Abalones belong to the genus of Haliotis and are economically important marine invertebrates for fisheries and aquaculture industries worldwide. The disk and pacific abalone, Haliotis discus, is an important species in Korean abalone culture. However, the global climate changes steadily warming the water temperature in coastal areas of Korea in summer, causing higher mortality in abalone farms. In addition, to prevent the potential inferiority in hatchery stock due to prolonged farming activities in limited areas, efforts are also being made to improve the genetic diversity of H. discus. Accordingly, single nucleotide polymorphisms (SNPs) analysis using molecular inversion probes were performed to analyze genetic characteristics related to thermotolerance and growth.
Initially, Genotyping By Sequencing (GBS) was done to find genome modification of 55 abalones which are F0 parents to produce F1 offsprings. After the sequence mapping and variant calling, 202,434 SNPs were confirmed. As a result of specific filtering steps, 27,771 SNPs were filtered as high-quality SNPs. Among them, 500 SNPs were selected to analyze the genotypes as molecular inversion probes (MIPs). Subsequently, MIPs and adapters containing a barcode sequence were designed.
For the MIPs analysis, 973 and 673 abalones were selected for the growth and thermotolerance tests respectively. MIPs experiments were performed with several steps such as probe pooling, target capture & library construction, gap filling & ligation reaction, degradation, multiplex PCR & purification. As a result, insert sequences of 180 bp were obtained from the genomic DNA of 1,646 abalones and processed to collect the data by Illumina Next-Seq. Based on the sequencing data, individual genotyping was profiled for the selected specific variations of growth and thermotolerance.
In conclusion, the specific MIPs were suitably developed from H. discus. Also, the genotype data were constructed and characterized for important traits such as growth and thermotolerance. In future, these results will be applied to improve the abalone with desirable qualities for the abalone aquaculture industry.