Benchmarking of low coverage sequencing workflows for precision genotyping in eggplant.

ABSTRACT: Low-coverage whole-genome sequencing (lcWGS) presents a cost-effective solution for genotyping, particularly in applications requiring high marker density and reduced costs. In this study, we evaluated lcWGS for eggplant genotyping using eight founder accessions from the first eggplant MAGIC population (MEGGIC). We tested various sequencing coverages and minimum depth of coverage thresholds with two SNP callers, Freebayes and GATK. Reference SNP panels were used to estimate the percentage of common biallelic SNPs (i.e., true positives) relative to the low coverage datasets (accuracy) and the SNP panels themselves (sensitivity). Furthermore, the percentage of true positives with the same genotype across both datasets was calculated to assess genotypic concordance. Sequencing coverages as lo

SUBMITTER: Baraja-Fonseca V 

PROVIDER: S-EPMC12379343 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature