Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity

KEYMESSAGE: Standardized microhaplotype databases for eight diverse crops enable multiallelic analyses, comparative genetics, and breeding decisions. Microhaplotypes are short genomic segments that contain multiple tightly linked variants, providing multi-allelic data that can enhance genetic resolution compared to traditional biallelic single nucleotide polymorphism (SNP) markers. Here, we present the creation and utilization of separate microhaplotype databases for eight crop species representing diverse genome sizes, ploidy levels, and breeding systems. We developed a standardized, species-agnostic pipeline for processing, filtering, and databasing microhaplotypes generated using the DArTag targeted genotyping platform. To enhance user accessibility, we developed a no-code, user-friendly application, HapApp, that uses an R Shiny front-end interface to allow breeders and researchers to add unique, standardized microhaplotype identities from raw DArTag reports and iteratively update the existing crop-specific database with the newly discovered microhaplotypes. Selected case studies with these databases highlight the operational advantages of microhaplotypes, especially for challenging, highly heterozygous, or polyploid species. They offer an informative alternative to traditional biallelic SNP analyses for resolving population structures and improving linkage map ordering. This integrated framework provides a reproducible and scalable foundation for managing and exploiting microhaplotype data in plant breeding and genetic research, enabling robust cross-project comparisons and facilitating trait discovery in both simple and complex crop genomes, while enabling comparative genomics and cross-species functional transfer that accelerates genetic gains across all crop species.

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Publication Details

Journal
Theoretical and Applied Genetics
Published
2026-08-25
DOI
https://doi.org/10.1007/s00122-026-05340-4
Primary Topic
Genetic diversity and population structure
Type
article
Field-Weighted Citation Impact
0.00

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article

Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity

John H. Price, Brian M. Irish, Dongyan Zhao, Moctar Kante et al.
Theoretical and Applied Genetics
Genetic diversity and population structure
article

Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity

John H. Price, Brian M. Irish, Dongyan Zhao, Moctar Kante, José Roberto Camacho, Jenyne Loarca, Seymour A. Webster, Heathcliffe Riday, Xinwang Wang, Alexander M. Sandercock, Deborah A. Samac, Chong-Wei Lee, Devinder Sandhu, E. Charles Brummer, Zhanyou Xu, Moira J. Sheehan, Shuyun Chen, Meng Lin, Lillian M. Hislop, Tae Hwa Kim, Ruth Mayela Castro Vásquez, James Polashock, Guilherme da Silva Pereira, Ebrahiem Babiker, Maria David, Reuben Ssali, Shufen Chen, Cristiane H. Taniguti, Po-Hsien Lu, Michael Hardigan, Warren Chatwin, Shaun J. Clare, G. Craig Yencho, Jose Fabian Jimenez Morales, Phillip A. Wadl, Simon Phillip Fraher, Craig. T. Beil, Nahla V. Bassil, Cesar Agusto Medina Culma, Angelyn Hilton, Hannele Lindqvist-Kreuze
article en

Abstract

KEYMESSAGE: Standardized microhaplotype databases for eight diverse crops enable multiallelic analyses, comparative genetics, and breeding decisions. Microhaplotypes are short genomic segments that contain multiple tightly linked variants, providing multi-allelic data that can enhance genetic resolution compared to traditional biallelic single nucleotide polymorphism (SNP) markers. Here, we present the creation and utilization of separate microhaplotype databases for eight crop species representing diverse genome sizes, ploidy levels, and breeding systems. We developed a standardized, species-agnostic pipeline for processing, filtering, and databasing microhaplotypes generated using the DArTag targeted genotyping platform. To enhance user accessibility, we developed a no-code, user-friendly application, HapApp, that uses an R Shiny front-end interface to allow breeders and researchers to add unique, standardized microhaplotype identities from raw DArTag reports and iteratively update the existing crop-specific database with the newly discovered microhaplotypes. Selected case studies with these databases highlight the operational advantages of microhaplotypes, especially for challenging, highly heterozygous, or polyploid species. They offer an informative alternative to traditional biallelic SNP analyses for resolving population structures and improving linkage map ordering. This integrated framework provides a reproducible and scalable foundation for managing and exploiting microhaplotype data in plant breeding and genetic research, enabling robust cross-project comparisons and facilitating trait discovery in both simple and complex crop genomes, while enabling comparative genomics and cross-species functional transfer that accelerates genetic gains across all crop species.

Theoretical and Applied GeneticsVol. 139(9)
University of Minnesota (US), Agricultural Research Service (US), International Potato Center (PE), North Carolina State University (US), Universidade Federal de Viçosa (BR), National Chung Hsing University (TW), National Chiayi University (TW), Carlsberg Laboratory (DK), Rural Development Administration (KR), University of Florida (US), Instituto Nacional de Tecnologia (BR), National Clonal Germplasm Repository (US), International Potato Center (UG), Taiwan Agricultural Research Institute Council of Agriculture, Executive Yuan (TW), Agriculture and Food (AU), U.S. Dairy Forage Research Center (US), Medical Education Institute (US), U.S. Salinity Laboratory (US), Horticultural Crops Research Laboratory (US), Cereal Disease Laboratory (US), U.S. Vegetable Laboratory (US), University of California, Davis (US), Mississippi State University (US)
U.S. Department of Agriculture, Bill and Melinda Gates Foundation, Rural Development Administration, Consortium of International Agricultural Research Centers, National Institute of Food and Agriculture, Agricultural Research Service
Openalex Percentile: Top 10%
Genetic diversity and population structure
DOIOpen Access PDFOpenAlex
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