Publication
Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity
Breeding Insight microhaplotypeDB
Process your DArTag reports against the public Breeding Insight microhaplotype database reference
HapApp performs QC and filters raw DArTag Missing Allele Discovery Count (MADC) reports, assigns every allele a fixed microhaplotype ID from the public Breeding Insight microhaplotype database for your species, and adds any newly discovered microhaplotypes to it.
Access is limited to registered users. To request access, please email bi-science-team@ufl.edu.
What makes MADC files different?
Most genotyping reports reduce each marker to two alleles, a reference and an alternative, discarding any additional variation found at that locus. A DArTag Missing Allele Discovery Count (MADC) report contains all alleles, including those “missing” from the initial panel design, which are now recognized as newly discovered variants. Specifically, an MADC report retains the full microhaplotype sequences found at each marker locus, along with read counts for every allele at every locus across every sample. This means a single locus can carry many alleles rather than just two, preserving the full scope of genetic variation captured by the sequencing read. HapApp works directly with this multi-allelic data by processing the microhaplotype sequences in the MADC report, rather than collapsing them to biallelic SNPs before analysis.
The practical advantage of keeping multi-allelic data is that nearby SNPs within a sequencing read are inherited together on the same genomic segment. Therefore, the combination of variants is recorded rather than each variant being called independently. Collapsing into a single SNP discards this co-occurrence information, reducing a potentially highly informative multi-allelic marker to a simple presence/absence call.
How HapApp works
HapApp runs the same Breeding Insight pipeline that built the published databases, so your report is processed the same way the reference was. There's no software to install and no command line.
- File checks. HapApp confirms that your upload is a raw, unprocessed DArTag MADC report and that its markers match a supported species panel.
- Quality control. Marker IDs are converted to a standard chromosome-and-position format. Microhaplotypes are kept only if they appear in at least 10 samples or 5% of samples (whichever is smaller) with at least 2 reads each, which removes rare sequencing artifacts.
- Fixed IDs. Each microhaplotype is compared with the database for your species using BLAST. Known microhaplotypes keep their established IDs, new ones get new unique IDs, and duplicate sequences are merged so each has exactly one ID.
- Download your results. You receive a processed MADC with fixed allele IDs, ready for downstream analysis. New microhaplotypes are added to the database, and your processed report, metadata and workflow log are shared with Breeding Insight for review.
Why process against a public reference?
DArTag reports name alleles project by project, so the same microhaplotype can carry different labels in different projects, even within your own program. Processing against the public database gives each microhaplotype one permanent ID. You can combine data across years and projects, compare your germplasm with other programs, and move straight into downstream analysis.
Breeding Insight's Microhaplotype Database
Breeding Insight maintains standardized, species-specific microhaplotype databases built from DArTag data from USDA-ARS and university breeding programs. Each processed report makes the reference more complete for everyone who uses it. The framework and the initial databases are described in a peer-reviewed publication.
- Alfalfa
- Blueberry
- Cranberry
- Cucumber
- Pecan
- Potato
- Strawberry
- Sweetpotato
Continue your analysis with Breeding Insight tools
Processed MADC files with fixed microhaplotype IDs are ready for downstream genomic analysis in Breeding Insight's open-source software.
Genomic analysis
BIGapp
A user-friendly Shiny app for genotype calling from read counts, population structure, GWAS, and genomic selection in diploid and polyploid species.
Ploidy and CNV
Qploidy2
Estimates ploidy, aneuploidy, and large-scale copy number variation from genetic marker data.
Mate allocation
AlloMate
A Shiny app that simplifies mate allocation decisions for breeders.
R package
BIGr
Functions developed by Breeding Insight to analyze diploid and polyploid breeding and genetic data.
Panel evaluation
GenoBrew
A Shiny app for evaluating marker panel efficiency and visualizing copy number variation profiles.
Data management
DeltaBreed
Open-source breeding data management software for specialty crop and animal breeders.
Sign in with your ORCID iD to process a MADC report. Your ORCID iD and metadata are recorded with each submission, so any new microhaplotypes from your data are credited to you.