Rapid identification of candidate genes controlling male-sterility in Foxtail millet (Setaria italica)
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ABSTRACT: Supplementary Information
The online version contains supplementary material available at 10.1007/s11032-021-01269-2.
SUBMITTER: Wei W
PROVIDER: S-EPMC10236058 | biostudies-literature | 2021 Nov
REPOSITORIES: biostudies-literature
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Project description:Terpenoid metabolism plays vital roles in stress defense and the environmental adaptation of monocot crops. Here, we describe the identification of the terpene synthase (TPS) gene family of the panicoid food and bioenergy model crop foxtail millet (Setaria italica). The diploid S. italica genome contains 32 TPS genes, 17 of which were biochemically characterized in this study. Unlike other thus far investigated grasses, S. italica contains TPSs producing all three ent-, (+)- and syn-copalyl pyrophosphate stereoisomers that naturally occur as central building blocks in the biosynthesis of distinct monocot diterpenoids. Conversion of these intermediates by the promiscuous TPS SiTPS8 yielded different diterpenoid scaffolds. Additionally, a cytochrome P450 monooxygenase (CYP99A17), which genomically clustered with SiTPS8, catalyzes the C19 hydroxylation of SiTPS8 products to generate the corresponding diterpene alcohols. The presence of syntenic orthologs to about 19% of the S. italica TPSs in related grasses supports a common ancestry of selected pathway branches. Among the identified enzyme products, abietadien-19-ol, syn-pimara-7,15-dien-19-ol and germacrene-d-4-ol were detectable in planta, and gene expression analysis of the biosynthetic TPSs showed distinct and, albeit moderately, inducible expression patterns in response to biotic and abiotic stress. In vitro growth-inhibiting activity of abietadien-19-ol and syn-pimara-7,15-dien-19-ol against Fusarium verticillioides and Fusarium subglutinans may indicate pathogen defensive functions, whereas the low antifungal efficacy of tested sesquiterpenoids supports other bioactivities. Together, these findings expand the known chemical space of monocot terpenoid metabolism to enable further investigations of terpenoid-mediated stress resilience in these agriculturally important species.
| S-EPMC7497057 | biostudies-literature
Project description:Transcriptome sequencing of Foxtail millet Setaria italica (Zhang-gu) for different tissues.
2012-03-31 | GSE36391 | GEO
Project description:Pollen development and germination play a crucial role in the sexual reproduction of plants. This study analysis of transcriptional dynamics of foxtail millet pollen with other tissues and organs (ovule, glume, seedling and root) through RNA-sequencing revealed that a total of 940 genes were up-regulated in foxtail millet pollen. Based on this, we analyzed the genes involved in pollen tube growth of receptor kinases and small peptides, calcium signaling, small G proteins, vesicle transport, cytoskeleton, cell wall correlation, and transcription factors that are up-regulated in pollen. At the same time, we compared the gene expression of foxtail millet pollen and mature anthers, and found that a large number of transcription factors were specific expressed in mature anthers. In addition, we verified the accuracy of the transcriptome data using RT-qPCR. Finally, employed the antisense Oligonucleotide (as-ODN) system found that inhibiting SiPME67 expression would cause abnormal growth of pollen tube subapical. In summary, we preliminarily analyzed the genes that were up-regulated in foxtail millet pollen, which provided a reference for understanding the male sterility mechanism of foxtail millet in the future and theoretical basis for creating new male sterility lines.
| S-EPMC11660619 | biostudies-literature
Project description:BackgroundMicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. Although many miRNAs have been identified in a large number of organisms, the miRNAs in foxtail millet (Setaria italica) have, until now, been poorly understood.ResultsIn this study, two replicate small RNA libraries from foxtail millet shoots were sequenced, and 40 million reads representing over 10 million unique sequences were generated. We identified 43 known miRNAs, 172 novel miRNAs and 2 mirtron precursor candidates in foxtail millet. Some miRNA*s of the known and novel miRNAs were detected as well. Further, eight novel miRNAs were validated by stem-loop RT-PCR. Potential targets of the foxtail millet miRNAs were predicted based on our strict criteria. Of the predicted target genes, 79% (351) had functional annotations in InterPro and GO analyses, indicating the targets of the miRNAs were involved in a wide range of regulatory functions and some specific biological processes. A total of 69 pairs of syntenic miRNA precursors that were conserved between foxtail millet and sorghum were found. Additionally, stem-loop RT-PCR was conducted to confirm the tissue-specific expression of some miRNAs in the four tissues identified by deep-sequencing.ConclusionsWe predicted, for the first time, 215 miRNAs and 447 miRNA targets in foxtail millet at a genome-wide level. The precursors, expression levels, miRNA* sequences, target functions, conservation, and evolution of miRNAs we identified were investigated. Some of the novel foxtail millet miRNAs and miRNA targets were validated experimentally.
