ArticleBMC plant biology2025
Benchmarking of low coverage sequencing workflows for precision genotyping in eggplant.
Article in BMC plant biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Development of a low-coverage whole genome sequencing screen for apomixis using a diverse set of Malus germplasm.PLoS genetics · 2026Article
- A Pseudohaploid-Based Imputation Strategy for Interspecific FMolecular ecology · 2026Article
- Water stress tolerance, genomic selection and identification of genomic regions in a MAGIC population of eggplant.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Skim-sequencing for genomic selection in wheat: a comparison of marker platforms.The plant genome · 2026Article
- Identification of phenological QTLs using a combination of high- and low-coverage whole genome sequencing in Japanese plum (Horticulture research · 2026Article
- Whole-genome sequencing reveals genomic diversity and selection signatures for adaptation in South African Afrikaner and Bonsmara cattle.Frontiers in genetics · 2026Article
- Resequencing and phenotyping of the first highly inbred eggplant multiparent population revealHorticulture research · 2025Article
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Authors and funding
7 authors.
Funding
Abstract
backgroundLow-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.
resultsSequencing coverages as low as 1X and 2X achieved high accuracy but lacked sufficient sensitivity and genotypic concordance. However, 3X sequencing reached approximately 10% less sensitivity than 5X while maintaining genotypic concordance above 90% at any depth of coverage threshold. Freebayes outperformed GATK in terms of sensitivity and genotypic concordance. Therefore, we used this software to conduct a pilot test with some MEGGIC lines from the fifth generation of selfing, comparing their datasets with a gold standard. Sequencing coverages as low as 1X identified a substantial number of true positives, with 3X significantly increasing the yield, particularly at moderate depth of coverage thresholds. Additionally, at least 30% of the true positives were consistently genotyped in all lines when using coverages greater than 2X, regardless of the depth of coverage threshold applied.
conclusionsThis study highlights the importance of using a gold standard to reduce false positives and demonstrates that lcWGS, with proper filtering, is a valuable alternative to high-coverage sequencing for eggplant genotyping, with potential applications to other crops.
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