DOI: 10.5061/dryad.wstqjq2jb
title: A haplotype-led approach to increase the precision of wheat breeding

description: Crop productivity must increase at unprecedented rates to meet the needs
 of the growing worldwide population. Exploiting natural variation for the
 genetic improvement of crops plays a central role in increasing
 productivity. Although current genomic technologies can be used for
 high-throughput identification of genetic variation, methods for
 efficiently exploiting this genetic potential in a targeted, systematic
 manner are lacking. Here, we developed a haplotype-based approach to
 identify genetic diversity for crop improvement using genome assemblies
 from 15 bread wheat (Triticum aestivum) cultivars. We used stringent
 criteria to identify identical-by-state haplotypes and distinguish these
 from near-identical sequences (~99.95% identity). We showed that each
 cultivar shares ~59 % of its genome with other sequenced cultivars and we
 detected the presence of extended haplotype blocks containing hundreds to
 thousands of genes across all wheat chromosomes. We found that genic
 sequence alone was insufficient to fully differentiate between haplotypes,
 as were commonly used array-based genotyping chips due to their gene
 centric design. We successfully used this approach for focused discovery
 of novel haplotypes from a landrace collection and documented their
 potential for trait improvement in modern bread wheat. This study provides
 a framework for defining and exploiting haplotypes to increase the
 efficiency and precision of wheat breeding towards optimising the
 agronomic performance of this crucial crop.
description: Here, we defined haplotype blocks in hexaploid bread wheat using
 genome assemblies of cultivars representing modern-day diversity across
 wheat breeding programmes. We used chromosome-scale genome assemblies
 corresponding to 9 wheat lines (ArinaLrFor, Jagger, Julius, Lancer,
 Landmark, Mace, Norin61, Stanley, SY-Mattis) and the Chinese Spring
 RefSev1.0 assembly, alongside 5 scaffold-level assemblies corresponding to
 cultivars Cadenza, Claire, Paragon, Robigus and Weebill. Thirteen of these
 15 lines are considered cultivars (cultivated varieties of wheat), whereas
 ArinaLrFor is a line derived from cultivar Arina and Chinese Spring is a
 landrace collected in the early 1900’s from China. To avoid multiple
 designations, for the purposes of this study we will refer to all 15 lines
 as cultivars.
description: The data corresponds to the underlying source data for the graphs
 and figures presented in Brinton et al 2020 <b>A haplotype-led
 approach to increase the precision of wheat
 breeding</b> <em>Communications Biology.</em>
 # Figure 1<br> ## Fig 1a,b,c,d<br>
 mace_v_stanley.all_6A_filtered_L20Kb_rq.delta ## Fig
 1d,e,f (pink box coordinates)<br>
 whole_genome_mummer_BLAST_5000000_blocks_combined_updated_ref_coords_10g_corrected_2gap_no_spelta.tsv ## Fig 1f<br> ### heatmaps<br> varieties_6A_identites_cdsbp.tab.gz<br> varieties_6A_identites_0bp.tab.gz<br> varieties_6A_identites_1000bp.tab.gz<br> varieties_6A_identites_2000bp.tab.gz<br> varieties_6A_identites_5000bp.tab.gz ### purple box coordinates<br> chr6A_haplotype_blocks_aln_25_gene_window_drop3.tsv # Figure 2<br> ## Fig 2a <br> Block_slice500k_stats_Tae_5000kbp.tsv.gz<br> 161010_Chinese_Spring_v1.0_pseudomolecules.fai ## Fig 2b,c<br> blocks_coverage_5000kbp.csv<br> combined_fai.txt<br> 161010_Chinese_Spring_v1.0_pseudomolecules.fai # Figure 3<br> ## Fig 3a<br> Brinton et al_Supplementary Table 4_Previously_identified_QTL_on_chromosome_6A.xlsx ## Fig 3b<br> Supplementary_Table_2_Sheet1_6A_only.xlsx # Figure 4<br> ## Fig 4a<br> all.GP08_mm75_het3_publication01142019.vcf.gz_all6A_HCLC_GT_only.GT.FORMAT_position_only.tsv<br> 35k_probe_set_IWGSCv1_chr6A.csv<br> voss_fells_marker_positions_6A.csv<br> pangenome_snp_dist_6A_CS_ref.tsv ## Fig 4b<br> 35K_cerealsdb_hap_examples.csv<br> voss_fells_hap_examples.csv<br> akhunov_hap_examples.csv<br> haplotype_specific_markers_pangenome.csv ## Fig 4c (also in Supplementary Table 7)<br> pangenome_haplotype_allocations_35K_all_AK_USA_capture_vossfells_updated_May2020_FINAL_SET_TO_INCLUDE.csv ## Fig 4d (also in Supplementary Table 9)<br> final_haplotypes_watkins_UKRL.csv ## Fig 4e<br> Extended Data Table 1 (in manuscript)<br>