biostudies-literatureUnknown17(1)Zhang WTea plants possess a highly heterozygous genome and produce diverse beneficial metabolites, yet the genomic basis of its metabolic diversity remains fully elusive. Here, we show that single-cell sequencing of 107 sperm cells, combined with PacBio HiFi and ONT ultra-long sequencing, enables an accurate haplotype-resolved genome assembly of Fuding Dabaicha (FDDB). Structural variations (SVs) between the two haplotypes comprise 23.8% of the genome and strongly influence crossover patterns. Using these phased genomes, we establish a half-sib-based QTL mapping platform and identify a Gypsy LTR insertion in the promoter of CsDFRb, which associated with the increasing of p-coumaroylquinate levels in young leaves. Moreover, mGWAS reveals 2649 additional loci associated with 2837 metabolites when uNature communications1754https://www.ebi.ac.uk/biostudies/studies/S-EPMC12913673biostudies-literatureThe Camellia sinensis var. sinensis cv. Fuding Dabaicha genome unveils structural variation-driven metabolic innovation.PMC12913673Zhang WFernie ARJiang XTariq AZhang XBuchmann JLuo SUsadel BWen WGao DfalseThe Camellia sinensis var. sinensis cv. Fuding Dabaicha genome unveils structural variation-driven metabolic innovation.Tea plants possess a highly heterozygous genome and produce diverse beneficial metabolites, yet the genomic basis of its metabolic diversity remains fully elusive. Here, we show that single-cell sequencing of 107 sperm cells, combined with PacBio HiFi and ONT ultra-long sequencing, enables an accurate haplotype-resolved genome assembly of Fuding Dabaicha (FDDB). Structural variations (SVs) between the two haplotypes comprise 23.8% of the genome and strongly influence crossover patterns. Using these phased genomes, we establish a half-sib-based QTL mapping platform and identify a Gypsy LTR insertion in the promoter of CsDFRb, which associated with the increasing of p-coumaroylquinate levels in young leaves. Moreover, mGWAS reveals 2649 additional loci associated with 2837 metabolites when u2026-01-01T00:00:00Z2026 Jan2026-07-16T06:52:09.038Z2026-07-09T10:42:18.628ZS-EPMC129136734153530510.1038/s41467-026-68463-8