Genome-Wide Characterization and Haplotypic Variation Analysis of the IDD Gene Family in Foxtail Millet (Setaria italica)
Abstract
:1. Introduction
2. Results
2.1. Phylogenetic Analysis and Structural Characterization of IDD Genes in Foxtail Millet
2.2. Protein Property and Spatial Structure of IDD Proteins
2.3. Putative Cis-Acting Regulatory Elements (CAREs or Cis-Elements) Analysis of SiIDD Genes
2.4. Chromosomal Distribution and Colinearity Analysis of the IDD Genes
2.5. Transcriptional Profiling of SiIDD Genes and Subcellular Localization of SiIDD Proteins
2.6. Superior Haplotypes of SiIDD8 and SiIDD14 Correlate with Early Heading Date and High Thousand Seed Weight
3. Discussion
3.1. IDD Genes Are Conserved between Foxtail Millet and Rice
3.2. Expression Profiling of SiIDD Genes Indicating Their Role in Plant Growth and Development
3.3. Function of IDD Genes in Arabidopsis and Rice Facilitate the Functional Prediction of IDD Genes in Foxtail Millet
3.4. Haplotypic Analysis Facilitate Identification of Superior Haplotypes with Agronomic Importance
4. Materials and Methods
4.1. Identification and Phylogenetic Analysis of IDD Genes in Foxtail Millet, Arabidopsis and Rice
4.2. Protein Property Analysis of SiIDD Genes
4.3. Cis-Elements Analysis of the SiIDD Gene Promoters
4.4. Chromosomal Distribution and Colinearity Analysis of SiIDD Genes
4.5. Transcriptional Profiling and Subcellular Localization of SiIDD Genes
4.6. Haplotypic Analysis of the SiIDD Genes and Association Study with Agronomic Traits in Foxtail Millet
4.7. Development of dCAPS Marker for SiIDD8 and SiIDD14
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Wu, H.; Zhang, R.; Diao, X. Genome-Wide Characterization and Haplotypic Variation Analysis of the IDD Gene Family in Foxtail Millet (Setaria italica). Int. J. Mol. Sci. 2024, 25, 8804. https://doi.org/10.3390/ijms25168804
Wu H, Zhang R, Diao X. Genome-Wide Characterization and Haplotypic Variation Analysis of the IDD Gene Family in Foxtail Millet (Setaria italica). International Journal of Molecular Sciences. 2024; 25(16):8804. https://doi.org/10.3390/ijms25168804
Chicago/Turabian StyleWu, Hongpo, Renliang Zhang, and Xianmin Diao. 2024. "Genome-Wide Characterization and Haplotypic Variation Analysis of the IDD Gene Family in Foxtail Millet (Setaria italica)" International Journal of Molecular Sciences 25, no. 16: 8804. https://doi.org/10.3390/ijms25168804