Axiom™ Multispecies Shrimp and Tilapia Genotyping Array (Axiom™ TilShrv1), 384HT format

The Axiom Multispecies Shrimp and Tilapia Genotyping Array (Axiom TilShrv1) was designed in collaboration with João Campos and Jose Fernando Garcia from Trigene, Brazil, with financial support from PIPE-FAPESP. The array contains 60,886 SNPs from tilapia and 6,453 SNPs from shrimp. It is also available in mini-96 format.

Tilapia content
• Contains 60,886 SNPs from tilapia
• Twelve different strains of Nile tilapia from wild African samples to farmed GIFT, Chitralada, Stirling, and other strains obtained from different origins in Brazil and North America, representing most of the variability of Nile tilapia in the world
• A total of 16 million variants identified after mapping reads from 158 samples to the Nile tilapia reference genome (GCF001858045.2 O. niloticus UMD-NMBU)
• Post-filtering, more than 2 million bi-allelic SNPs investigated for inclusion on the array
• Highly polymorphic SNPs with the no adjacent polymorphisms were selected
• Final set of SNPs had an average distance of 14 kbp on the 22 linkage groups and high allele frequency, with only a few having >5% SNPs with a minor allele frequency lower than 0.05

Applications for tilapia array
• Genome wide association studies
• Molecular breeding—association mapping and genomic selection
• Population genetics—distinguish among fish origin
• Distinguish between different strains of Nile tilapia

Shrimp content
• Contains 6,453 SNPs from shrimp
• Markers selected within the L. vannamei genome from a dataset of over 350,00 putative variants (1,2)
• Evenly spaced markers

Applications for shrimp array
• Genomic selection and evaluation for family identification within Pacific white shrimp (Litopenaeus vannamei)

References
1. Du ZQ, Ciobanu DC, Onteru SK, Gorbach D, Mileham AJ, Jaramillo G, Rothschild MF. A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei. Anim Genet. 2010 Jun;41(3):286-94.
2. Jones DB, Jerry DR, Khatkar MS, Raadsma HW, Steen HV, Prochaska J, Forêt S, Zenger KR. A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei. Sci Rep. 2017 Sep 4;7(1):10360.

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