Advancing rust resistance in elite wheat with haplotype mapping and a novel introgression strategy

File Names:

1. combined_Oz_haplotype-sum_Yr_0.5r2_0Tol – Combined haplotype effect summary for stripe rust across environments and years (includes block names, positions, chromosome names, haplotypes, and effect values).
2. combined_oz_Yr_top_100_blocks_info – Top 100 haplotype blocks for stripe rust based on variance of haplotype effects.
3. combined_vav_haplotype-sum_Yr_0.5r2_0Tol – Same as (1) but for Vavilov panel.
4. combined_vav_Yr_top_100_blocks_info – Top 100 blocks for Vavilov panel.
5. final_block_summary_combined – Summary of total haplotype blocks developed using the above thresholds.
6. GebvS_LR_Shenton_combined – Genomic estimated breeding values (GEBVs) for leaf rust in Shenton panel across years.
7. GebvS_Yr_combined – GEBVs for stripe rust across locations and years.
8. gene_extraction.r – R script for gene extraction using Chinese reference genome v1.0.
9. iwgsc_refseqv1.0_FunctionalAnnotation_v1 – Functional annotation file from IWGSC reference.
10. iwgsc_refseqv1.0_HighConf_2017Mar13.gff3 – High-confidence annotation file used in gene extraction.
    11–14. oz_top100_significant_blocks_LR / Yr, SelectedBlocks_CandidateGenes_ALL / DEFENCE – Significant haplotype blocks and candidate gene lists.
11. selectedParents_usingcompositefun – Selected parents list using composite fitness function for introgression.
    16–19. shenton_Oz_haplotype-sum_LR_0.5r2_0Tol, shenton_oz_LR_top_100_blocks_info, shenton_vav_haplotype-sum_LR_0.5r2_0Tol, shenton_vav_LR_top_100_blocks_info – Leaf rust haplotype summaries and top blocks for OzWheat and Vavilov panels.
12. StripeRust_TopBlocks_Overlap – Stripe rust top blocks overlapped with literature positions.
13. summary_per_chromosome_block_hb_0.5r2_0Tol-29972_combined – Summary of haplotype blocks per chromosome (SNP count, block span, positions).

Notes:

• “Yr” stands for stripe rust; “LR” stands for leaf rust.
• Haplotype blocks were constructed using r² ≥ 0.5 and 0 tolerance.
• File names are self-explanatory and indicate panel, trait, and threshold details.
• File names are not in order