ArticleBMC plant biology2021
Genome-wide association study uncovers major genetic loci associated with seed flooding tolerance in soybean.
Article in BMC plant biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 38 citations in OpenAlex.
- Article
- Integrating natural variation through GWAS - genetics of drought and flood tolerance in grass pea reveal independent yet interconnected mechanisms.BMC plant biology · 2026Article
- YOLO-based high-throughput phenotyping pipeline for soybean nodulation traits in genomic research.Frontiers in plant science · 2026Article
- Crop wild relatives of legumes: evolutionary resources for climate-responsive pre-breeding.Frontiers in plant science · 2026Review
- Unraveling the genetic architecture of anti-nutritional factors in soybean (Glycine max.) for nutritional enhancement.Scientific reports · 2025Article
- Unveiling key genetic determinants of charcoal rot resistance in soybean via genome-wide association studies.Frontiers in plant science · 2025Article
- Integrating dynamic high-throughput phenotyping and genetic analysis to monitor growth variation in foxtail millet.Plant methods · 2024Article
- Genome-Wide Association study for root system architecture traits in field soybean [Glycine max (L.) Merr.].Scientific reports · 2024Article
- From phenotyping to genetic mapping: identifying water-stress adaptations in legume root traits.BMC plant biology · 2024Review
- Biochemical Analysis to Understand the Flooding Tolerance of Mutant Soybean Irradiated with Gamma Rays.International journal of molecular sciences · 2023Article
- Physiological, Epigenetic, and Transcriptome Analyses Provide Insights into the Responses of Wheat Seedling Leaves to Different Water Depths under Flooding Conditions.International journal of molecular sciences · 2023Article
- Genetic Dissection of Extreme Seed-Flooding Tolerance in a Wild Soybean PI342618B by Linkage Mapping and Candidate Gene Analysis.Plants (Basel, Switzerland) · 2023Article
- A novel method for irrigating plants, tracking water use, and imposing water deficits in controlled environments.Frontiers in plant science · 2023Article
- Identification of Functional Genetic Variations Underlying Flooding Tolerance in Brazilian Soybean Genotypes.International journal of molecular sciences · 2022Article
- Discovery of genetic loci and causal genes for seed germination via deep re-sequencing in soybean.Molecular breeding : new strategies in plant improvement · 2022Article
- Genetic and Genomic Resources for Soybean Breeding Research.Plants (Basel, Switzerland) · 2022Review
- Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes.Frontiers in plant science · 2022Review
- The intervention of classical and molecular breeding approaches to enhance flooding stress tolerance in soybean - An review.Frontiers in plant science · 2022Review
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Authors and funding
10 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSeed flooding stress is one of the threatening environmental stressors that adversely limits soybean at the germination stage across the globe. The knowledge on the genetic basis underlying seed-flooding tolerance is limited. Therefore, we performed a genome-wide association study (GWAS) using 34,718 single nucleotide polymorphism (SNPs) in a panel of 243 worldwide soybean collections to identify genetic loci linked to soybean seed flooding tolerance at the germination stage.
resultsIn the present study, GWAS was performed with two contrasting models, Mixed Linear Model (MLM) and Multi-Locus Random-SNP-Effect Mixed Linear Model (mrMLM) to identify significant SNPs associated with electrical conductivity (EC), germination rate (GR), shoot length (ShL), and root length (RL) traits at germination stage in soybean. With MLM, a total of 20, 40, 4, and 9 SNPs associated with EC, GR, ShL and RL, respectively, whereas in the same order mrMLM detected 27, 17, 13, and 18 SNPs. Among these SNPs, two major SNPs, Gm_08_11971416, and Gm_08_46239716 were found to be consistently connected with seed-flooding tolerance related traits, namely EC and GR across two environments. We also detected two SNPs, Gm_05_1000479 and Gm_01_53535790 linked to ShL and RL, respectively. Based on Gene Ontology enrichment analysis, gene functional annotations, and protein-protein interaction network analysis, we predicted eight candidate genes and three hub genes within the regions of the four SNPs with Cis-elements in promoter regions which may be involved in seed-flooding tolerance in soybeans and these warrant further screening and functional validation.
conclusionsOur findings demonstrate that GWAS based on high-density SNP markers is an efficient approach to dissect the genetic basis of complex traits and identify candidate genes in soybean. The trait associated SNPs could be used for genetic improvement in soybean breeding programs. The candidate genes could help researchers better understand the molecular mechanisms underlying seed-flooding stress tolerance in soybean.
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