Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China

Munage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is renowned for its exceptional fruit traits. There are two main types of Munage: white fruit (WM) and red fruit (RM). However, the lack of a high-quality genomic resources has impeded effective breeding and restricted the potential for expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies for WM and RM, alongside integrated whole genome resequencing (WGS) data and transcriptome data to illuminate the origin, private mutations and selection in Munage. Our analyses suggest that Munage likely shares a common ancestor with Eurasian grapes that originated in West Asia. Selective analysis between Munage clones and Eurasian grapes mapped genomic signals of selection in Munage grapes, with genes enriched in processes including cell maturation, plant epidermal cell differentiation, and root epidermal cell differentiation. We also identified 283 somatic mutation sites between WM and RM, along with differential selection on genome and expressed genes. These findings provide crucial genetic resources for investigating the genetics of the ancient Chinese grape variety, Munage, and will facilitate the genetic improvement in grapevine using this ancient cultivar as a gene donor.

Authors

Institutions

Publication Details

Journal
Horticulture Research
Published
2025-10-20
DOI
https://doi.org/10.1093/hr/uhaf274
Primary Topic
Horticultural and Viticultural Research
Type
article
Field-Weighted Citation Impact
0.00
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China

Xiaoming Zhou, Zhongqi Liu, Mengyan Zhang, Wenrui Wang et al.
Horticulture Research
Horticultural and Viticultural Research
article

Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China

Xiaoming Zhou, Zhongqi Liu, Mengyan Zhang, Wenrui Wang, Zhongjie Liu, Ling Tian, Jiacui Li, Ruirui Liu, Vivek Yadav, Chuan Zhang, Zhong Haixia, Hua Xiao, Tianhao Zhang, Songlin Zhang, Yingchun Zhang, Hao Wang, Xinyu Wu, Shuo Cao, Hui Xue, Xiaoya Shi, Tianxiang Fan, Jin Yao, Yuting Liu, Fuchun Zhang, Ruoyan Zhao, Yongfeng Zhou, Jiangxia Qiao, Xu Wang
article en

Abstract

Munage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is renowned for its exceptional fruit traits. There are two main types of Munage: white fruit (WM) and red fruit (RM). However, the lack of a high-quality genomic resources has impeded effective breeding and restricted the potential for expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies for WM and RM, alongside integrated whole genome resequencing (WGS) data and transcriptome data to illuminate the origin, private mutations and selection in Munage. Our analyses suggest that Munage likely shares a common ancestor with Eurasian grapes that originated in West Asia. Selective analysis between Munage clones and Eurasian grapes mapped genomic signals of selection in Munage grapes, with genes enriched in processes including cell maturation, plant epidermal cell differentiation, and root epidermal cell differentiation. We also identified 283 somatic mutation sites between WM and RM, along with differential selection on genome and expressed genes. These findings provide crucial genetic resources for investigating the genetics of the ancient Chinese grape variety, Munage, and will facilitate the genetic improvement in grapevine using this ancient cultivar as a gene donor.

Horticulture ResearchVol. 13(1)
Chinese Academy of Tropical Agricultural Sciences (CN), Shenzhen Polytechnic University (CN), Arkansas Agricultural Experiment Station (US), Longdong University (CN), Agricultural Genomics Institute at Shenzhen (CN), Tropical Crops Genetic Resources Institute (CN), Xinjiang Academy of Agricultural Sciences (CN)
Openalex Percentile: Top 78%
Horticultural and Viticultural Research
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.