Fig. 4: Identifying and exploiting novel haplotypes from the Watkins landraces.

a Physical distribution of SNPs in 5-Mbp bins across chromosome 6A based on the 15 sequenced cultivars and other genotyping platforms (15K iSelect, 35K Axiom, exome capture). Beige shading indicates minimum haplotype block (MHB). b Allele calls extracted from sequenced cultivars for informative SNPs in MHB based on the genotyping platforms shown in (a) and allele calls for 6A haplotype-informed (Hap. informed) markers. Physical positions of SNPs are shown above each panel. Grey = reference allele, black = alternative allele. c 6A haplotypes present in germplasm panels based on genotyping platforms in (b) (number of cultivars in parentheses). ‘UK’ = UK Recommended List (35 K)²⁴, ‘Eur.’ = European elite winter wheat (15K)²³, ‘Aus.’ = Australian cultivars (35K)²⁴, ‘USA’ = USA cultivars (exome capture)¹¹, ‘CIM’ = CIMMYT Core Germplasm (CIMCOG) lines (35K)²⁴. d 6A haplotypes in the Watkins landrace panel (n = 806) based on 35K array (left)⁶¹ and haplotype-informed markers (right). Full details of lines and haplotype allocations in Supplementary Data 10. Fill colour legend corresponds to both (c) and (d). e Summary of Paragon (H2) x Watkins bi-parental populations with QTL for increased thousand grain weight (TGW) across the MHB. See Supplementary Table 1 for additional phenotypes.