| S-EPMC3878754 | biostudies-literature
Project description:Foxtail millet (Setaria italica (L.) P. Beauv.), the second most cultivated millet species, is well adapted to diverse environments and remains an important cereal food and forage crop in arid and semiarid regions worldwide. A symbolic crop for indigenous Austronesian peoples, foxtail millet has been cultivated in Taiwan for more than 5,000 years, and landraces reflect diversifying selection for various food applications. A total of 124 accessions collected within Taiwan were assessed for Wx genotypes. Four identified Wx alleles, I, III, IV, and IX were caused by insertion of various transposable elements (TEs) and resulted in endosperm with non-waxy, low amylose content (AC), and waxy, respectively. A total of 16.9%, 4.0%, 49.2%, and 29.8% of accessions were classified as type I, III, IV, and IX, respectively; approximately half of the accessions belonged to the waxy type, indicating that glutinous grains were favored for making traditional food and wine. The TE insertion affected splicing efficiency rather than accuracy, leading to significantly reduced expression of wx in types III, IV, and IX, although their transcripts were the same as wild-type, type I. Consequently, the granule-bound starch synthase I (GBSSI) contents of the three mutated genotypes were relatively low, leading to waxy or low AC endosperm, and the Wx genotypes could explain 78% of variance in AC. The geographic distribution of Wx genotypes are associated with culinary preferences and migration routes of Taiwanese indigenous peoples-in particular, the genotype of landraces collected from Orchid Island was distinct from those from Taiwan Island. This information on the major gene regulating starch biosynthesis in foxtail millet endosperm can be applied to breeding programs for grain quality, and contributes to knowledge of Austronesian cultures.
| S-EPMC6312202 | biostudies-literature
Project description:Transcriptome sequencing of Foxtail millet Setaria italica (Zhang-gu) for different tissues. Four RNA pools were created corresponding to four different tissues: root, leaf, stem, spica (tassel) at developmental stage, then each pool was sequenced.
2012-03-31 | E-GEOD-36391 | biostudies-arrayexpress
Project description:BackgroundAs modern industrial activities have advanced, the prevalence of microplastics and nanoplastics in the environment has increased, thereby impacting plant growth. Potassium is one of the most crucial nutrient cations for plant biology. Understanding how polyethylene terephthalate (PET) treatment affects potassium uptake will deepen our understanding of plant response mechanisms to plastic pollution.ResultsIn this study, we examined the impact of PET micro- and nanoplastics on foxtail millet seedling growth and potassium accumulation. Additionally, we measured reactive oxygen species (ROS) production, antioxidant enzyme activities, and the expression levels of the corresponding enzyme-encoding genes. Our findings indicated that the germination and seedling growth of foxtail millet were not significantly affected by exposure to PET plastics. However, the ROS levels in foxtail millet increased under these conditions. This increase in ROS led to the upregulation of several genes involved in K+ uptake and transport (SiHAK1, SiHAK2, SiAKT2/3, SiHKT2;2, SiHKT1;1, SiGORK, and SiSKOR), thereby increasing K+ accumulation in foxtail millet leaves. Further research revealed that higher K+ concentrations in plant leaves were correlated with increased expression of the antioxidant-related genes SiCAT1, SiPOD1, and SiSOD3, as well as increased activities of the corresponding antioxidant enzymes. This response helps mitigate the excessive accumulation and damage caused by ROS in plant cells after PET nanoplastic treatment, suggesting a potential stress response mechanism in foxtail millet against nanoplastic pollution.ConclusionsOur research indicates that PET nanoplastic treatment induces the expression of genes related to K+ uptake in foxtail millet through ROS signaling, leading to increased K+ accumulation in the leaves. This process mitigates the ROS damage caused by PET nanoplastic treatment by increasing the expression and activity of genes encoding antioxidant enzymes. The present research has unveiled the K+ accumulation-related response mechanism of foxtail millet to PET nanoplastic treatment, contributing significantly to our understanding of both the potassium absorption regulation mechanism in plants and the broader impact of plastic pollution on agricultural crops. This discovery not only highlights the complexity of plant responses to environmental stressors but also underscores the importance of considering such responses when evaluating the ecological and agricultural implications of plastic pollution.
