maize.md

---

Maize

Genome annotation data

Maize Association Panel (MAP, n=282 lines, aka 282 panel)

• Genotype: Whole genome sequencing (>10 M SNPs)
  • Raw sequencing data (Bukowski et al., 2018)
  • Row VCF file on HCC: path?
    • AGPV5 genome filtration MAF < 0.05 and MR > 0.6: vcf
  • Randomly sampled 50k SNPs
    • GitHub Path: data/01Genotype/282_agpv5_50.recode.vcf
    • data/01Genotype/282_agpv5_50k.txt
• RNA-seq
  • RNA-seq in seven tissues: CyVerse (Kremling et al., 2018)
  • Root RNA-seq?
    • Raw data?
    • Process version?
• 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 (Z. Yang et al., 2022)
• Aboveground phenotypes
  • More than 50 traits BLUP values
    • data/03Phenotype/MAP/public_pheno_282_37traits.xlsx
    • data/03Phenotype/MAP/public_pheno_282_mineral_ziegler.xlxs
  • 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.