Development and application of an updated haplotype reference panel for association analysis of spontaneous sex reversal in XX rainbow trout
With the rapid cost reduction of next-generation sequencing, low-coverage whole-genome sequencing (lcWGS) followed by genotype imputation is becoming a cost-effective alternative to SNP (single nucleotide polymorphism) array genotyping. Previously, we constructed a reference panel consisting of 410 samples representing five breeding populations of rainbow trout (Oncorhynchus mykiss). However, the reference panel had a limited representation of the major commercial populations in the U.S. The objectives of this study were two-fold: 1) to update the haplotype reference panel of rainbow trout by adding more reference populations and more samples from the previous reference populations; and 2) to identify SNPs associated with spontaneous sex reversal to males in XX rainbow trout.