Graph pangenome captures missing heritability and empowers tomato breeding

Abstract Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits 1,2 . The solution to this problem is to identify all causal genetic variants and to measure their individual contributions 3,4 . Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41 compared with 0.33 when using the single linear reference genome. This…

• NS
  National Science Foundation

  Awards: IOS-1855585, 1855585
• NN
  National Natural Science Foundation of China

  Award: 31991180
• CA
  Chinese Academy of Agricultural Sciences
• NK
  National Key Research and Development Program of China

  Award: 2019YFA0906200
• AS
  Agricultural Science and Technology Innovation Program

  Award: CAAS-ZDRW202103
• SP
  Special Project for Research and Development in Key areas of Guangdong Province

  Award: 2021B0707010005