Multiple across-strain and within-strain QTLs suggest highly complex genetic architecture for hypoxia tolerance in channel catfish

Abstract

The ability to survive hypoxic conditions is important for various organisms, especially for aquatic animals. Teleost fish, representing more than 50 % of vertebrate species, are extremely efficient in utilizing low levels of dissolved oxygen in water. However, huge variations exist among various taxa of fish in their ability to tolerate hypoxia. In aquaculture, hypoxia tolerance is among the most important traits because hypoxia can cause major economic losses. Genetic enhancement for hypoxia tolerance in catfish is of great interest, but little was done with analysis of the genetic architecture of hypoxia tolerance. The objective of this study was to conduct a genome-wide association study to identify QTLs for hypoxia tolerance using the catfish 250K SNP array with channel catfish families from six strains. Multiple significant and suggestive QTLs were identified across and within strains. One significant QTL and four suggestive QTLs were identified across strains. Six significant QTLs and many suggestive QTLs were identified within strains. There were rare overlaps among the QTLs identified within the six strains, suggesting a complex genetic architecture of hypoxia tolerance. Overall, within-strain QTLs explained larger proportion of phenotypic variation than across-strain QTLs. Many of genes within these identified QTLs have known functions for regulation of oxygen metabolism and involvement in hypoxia responses. Pathway analysis indicated that most of these genes were involved in MAPK or PI3K/AKT/mTOR signaling pathways that were known to be important for hypoxia-mediated angiogenesis, cell proliferation, apoptosis and survival.

A Review of Molecular Responses of Catfish to Bacterial Diseases and Abiotic Stresses

“…In pathway analysis, annotated genes within QTL associated with hypoxia tolerance belonged to several pathways, for instance, PI3K/Akt/mTOR signaling pathway (Zhong et al, 2017). The QTL identified from the interspecific hybrid catfish, for the most part, had rare overlaps with the QTL within the six strains from channel catfish (Wang et al, 2017b), further supporting the notion that the genetic architecture of low oxygen tolerance in catfish is extremely complex (Zhong et al, 2017). …”

“…With a well-assembled reference genome sequence, potential candidate genes within QTLs can be identified simultaneously, which is a useful way to understand the molecular mechanisms of a trait by identification of genes in proximity to QTL (Dikmen et al, 2013; Geng et al, 2015). As described above, GWAS was conducted to identify QTL associated with several important traits, including disease resistance for columnaris (Geng et al, 2015) and ESC (Zhou et al, 2017b; Shi et al, 2018; Tan et al, 2018), growth rate (Li et al, 2017), head size (Geng et al, 2016), body conformation (Geng et al, 2017), and low oxygen tolerance (Wang et al, 2017b; Zhong et al, 2017). As the global climate change worsens over time, it is important to develop heat-tolerant lines.…”

“…Two GWAS studies were recently conducted on hypoxia tolerance, using channel catfish (Wang et al, 2017b) and hybrid catfish (Zhong et al, 2017). In one experiment with six strains of channel catfish, QTL were identified in all six strains, but they rarely overlaped, suggesting the complexity of the genetic architecture of hypoxia tolerance in different channel catfish strains (Wang et al, 2017b).…”

“…In one experiment with six strains of channel catfish, QTL were identified in all six strains, but they rarely overlaped, suggesting the complexity of the genetic architecture of hypoxia tolerance in different channel catfish strains (Wang et al, 2017b). Genes annotated within QTL were involved in not only MAPK signaling pathway but also PI3K/AKT/mTOR signaling pathways (Wang et al, 2017b). It is apparent that mutations in any of the several gene pathways can lead to QTL associated with tolerance to low oxygen.…”

“…For the later, great genetic variations among catfish species and strains in response to diseases and stresses provide biological sources for the analysis of genetic and epigenetic regulation of disease resistance. After the publication of the channel catfish reference genome sequence (Liu et al, 2016), rapid progress has been made for the determination of QTL associated with disease resistance (Geng et al, 2015; Zhou et al, 2017b; Shi et al, 2018; Tan et al, 2018) and stress tolerance (Jin et al, 2017; Wang et al, 2017b; Zhong et al, 2017). …”