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Outline
Foxtail millet (Setaria italica) is a typical short-day plant, and its photoperiod sensitivity severely restricts regional adaptation. This study aims to identify core genes involved in the photoperiod response, elucidate the underlying molecular mechanism and provide a theoretical basis for breeding widely adaptable varieties.
Foxtail millet cultivar ‘Jingu 21’ was grown under long-day (LD, 16 h light/8 h dark) or short-day (SD, 10 h light/14 h dark) conditions. The second leaf from the top was sampled at 21 and 45 days after emergence. Total RNA was extracted using a plant RNA kit. RNA-seq libraries were prepared and sequenced on an Illumina NovaSeqTM X Plus platform. Differentially expressed genes (DEGs) were identified with |log2(Fold Change)|≥1 and adjusted P≤0.05. RT-qPCR was performed to validate the RNA-seq data using the reference gene SiH3.3. Gene expression was calculated using the 2−ΔΔCt method. Functional annotation of DEGs was performed using the ‘Xiaomi’ reference genome, followed by gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.
A total of 3 771 and 4 514 DEGs were identified in the SD21/LD21 and SD45/LD45 comparisons, respectively, with 1 291 common DEGs shared between the two stages. KEGG and GO analyses revealed that the DEGs were significantly enriched in pathways such as photoperiod response, porphyrin metabolism, and secondary metabolite biosynthesis. Under SD conditions, florigen genes SiFTa and SiFTL9 and flowering-promoting factor SiEhd1 were up-regulated, while under LD conditions, flowering repressor SiGhd7, circadian clock gene SiPRR37, and multiple SiCOL genes were significantly up-regulated.
Notably, eight key heading-date regulatory genes—SiMADS14, SiFTa, SiGhd7, SiPCL1, SiFTL9, SiCOL9, SiHd1, and SiFPFL4—were differentially expressed at both stages, suggesting that they may constitute core regulatory components of the photoperiod response. This study provides a theoretical basis for clarifying the molecular mechanism of photoperiod regulation in foxtail millet and for breeding widely adaptable varieties.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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