Development of a low-density SNP genotyping panel by a novel technology mGPS and its application in germplasm identification of abalone

Abalones (genus Haliotis) are important shellfish in fisheries and aquaculture industries in China. Genetic in-teractions between abalone species are common in Chinese fisheries since their artificial breeding involves the production of interspecific hybrids of Pacific abalone (H. dicus hannai) and Green abalone (H. fulgens) as well as Pacific abalone (H. dicus hannai) and Xishi abalone (H. gigantea). To achieve better abalone breeding manage-ment and investigate the discrepancies between different abalone groups, this study developed and validated an SNP genotyping tool by the methods of genomic resequencing and Genotyping by Pinpoint Sequencing of multiplex PCR products (mGPS). We established a DNA fingerprint for five abalone groups through target SNPs located in 59 segments identified from 130 abalone resequencing datasets. Five distinct groups were successfully discriminated from 244 abalone individuals based on the group discrepancy analysis. The results indicated that the genetic distances between Pacific abalone, Green abalone, and H. fulgens female x H. discus hannai male and between Pacific abalone, Xishi abalone, and H. gigantea female x H. discus hannai male were relatively close. However, H. fulgens female x H. discus hannai male and H. gigantea female x H. discus hannai male had a closer genetic relationship with their original female parents Pacific abalone and Xishi abalone, respectively. In addition, a core set of two specific SNPs sourced from 59 segments was diagnostic in identifying the five abalone groups. Our results present a novel method with the advantages of high efficiency and low cost and thus have potential applications in genetic research. The identified genotyping panel developed based on this method is a valuable tool that can improve our understanding of the connectivity and difference between five abalone groups. Furthermore, the core SNP markers could contribute to future authentication and conservation of abalone germplasm resources.

Automated summary

This study developed and validated an SNP genotyping tool using genomic resequencing and Genotyping by Pinpoint Sequencing of multiplex PCR products (mGPS). Five abalone groups were identified, and genetic distances between them were analyzed. The results showed close genetic relationships between certain abalone groups, and core SNP markers were identified for future authentication and conservation of abalone resources.