ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2024
Efficient identification of QTL for agronomic traits in foxtail millet (Setaria italica) using RTM- and MLM-GWAS.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 21 citations in OpenAlex.
- Genome-wide association analysis and candidate gene identification for plant height in Shanxi local foxtail millet varieties.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Pan-Genome Analysis of the Fructokinase Gene Family Reveals a Light-Regulated SiPhyC-SiFRK4 Module Controlling Carbon Partitioning in Foxtail Millet.Plants (Basel, Switzerland) · 2026Article
- Identifying genetic loci associated with drought tolerance in foxtail millet (Setaria italica).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 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
- Multi-omics analysis reveals the phenylalanine pathway associated with stem development under organic and compound fertilizers inFrontiers in plant science · 2026Article
- Genome-wide association study, linkage mapping and transcriptomic analysis reveal candidate genes associated with nitrogen use efficiency in wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Leveraging GWAS-Identified Markers in Combination with Bayesian and Machine Learning Models to Improve Genomic Selection in Soybean.International journal of molecular sciences · 2025Article
- Genetic linkage map construction and QTL mapping for panicle-related traits in foxtail millet (Molecular breeding : new strategies in plant improvement · 2025Article
- Construction of a genetic linkage map and QTL mapping of the agronomic traits in Foxtail millet (Setaria italica).BMC genomics · 2025Article
- Expression of Foxtail MilletBiomolecules · 2024Article
- Assessment of Breeding Potential of Foxtail Millet Varieties Using a TOPSIS Model Constructed Based on Distinctness, Uniformity, and Stability Test Characteristics.Plants (Basel, Switzerland) · 2024Article
- Genetic dissection of ten photosynthesis-related traits based on InDel- and SNP-GWAS in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Identification, function validation and haplotype analysis of salt-tolerant genes of lectin receptor kinase gene family in sorghum (Frontiers in genetics · 2024Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
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Abstract
key messageEleven QTLs for agronomic traits were identified by RTM- and MLM-GWAS, putative candidate genes were predicted and two markers for grain weight were developed and validated. Foxtail millet (Setaria italica), the second most cultivated millet crop after pearl millet, is an important grain crop in arid regions. Seven agronomic traits of 408 diverse foxtail millet accessions from 15 provinces in China were evaluated in three environments. They were clustered into two divergent groups based on genotypic data using ADMIXTURE, which was highly consistent with their geographical distribution. Two models for genome-wide association studies (GWAS), namely restricted two-stage multi-locus multi-allele (RTM)-GWAS and mixed linear model (MLM)-GWAS, were used to dissect the genetic architecture of the agronomic traits based on 13,723 SNPs. Eleven quantitative trait loci (QTLs) for seven traits were identified using two models (RTM- and MLM-GWAS). Among them, five were considered stable QTLs that were identified in at least two environments using MLM-GWAS. One putative candidate gene (SETIT_006045mg, Chr4: 744,701-746,852) that can enhance grain weight per panicle was identified based on homologous gene comparison and gene expression analysis and was validated by haplotype analysis of 330 accessions with high-depth (10×) resequencing data (unpublished). In addition, homologous gene comparison and haplotype analysis identified one putative foxtail millet ortholog (SETIT_032906mg, Chr2: 5,020,600-5,029,771) with rice affecting the target traits. Two markers (cGWP6045 and kTGW2906) were developed and validated and can be used for marker-assisted selection of foxtail millet with high grain weight. The results provide a fundamental resource for foxtail millet genetic research and breeding and demonstrate the power of integrating RTM- and MLM-GWAS approaches as a complementary strategy for investigating complex traits in foxtail millet.
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