ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2018
Efficient QTL detection of flowering date in a soybean RIL population using the novel restricted two-stage multi-locus GWAS procedure.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Constitution and function of intergenic genome regions in cultivated versus annual wild soybean in China.Journal of integrative plant biology · 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
- Characterization of shade tolerance gene network in soybean revealed by forward integrated reverse genetic studies.Horticulture research · 2025Article
- 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
- Integration of genetic and genomics resources in einkorn wheat enables precision mapping of important traits.Communications biology · 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
- The Identification of a Yield-Related Gene Controlling Multiple Traits Using GWAS in Sorghum (Plants (Basel, Switzerland) · 2023Article
- Genome-wide association study as a powerful tool for dissecting competitive traits in legumes.Frontiers in plant science · 2023Review
- A study using single-locus and multi-locus genome-wide association study to identify genes associated with teat number in Hu sheep.Animal genetics · 2022Article
- Characterization of Root System Architecture Traits in Diverse Soybean Genotypes Using a Semi-Hydroponic System.Plants (Basel, Switzerland) · 2021Article
- Uncovering the Novel QTLs and Candidate Genes of Salt Tolerance in Rice with Linkage Mapping, RTM-GWAS, and RNA-seq.Rice (New York, N.Y.) · 2021Article
- Linkage and association study discovered loci and candidate genes for glycinin and β-conglycinin in soybean (Glycine max L. Merr.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 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
- Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean.International journal of molecular sciences · 2021Article
- Genome-Wide Association Study Identifies Genomic Regions for Important Morpho-Agronomic Traits in Mesoamerican Common Bean.Frontiers in plant science · 2021Article
- Genetic dynamics of earlier maturity group emergence in south-to-north extension of Northeast China soybeans.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Genomic Prediction Accuracy of Seven Breeding Selection Traits Improved by QTL Identification in Flax.International journal of molecular sciences · 2020Article
- Identification of Additive-Epistatic QTLs Conferring Seed Traits in Soybean Using Recombinant Inbred Lines.Frontiers in plant science · 2020Article
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8 authors.
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Abstract
key messageEighty-six R1 QTLs accounting for 89.92% phenotypic variance in a soybean RIL population were identified using RTM-GWAS with SNPLDB marker which performed superior over CIM and MLM-GWAS with BIN/SNPLDB marker. A population (NJRIKY) composed of 427 recombinant inbred lines (RILs) derived from Kefeng-1 × NN1138-2 (MGII × MGV, MG maturity group) was applied for detecting flowering date (R1) quantitative trait locus (QTL) system in soybean. From a low-depth re-sequencing (~ 0.75 ×), 576,874 SNPs were detected and organized into 4737 BINs (recombination breakpoint determinations) and 3683 SNP linkage disequilibrium blocks (SNPLDBs), respectively. Using the association mapping procedures "Restricted Two-stage Multi-locus Genome-wide Association Study" (RTM-GWAS), "Mixed Linear Model Genome-wide Association Study" (MLM-GWAS) and the linkage mapping procedure "Composite Interval Mapping" (CIM), 67, 36 and 10 BIN-QTLs and 86, 14 and 23 SNPLDB-QTLs were detected with their phenotypic variance explained (PVE) 88.70-89.92% (within heritability 98.2%), 146.41-353.62% (overflowing) and 88.29-172.34% (overflowing), respectively. The RTM-GWAS with SNPLDBs which showed to be more efficient and reasonable than the others was used to identify the R1 QTL system in NJRIKY. The detected 86 SNPLDB-QTLs with their PVE from 0.02 to 30.66% in a total of 89.92% covered 51 out of 104 R1 QTLs in 18 crosses in SoyBase and 26 out of 139 QTLs in a nested association mapping population, while the rest 29 QTLs were novel ones. From the QTL system, 52 candidate genes were annotated, including the verified gene E1, E2, E9 and J, and grouped into 3 categories of biological processes, among which 24 genes were enriched into three protein-protein interaction networks, suggesting gene networks working together. Since NJRIKY involves only MGII and MGV, the QTL/gene system among MG000-MGX should be explored further.
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