Development of SNP markers for identification of thermo-resistant families of the Pacific oyster Crassostrea gigas based on RNA-seq

The Pacific oyster Crassostrea gigas is the most cultivated oyster species around the world. However, massive mortalities linked to high temperatures have been reported in different countries, becoming one of the most significant challenges for oyster culture. High mortality episodes have been reported also in Mexico due to temperature stress, mainly in Sonora and Baja California Sur. In this region, areas with shallow waters can reach 34 °C, causing severe physiological stress, mostly in juvenile oysters. Recently and as a strategy to address this problem in Mexico, a selective breeding program has been implemented, aiming to develop families with high survival at high temperatures through marker-aided selection. The objective of the present study was the identification of SNP markers from the transcriptome of families phenotypically different: thermo-resistant (‘R’) versus thermo-susceptible (‘S’) and analyzing whether these variants were present in transcripts potentially involved in thermal resistance. Several SNP variants were detected between ‘R’ and ‘S’ families, affecting multiple transcripts and molecular pathways. Four SNP markers provided accurate differentiation between ‘R’ and ‘S’ oysters. Additionally, 66 SNPs were suitable for pedigree reconstruction and sibling clustering. The discriminant SNPs were associated with changes in gene transcripts that were related to biological processes such as the activation of HSP90, zinc uptake, collagen biosynthesis, ion transport, and the immune response. The use of SNPs markers associated with thermo-resistant families can help to improve the yields in oyster production at high temperatures, especially in Mexico. •Four SNP markers are provided for selection of thermo-resistant C. gigas oysters.•Additional SNPs (66) were useful for pedigree inference and sibling clustering.•These SNPs will allow for reduced mortalities of oysters at high temperature.•Discriminant SNPs were associated with changes in annotated gene transcripts.