Publication
Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity
Breeding Insight microhaplotype search
Search microhaplotypes across species, projects, and breeding programs
HapSearch is a searchable interface to Breeding Insight’s microhaplotype databases. Look up a marker, sequence, or sample, compare every allele at a locus in a sequence alignment, and trace each allele to the breeding projects, samples, and collaborators behind it.
Access is limited to registered users. To request access, please email bi-science-team@ufl.edu.
About Microhaplotypes
Microhaplotypes are short genomic segments (typically 54-109 bp) containing two or more closely spaced variants that are inherited together as a single unit. Unlike single SNPs which are bi-allelic, microhaplotypes are multi-allelic markers that provide significantly higher information content for diversity analysis, QTL discovery, and genomic selection in plant breeding.
Because the SNPs within a microhaplotype are sequenced together in the same short read, their phase is directly observed, making them highly informative, phase-known markers. This multi-allelic nature and strong linkage make microhaplotypes especially powerful for characterizing germplasm, where unique and trait-associated microhaplotypes can be tracked within and across breeding populations to inform designing crosses.
HapSearch Platform
HapSearch centralizes fragmented microhaplotype data generated from the DArTag targeted genotyping platform across multiple breeding programs. The platform enables targeted mining of alleles of interest by crop species, sequence similarity, and project-specific keywords, with integrated filters to narrow results to specific loci. It also provides multiple sequence alignment views to display locus-level variation and help users identify accessions carrying unique microhaplotype alleles, while connecting sequence-level information to breeding projects and samples for marker evaluation and decision support. By improving data discoverability and cross-project visibility, HapSearch supports collaboration and resource exchange across breeding and research communities.
Breeding Insight’s Microhaplotype Database
Breeding Insight maintains standardized, species-specific microhaplotype databases built from DArTag data contributed by USDA-ARS, university, and other breeding programs. Each allele has one permanent ID, so results line up across years, projects, and institutions. New reports processed with HapApp add newly discovered alleles, so the databases HapSearch draws on keep growing. 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.
Microhaplotypes
HapApp
Processes DArTag MADC reports against Breeding Insight’s microhaplotype databases and assigns fixed allele IDs ready for downstream analysis.
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.
Mate allocation
AlloMate
A Shiny app that simplifies mate allocation decisions for breeders.
Ploidy and CNV
Qploidy2
Estimates ploidy, aneuploidy, and large-scale copy number variation from genetic marker data.
R package
BIGr
Functions developed by Breeding Insight to analyze diploid and polyploid breeding and genetic data.
Data management
DeltaBreed
Open-source breeding data management software for specialty crop and animal breeders.
Sign in with your ORCID iD to search Breeding Insight’s microhaplotype databases with HapSearch.