ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2017
An innovative procedure of genome-wide association analysis fits studies on germplasm population and plant breeding.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 117 citations in OpenAlex.
- 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
- Genomic and Phenotypic Differentiation of Ardi Goat Lines with Distinct Facial Pigmentation in Bahrain: Implications for Conservation.Animals : an open access journal from MDPI · 2026Article
- Multi-locus genome-wide association mapping reveals loci underlying malt quality traits in heterogeneous Ethiopian Barley (Hordeum vulgare L.) germplasm.Scientific reports · 2026Article
- Detection of QTLs and QTL-environment interactions for fruit branch number in Upland cotton (Gossypium hirsutum L.) using a restricted two-stage multi-locus genome-wide association study.BMC plant biology · 2026Article
- Article
- Genome-wide locus-allele comparison reveals differential evolution dynamics from annual wild to landrace and released cultivar soybeans.The plant genome · 2025Article
- Genome-wide association analyses for revealing QTN, QTN-by-environment and QTN-by-QTN interactions in soybean phenology.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- The integration of quantile regression with 3VmrMLM identifies more QTNs and QTN-by-environment interactions using SNP- and haplotype-based markers.Plant communications · 2025Article
- A comprehensive map of DNA-segment copy number variation in 491 genomes of common wheat uncovers genes associated with multiple agronomic traits.Plant communications · 2025Article
- Characterization of a G. max × G. soja nested association mapping population and identification of loci controlling seed composition traits from wild soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Characterization of shade tolerance gene network in soybean revealed by forward integrated reverse genetic studies.Horticulture research · 2025Article
- Genome-Wide Genetic Architecture for Common Scab (International journal of molecular sciences · 2025Article
- Genome-wide association study and transcriptome analysis reveal candidate genes related to drought stress in the germination stage of soybean.Frontiers in plant science · 2025Article
- Genome-wide association study provides new insight into the underlying mechanism of drought tolerance during seed germination stage in soybean.Scientific reports · 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
- Identification of Gene-Allele System Conferring Alkali-Tolerance at Seedling Stage in Northeast China Soybean Germplasm.International journal of molecular sciences · 2024Article
- Identification of adult resistant genes to stripe rust in wheat from southwestern China based on GWAS and WGCNA analysis.Plant cell reports · 2024Article
- Fine-mapping of a major locus for Fusarium wilt resistance in flax (Linum usitatissimum L.).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
8 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
key messageThe innovative RTM-GWAS procedure provides a relatively thorough detection of QTL and their multiple alleles for germplasm population characterization, gene network identification, and genomic selection strategy innovation in plant breeding. The previous genome-wide association studies (GWAS) have been concentrated on finding a handful of major quantitative trait loci (QTL), but plant breeders are interested in revealing the whole-genome QTL-allele constitution in breeding materials/germplasm (in which tremendous historical allelic variation has been accumulated) for genome-wide improvement. To match this requirement, two innovations were suggested for GWAS: first grouping tightly linked sequential SNPs into linkage disequilibrium blocks (SNPLDBs) to form markers with multi-allelic haplotypes, and second utilizing two-stage association analysis for QTL identification, where the markers were preselected by single-locus model followed by multi-locus multi-allele model stepwise regression. Our proposed GWAS procedure is characterized as a novel restricted two-stage multi-locus multi-allele GWAS (RTM-GWAS, https://github.com/njau-sri/rtm-gwas ). The Chinese soybean germplasm population (CSGP) composed of 1024 accessions with 36,952 SNPLDBs (generated from 145,558 SNPs, with reduced linkage disequilibrium decay distance) was used to demonstrate the power and efficiency of RTM-GWAS. Using the CSGP marker information, simulation studies demonstrated that RTM-GWAS achieved the highest QTL detection power and efficiency compared with the previous procedures, especially under large sample size and high trait heritability conditions. A relatively thorough detection of QTL with their multiple alleles was achieved by RTM-GWAS compared with the linear mixed model method on 100-seed weight in CSGP. A QTL-allele matrix (402 alleles of 139 QTL × 1024 accessions) was established as a compact form of the population genetic constitution. The 100-seed weight QTL-allele matrix was used for genetic characterization, candidate gene prediction, and genomic selection for optimal crosses in the germplasm population.
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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.