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Transcriptome sequencing of Foxtail millet Setaria italica for different tissues

ABSTRACT: 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.

ORGANISM(S): Setaria italica

SUBMITTER: Zhijun Zheng

PROVIDER: E-GEOD-36391 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential.

Zhang Gengyun G Liu Xin X Quan Zhiwu Z Cheng Shifeng S Xu Xun X Pan Shengkai S Xie Min M Zeng Peng P Yue Zhen Z Wang Wenliang W Tao Ye Y Bian Chao C Han Changlei C Xia Qiuju Q Peng Xiaohua X Cao Rui R Yang Xinhua X Zhan Dongliang D Hu Jingchu J Zhang Yinxin Y Li Henan H Li Hua H Li Ning N Wang Junyi J Wang Chanchan C Wang Renyi R Guo Tao T Cai Yanjie Y Liu Chengzhang C Xiang Haitao H Shi Qiuxiang Q Huang Ping P Chen Qingchun Q Li Yingrui Y Wang Jun J Zhao Zhihai Z Wang Jian J

Nature biotechnology 20120513 6

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuff ...[more]

PMID: 22580950

Similar Datasets

Transcriptome sequencing of Foxtail millet Setaria italica for different tissues

Project description:Transcriptome sequencing of Foxtail millet Setaria italica (Zhang-gu) for different tissues.

2012-03-31 | GSE36391 | GEO

Whole genome sequencing of six strains of Philippine local foxtail millet (Setaria italica) accessions

Project description:The study aims to identify molecular variations across these six lines of foxtail millet.

2023-02-15 | E-MTAB-12658 | biostudies-arrayexpress

Whole genome sequencing of two strains of Philippine local foxtail millet (Setaria italica) accessions

Project description:The study aims to identify molecular variations across these six lines of foxtail millet.

2023-06-10 | E-MTAB-13027 | biostudies-arrayexpress

Transcriptome Analysis of Responses to Saline-Alkali Stress in Two Different Genotypes of foxtail millet (Setaria italica L.)at the Seedling Stage

Project description:We present here a transcriptome dataset of millet seedling leaves based on RNA-seq technology. The purpose of this study was to mine the salt and alkali tolerance genes of millet and further explore the mechanism of salt and alkali tolerance of millet. We selected 18 representative samples and conducted in-depth sequencing using the latest sequencing platform to ensure the accuracy and reliability of the data.

2024-10-10 | GSE278652 | GEO

Setaria italica cultivar:foxtail millet

Project description:Setaria italica cultivar:foxtail millet Raw sequence reads

| PRJNA287886 | ENA

Waxy allele diversification in foxtail millet (Setaria italica) landraces of Taiwan.

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-other

The foxtail millet (Setaria italica) terpene synthase gene family.

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

Genome-wide characterization of microRNA in foxtail millet (Setaria italica).

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

Generation and Characterization of a Foxtail Millet (<i>Setaria italica</i>) Mutant Library.

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

Transcriptome Analysis Provides Insights into Grain Filling in Foxtail Millet (Setaria italica L.).

Project description:Grain filling is an importantly developmental process which is associated with the yield and quality of foxtail millet (Setaria italic L.). However, the molecular mechanisms of grain filling are rarely reported in foxtail millet. In our study, RNA-seq was performed to investigate the transcriptional dynamics and identify the key genes involved in grain filling in foxtail millet at five different developmental stages. A total of 11,399 differentially expressed genes (DEGs), including 902 transcription factors (TFs), were identified. Certain important genes involved in grain filling were discovered through a function annotation and temporal expression patterns analysis. These genes included genes associated with starch biosynthesis, cell-wall invertases, hormone signal transduction, and polyamine metabolism pathways. The expression levels of seven randomly selected DEGs were validated by a quantitative real-time polymerase chain reaction (qRT-PCR). This study provides the first insight into the changes in the gene expression of grain filling at different developmental stages in foxtail millet. These results could help understand the complex molecular mechanisms of the panicle formation in foxtail millet and other cereal crops.

| S-EPMC7403974 | biostudies-literature

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