Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat.

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  • Additional Information
    • Source:
      Publisher: Published by the Plant Communications Shanghai Office in association with Cell Press, an imprint of Elsevier Inc Country of Publication: China NLM ID: 101769147 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2590-3462 (Electronic) Linking ISSN: 25903462 NLM ISO Abbreviation: Plant Commun Subsets: MEDLINE
    • Publication Information:
      Original Publication: [Shanghai] : Published by the Plant Communications Shanghai Office in association with Cell Press, an imprint of Elsevier Inc., [2020]-
    • Subject Terms:
      Triticum*/genetics ; Triticum*/growth & development ; Gene Regulatory Networks* ; Quantitative Trait Loci*/genetics ; Genome-Wide Association Study* ; Genetic Variation*; Gene Expression Regulation, Plant ; Phenotype
    • Abstract:
      Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.
      (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)
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    • Contributed Indexing:
      Keywords: bread wheat; gene regulatory network; genetic variation; protein–protein interaction; spike traits
    • Publication Date:
      Date Created: 20240315 Date Completed: 20240514 Latest Revision: 20240526
    • Publication Date:
      20240526
    • Accession Number:
      PMC11121755
    • Accession Number:
      10.1016/j.xplc.2024.100879
    • Accession Number:
      38486454