Abstract
The RPD3/HDA1 histone deacetylase family members play crucial roles in plant development, influencing traits such as plant height, stress response and fertility. Although, the RPD3/HDA1 family has been characterized in several plant species, its members and functions in foxtail millet remain largely unknown. In this study, we identified 13 SiRPD3/HDA1 genes in foxtail millet and classified them into four distinct phylogenetic groups. Structural analysis revealed conserved exon-intron patterns and motif compositions within each group, implying functional conservation. Two segmental duplication events were detected. The Ka/Ks ratios (<1) suggested that these gene pairs have undergone strong purifying selection. Expression profiling showed that most SiRPD3/HDA1 genes were expressed during reproductive stages, particularly in shoot apical meristem. Promoter analysis revealed multiple phytohormone-responsive cis -elements. Consistently, qRT-PCR assays confirmed that exogenous GA, ABA, MeJA, and IAA triggered distinct, gene-specific expression responses, together suggesting functional divergence of SiRPD3/HDA1 genes in hormone signaling. Importantly, we performed haplotype-based association analysis across 942 natural accessions, covering the entire SiRPD3/HDA1 gene family. This analysis revealed extensive natural variations and identified five candidate genes ( Seita.1G034500 , Seita.2G042600 , Seita.4G235100 , Seita.5G190100 , and Seita.5G255900 ) showing strong association with plant height. Subsequently, subcellular localization analysis showed that Seita.2G042600 and Seita.5G190100 are targeted to the nucleus and plasma membrane, respectively, suggesting their distinct functional roles. This study provides a comprehensive characterization of the RPD3/HDA1 family in foxtail millet, identifies potential regulators associated with plant height, and lays a foundation for future functional studies and molecular breeding efforts.
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Claims 10
Claim · model-written summary
Thirteen SiRPD3/HDA1 genes were identified in four groups.
- Taxon
- foxtail millet
Setaria italicae0 - Gene
- SiRPD3/HDA1e0
- Outcome
- genese0
- Value
- 13e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“identified 13 SiRPD3/HDA1 genes in foxtail millet and classified them into four distinct phylogenetic groups”
Claim · model-written summary
Gene groups had conserved exon-intron patterns and motifs.
- Taxon
- foxtail milletSetaria italicat0
- Outcome
- exon-intron patterns and motif compositionse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“conserved exon-intron patterns and motif compositions within each group”
t0“foxtail millet”
Claim · model-written summary
Two segmental duplication events were detected.
- Taxon
- foxtail milletSetaria italicat0
- Outcome
- segmental duplication eventse0
- Value
- Twoe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Two segmental duplication events were detected.”
t0“foxtail millet”
Claim · model-written summary
Ka/Ks ratios suggested strong purifying selection.
- Taxon
- foxtail milletSetaria italicat0
- Gene
- gene pairse0
- Outcome
- strong purifying selectione0
- Value
- <1e0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The Ka/Ks ratios (<1) suggested that these gene pairs have undergone strong purifying selection.”
t0“foxtail millet”
Claim · model-written summary
Most genes were expressed in reproductive stages, especially shoot apical meristem.
- Taxon
- foxtail milletSetaria italicat0
- Organ / stage
- shoot apical meristeme0
- Gene
- SiRPD3/HDA1e0
- Outcome
- expressede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“most SiRPD3/HDA1 genes were expressed during reproductive stages, particularly in shoot apical meristem”
t0“foxtail millet”
Claim · model-written summary
Promoters contained multiple phytohormone-responsive cis-elements.
- Taxon
- foxtail milletSetaria italicat0
- Outcome
- phytohormone-responsive cis -elementse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Promoter analysis revealed multiple phytohormone-responsive cis -elements.”
t0“foxtail millet”
Claim · model-written summary
GA, ABA, MeJA, and IAA induced gene-specific expression responses.
- Taxon
- foxtail milletSetaria italicat0
- Treatment
- exogenous GA, ABA, MeJA, and IAAe0
- Outcome
- gene-specific expression responsese0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“exogenous GA, ABA, MeJA, and IAA triggered distinct, gene-specific expression responses”
t0“foxtail millet”
Claim · model-written summary
Five candidate genes showed strong association with plant height.
- Taxon
- foxtail milletSetaria italicat0
- Gene
- Seita.1G034500e0
- Outcome
- plant heighte0
- Value
- fivee0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“five candidate genes ( Seita.1G034500 , Seita.2G042600 , Seita.4G235100 , Seita.5G190100 , and Seita.5G255900 ) showing strong association with plant height”
t0“foxtail millet”
Claim · model-written summary
Seita.2G042600 localized to the nucleus.
- Taxon
- foxtail milletSetaria italicat0
- Gene
- Seita.2G042600e0
- Outcome
- nucleuse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Seita.2G042600 and Seita.5G190100 are targeted to the nucleus and plasma membrane, respectively”
t0“foxtail millet”
Claim · model-written summary
Seita.5G190100 localized to the plasma membrane.
- Taxon
- foxtail milletSetaria italicat0
- Gene
- Seita.5G190100e0
- Outcome
- plasma membranee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Seita.2G042600 and Seita.5G190100 are targeted to the nucleus and plasma membrane, respectively”
t0“foxtail millet”