Elsevier

Aquaculture

Volume 536, 15 April 2021, 736436
Aquaculture

A genome-wide association study of heat tolerance in Pacific abalone based on genome resequencing

https://doi.org/10.1016/j.aquaculture.2021.736436Get rights and content

Highlights

  • A genome-wide association study (GWAS) was performed to find the associated SNPs with heat tolerance of Pacific abalone.

  • The adhesion ability was important for abalone and attachment duration was hired to assess the heat tolerance of abalone in this study.

  • The linkage disequilibrium (LD) decay was rapid within the abalone samples and a great number of SNPs were required for GWAS.

Abstract

China produces nearly 90% of the world's abalone. The Pacific abalone, Haliotis discus hannai, is the main cultured species. Because of the southward migration to subtropical areas from its natural temperate habitat, abalone can be grown at suitable temperatures for an extended time, and the growth period has been greatly shortened. However, the survival rate declines sharply with high temperatures, especially in summer. Therefore, heat tolerance has been one of the most important economic traits for abalone farming, and accelerating genetic improvements has become the priority of breeding research. In this study, a genome-wide association study (GWAS) was performed using genome resequencing to identify the loci associated with the heat tolerance of abalone. A total of 1,431,014 single nucleotide polymorphisms (SNPs) were identified. Among these, 27 SNPs showed significant associations with heat tolerance. Thirty candidate genes were identified near these SNPs. Most of these genes were related to metabolism, ion channels, signal transduction, or DNA repair. In particular, genes mdhc (malate dehydrogenase, cytoplasmic), achβ3 and ach92 (acetylcholine receptors), and cah2 and cah7 (carbonic anhydrase) have been demonstrated to be associated with heat response in previous studies in mollusks, corroborating the accuracy and reliability of the GWAS results. The results should be useful for marker-assisted selection (MAS), which would accelerate the genetic improvement of heat tolerance of abalone, and promote the understanding of the molecular mechanisms underlying heat tolerance in Pacific abalone or other shellfish.

Introduction

The Pacific abalone, Haliotis discus hannai, is an important fishery and food resource that has been widely farmed in East Asia (Nguyen et al., 2013). In China, the Pacific abalone is endemic to the coastal areas of Shandong and Liaoning Peninsulas, and its large-scale farming began in the late 1980s (Guo et al., 1999; Li et al., 2007; Chen et al., 2017). During the first 20 years, the Pacific abalone farming remained restricted to the coastal areas within or close to its natural habitats. Around 2000, the farming activities were gradually extended from the northern Yellow Sea (a temperate area) to the East China Sea (a subtropical area) (Chen et al., 2016). Since then, the abalone farming in China has developed rapidly. In 2018, the production was 163,169 tons, producing more than three billion US dollars (Xu and Wu, 2019). Fujian Province accounts for approximately 80% of the country's production, making it the largest producer of abalone in the world (Xu and Wu, 2019).

Because of the southward migration, the Pacific abalone can be grown at suitable temperatures for an extended time, and the growth period has been greatly shortened. However, the highest seawater temperature in Fujian is close to 30 °C (Fig. S1), which is much higher than that in the abalone's the natural habitats. It has been reported that the optimal temperature was around 20 °C for the Pacific abalone, and deviations from this temperature would result in reduceding immune activity, increaseding susceptibility to disease outbreaks, leading to higher mortality (Cheng et al., 2004; Dang et al., 2012; Kyeong et al., 2020). In addition, the increasing temperature would lead to hypoxic condition easily, and suppress the respiration and metabolism of marine organisms, causing internal energy imbalance (Hamburger et al., 1994; Hoegh-Guldberg and Bruno, 2010; Chen et al., 2016). Therefore, high temperature has been one of the major reasons for summer mortality. More worryingly, the average sea surface temperatures have increased by 0.6 °C in the last 100 years, and this upward trend is ongoing (Hoegh-Guldberg and Bruno, 2010). Therefore, accelerating the genetic improvement in abalone heat tolerance has become the priority of breeding research.

