ArticleBMC bioinformatics2018
A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- GenoTriplo: A SNP genotype calling method for triploids.PLoS computational biology · 2024Article
- Genome-wide family prediction unveils molecular mechanisms underlying the regulation of agronomic traits inFrontiers in plant science · 2023Article
- Allele expression biases in mixed-ploid sugarcane accessions.Scientific reports · 2022Article
- Genomic prediction with allele dosage information in highly polyploid species.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR.F1000Research · 2022Article
- Strategies to Increase Prediction Accuracy in Genomic Selection of Complex Traits in Alfalfa (Cells · 2021Review
- Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR.Bioinformatics (Oxford, England) · 2021Article
- Genome-wide approaches for the identification of markers and genes associated with sugarcane yellow leaf virus resistance.Scientific reports · 2021Article
- Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species.BMC bioinformatics · 2021Article
- Genomic Selection in an Outcrossing Autotetraploid Fruit Crop: Lessons From Blueberry Breeding.Frontiers in plant science · 2021Article
- Construction of a High-Density Genetic Map ofFrontiers in plant science · 2021Article
- Applying Molecular Phenotyping Tools to Explore Sugarcane Carbon Potential.Frontiers in plant science · 2021Review
- A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses.Frontiers in plant science · 2021Article
- Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance.Scientific reports · 2020Article
- Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population.Genetics · 2020Article
- Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa (International journal of molecular sciences · 2020Article
- Genotype calling of triploid offspring from diploid parents.Genetics, selection, evolution : GSE · 2020Article
- High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass (Frontiers in plant science · 2020Article
- Quantitative trait loci and differential gene expression analyses reveal the genetic basis for negatively associated β-carotene and starch content in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.].TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundGenotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because genotype calling software generally fails to properly distinguish heterozygous classes based on allele dosage.
resultsVCF2SM is a Python script that integrates sequencing depth information of polymorphisms in variant call format (VCF) files and SUPERMASSA software for quantitative genotype calling. VCFs can be obtained from any variant discovery software that outputs exact allele sequencing depth, such as a modified version of the TASSEL-GBS pipeline provided here. VCF2SM was successfully applied in analyzing GBS data from diverse panels (alfalfa and potato) and full-sib mapping populations (alfalfa and switchgrass) of polyploid species.
conclusionsWe demonstrate that our approach can help plant geneticists working with autopolyploid species to advance their studies by distinguishing allele dosage from GBS data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.