Genome-Wide Association Study Reveals Multiple Novel QTL Associated with Low Oxygen Tolerance in Hybrid Catfish

Xiaoxiao Zhong, Xiaozhu Wang, Tao Zhou, Yulin Jin, Suxu Tan, Chen Jiang, Xin Geng, Ning Li, Huitong Shi, Qifan Zeng, Yujia Yang, Zihao Yuan, Lisui Bao, Shikai Liu, Changxu Tian, Eric Peatman, Qi Li, Zhanjian "John" Liu

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Hypoxic condition is common in aquaculture, leading to major economic losses. Genetic analysis of hypoxia tolerance, therefore, is not only scientifically significant, but also economically important. Catfish is generally regarded as being highly tolerant to low dissolved oxygen, but variations exist among various populations, strains, and species. In this study, we conducted a genome-wide association study (GWAS) using the catfish 250 K SNP array to identify quantitative trait locus (QTL) associated with tolerance to low dissolved oxygen in the channel catfish × blue catfish interspecific system. Four linkage groups (LG2, LG4, LG23, and LG29) were found to be associated with low oxygen tolerance in hybrid catfish. Multiple significant SNPs were found to be physically linked in genomic regions containing significant QTL for low oxygen tolerance on LG2 and LG23, and in those regions containing suggestively significant QTL on LG2, LG4, LG23, and LG29, suggesting that the physically linked SNPs were genuinely segregating and related with low oxygen tolerance. Analysis of genes within the associated genomic regions suggested that many of these genes were involved in VEGF, MAPK, mTOR, PI3K-Akt, P53-mediated apoptosis, and DNA damage checkpoint pathways. Comparative analysis indicated that most of the QTL at the species level, as analyzed by using the interspecific system, did not overlap with those identified from six strains of channel catfish, confirming the complexity of the genetic architecture of hypoxia tolerance in catfish.

Original languageEnglish (US)
Pages (from-to)379-390
Number of pages12
JournalMarine Biotechnology
Volume19
Issue number4
DOIs
StatePublished - Aug 1 2017
Externally publishedYes

Fingerprint

Catfishes
Quantitative Trait Loci
Genome-Wide Association Study
catfish
quantitative trait loci
genome
tolerance
Oxygen
oxygen
Ictaluridae
Ictalurus punctatus
Single Nucleotide Polymorphism
dissolved oxygen
hypoxia
Ictalurus furcatus
genomics
phosphatidylinositol 3-kinase
Aquaculture
linkage groups
anaerobic conditions

Keywords

  • Fish
  • Genome
  • GWAS
  • Hypoxia
  • Low oxygen tolerance
  • SNP

ASJC Scopus subject areas

  • Biotechnology
  • Aquatic Science

Cite this

Genome-Wide Association Study Reveals Multiple Novel QTL Associated with Low Oxygen Tolerance in Hybrid Catfish. / Zhong, Xiaoxiao; Wang, Xiaozhu; Zhou, Tao; Jin, Yulin; Tan, Suxu; Jiang, Chen; Geng, Xin; Li, Ning; Shi, Huitong; Zeng, Qifan; Yang, Yujia; Yuan, Zihao; Bao, Lisui; Liu, Shikai; Tian, Changxu; Peatman, Eric; Li, Qi; Liu, Zhanjian "John".

In: Marine Biotechnology, Vol. 19, No. 4, 01.08.2017, p. 379-390.

Research output: Contribution to journalArticle

Zhong, X, Wang, X, Zhou, T, Jin, Y, Tan, S, Jiang, C, Geng, X, Li, N, Shi, H, Zeng, Q, Yang, Y, Yuan, Z, Bao, L, Liu, S, Tian, C, Peatman, E, Li, Q & Liu, ZJ 2017, 'Genome-Wide Association Study Reveals Multiple Novel QTL Associated with Low Oxygen Tolerance in Hybrid Catfish', Marine Biotechnology, vol. 19, no. 4, pp. 379-390. https://doi.org/10.1007/s10126-017-9757-5
Zhong, Xiaoxiao ; Wang, Xiaozhu ; Zhou, Tao ; Jin, Yulin ; Tan, Suxu ; Jiang, Chen ; Geng, Xin ; Li, Ning ; Shi, Huitong ; Zeng, Qifan ; Yang, Yujia ; Yuan, Zihao ; Bao, Lisui ; Liu, Shikai ; Tian, Changxu ; Peatman, Eric ; Li, Qi ; Liu, Zhanjian "John". / Genome-Wide Association Study Reveals Multiple Novel QTL Associated with Low Oxygen Tolerance in Hybrid Catfish. In: Marine Biotechnology. 2017 ; Vol. 19, No. 4. pp. 379-390.
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AU - Tan, Suxu

AU - Jiang, Chen

AU - Geng, Xin

AU - Li, Ning

AU - Shi, Huitong

AU - Zeng, Qifan

AU - Yang, Yujia

AU - Yuan, Zihao

AU - Bao, Lisui

AU - Liu, Shikai

AU - Tian, Changxu

AU - Peatman, Eric

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AU - Liu, Zhanjian "John"

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N2 - Hypoxic condition is common in aquaculture, leading to major economic losses. Genetic analysis of hypoxia tolerance, therefore, is not only scientifically significant, but also economically important. Catfish is generally regarded as being highly tolerant to low dissolved oxygen, but variations exist among various populations, strains, and species. In this study, we conducted a genome-wide association study (GWAS) using the catfish 250 K SNP array to identify quantitative trait locus (QTL) associated with tolerance to low dissolved oxygen in the channel catfish × blue catfish interspecific system. Four linkage groups (LG2, LG4, LG23, and LG29) were found to be associated with low oxygen tolerance in hybrid catfish. Multiple significant SNPs were found to be physically linked in genomic regions containing significant QTL for low oxygen tolerance on LG2 and LG23, and in those regions containing suggestively significant QTL on LG2, LG4, LG23, and LG29, suggesting that the physically linked SNPs were genuinely segregating and related with low oxygen tolerance. Analysis of genes within the associated genomic regions suggested that many of these genes were involved in VEGF, MAPK, mTOR, PI3K-Akt, P53-mediated apoptosis, and DNA damage checkpoint pathways. Comparative analysis indicated that most of the QTL at the species level, as analyzed by using the interspecific system, did not overlap with those identified from six strains of channel catfish, confirming the complexity of the genetic architecture of hypoxia tolerance in catfish.

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