Fig. 4: A Genome–phenome association map for the identification of genetic loci that confer agronomic traits.
a, Summary of the most significant trait–marker associations underlying a variety of agronomic traits presented as a combined Manhattan plot. Gene symbols shown in a circle correspond to Mendel’s loci. b, Manhattan plot of GWAS data for seed protein content, showing a peak overlapped with the R gene locus. c, Manhattan plot of GWAS data for the presence or absence of axial ring pigmentation, on a subset of phenotypic data excluding accessions carrying white flowers (a/a). These data were collected at Harbin (northern China, 2022). A peak at the expected genomic position of D is significantly associated with the accumulation of axillary anthocyanin, and the peak at chromosome 6 is the location of A. d, Genomic interval of D locus on chromosome 2 defined by recombinant inbred lines (RIL) mapping and GWAS analyses, further defined by bioinformatic analysis of FN mutants as a MYB gene cluster7,47,48, with the genes PsMYB104 and PsMYB106 both deleted in the d mutant line FN1218/6. The region outlined in red line indicates the approximate position of the deletion detected in FN1218/6 from mapping of sequence reads. e, Manhattan plot of GWAS data for Af/af (semi-leafless phenotype). Scale bar, 5 cm. f, Manhattan plot of GWAS data for hundred seed weight (HSW) and pod width (PW). The HSW and pod width genomic intervals span the same 8 Mb genomic region, named Organ Size 1 (PsOs1). Scale bar, 2 cm. g, Narrowed genomic interval of PsOs1 on chromosome 2 defined by two F2 mapping populations and BSA analysis (Methods) as a 1.01-Mb region encompassing 11 protein-coding genes, of which Psat02G0011300 (marked in yellow) is the most highly expressed gene. Photographs in c,e,f show the corresponding contrasting phenotypes.
