ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2016
Detecting the QTL-allele system of seed isoflavone content in Chinese soybean landrace population for optimal cross design and gene system exploration.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 57 citations in OpenAlex.
- GmDOF3.1-GmCPX Module Regulates Nodulation and Nitrogen Fixation Abilities in Soybean.Plant biotechnology journal · 2026Article
- A Restricted Two-Stage Multi-Locus Multi-Allele Genome-Wide Association Study Reveals Genomic Loci and Candidate Genes Controlling Plant-Height-Related Traits in Soybean Under Normal and Shade Conditions.International journal of molecular sciences · 2026Article
- A balance between glycitein and glyceollins governed by isoflavone 6-hydroxylase confers soybean resistance toProceedings of the National Academy of Sciences of the United States of America · 2025Article
- The analysis of the genetic loci affecting phenotypic plasticity of soybean isoflavone content by dQTG.seq model.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- High-quality genome of a modern soybean cultivar and resequencing of 547 accessions provide insights into the role of structural variation.Nature genetics · 2024Article
- Integrating RTM-GWAS and meta‑QTL data revealed genomic regions and candidate genes associated with the first fruit branch node and its height in upland cotton.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Efficient identification of QTL for agronomic traits in foxtail millet (Setaria italica) using RTM- and MLM-GWAS.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Identification of Genes Responsible for the Synthesis of Glycitein Isoflavones in Soybean Seeds.Plants (Basel, Switzerland) · 2024Article
- The Identification of a Quantative Trait Loci-Allele System of Antixenosis against the Common Cutworm (International journal of molecular sciences · 2023Article
- Gene-allele system of shade tolerance in southern China soybean germplasm revealed by genome-wide association study using gene-allele sequence as markers.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Review
- An Improved Genome-Wide Association Procedure Explores Gene-Allele Constitutions and Evolutionary Drives of Growth Period Traits in the Global Soybean Germplasm Population.International journal of molecular sciences · 2023Article
- Identification of Loci Governing Agronomic Traits and Mutation Hotspots via a GBS-Based Genome-Wide Association Study in a Soybean Mutant Diversity Pool.International journal of molecular sciences · 2022Article
- Resequencing 250 Soybean Accessions: New Insights into Genes Associated with Agronomic Traits and Genetic Networks.Genomics, proteomics & bioinformatics · 2022Article
- Germplasm Sources, Genetic Richness, and Population Differentiation of Modern Chinese Soybean Cultivars Based on Pedigree Integrated With Genomic-Marker Analysis.Frontiers in plant science · 2022Article
- Genome wide association study to detect genetic regions related to isoflavone content in a mutant soybean population derived from radiation breeding.Frontiers in plant science · 2022Article
- Transgressive Potential Prediction and Optimal Cross Design of Seed Protein Content in the Northeast China Soybean Population Based on Full Exploration of the QTL-Allele System.Frontiers in plant science · 2022Article
- Genetic loci and causal genes for seed fatty acids accumulation across multiple environments and genetic backgrounds in soybean.Molecular breeding : new strategies in plant improvement · 2021Article
- Evolutionary QTL-allele changes in main stem node number among geographic and seasonal subpopulations of Chinese cultivated soybeans.Molecular genetics and genomics : MGG · 2021Article
- A Genome-Wide Genetic Diversity Scan Reveals Multiple Signatures of Selection in a European Soybean Collection Compared to Chinese Collections of Wild and Cultivated Soybean Accessions.Frontiers in plant science · 2021Article
- An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton.BMC plant biology · 2020Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageUtilizing an innovative GWAS in CSLRP, 44 QTL 199 alleles with 72.2 % contribution to SIFC variation were detected and organized into a QTL-allele matrix for cross design and gene annotation. The seed isoflavone content (SIFC) of soybeans is of great importance to health care. The Chinese soybean landrace population (CSLRP) as a genetic reservoir was studied for its whole-genome quantitative trait loci (QTL) system of the SIFC using an innovative restricted two-stage multi-locus genome-wide association study procedure (RTM-GWAS). A sample of 366 landraces was tested under four environments and sequenced using RAD-seq (restriction-site-associated DNA sequencing) technique to obtain 116,769 single nucleotide polymorphisms (SNPs) then organized into 29,119 SNP linkage disequilibrium blocks (SNPLDBs) for GWAS. The detected 44 QTL 199 alleles on 16 chromosomes (explaining 72.2 % of the total phenotypic variation) with the allele effects (92 positive and 107 negative) of the CSLRP were organized into a QTL-allele matrix showing the SIFC population genetic structure. Additional differentiation among eco-regions due to the SIFC in addition to that of genome-wide markers was found. All accessions comprised both positive and negative alleles, implying a great potential for recombination within the population. The optimal crosses were predicted from the matrices, showing transgressive potentials in the CSLRP. From the detected QTL system, 55 candidate genes related to 11 biological processes were χ (2)-tested as an SIFC candidate gene system. The present study explored the genome-wide SIFC QTL/gene system with the innovative RTM-GWAS and found the potentials of the QTL-allele matrix in optimal cross design and population genetic and genomic studies, which may have provided a solution to match the breeding by design strategy at both QTL and gene levels in breeding programs.
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