Plot genotype per NIL. Characterize linkage disequilibrium between the Inv4m chromosomal inversion and genome-wide markers in maize near-isogenic lines.

Testing whether: Inv4m constitutively upregulates DNA replication genes (PCNA2, MCM5, others) across tissues, accelerating cell cycle in the SAM, leading to: - Larger SAM size (9% increase at 3 weeks) - Taller plants - Earlier flowering

This analysis performs differential gene expression analysis on RNA-seq data from Crow et al. (2020), examining maize apical tissue samples across multiple experimental factors: Tissue type: V1_Leaf, V1_Root, V3_Leaf, V3_Root, V3_SAM temperature treatment: CTRL (warm) vs cold Genotype: CTRL (B73) vs Inv4m (inverted karyotype) Donor: PT vs Mi21 (treated as batch effect)

Identify and characterize trans-regulatory networks mediated by genes within the Inv4m introgression region. This analysis integrates differential expression results with co-expression data from MaizeNetome to construct regulatory networks.

**Purpose**: GO over-representation analysis for differential expression across Leaf development and Phosphorus deficiency. **Experimental predictors**: - **Leaf**: Leaf development/senescence (FC threshold: ±0.7) - **-P**: Phosphorus deficiency (FC threshold: ±2) - **Leaf:-P**: Interaction term

GO KEGG analysis of Inv4m experiment

Analysis dropping Inv4m x P interaction and adding Leaf x P interaction

PSU2022 INv4m P Leaf Differential gene expression

Teosinte Introgression Lines Ancestry Analysis by bins

Extreact P retention Potential for selected maize accessions.

Extracting soil retention potential for maize accessions in root phenotype study

Loading ISRIC Phosphorous Retention Potential Main Clases, and make it a continuous variable

Load ISRIC. Linearize categorical data

Extract P data from root phenotype set, Burton et. al. 2013.

Extract P data from ISRIC and Oak Ridge models.

Local adaptation to Phosphorus Availability This package helps in the extraction from geographical coordinates of phosphorus data from two sources, ISRIC for soil retention, and Oakridge National Laboratory for soil availabilty.