From West Asia to Xinjiang: The genome secrets behind China’s legendary Munage grape

An international research team has generated the first haplotype-resolved genome assemblies of Munage, one of China's oldest grape cultivars of Vitis vinifera. By integrating high-fidelity long-read sequencing, population genomics, and transcriptome analyses, the study reveals the evolutionary origin, adaptive selection, and clonal divergence of white and red Munage grapes. The results indicate that Munage shares ancestry with West Asian Eurasian grapes but underwent distinct genomic adaptation after its introduction to Xinjiang. The work also identifies somatic mutations and differential gene expression associated with berry color variation. These findings provide valuable genomic resources for grape breeding and deepen understanding of how domestication and clonal propagation shape fruit diversity.

The cultivated grapevine, Vitis vinifera, was domesticated in West Asia and later spread across Europe and Asia. Although archaeological evidence suggests grapes reached Xinjiang over two millennia ago, the genetic origin and domestication trajectory of ancient local cultivars remain unclear. Munage, a traditional Xinjiang variety prized for large berries and distinctive flavor, exists in white and red forms believed to have arisen through bud mutation. However, the lack of high-quality genomic references has limited systematic genetic investigation. Based on these challenges, in-depth genomic research is needed to clarify the evolutionary history of Munage and uncover the genetic mechanisms underlying its unique traits.

Researchers from the Xinjiang Academy of Agricultural Sciences and collaborating institutions reported (DOI: 10.1093/hr/uhaf274) haplotype-resolved genome assemblies of white and red Munage in Horticulture Research (2026). Using PacBio HiFi sequencing and Hi-C scaffolding technology, the team constructed high-quality diploid genomes and integrated resequencing data from 59 grape accessions. Their analyses traced the evolutionary origin of Munage within Vitis vinifera, identified selective sweeps linked to environmental adaptation, and uncovered somatic mutations and transcriptional divergence associated with berry color variation between the two clones.

The team generated four chromosome-level haplotypes with genome sizes ranging from 480–490 Mb and BUSCO completeness above 98%, demonstrating high assembly quality. Comparative analyses revealed strong collinearity with the telomere-to-telomere reference genome while identifying structural variations, including large chromosomal inversions.

Population genomic analysis showed that Munage clusters with Eurasian cultivated grapes and is closely related to a West Asian table grape, supporting shared ancestry. However, principal component and population branch statistic analyses revealed distinct selective sweeps across 19 chromosomes, indicating genomic adaptation to Xinjiang's arid continental climate. Genes within these regions included immune-related genes such as RPM1 and cysteine-rich receptor-like kinases, hormone-regulating genes such as BIG, and genes involved in photosynthesis and epidermal differentiation.

Although white and red Munage are nearly genetically identical (IBD = 0.98), 283 somatic mutation sites were identified between them. Many were located in regulatory regions rather than coding sequences. Transcriptome profiling further identified 578 differentially expressed genes, including genes enriched in anthocyanin biosynthesis and pigment metabolism pathways, suggesting that regulatory divergence contributes to berry color differences.

“Our haplotype-resolved assemblies allow us to see genomic variations that are often hidden in highly heterozygous crops like Vitis vinifera,” the authors said. “By identifying selection signals and somatic mutations, we provide molecular evidence explaining how long-term adaptation and clonal propagation shaped Munage. This ancient cultivar contains valuable alleles that can support future grape breeding and climate resilience strategies.”

The high-quality genomic resources generated in this study establish a foundation for precision breeding in Vitis vinifera, particularly for improving stress tolerance, fruit quality, and pigmentation traits. Identifying adaptive selection signals related to immune response, root development, and metabolic regulation offers candidate genes for breeding cultivars better suited to changing climates. Moreover, understanding somatic mutation accumulation during clonal propagation may guide targeted selection in perennial fruit crops. Beyond grape improvement, the research demonstrates how haplotype-resolved assemblies combined with population genomics can reconstruct the domestication and adaptation history of ancient germplasm resources.

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References

DOI

10.1093/hr/uhaf274

Original Source URL

https://doi.org/10.1093/hr/uhaf274

Funding information

The financial assistance for this research is received from the Project of Fund for Stable Support to Agricultural Sci-Tech Renovation (xjnkywdzc-2025001-07, xjnkywdzc-2026001-18, xjnkywdzc-2025001-39), Tianshan Autonomous Region Talent Youth Top notch Talent - Young Science and Technology Innovation Talent Project (2024TSYCCX0097), the National Natural Science Foundation of China (No.32160682, No.32260732 and No.32460722), Xinjiang Uygur Autonomous Region Tianchi Talent - Special Expert Project (Whole genome design and breeding of grapes), Key research and development project of autonomous region (2022B02045-1-1, 2023B02029-1-1), National Key Laboratory of Tropical Crop Breeding (No.NKLTCB-RC202501), the China Agriculture Research System of MOF and MARA and Shenzhen Polytechnic University Research Project (6024330001K) to Tian Ling.

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.