Low-Coverage Whole-Genome Sequencing with Imputation Achieves High Accuracy in Aquatic Species

Strategic Insights -

Recent research from the Chinese Academy of Sciences has demonstrated the potential of low-coverage whole-genome sequencing (lcWGS) with imputation as a cost-effective method for generating large numbers of single nucleotide polymorphism (SNP) in highly heterozygous and complex genomes of aquatic species. This study represents the first systematic investigation into the application of lcWGS with imputation in Pacific abalone (Haliotis discus hannai) without a reference panel. The findings suggest that lcWGS with imputation can achieve high accuracy with moderate sample sizes (n = 400) in Pacific abalone, offering a cost-effective approach for genotyping in aquaculture species.

Key Takeaways:

  • The research utilized 1059 Pacific abalone individuals sequenced at an average depth of 7.86x, as well as 16 individuals sequenced at 20x, as sample materials.
  • To assess the genotype imputation accuracy for lcWGS without a reference panel, the researchers simulated data with varying sequencing depths (0.5-4x) and examined the effects of sample size, chromosome length, and minor allele frequency (MAF).
  • The BaseVar strategy achieved high accuracy when the sample size exceeded 400, with a genotype correlation (R-2) of 0.98 +/- 0.002 and genotype concordance (GC) of 0.99 +/- 0.001.
  • Imputation accuracy plateaued when the sample size exceeded 400 and sequencing depth surpassed 1x.
  • Chromosome length had minimal effects, with all three chromosomes achieving an accuracy of approximately 0.98.
  • The accuracy for rare MAF was affected by sample size and sequencing depth, with lower accuracy at lower sequencing depths.
  • The researchers used the STITCH strategy which achieved high accuracy when the sample size exceeded 400.
  • The BaseVar and STITCH strategies achieved high accuracy in Pacific abalone with lcWGS and imputation.

Statistics:

  • 1059 Pacific abalone individuals were sequenced at an average depth of 7.86x.
  • 16 Pacific abalone individuals were sequenced at 20x.
  • The sample size of 400 achieved high accuracy with the BaseVar and STITCH strategies.
  • The genotype correlation (R-2) and genotype concordance (GC) reached 0.98 +/- 0.002 and 0.99 +/- 0.001, respectively.
  • Chromosome length had minimal effects on accuracy, with an average accuracy of 0.98 across all three chromosomes.
  • Rare MAF had a lower accuracy at lower sequencing depths.

Sources:

  • Evaluation of Low-coverage Sequencing Strategies for Whole-genome Imputation In Pacific Abalone haliotis Discus Hannai. International Journal of Molecular Sciences, 2025;26(10).
  • Chinese Academy of Sciences, Institute of Oceanology, Ctr Ocean Mega Sci, Cas & Shandong Prov Key Lab Expt Marine Biol, Qingdao 266000, People's Republic of China.