Maize and Sorghum Omics Data Curation

We focus on population-wide omics datasets. By curating these existing datasets, we can ensure the development of robust computational models.

Maize

Genome annotation data

Maize Association Panel (MAP, n=300 lines)

• Genotype: Whole genome sequencing (>10 M SNPs)
  • V5 genome filteration MAF < 0.05 and MR > 0.6: vcf (Bukowski et al., 2018)
• RNA-seq
  • RNA-seq in seven tissues: CyVerse (Kremling et al., 2018)
• Microbiome
  • under high N and low N conditions (n=230 gentoypes x 2 N x 2 reps) (Meier et al., 2022)
• Root exudates
  • collected using GC-MS method
• Metabolomics
  • From seedling tissue with three replications (unpublished)
• Aboveground phenotypes
  • More than 50 traits BLUP values
  • Six ear-related traits under different N conditions
• Belowground Phenotypes
  • NA

Backcrossed GEM (BGEM) DH lines (BGEM-DH, n=300 lines)

Maize off-PVP lines (PVP, n=x lines)

Chinese Elite Inbreds (CEI, n=300 lines)

Some big data were stored at OneDrive.

Sorghum

Sorghum Association Panel (SAP, n=400 lines)

Sorghum Carbon-Partitioning NAM (CP-NAM, n=2,500 RILs)

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Project Guideline

• To guide group members having a better sense about the project layout, here we briefly introduce the specific purposes of the dir system. The layout of dirs is based on the idea borrowed from ProjectTemplate.

• The guideline for the collaborative workflow.

• Check out progress and things to-do and throw ideas via the wiki page.

License

This is an ongoing research project. It was intended for internal lab usage. It has not been extensively tested. Use at your own risk. It is a free and open source software, licensed under GPLv3.