Integrative genomics reveals the polygenic basis of seedless in grapevine

To explore the evolutionary patterns of seed abortion in grapes, we generated four haplotype-resolved T2T genomes using high-depth PacBio HiFi long-reads and Illumina Hi-C reads for two grape varieties: Thompson Seedless (B7) and Black Monukka (Z1). The RNA-seq of thses two grape varieties were extracted from mixed tissues, including roots, stems, buds, and tendrils, for genome annotation. Additionally, we performed high-depth Whole Genome Sequencing (WGS) on 29 different grape cultivars, including B7 and Z1. Our study involved the construction of a phylogenetic tree, PCA analysis, Identity by Descent (IBD) analysis, Genome-Wide Association Study (GWAS), RNA-seq analysis, and other relevant analyses.