Axiom™ Multispecies Tambaqui and Pacu Genotyping Array (Axiom SerraSNP), 384HT format

The Axiom Multispecies Tambaqui and Pacu Genotyping Array (Axiom SerraSNP) is a component of our Axiom Genotyping Solution in which target genomic DNA is prepared and processed on the GeneTitan Multi-Channel Instrument. The automated process includes hybridization of the gDNA to this high-throughput microarray, followed by staining, washing, imaging, and output of SNP genotyping data for further analysis.

The Axiom Multispecies Tambaqui and Pacu Genotyping Array was designed in collaboration with Dr. Diogo Teruo Hashimoto from São Paulo State University (UNESP, CAUNESP, Jaboticabal - Brazil) and Dr. José Manuel Yáñez from University of Chile. The array contains 29,575 SNPs from tambaqui (Colossoma macropomum) and 29,612 SNPs from pacu (Piaractus mesopotamicus). Moreover, 3000 polymorphic SNPs were validated for a closely related serrasalmid species, pirapitinga (Piaractus brachypomus), by conversion rate using the SNP markers of tambaqui and pacu as a valuable resource for the application to selective breeding programs and conservation/population studies. This array is also available in mini-96 format (Cat. No. 551219).

Tambaqui content
• Contains 29,575 SNPs
• Samples for SNP discovery obtained from broodstocks of commercial hatcheries in South America (Brazil, Colombia and Peru) and breeding nucleus of Aquaculture Center (Caunesp) of São Paulo State University (Unesp), Brazil
• 81,848 SNPs originated by ddRADseq, GBS1, and RNAseq2,3 techniques initially identified
• in silico prediction to select best probes according to Axiom array criteria resulted in 42,851 recommended markers
• Polymorphic SNPs with Polyhigh resolution and no adjacent polymorphisms selected for final set
• Array verified by genotyping samples from Brazil, Colombia, and Peru
• Average MAF value was 0.247 presenting SNPs with high allele frequency

Pacu content
• Contains 29,612 SNPs
• Pacu used for SNP discovery obtained from full-sib families of breeding nucleus of Aquaculture Center (Caunesp) of São Paulo State University (Unesp), Brazil
• 130,403 SNPs originated by RADseq4, ddRADseq, and RNAseq5 techniques initially identified
• in-silico prediction to select best probes according to Axiom array criteria resulted in 99,682 recommended markers
• Polymorphic SNPs with Polyhigh resolution and no adjacent polymorphisms selected for final set
• Array verified by genotyping samples from broodstocks of different commercial hatcheries in Brazil
• Average MAF value was 0.203 presenting SNPs with high allele frequency

Applications
• Genome-wide association studies
• Molecular breeding (association mapping and genomic selection)
• Population genetics (to distinguish among fish origin)

Required products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument
Axiom Analysis Suite Software
Axiom Long Format Export Tool (AxLE)

References
1. Nunes, J. R. S., Liu, S., Pértille, F., Perazza, C. A., Villela, P. M. S., Almeida-Val, V. M. F., Hilsdorf, A. W. S., Liu, Z. & Coutinho, L. L. Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing. Sci. Rep. 7, 46112 (2017).
2. Ariede, R.B., Freitas, M.V., Hata, M.E., Mastrochirico-Filho, V.A., Pilarski, F., Batlouni, S. R., Porto-Foresti, F. & Hashimoto, D. T. Microsatellites associated with growth performance and analysis of resistance to Aeromonas hydrophila in tambaqui Colossoma macropomum. Front. Genet. 9, 3 (2018).
3. Gomes, F., Watanabe, L., Vianez, J., Nunes, M., Cardoso, J., Lima, C., Schneider, H. & Sampaio, I. Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing. PloS One 14, e0212755 (2019).
4. Mastrochirico-Filho, V. A., Borges, C. H. S., Freitas, M. V., Ariede, R. B., Pilarski, F., Utsunomia, R., Carvalheiro, R., Gutierrez, A. P., Peñaloza, C., Yáñez, J. M., Houston, R. D. & Hashimoto, D. T. Development of a SNP linkage map and genome-wide association study for resistance to Aeromonas hydrophila in pacu (Piaractus mesopotamicus). BMC Genomics 21, 672 (2020).
5. Mastrochirico-Filho, V. A., Hata, M. E., Kuradomi, R. Y., Freitas, M. V., Ariede, R. B., Pinheiro, D. G., Robledo, D., Houston, R. & Hashimoto, D. T. Transcriptome profiling of pacu (Piaractus mesopotamicus) challenged with pathogenic Aeromonas hydrophila: inference on immune gene response. Front. Genet. 11, 604 (2020).