Pan-genome-based characterization of SiGRAS transcription factors and prediction of hub genes correlated with plant height in foxtail millet (Setaria italica L.)
- 1Houji Laboratory; Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding (Ministry–Province Co-construction); Shanxi Engineering Research Center for Foxtail Millet Genetic Improvement; Changzhi Key Laboratory of Foxtail Millet Genetic Improvement; Millet Research Institute, Shanxi Agricultural University, Changzhi, 046000 China
- 2College of Agriculture, Shanxi Agricultural University, Taigu, 030800 China
Abstract
Background: The GRAS gene family, a class of plant-specific transcription factors, plays pivotal roles in diverse biological processes, including plant growth, development, and stress responses. Although the SiGRAS family has been previously characterized in foxtail millet, those studies were restricted to a single reference genome, overlooking critical genetic variations.
Results: To overcome the inherent limitations of gene family analysis using a single reference, we systematically investigated the SiGRAS gene family using pan-genome data generated from 110 foxtail millet accessions together with the xiaomi and Yugu1 genomes. Based on a rigorously filtered pan-genome catalog, we identified a total of 949 SiGRAS pan-genes, comprising 1 core, 20 near-core, 50 dispensable, and 878 private genes. Phylogenetic analysis classified these genes into 9 distinct subfamilies. Evolutionary analysis based on Ka/Ks ratios revealed that 8 SiGRAS genes underwent purifying selection, while SiGRAS17 and SiGRAS2 were subjected to positive selection in the majority of accessions. Notably, we observed that structural variations (SVs) significantly influenced the expression levels of SiGRAS63, and altered both conserved domains and gene structure in specific accessions. Furthermore, we identified four hub genes correlated with plant height by integrating RNA-seq data with gene co-expression regulatory network.
Conclusions: This study lays a foundation for understanding the diversity of the SiGRAS gene family and provides a valuable resource for future function studies of SiGRAS genes in foxtail millet.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12870-026-09696-z.
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BibTeX
@article{han2026pangenomebased,
title = {{Pan-genome-based characterization of SiGRAS transcription factors and prediction of hub genes correlated with plant height in foxtail millet (Setaria italica L.)}},
author = {Kangni Han and Zhilan Wang and Ziyi Li and Shichao Lian and Hongpo Wu and Xiaofen Du and Yuxin Li and Yanfang Li and Huan Yang and Linyi Zhang and Jun Wang},
journal = {BMC Plant Biology},
year = {2026},
month = aug,
doi = {10.1186/s12870-026-09696-z},
url = {https://doi.org/10.1186/s12870-026-09696-z},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Pan-genome-based characterization of SiGRAS transcription factors and prediction of hub genes correlated with plant height in foxtail millet (Setaria italica L.)
AU - Kangni Han
AU - Zhilan Wang
AU - Ziyi Li
AU - Shichao Lian
AU - Hongpo Wu
AU - Xiaofen Du
AU - Yuxin Li
AU - Yanfang Li
AU - Huan Yang
AU - Linyi Zhang
AU - Jun Wang
PY - 2026
DA - 2026/08/07
JO - BMC Plant Biology
DO - 10.1186/s12870-026-09696-z
UR - https://doi.org/10.1186/s12870-026-09696-z
AB - Background: The GRAS gene family, a class of plant-specific transcription factors, plays pivotal roles in diverse biological processes, including plant growth, development, and stress responses. Although the SiGRAS family has been previously characterized in foxtail millet, those studies were restricted to a single reference genome, overlooking critical genetic variations. Results: To overcome the inherent limitations of gene family analysis using a single reference, we systematically investigated the SiGRAS gene family using pan-genome data generated from 110 foxtail millet accessions together with the xiaomi and Yugu1 genomes. Based on a rigorously filtered pan-genome catalog, we identified a total of 949 SiGRAS pan-genes, comprising 1 core, 20 near-core, 50 dispensable, and 878 private genes. Phylogenetic analysis classified these genes into 9 distinct subfamilies. Evolutionary analysis based on Ka/Ks ratios revealed that 8 SiGRAS genes underwent purifying selection, while SiGRAS17 and SiGRAS2 were subjected to positive selection in the majority of accessions. Notably, we observed that structural variations (SVs) significantly influenced the expression levels of SiGRAS63, and altered both conserved domains and gene structure in specific accessions. Furthermore, we identified four hub genes correlated with plant height by integrating RNA-seq data with gene co-expression regulatory network. Conclusions: This study lays a foundation for understanding the diversity of the SiGRAS gene family and provides a valuable resource for future function studies of SiGRAS genes in foxtail millet. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12870-026-09696-z.
SN - 1471-2229
ER -