Development and performance of a SNP array for black tiger shrimp and a GWAS for sex determination

Black tiger shrimp ( Penaeus monodon ) is a high value aquaculture species however development of genomic tools and advanced breeding programs remain behind that of many other domestic animals. To develop a SNP array with high rates of informativeness across diverse populations, we sequenced both wild and farmed shrimp to an average of 18-fold coverage. Application of stringent filters identified 4.27 M high quality SNP. Allele frequency, genome spacing and high local linkage disequilibrium (LD) were used to select 8472 SNP for manufacture of an Illumina Infinium custom SNP array. Validation was performed by genotyping 972 individuals, revealing high rates of assay conversion. The prospects to support genomic selection was evaluated using two approaches. First, the accuracy of genomic relationship matrices was evaluated. Secondly, LD was found to decay rapidly in one population but persisted over larger physical distances in a second population with reduced genetic diversity. This suggested that for at least some populations the array is likely to capture a significant proportion of genetic variability. We also tested the ability of the array to discover association signals by mapping the sex determination locus to a single critical interval of 4.2 Mb on chromosome 19. Transcriptomic analysis prioritised Feminization-1 ( Fem-1 ) and Cyclic-AMP responsive element modulator like-1 ( CrebB ) as positional candidate genes. We report the construction and performance of a high-quality genotyping tool suitable for a range of applications including genomic selection. • Availability of a tiger shrimp SNP array opens options for advanced breeding. • Validation testing revealed high rates of polymorphism. • GWAS identifies a small region on chromosome 19 associated with sex determination.