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Genetic diversity of grain yield traits and identification of a grain weight gene SiTGW6 in foxtail millet

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Abstract

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Agronomic traits were evaluated in 1250 foxtail millet accessions, and a crucial gene SiTGW6 governing grain yield was identified. Elite haplotypes and dCAPS markers developed for SiTGW6 facilitate molecular breeding.

Abstract

A comprehensive evaluation of phenotypic characteristics and genetic diversity in germplasm resources are important for gene discovery and breeding improvements. In this study, we conducted a comprehensive evaluation of 1250 foxtail millet varieties, assessing seven grain yield-related traits and fourteen common agronomic traits over two years. Principal component analysis, correlation analysis, and cluster analysis revealed a strong positive correlation between 1000-grain weight and grain width with grain yield, emphasizing their importance in foxtail millet breeding. Additionally, we found that panicle weight positively correlated with 1000-grain weight but negatively correlated with branch and tiller numbers, indicating selection factors during domestication and breeding. Using this information, we identified 27 germplasm resources suitable for high-yield foxtail millet breeding. Furthermore, through an integration of haplotype variations and phenotype association analysis, we pinpointed a crucial gene, SiTGW6, responsible for governing grain yield in foxtail millet. SiTGW6 encodes an IAA-glucose hydrolase, primarily localized in the cytoplasm and predominantly expressed in flowering panicles. Employing RNAseq analysis, we identified 1439 differentially expressed genes across various SiTGW6 haplotypes. Functional enrichment analysis indicating that SiTGW6 regulates grain yield through the orchestration of auxin and glucan metabolism, as well as plant hormone signaling pathways. Additionally, we have identified elite haplotypes and developed dCAPS markers for SiTGW6, providing valuable technical tools to facilitate molecular breeding efforts in foxtail millet.

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Data availability

The resequencing datasets of 1250 foxtail millet accessions can be obtained from our previous research (He et al. 2023). The transcriptome sequencing data obtained in this study had been deposited at EMBL-EBI in the European Nucleotide Archive database under the accession number PRJEB67280. Other datasets related to the paper are present in the paper and/or the Supplementary Information. Foxtail millet germplasm resources are available from the corresponding author on reasonable request.

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Acknowledgements

We thank Dr. Dongdong Li from Iowa State University for his technical support in bioinformatic analysis.

Funding

This work was supported by grants from National Key Research and Development Program of China (2021YFF1000104), the National Natural Science Foundation of China (32241038), the China Agricultural Research System (CARS06-13.5-A04), and the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences.

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Authors and Affiliations

  1. College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi Province, China

    Hui Zhang, Honglu Wang, Qian Ma & Baili Feng

  2. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Hui Zhang, Sha Tang, Yannan Wang, Hui Zhi, Bin Liu, Renliang Zhang, Guanqing Jia & Xianmin Diao

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  1. Hui Zhang
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  2. Sha Tang
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  3. Honglu Wang
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  11. Xianmin Diao
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Contributions

XD, BF, and ST provided funding acquisition and project administration. HZ and ST conceived and designed the project, data analysis, and wrote the manuscript. HW, YW, BL, RZ, and QM made the data collection. HZ conducted field management. GJ provided technical assistance. All authors read and approved the final manuscript.

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Correspondence to Sha Tang, Baili Feng or Xianmin Diao.

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These experiments complied with the ethical standards in China.

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Communicated by Hai-Chun Jing.

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Zhang, H., Tang, S., Wang, H. et al. Genetic diversity of grain yield traits and identification of a grain weight gene SiTGW6 in foxtail millet. Theor Appl Genet 137, 84 (2024). https://doi.org/10.1007/s00122-024-04586-0

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