei Agricultural University, Qinhuangdao 066003, China

  • 2.

    South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Areas, Guangzhou 510300, China

  • 3.

    Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China

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  • Received Date: November 23, 2021
  • Revised Date: February 05, 2022
  • Accepted Date: February 17, 2022
  • Available Online: March 02, 2022
    Graphical Abstract
    • Abstract
  • Trachinotus ovatus is a fish with high oxygen consumption rate, and hypoxia can easily lead to its death. Screening for InDel molecular markers for hypoxia tolerance traits in T. ovatus and discovering functional genes affecting hypoxia tolerance traits can provide guidances for selecting and breeding T. ovatus with strong hypoxia tolerance. In this study, we applied the whole genome resequencing technology to analyze the InDel differences of T. ovatus gene, excavated the InDel sites that were significantly associated with hypoxia tolerance traits in T. ovatus, and explored the candidate genes related to hypoxia tolerance traits. Altogether 693.48 Gb was obtained by sequencing, and the average value of Q30 was 90.8%. A total of 2 574 178 InDel markers were found by annotation analysis. A total of 249 395 InDel markers were found in the 50 individuals in the tolerance group, of which 2 209 were located in exons. It is found that there were mutated genes in the nucleotide excise repair signaling pathway and cell adhesion molecules. Three InDel markers (InDel 22883061, InDel 24919481 and InDel 14451779) were found to be close to the significance threshold by association analysis between InDel markers and hypoxia tolerance trait. Nine candidate genes were obtained by annotation analysis. The selected InDel markers were of great value for selecting and identifying molecular marker selection breeding. The annotated candidate genes provide a basis and references for the study of the hypoxia tolerance mechanism of T. ovatus.
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