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Comparative transcriptome analysis and genetic dissection of vegetative branching traits in foxtail millet (Setaria italica)

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Abstract

Key message

Two major genetic loci, qTN5.1 and qAB9.1, were identified and finely mapped to the 255 Kb region with one potential candidate gene for tiller number and the 521 Kb region with eight candidate genes for axillary branch number, respectively.

Abstract

Vegetative branching including tillering and axillary branching are vital traits affecting both the plant architecture and the biomass in cereal crops. However, the mechanism underlying the formation of vegetative branching in foxtail millet is largely unknown. Here, a foxtail millet cultivar and its bushy wild relative Setaria viridis accession were used to construct segregating populations to identify candidate genes regulating tiller number and axillary branch number. Transcriptome analysis using vegetative branching bud samples of parental accessions was performed, and key differentially expressed genes and pathways regulating vegetative branching were pointed out. Bulk segregant analysis on their F2:3 segregating population was carried out, and a major QTL for tiller number (qTN5.1) and two major QTLs for axillary branch number (qAB2.1 and qAB9.1) were detected. Fine-mapping strategy was further performed on F2:4 segregate population, and Seita.5G356600 encoding β-glucosidase 11 was identified as the promising candidate gene for qTN5.1, and eight genes, especially Seita.9G125300 and Seita.9G125400 annotated as B-S glucosidase 44, were finally identified as candidate genes for regulating axillary branching. Findings in this study will help to elucidate the genetic basis of the vegetative branching formation of foxtail millet and lay a foundation for breeding foxtail millet varieties with ideal vegetative branching numbers.

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Funding

This study was financially supported by the China Agriculture Research System (CARS-06-14.5-A8); Natural Science Foundation of China (31960419), Special Project of Agricultural Science and Technology innovation of GAAS (2021GAAS02); Top-notch talent project in Gansu Province (2022); Doctoral Fund of Gansu Academy of Agricultural Sciences(2023GAAS26).

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Authors and Affiliations

  1. Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China

    Tianpeng Liu, Jihong He, Kongjun Dong, Lei Zhang, Yawei Li, Ruiyu Ren & Tianyu Yang

  2. College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China

    Tianpeng Liu & Xueying Liu

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  1. Tianpeng Liu
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Contributions

TL contributed to the conceptualization, methodology, software, validation, formal analysis, investigation, data curation, writing—original draft, visualization and funding acquisition. XL assisted in the data curation, writing—original draft and visualization. JH, LZ, YL and RY were involved in the investigation, resources and data curation. KJ contributed to the resources, investigation, data curation and funding acquisition. TY assisted in the writing—review and editing, supervision, project administration and funding acquisition. All authors have read and approved the final manuscript.

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Correspondence to Tianyu Yang.

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Liu, T., Liu, X., He, J. et al. Comparative transcriptome analysis and genetic dissection of vegetative branching traits in foxtail millet (Setaria italica). Theor Appl Genet 137, 39 (2024). https://doi.org/10.1007/s00122-023-04524-6

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