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Benchmarking of low coverage sequencing workflows for precision genotyping in eggplant
Virginia Baraja-Fonseca1, Andrea Arrones2, Santiago Vilanova2
1Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain. vbarfon@posgrado.upv.es.
BMC Plant Biology
|August 25, 2025
Summary
Low-coverage whole-genome sequencing (lcWGS) is a cost-effective method for eggplant genotyping. Even at 3X coverage, lcWGS provides high accuracy and genotypic concordance, making it a viable alternative to high-coverage sequencing.
Area of Science:
- Genomics
- Plant Breeding
- Bioinformatics
Background:
- Low-coverage whole-genome sequencing (lcWGS) offers a cost-effective approach for high-density genotyping.
- Evaluating lcWGS for eggplant genotyping is crucial for advancing breeding programs.
- The study utilized the first eggplant MAGIC population (MEGGIC) for evaluation.
Purpose of the Study:
- To assess the effectiveness of lcWGS for eggplant genotyping across various sequencing coverages and depth thresholds.
- To compare the performance of Freebayes and GATK SNP callers under lcWGS conditions.
- To determine optimal parameters for accurate and sensitive eggplant genotyping using lcWGS.
Main Methods:
- Tested lcWGS with coverages from 1X to 5X and varying minimum depth thresholds.
- Employed Freebayes and GATK for SNP calling.
- Utilized reference SNP panels to calculate accuracy, sensitivity, and genotypic concordance.
- Conducted a pilot test on MEGGIC lines using a gold standard comparison.
Main Results:
- Coverages of 1X and 2X showed high accuracy but limited sensitivity and concordance.
- 3X sequencing achieved >90% genotypic concordance and near 5X sensitivity.
- Freebayes demonstrated superior sensitivity and genotypic concordance compared to GATK.
- 3X coverage significantly increased true positive yield, especially at moderate depths.
- Consistent genotyping (>30% true positives) was achieved with >2X coverage.
Conclusions:
- lcWGS, with appropriate filtering and a gold standard, is a reliable method for eggplant genotyping.
- 3X coverage offers a strong balance between sensitivity, accuracy, and concordance.
- This approach has potential applications for genotyping in other crop species.
