Inheritance-of-HEB-in-wheat

Background:

This repository contains scripts and links to data tables and raw sequencing data to a pre-print: "Rapid reprogramming and stabilisation of homoeolog expression bias in hexaploid wheat biparental populations" (link)

In this study, we analyse Homoeolog Expression Bias inheritance patterns in two F₅ biparental populations with a common parent: Paragon (W10074 PF-1) x Charger (WPxCHA – 1001), and Paragon (W10074 PF-1) x Watkins (WATDE0228).

Data availability:

All RNA-seq data were uploaded to Sequence Read Archive (SRA) under the BioProject ID PRJNA1128551.

The wheat genome reference used to map/pseudoalign the RNA-seq data to is The IWGSC RefSeq v1.0 assembly available here.

The wheat transcriptome reference and genome annotation used to map SNPs to is The IWGSC RefSeq v1.1 annotation available here.

The triad identification file "homoeologs_1_1_1_synt_and_non_synt.csv" is adapted from HCtriads.tsv published as a part of dataset in Ramírez-González et al. (2018).

All data tables necessary to run scripts associated with this project are located in the figshare repository, organised by Methods sections just like scripts (see below).

Methodology:

Scripts are organised by Methods sections as outlined in the manuscript in the scripts folder.

1. HEB analysis

2. Gene ontology term enrichment

3. Variant calling, genotyping and association between genotype and homoeolog expression

4. SNP genotyping of F₅ lines for eQTL mapping

5. Quantification of gene expression levels and correction for batch effects

6. Detection of eQTL

Note: Sections 4 and 6 are coupled together due to overlapping code sections.

Figures:

The code for recreating figure panels is in the figures folder. The ready to plot data are located in the figshare repository associated with this project.