Marker-assisted selection demonstrates high efficacy without the time-consuming and labor-intensive methods that limit traditional breeding programs. However, marker-assisted selection must be based on effective loci that must be identified via genetic dissection (Jia et al., 2020). Genome-wide association study (GWAS) with high-throughput genotyping data can help to discover important genes or genetic loci, even with small sample size. Thus, GWAS has become an efficient and powerful tool to illustrate the target traits. In economically important fishes, some GWAS studies have been performed, and most focused on growth traits and disease resistance (Liu et al., 2015; Geng et al., 2015; Tsai et al., 2015; Correa et al., 2017; Geng et al., 2016; Zhou et al., 2017; Li et al., 2018; Zhou et al., 2019). In addition, 3 significant associated single nucleotide polymorphisms (SNPs) and 14 genes with heat stress-related functions were detected by GWAS analyses in catfish (Jin et al., 2017). With the rapid development of sequencing technology, GWAS analyses in shellfish have been developed in recent years. For example, a significant quantitative trait locus (QTL) affecting host resistance to Ostreid herpesvirus (Gutierrez et al., 2018) and 12/11 SNPs of Zn/Cu contents-related (Meng et al., 2020) were revealed in the Pacific oyster (Crassostrea gigas). One genomic region on chromosome 11 that is associated with shell color (Zhao et al., 2017) and two significantly growth-associated SNPs (Ning et al., 2019) were reported in the scallop. However, there have been no reports of GWAS analyses on heat tolerance in shellfish.

Usually, GWAS approaches call for high-throughput genotyping data by SNP chip or restriction-site associated DNA sequencing (RAD-seq). However, these methods have their limitations. Chip data consist of only a few variants selected based on their quality (Talouarn et al., 2020), and there is no suitable array that can be used in recent studies of abalone. RAD-seq data cover less than 10% of the examined genome (Xu et al., 2019). The number of SNPs available in these methods also limited the efficacy of GWAS, leading to an inability to identify the causal loci of complex traits. Whole-genome sequence data containing the majority of SNPs were optimized to enhance the accuracy and power of GWAS and the detection of QTLs associated with complex traits (Wu et al., 2019).

Therefore, this study aimed to identify SNPs associated with heat tolerance in abalone by conducting whole genome resequencing and GWAS analysis. The results would offer candidate loci for the marker-assisted selection (MAS) of novel abalone varieties with better heat tolerance and provide a basis for further research on the function of related genes, thereby promoting the understanding of the molecular mechanisms underlying heat tolerance in Pacific abalone or other shellfish.

Section snippets

Heat stress experiment and sample collection

In this study, the attachment duration (the length of time that an abalone remained adhered to the substrate) at high temperature was employed to assess the heat tolerance. First, a suitable temperature was selected. A total of 360 abalones (shell length 60.41 ± 3.35 mm) were randomly divided into six groups; each group was transferred to a tank that contained 270 L fresh seawater. The acclimation followed the procedures conducted by Chen et al. (2016). The abalones were acclimated at 20 °C for

The selection of heat stress temperature

A total of five temperatures (29, 30, 31, 32, and 33 °C) were used for choosing the optimal stress conditions. As shown in Fig. 1, all individuals remained attached in the control group (20 °C) within 12 h, and the result was the same when the temperature was set at 29 °C. When the temperatures were kept at 30 and 31 °C, there were four and eight individuals respectively, dropping from the substrates within 12 h (Table S1). When the temperature was raised to 32 °C, the abalone gradually

Discussion

Because of the southward migration, heat stress has been one of the paramount challenges for abalone culture in China, and heat tolerance has become an economically important trait (Chen et al., 2016; Chen et al., 2019). In this study, a GWAS analysis was conducted to obtain key loci/SNPs for abalone heat tolerance. The first step was to assess the different tolerance levels of individuals. It has been reported that the adhesion ability of abalone is influenced by temperature (Park et al., 2015

Conclusions

Using genome resequencing, the first GWAS analysis for heat tolerance of abalone was performed in this study. A total of 27 heat-tolerant SNPs and 30 candidate genes were identified. Among the identified genes, mdhc, Ach, and cah have been shown to be associated with heat response in mollusks, thus demonstrating the accuracy and reliability of the results. And it provided valuable information for further researches on the function of related genes. Meanwhile, both the moderate level

Author statement

Feng Yu: Measurement, Sampling, Data curation, Visualization, Formal analysis, Writing - Original draft, Writing - Review and Editing.

Wenzhu Peng: Sampling, Visualization, Software, Formal analysis, Writing - Original draft, Writing - Review and Editing.

Bin Tang: Measurement, Sampling.

Yifang Zhang: Measurement, Sampling, Formal analysis.

Yi Wang: Measurement, Writing - Original draft.

Yang Gan: Sampling, Visualization.

Xuan Luo: Materials, Investigation,Validation.

Weiwei You: Investigation,

Declaration of Competing Interest

We declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled, “A genome-wide association study of heat tolerance in Pacific abalone based on genome resequencing”.

Acknowledgements

This work was supported by grants from the National Key Research and Development Program of China (2018YFD0901401), National Natural Science Foundation of China (U1605213, 31802294 and 31872564) and Fujian Provincial S & T Project (2019 N0001).

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