Expression quantitative traits locus analysis using EMMAX software

Download RNA-seq and genome-wide marks from public database.

The marks file in VCF format is from Yan's Lab website: http://www.maizego.org/

The RNA-seq data of kernel in 15 DAP were downloaded from NCBI.

Reference: Liu H, Luo X, Niu L, Xiao Y, Chen L, Liu J, Wang X, Jin M, Li W, Zhang Q, Yan J. Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize. Mol Plant. 2017 Mar 6;10(3):414-426. doi: 10.1016/j.molp.2016.06.016. Epub 2016 Jul 2. PMID: 27381443.

QC, mapping and calculate the expression level of genes in each sample.

Merge expression level of each gene in different samples to one file.

Filter marks of 368 maize inbred lines

Using Genome-wide association stduy, identify significant marks potentially regulating expression of each genes.

Visualization using R.