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Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses
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MDSi: Multi-omics Database for Setaria italica.

Xukai Li1,2, Siyu Hou1,3, Mengmeng Feng2

  • 1Hou Ji Laboratory in Shanxi Province, Shanxi Agricultural University, Taiyuan, Shanxi, 030031, China.

BMC Plant Biology
|April 26, 2023
PubMed
Summary
This summary is machine-generated.

A new database, MDSi, integrates foxtail millet genomics, transcriptomics, and metabolomics data. This resource provides valuable insights into Setaria italica germplasm variation and supports agricultural research.

Keywords:
DatabaseFoxtail milletMulti-omicsSetaria italicaTools

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Area of Science:

  • Plant genomics and bioinformatics
  • Agricultural science and crop improvement

Background:

  • Foxtail millet (Setaria italica) is a valuable grass species with a small genome, making it a model for C4 research.
  • A mini foxtail millet, xiaomi, was developed with a fast life cycle, high-quality genome data, and genetic transformation system.
  • The research community requires a user-friendly platform for analyzing foxtail millet data.

Purpose of the Study:

  • To develop a comprehensive, user-friendly database for foxtail millet data analysis.
  • To integrate multi-omics data, including genomics, transcriptomics, and metabolomics.
  • To provide access to germplasm variation data for Setaria italica.

Main Methods:

  • Construction of the Multi-omics Database for Setaria italica (MDSi).
  • Inclusion of genome annotations, gene expression data (xEFP), and whole-genome resequencing (WGS) data.
  • Integration of metabolic data and pre-called SNPs/Indels for 398 germplasms.

Main Results:

  • MDSi contains 161,844 annotations and 34,436 protein-coding genes with expression data in 29 tissues.
  • The database hosts WGS data for 398 foxtail and green foxtail germplasms, along with metabolic data.
  • Interactive tools such as BLAST, GBrowse, JBrowse, and a map viewer are implemented for data exploration.

Conclusions:

  • MDSi successfully integrates and visualizes genomics, transcriptomics, and metabolomics data for foxtail millet.
  • The database provides valuable information on germplasm variation, supporting research in the field.
  • MDSi meets the needs of the research community for exploratory data analysis in Setaria italica.