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

Abstract

Abalones (genus Haliotis) are important shellfish in fisheries and aquaculture industries in China. Genetic interactions 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 management 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 ♀ × H. discus hannai ♂ and between Pacific abalone, Xishi abalone, and H. gigantea ♀ × H. discus hannai ♂ were relatively close. However, H. fulgens ♀ × H. discus hannai ♂ and H. gigantea ♀ × H. discus hannai ♂ 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.