ArticleBMC plant biology2022
Combining QTL mapping and gene co-expression network analysis for prediction of candidate genes and molecular network related to yield in wheat.
Article in BMC plant biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 28 citations in OpenAlex.
- Identification and Validation of Stable Loci Underlying Productivity-Related Traits in Common Wheat.International journal of molecular sciences · 2026Article
- A Comparative Transcriptome and WGCNA of Tomato Reveals Hub Genes and a Hormone-Mediated Defense Network AgainstBiology · 2026Article
- Integrating Genetic Mapping and BSR-Seq Analysis to Identify Candidate Genes Controlling Fruitfulness inPlants (Basel, Switzerland) · 2025Article
- WGCNA analysis reveals hub genes in the Hemarthria compressa roots in response to waterlogging stress.Scientific reports · 2025Article
- A spectral framework to map QTLs affecting joint differential networks of gene co-expression.PLoS computational biology · 2025Article
- Identification of candidate genes associated with resistance to aflatoxin production in peanut through genetic mapping and transcriptome analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Genomic analysis of Zhou8425B, a key founder parent, reveals its genetic contributions to elite agronomic traits in wheat breeding.Plant communications · 2025Article
- Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects.International journal of molecular sciences · 2025Review
- Comparative transcriptomes and WGCNA reveal hub genes for spike germination in different quinoa lines.BMC genomics · 2024Article
- Integrated meta-QTL and in silico transcriptome assessment pinpoint major genomic regions responsible for spike length in wheat (Triticum aestivum L.).The plant genome · 2024Article
- Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley.Journal of experimental botany · 2024Article
- Overexpression of Taetr1-1 promotes enhanced seed dormancy and ethylene insensitivity in wheat.Planta · 2023Article
- QTL Mapping and Transcriptome Analysis Reveal Candidate Genes Regulating Seed Color inInternational journal of molecular sciences · 2023Article
- Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses.Plants (Basel, Switzerland) · 2022Review
- Transcriptome analysis and mining of genes related to shade tolerance in foxtail millet (Royal Society open science · 2022Article
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Authors and funding
10 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWheat (Triticum aestivum L.) is an important cereal crop. Increasing grain yield for wheat is always a priority. Due to the complex genome of hexaploid wheat with 21 chromosomes, it is difficult to identify underlying genes by traditional genetic approach. The combination of genetics and omics analysis has displayed the powerful capability to identify candidate genes for major quantitative trait loci (QTLs), but such studies have rarely been carried out in wheat. In this study, candidate genes related to yield were predicted by a combined use of linkage mapping and weighted gene co-expression network analysis (WGCNA) in a recombinant inbred line population.
resultsQTL mapping was performed for plant height (PH), spike length (SL) and seed traits. A total of 68 QTLs were identified for them, among which, 12 QTLs were stably identified across different environments. Using RNA sequencing, we scanned the 99,168 genes expression patterns of the whole spike for the recombinant inbred line population. By the combined use of QTL mapping and WGCNA, 29, 47, 20, 26, 54, 46 and 22 candidate genes were predicted for PH, SL, kernel length (KL), kernel width, thousand kernel weight, seed dormancy, and seed vigor, respectively. Candidate genes for different traits had distinct preferences. The known PH regulation genes Rht-B and Rht-D, and the known seed dormancy regulation genes TaMFT can be selected as candidate gene. Moreover, further experiment revealed that there was a SL regulatory QTL located in an interval of about 7 Mbp on chromosome 7A, named TaSL1, which also involved in the regulation of KL.
conclusionsA combination of QTL mapping and WGCNA was applied to predicted wheat candidate genes for PH, SL and seed traits. This strategy will facilitate the identification of candidate genes for related QTLs in wheat. In addition, the QTL TaSL1 that had multi-effect regulation of KL and SL was identified, which can be used for wheat improvement. These results provided valuable molecular marker and gene information for fine mapping and cloning of the yield-related trait loci in the future.
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