High‐Contiguity Haplotype‐Resolved Genome Assembly of the Hexaploid <i>Actinidia valvata</i> Rootstock Sheds Light on Waterlogging Resistance Gene

Polyploidisation, creating redundant or diverged copies of the genome, is a major driving force in plant evolution, diversification and environmental adaptation, including for the kiwifruit genus (Actinidia Lindl.). We present a high-contiguity, haplotype-resolved genome assembly of the hexaploid Actinidia valvata rootstock cultivar 'Zhongmikangzhen No. 2' (ZK2), a novel rootstock and the first of its kind to receive Plant Variety Protection in China, exhibiting superior waterlogging tolerance. The assembly, ZK2, contains 174 chromosomes in 6 haplotypes (2n = 6x = 174), where > 82% of chromosomes per haplotype are telomere-capped at one or both ends, including three haplotypes achieved with 100% telomeric representation. In total, 212 055 protein-coding genes are predicted, or about 35 000 genes per haplotype on average. Our work on comparative genomics, including analyses of TE composition, collinearity, orthologs and phylogenies, strongly reveals an AABBBB subgenome structure derived from ancestral donors A. polygama (A1 and A2) and A. macrosperma (B1 to B4). Transcriptome analysis showed differential expressions between the homeologs under waterlogging stress, highlighting subgenome-specific regulatory dynamics. A key example involves an ethylene-response factor (ERF) gene: when the B1 copy of ERF was overexpressed in the kiwifruit transgenic lines, they illustrated an enhanced waterlogging resistance. In addition, this high-quality haplotype-resolved A. valvata genome assembly enables functional trait discovery, homeolog-aware genome-wide association studies, and targeted editing of beneficial alleles or homologous gene sets, supporting the breeding of resilient polyploid kiwifruit cultivars and rootstocks. This resource provides a foundation for future research in kiwifruit, particularly for rootstock-mediated crop improvement.