Extended Data Fig. 8: Identification of genomic loci associated with major agronomic traits.

a, Multi-site phenotyping experiments were conducted to measure 79 traits in total from distinct climate zones at three different locations: Southern China (22°N, Shenzhen), Northern China (45°N, Harbin), and the UK (52°N, Norwich). Map created using the maps package (3.4.0) in R (version 4.2). b, Illustrative photographs and drawings of phenotypic data collected for different trait categories scored in this study. The points in the hexagon represent the total number of sub-traits collected for each category, with the red line indicating the total number of phenotypes assessed (Supplementary Table 37). c, Significant marker-trait associations (MTAs) and their genetic effects for component traits from seeds, pods, leaves, flowers, roots and plant architecture. The number of sub-traits for each category is shown in parentheses. Specific examples for some of the selected Manhattan plots are shown to explain: d, The acute vs. blunt pod tip phenotypes, corresponding to the Bt locus (a locus known from classical genetics alone)⁸⁵. e, The pod neoplasm phenotype, the development of pustular-like growths, known as ‘neoplasms’. The locus known from classical genetics is Np⁸⁶. f, Green pod vs purple pod phenotypes corresponding to the known genetic loci: Pur and Pu⁴⁵. g, A new locus at the end of chromosome 3, underlying the seed number (SDN) per pod. h, Variations in flower number per axillary inflorescence corresponding to the known genetic loci: Fn and Fna⁸⁷. i, A new locus on chromosome 3, underlying the total seed weight per plant (SDY), a yield component trait. j, Variation in flowering time corresponding to the Hr locus⁸⁸. k, A new locus underlying flower size (FLS), on chromosome 1. l, Brown vs black hilum colour phenotypes, corresponding to the Pl locus⁸⁹. m, A historical locus (Ser1) at chromosome 5, explaining the phenotypic variation in leaflet margin serration.