SNP Identification by Transcriptome Sequencing and Candidate Gene-Based Association Analysis for Heat Tolerance in the Bay Scallop Argopecten irradians

Abstract

The northern bay scallop Argopecten irradians irradians (Lamarck) and the southern bay scallop Argopecten irradians concentricus (Say) were introduced into China in the 1980s and 1990s, and are now major aquaculture molluscs in China. Here, we report the transcriptome sequencing of the two subspecies and the subsequent association analysis on candidate gene on the trait of heat tolerance. In total, RNA from six tissues of 67 and 42 individuals of northern and southern bay scallops, respectively, were used and 55.5 and 34.9 million raw reads were generated, respectively. There were 82,267 unigenes produced in total, of which 32,595 were annotated. Altogether, 32,206 and 23,312 high-quality SNPs were identified for northern and southern bay scallops, respectively. For case-control analysis, two intercrossed populations were heat stress treated, and both heat-susceptible and heat-resistant individuals were collected. According to annotation and SNP allele frequency analysis, 476 unigenes were selected, and 399 pairs of primers were designed. Genotyping was conducted using the high-resolution melting method, and Fisher’s exact test was performed for allele frequency comparison between the heat-susceptible and heat-resistant groups. SNP all-53308-760 T/C showed a significant difference in allele frequency between the heat-susceptible and heat-resistant groups. Notably, considerable difference in allele frequency at this locus was also observed between the sequenced natural populations. These results suggest that SNP all-53308-760 T/C may be related to the heat tolerance of the bay scallop. Moreover, quantitative expression analysis revealed that the expression level of all-53308 was negatively correlated with heat tolerance of the bay scallop.

Integrating intraspecific differentiation in species distribution models: Consequences on projections of current and future climatically suitable areas of species

“…This would suggest that heat tolerance may also be conserved within species. However, several empirical studies (including studies on bumblebee species) underlined differentiations in genes coding for heat tolerance (Du, Li, Zhang, Meng, & Zhang, 2014) or in heat resistance (Homburg et al, 2014;Martinet, Lecocq et al, 2015;Oyen et al, 2016;Slatyer, Nash, & Hoffmann, 2016;Sorte, Jones, & Miller, 2011) among conspecific populations or ESUs. Therefore, such assessments require experiments to determine the tolerances to all climatic parameters of differentiated populations.…”

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…A SNP genotype was identified as significantly related to cold tolerance among individual shrimps. SNP identification by transcriptome sequencing and candidate gene-based association analysis was performed for heat tolerance in the bay scallop Argopecten irradians (Du et al, 2014). SNP all-53308-760 T/C showed a significant difference in allele frequency between the heat-susceptible and heat-resistant groups.…”

A genotype–phenotype association approach to reveal thermal adaptation in Daphnia galeata

“…Genotype–phenotype relationships are still mostly examined in studies concerning human diseases and traits of agricultural importance by applying data‐driven genome‐wide association analyses. Now that simultaneous genotyping of high numbers of individuals and therefore genotype–phenotype association analyses have become feasible for a wide range of species through high throughput sequencing (reviewed in Korte & Farlow, ), efforts are made to utilize this approach for ecological research and toward hypothesis‐driven candidate gene association analysis (e.g., Du, Li, Zhang, Meng, & Zhang, ).…”