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

This dataset contains haplotype block information and genomic prediction results for wheat resistance to leaf rust (LR) and stripe rust (Yr). The data were generated using OzWheat and Vavilov panel datasets, combined across multiple environments and years. Haplotype blocks were constructed using an r² threshold of 0.5 and 0 tolerance, and the dataset includes summaries of haplotype effects, top blocks based on variance, and candidate gene extractions. File Names: 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). combined_oz_Yr_top_100_blocks_info – Top 100 haplotype blocks for stripe rust based on variance of haplotype effects. combined_vav_haplotype-sum_Yr_0.5r2_0Tol – Same as (1) but for Vavilov panel. combined_vav_Yr_top_100_blocks_info – Top 100 blocks for Vavilov panel. final_block_summary_combined – Summary of total haplotype blocks developed using the above thresholds. GebvS_LR_Shenton_combined – Genomic estimated breeding values (GEBVs) for leaf rust in Shenton panel across years. GebvS_Yr_combined – GEBVs for stripe rust across locations and years. gene_extraction.r – R script for gene extraction using Chinese reference genome v1.0. iwgsc_refseqv1.0_FunctionalAnnotation_v1 – Functional annotation file from IWGSC reference. 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. 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. StripeRust_TopBlocks_Overlap – Stripe rust top blocks overlapped with literature positions. 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