The Effect of Haplotype Size on Genomic Selection Accuracy and Epistasis: An Empirical Study in Rice - Dataset

The Effect of Haplotype Size on Genomic Selection Accuracy and Epistasis: An Empirical Study in Rice
Author: Maria Montiel
Description: This study investigates how haplotype block size impacts genomic selection (GS) accuracy and the detection of epistatic interactions in rice breeding populations. It includes phenotypic and genotypic datasets across three years and uses various statistical models and genomic prediction pipelines.
This repository contains all the data and scripts used in the study, including phenotypic and genotypic datasets from multiple rice populations evaluated over three years, alongside R scripts for spatial adjustments, genomic selection analysis, and epistasis modeling.

Folders:
- 001 Phenotypic Data: Contains raw phenotypic data from MP6-8 (multi-parent) and MP2 (bi-parental) populations (2020–2022 trials). Includes Preliminary Yield Trials (PYT) data. Traits: grain yield, days to heading, chalk, and whole milling.
Example file: `project_20mp2.csv`

- 002 Genotypic Data: Contains genotypic data in dosage matrix format (0, 1, 2) for MP2, MP6-8, MP4 populations. Includes genotype data for PYTs (2020–2022), both imputed and non-imputed. Also contains "LDdistance.csv" with LSU500 SNP distances.

- 003 Scripts: R scripts used for data processing, spatial adjustment, genomic selection, and matrix computation.
- README.txt

Data Format:
- Phenotypic Data: .csv
- Genotypic Data: .csv
- Scripts: .R

For more information, please refer to the "README.txt" file.