Jiantao Zhao

TomatoPGFM is a graph-conditioned foundation model for tomato pangenomes that improves sequence representation using graph context, achieving higher classification performance than DNABERT-2.

This study constructs a watermelon super-pangenome from 138 genomes, identifies over a million structural variants, and develops genomic prediction models for 18 traits to advance precision breeding.

The paper constructs a cucumber pangenome to analyze structural variant dynamics during domestication and breeding, finding SVs are purged more than SNPs and improving genomic prediction accuracy.

This study identifies genes regulating lateral root development in tomato under salt stress, revealing ethylene and ROS signaling as key factors.