Introduction
The interest for the use of diagnostic molecular markers to genetically identify species and interspecific hybrids is increasing with both commercial and conservation purposes. Lowering costs and processing time is of primary relevance especially for routine applications in which pureness of individuals must be rapidly assessed such as in the enforcement of commercial controls and in the selection of captive breeders (Toews & Brelsford, 2012; Camacho-Sanchez et al., 2020).
We present a new class of nuclear molecular markers carrying interesting features potentially useful to investigate different levels of fish genetic diversity: introns’ polymorphisms.
Material and Methods
Based on an in silico analysis of available fish genomes, we isolated several intronic regions potentially conserved across teleosts to be characterized by an opportunely optimized targeted-amplicon high-throughput sequencing method.
A total of 122 intronic loci were selected for primer construction. All primer pairs were validated on 66 species also including important species for aquaculture and conservation purposes. Sequencing data allowed for evaluating suitability and reliability of such introns in detecting species and differentiating populations. We will also present a case study on the discrimination between the Solea solea and the very similar S. aegyptiaca.
Results
Introns has proven to be highly transferable across species with about 70 loci successfully amplified in over half of the species tested and their sequence variability has proven to have a very high-resolution power in differentiating at the species level. Focusing on the case study of the genus Solea, we identified 38 perfectly diagnostic loci with alternative private alleles between the two species. that These loci allowed for setting up fast and cheap identification tool base on introns’ polymorphisms.
Discussion
We presented the first panel of highly conserved intron markers, characterized by high transferability between species, and variability in terms of allelic richness, as well as remarkable diagnostic potential for analysis of species and hybrid identification. Obtained results are very encouraging also for many other applications such as detection of population origin and relatedness analysis. What showed in the case study can be optimized for many other fish species.
References
Toews DPL & Brelsford A (2012). The biogeography of mitochondrial and nuclear discordance in animals. Molecular Ecology, 21(16): 3907-30. http://doi.org/10.1111/j.1365-294X.2012.05664.x
Chamazo-Sanchez M, Velo-Antòn G, Hanson JO, et al. (2020). Comparative assessment of range-wide patterns of genetic diversity and structure with SNPs and microsatellites: a case study with Iberian amphibians. Ecology and Evolution, 10:10353-10363. https://doi.org/10.1002/ece3.6670.