Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.)

Abstract

Background GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted. Results In this study, 57 GRAS genes of foxtail millet (SiGRASs) were identified and renamed according to the chromosomal distribution of the SiGRAS genes. Based on the number of conserved domains and gene structure, the SiGRAS genes were divided into 13 subfamilies via phylogenetic tree analysis. The GRAS genes were unevenly distributed on nine chromosomes, and members of the same subfamily had similar gene structures and motif compositions. Genetic structure analysis showed that most SiGRAS genes lacked introns. Some SiGRAS genes were derived from gene duplication events, and segmental duplications may have contributed more to GRAS gene family expansion than tandem duplications. Quantitative polymerase chain reaction showed significant differences in the expression of SiGRAS genes in different tissues and stages of fruits development, which indicated the complexity of the physiological functions of SiGRAS. In addition, exogenous paclobutrazol treatment significantly altered the transcription levels of DELLA subfamily members, downregulated the gibberellin content, and decreased the plant height of foxtail millet, while it increased the fruit weight. In addition, SiGRAS13 and SiGRAS25 may have the potential for genetic improvement and functional gene research in foxtail millet. Conclusions Collectively, this study will be helpful for further analysing the biological function of SiGRAS. Our results may contribute to improving the genetic breeding of foxtail millet.

Genome-wide identification, expression and salt stress tolerance analysis of the GRAS transcription factor family in Betula platyphylla

“…All the genes involved in tandem duplication events belonged to the same subfamily. Except BpGRAS38 , BpGRAS39 and BpGRAS40 from PAT subfamily, 6 genes in tandem duplication events belonged to LISCL subfamily, indicating that LISCL group played an important role in expansion of GRASs as the largest subfamily ( Fan et al., 2021a ).…”

Genome‑wide identification, phylogenetic and expression pattern analysis of GATA family genes in foxtail millet (Setaria italica)

“…Foxtail millet plants at the seedling stage (28 days) were treated with eight abiotic stresses, including salt (5% NaCl), acid (HCl 0.1 mol/L), alkali (NaOH, 0.2 M), darkness (complete shading), flooding (whole plant), heat (40 °C), drought (30% PEG6000), and cold (4 °C). According to Fan et al’s method, acid, alkali, salt, and drought stress were applied [ 12 , 53 ]. That is, under the same stress conditions, different repetitions with the same volume of liquid immersion roots were used.…”

“…These proteins play important roles in plants, including controlling flower development [ 2 , 3 ], carbon and nitrogen metabolism [ 4 ], the circadian clock [ 5 ], cell differentiation [ 6 ], hormone response [ 7 ], and disease resistance [ 8 ]. At present, many TFs have been identified and analyzed in foxtail millet, such as NAC [ 9 ], bHLH [ 10 ], AP2/ERF [ 11 ], GRAS [ 12 ], WRKY [ 13 ], and bZIP [ 14 ]. However, few studies have focused on the GATA TF family in foxtail millet.…”

Multifaceted roles of GRAS transcription factors in growth and stress responses in plants

“…(2016) Rosa chinensis (rose) Rosaceae Eudicot 59 17 Kumari et al. (2022) Selaginella moellendorffii (lycophyte) Selaginellaceae Eudicot 45 15 Engstrom (2011) Setaria italica (foxtail millet) Poaceae Monocot 57 13 Fan et al. (2021a) Solanum lycopersicum (tomato) Solanaceae Eudicot 54 10 Niu et al.…”