TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026
Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity.
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Zhao Dongyan, Lin Meng, Taniguti Cristiane H, Sandercock Alexander M, Chen Shufen, Babiker Ebrahiem, Bassil Nahla V, Brummer E Charles, Camacho Jose Roberto, Chatwin Warren, Chen Shu-Yun, Clare Shaun J, da Silva Pereira Guilherme, David Maria, Fraher Simon Phillip, Hardigan Michael, Hilton Angelyn, Hislop Lillian M, Irish Brian M, Kante Moctar, Kim Tae Hwa, Lee Chong-Wei, Lindqvist-Kreuze Hannele, Loarca Jenyne, Lu Po-Hsien, Medina Culma Cesar Agusto, Jiménez Morales Jose Fabián, Polashock James, Price John H, Riday Heathcliffe, Samac Deborah A, Sandhu Devinder, Ssali Reuben, Castro Vásquez Ruth Mayela, Wadl Phillip A, Wang Xinwang, Webster Seymour A, Xu Zhanyou, Yencho G Craig, Beil Craig T, Sheehan Moira J
Аннотация
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.