| S-EPMC11670363 | biostudies-literature
Project description:Foxtail millet is very a drought-tolerant crop. Basic helix-loop-helix (bHLH) transcription factors are involved in many drought-stress responses, but foxtail millet bHLH genes have been scarcely examined. We identified 149 foxtail millet bHLH genes in a genome-wide analysis and performed Swiss-Prot, GO, and KEGG pathway analyses for these genes. Phylogenetic analyses placed the genes into 25 clades, with some remaining orphans. We identified homologs based on gene trees and Swiss-Prot annotation. We also inferred that some homologs underwent positive selection in foxtail millet ancestors, and selected motifs differed among homologs. Expression of eight foxtail millet bHLH genes varied with drought stress. One of these genes was localized to a QTL that contributes to drought tolerance in foxtail millet. We also perform a cis-acting regulatory element analysis on foxtail millet bHLH genes and some drought-induced genes. Foxtail millet bHLH genes were inferred to have a possible key role in drought tolerance. This study clarifies both the function of foxtail millet bHLH genes and drought tolerance in foxtail millet.
| S-EPMC6226204 | biostudies-literature
Project description:Foxtail millet (Setaria italica) is attractive to plant scientists as a model plant because of several distinct characteristics, such as its short stature, rapid life cycle, sufficient seed production per plant, self-compatibility, true diploid nature, high photosynthetic efficiency, small genome size, and tolerance to abiotic and biotic stress. However, the study on the genetic resources of foxtail millet largely lag behind those of the other model plants such as Arabidopsis, rice and maize. Mutagenized populations cannot only create new germplasm resources, but also provide materials for gene function research. In this manuscript, an ethyl methanesulfonate (EMS)-induced foxtail millet population comprising ∼15,000 individual M1 lines was established. Total 1353 independent lines with diverse abnormal phenotypes of leaf color, plant morphologies and panicle shapes were identified in M2. Resequencing of sixteen randomly selected M2 plants showed an average estimated mutation density of 1 loci/213 kb. Moreover, we provided an example for rapid cloning of the WP1 gene by a map-based cloning method. A white panicle mutant, named as wp1.a, exhibited significantly reduced chlorophyll (Chl) and carotenoid contents in leaf and panicle. Map-based cloning results showed an eight-base pair deletion located at the sixth exon of wp1.a in LOC101786849, which caused the premature termination. WP1 encoded phytoene synthase. Moreover, the sequencing analysis and cross test verified that a white panicle mutant wp1.b was an allelic mutant of wp1.a. The filed phenotypic observation and gene cloning example showed that our foxtail millet EMS-induced mutant population would be used as an important resource for functional genomics studies of foxtail millet.
| S-EPMC6455083 | biostudies-literature
Project description:RationaleCarbonised plant remains are analysed for reconstruction of past climates and agricultural regimes. Several recent studies have used C4 plants to address related questions, and correlations between modern C4 plant δ13 C values and rainfall have been found. The millets were important food crops in prehistoric Eurasia, yet little is known about causes of isotopic variation within millet species. Previous research has shown there to be significant isotopic variation between millet accessions. Here we compare isotope ratios from plants grown under different watering regimes. This allows for a consideration of whether or not Setaria italica is a good proxy for environmental reconstruction.MethodsWe compare stable isotope ratios of Setaria italica plants grown in a controlled environment chamber with different watering regimes. We compare the carbon isotope ratios of leaves and grains, and the nitrogen isotope ratios of grains, from 12 accessions of Setaria italica.ResultsWe find significant isotopic variability between watering regimes. Carbon isotope ratios are positively correlated with water availability, and on average vary by 1.9‰ and 1.7‰ for leaves and grains, respectively. Grain nitrogen isotope ratios also vary with watering regime; however, the highest isotope ratios are found with the 130-mL watering regime.ConclusionsThe carbon isotope ratios of Setaria italica are strongly correlated with water availability. However, the correlation is the opposite to that seen in studies of C3 plants. The difference in isotopic ratio due to watering regime is comparable with that seen between different accessions; thus distinguishing between changing varieties of Setaria italica and changing climate is problematic. In terms of grain nitrogen isotope ratios, the highest δ15 N values were not associated with the lowest watering regime. Again, δ15 N variation is comparable with that which would be expected from an aridity effect or a manuring effect, and thus distinguishing between these factors is probably problematic.
| S-EPMC7050514 | biostudies-literature