Evidence map›Paper›PMID 42640273›Full record

ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2026

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

Dongyan Zhao, Meng Lin, Cristiane H Taniguti, Alexander M Sandercock, Shufen Chen, Ebrahiem Babiker, Nahla V Bassil, E Charles Brummer, Jose Roberto Camacho, Warren Chatwin and 31 more

Abstract read
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Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. DNA extraction from sweetpotato (Molecular breeding : new strategies in plant improvement · 2026
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

41 authors.

Dongyan ZhaoBreeding Insight, University of Florida, Gainesville, FL, 32611, USA.
Meng LinBreeding Insight, University of Florida, Gainesville, FL, 32611, USA.
Cristiane H TanigutiBreeding Insight, University of Florida, Gainesville, FL, 32611, USA.
Alexander M SandercockBreeding Insight, University of Florida, Gainesville, FL, 32611, USA.
Shufen ChenBreeding Insight, University of Florida, Gainesville, FL, 32611, USA.
Ebrahiem BabikerUSDA ARS Corn Host Resistance Research Unit, Mississippi State, MS, 39762, USA.
Nahla V BassilUSDA ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA.
E Charles BrummerDepartment of Plant Sciences, University of California Davis, Davis, CA, 95616, USA.
Jose Roberto CamachoThe Instituto Nacional de Innovación y Transferencia en Tecnología Agropecuaria (INTA), San José, Costa Rica.
Warren ChatwinUSDA ARS Pecan Breeding and Genetics Program, College Station, TX, 77845, USA.
Shu-Yun ChenDepartment of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan.
Shaun J ClareCarlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark.
Guilherme da Silva PereiraDepartment of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil.
Maria DavidInternational Potato Center (CIP), Lima 12, Apartado, 1558, Peru.
Simon Phillip FraherDepartment of Horticulture Science, NC State University, Raleigh, NC, 27695, USA.
Michael HardiganUSDA ARS Horticultural Crops Production and Genetic Improvement Research Unit, Corvallis, OR, 97333, USA.
Angelyn HiltonUSDA ARS Pecan Breeding and Genetics Program, College Station, TX, 77845, USA.
Lillian M HislopSavanna Institute, 2453 Atwood Ave. Suite 209, Madison, WI, 53704, USA.
Brian M IrishUSDA ARS Plant Germplasm Introduction and Testing Research Unit, Prosser, WA, 99164, USA.
Moctar KanteInternational Potato Center (CIP), Lima 12, Apartado, 1558, Peru.
Tae Hwa KimValue Crop Research Institute, National Institute of Crop and Food Science, Rural Development Administration, Muan, 58545, Republic of Korea.
Chong-Wei LeeDepartment of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan.
Hannele Lindqvist-KreuzeInternational Potato Center (CIP), Lima 12, Apartado, 1558, Peru.
Jenyne LoarcaUSDA ARS Horticultural Crops Production and Genetic Improvement Research Unit, Corvallis, OR, 97333, USA.
Po-Hsien LuDepartment of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan.
Cesar Agusto Medina CulmaDepartment of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
Jose Fabián Jiménez MoralesThe Instituto Nacional de Innovación y Transferencia en Tecnología Agropecuaria (INTA), San José, Costa Rica.
James PolashockUSDA ARS Genetic Improvement for Fruits & Vegetables Laboratory, Chatsworth, NJ, 08019, USA.
John H PriceUSDA ARS Genetic Improvement for Fruits & Vegetables Laboratory, Chatsworth, NJ, 08019, USA.
Heathcliffe RidayUSDA ARS Dairy Forage Research Center, Madison, WI, 53706, USA.
Deborah A SamacUSDA ARS, Plant Science Research Unit, St. Paul, MN, 55108, USA.
Devinder SandhuUSDA ARS Agricultural Water Efficiency and Salinity Research Unit, Riverside, CA, 92507, USA.
Reuben SsaliInternational Potato Center (CIP), Ntinda II Road, Plot 47, Kampala, Uganda.
Ruth Mayela Castro VásquezThe Instituto Nacional de Innovación y Transferencia en Tecnología Agropecuaria (INTA), San José, Costa Rica.
Phillip A WadlUSDA ARS US Vegetable Laboratory, Charleston, SC, 24914, USA.
Xinwang WangUSDA ARS Pecan Breeding and Genetics Program, College Station, TX, 77845, USA.
Seymour A WebsterCollege of Agriculture, Science and Education, Faculty of Food and Agriculture Department of Plant, Soil Sciences, and Engineering, Passley Gardens, P.O. Box 170, Port Antonio, Portland, Jamaica.
Zhanyou XuPathology, and Genetics Research Unit, USDA ARS Soybean/Maize Germplasm, Urbana, IL, 61801, USA.
G Craig YenchoDepartment of Horticulture Science, NC State University, Raleigh, NC, 27695, USA.
Craig T BeilBreeding Insight, University of Florida, Gainesville, FL, 32611, USA.
Moira J SheehanBreeding Insight, University of Florida, Gainesville, FL, 32611, USA. moirasheehan@ufl.edu.ORCID https://orcid.org/0000-0002-3400-2165

Funding

Agricultural Research Service 8062-21000-043-004-ABill and Melinda Gates Foundation OPP1213329National Institute of Food and Agriculture 2019-70005-30361National Institute of Food and Agriculture 2023-70005-41081NIFA 2019-70005-30361Rural Development Administration PJ0188901USDA ARS 2072-21000-059-000D
6 · The paper itself

Abstract

keymessageStandardized 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.

Indexed as

Crops, AgriculturalDatabases, GeneticGenetic VariationHaplotypesGenome, PlantPlant BreedingPolymorphism, Single Nucleotide

Identifiers

PMID42640273
PMCPMC13506570

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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.