ArticlePlant biotechnology journal2021
Soybean (Glycine max) Haplotype Map (GmHapMap): a universal resource for soybean translational and functional genomics.
Article in Plant biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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53 citing papers in PubMed, 76 citations in OpenAlex.
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- Identification of Genomic Regions for Partial Resistance to Soybean Rust Under Field Conditions Using FarmCPU and Machine Learning Approaches.Plants (Basel, Switzerland) · 2026Article
- Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse.Scientific data · 2026Article
- Dissection of local haplotype diversity at soybean rust loci reveals resistance-associated and context-dependent variation patterns in diverse germplasm.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Allelic differences within DNA polymerase delta subunit 1 correlate with geminivirus resistance in diverse plants.G3 (Bethesda, Md.) · 2025Article
- Integrative genome-wide association and haplotype-based analyses reveal genetic structure and local adaptation in Korean landrace soybeans.BMC plant biology · 2025Article
- Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions.BMC plant biology · 2025Article
- Benchmarking of low coverage sequencing workflows for precision genotyping in eggplant.BMC plant biology · 2025Article
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- Genetic diversity and population structure of soybean (Glycine max (L.) Merril) germplasm.PloS one · 2025Article
- Genetic diversity, population structure in a historical panel of Brazilian soybean cultivars.PloS one · 2025Article
- A strategy for identification and characterization of genic mutations using a temperature-sensitive chlorotic soybean mutant as an example.Plant direct · 2024Article
- Enhancing Agrobacterium-mediated soybean transformation efficiency with an auxiliary solution.Crop health · 2024Article
- Integrating targeted genetic markers to genotyping-by-sequencing for an ultimate genotyping tool.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Allelic variability in the Rpp1 locus conferring resistance to Asian soybean rust revealed by genome-wide association.BMC plant biology · 2024Article
- A spatially resolved multiomic single-cell atlas of soybean development.bioRxiv : the preprint server for biology · 2024Article
- Omics-driven utilization of wild relatives for empowering pre-breeding in pearl millet.Planta · 2024Review
- Genetic insights into agronomic and morphological traits of drug-type cannabis revealed by genome-wide association studies.Scientific reports · 2024Article
- Identification and characterization of a temperature sensitive chlorotic soybean mutant.bioRxiv : the preprint server for biology · 2024Article
- Dissection of theFrontiers in plant science · 2024Article
Corrections and comments
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Authors and funding
11 authors at 8 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we describe a worldwide haplotype map for soybean (GmHapMap) constructed using whole-genome sequence data for 1007 Glycine max accessions and yielding 14.9 million variants as well as 4.3 M tag single-nucleotide polymorphisms (SNPs). When sampling random subsets of these accessions, the number of variants and tag SNPs plateaued beyond approximately 800 and 600 accessions, respectively. This suggests extensive coverage of diversity within the cultivated soybean. GmHapMap variants were imputed onto 21 618 previously genotyped accessions with up to 96% success for common alleles. A local association analysis was performed with the imputed data using markers located in a 1-Mb region known to contribute to seed oil content and enabled us to identify a candidate causal SNP residing in the NPC1 gene. We determined gene-centric haplotypes (407 867 GCHs) for the 55 589 genes and showed that such haplotypes can help to identify alleles that differ in the resulting phenotype. Finally, we predicted 18 031 putative loss-of-function (LOF) mutations in 10 662 genes and illustrated how such a resource can be used to explore gene function. The GmHapMap provides a unique worldwide resource for applied soybean genomics and breeding.
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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.