The inclusion of genomic information is expected to accelerate the genetic gain over time in comparison to traditional pedigree-based methods in shrimp breeding. The decay of linkage disequilibrium (LD) between single nucleotide polymorphisms (SNPs) is an important measure to evaluate the feasibility of implementing genomic selection (GS) and genome-wide association studies (GWAS) . Our aims were to show the first application of a 50K SNP to estimate the LD and the effective population size (Ne) of a breeding population of Pacific white shrimp.
A total of 96 animals (40 sires and 56 dams) from an Ecuadorian breeding population were genotyped using the novel Illumina AquaArray HD (50K) vannamei®. A q uality control of genotypes was performed consisting of four exclusion criteria: call-rate < 0.8 for SNPs and samples, Hardy-Weinberg equilibrium (p-value < 10-5 ) and minor allele frequency (MAF) with different threshold values, forming three quality control sets (QC): < 0.10 (QC1), < 0.05 (QC2) and < 0.01 (QC3). The LD was estimated using the r2 measure and the Ne was estimated using a method that takes into account LD and recombination rate. After QC, 34,425, 39,091 and 42,789 SNPs were retained for QC1, QC2 and QC3, respectively, validating the high informativeness of this SNP array to this particular shrimp population. LD decayed rapidly in the first 30Kb of distance between markers from 0.20 to 0.07 and then decreased to 0.02 in the long-range distance (Figure 1). These results suggest a relatively recent incorporation of animals from different populations in the broodstock. Ne size reduction was more significant in the last 300 generations with approximately 62% of total reduction in this period (Figure 2) . However, the contemporary Ne estimated was close to 86 showing that despite mass selection applied in this population, the effective population size is at an acceptable level. In conclusion, the level of LD estimated suggests that GS and GWAS are feasible in shrimp by using this SNP array.