1Institute of Fruits and Vegetables, Xinjiang Uygur Autonomous Region Academy of Agricultural Sciences, Biological Breeding Laboratory, Xinjiang Uygur Autonomous Region Academy of Agricultural Sciences, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Urumqi, China 2State Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China 3College of Enology, Heyang Viti-Viniculture Station, Ningxia Helan Mountain’s East Foothill Wine Experiment and Demonstration Station, Northwest A&F University, Yangling, China 4State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China 5School of Management, Shenzhen Polytechnic University, Shenzhen, China 6Gansu Key Laboratory of Conservation and Utilization of Biological Resources and Ecological Restoration in Longdong, School of Agriculture and Bioengineering, Longdong University, Qingyang, China *Corresponding author. E-mail: zhouyongfeng@caas.cn,tianling@szpu.edu.cn,wuxy@xaas.ac.cn,xiaohua01@caas.cn †Haixia Zhong,Xiaoya Shi,Fuchun Zhang contributed equally to the study.
Received: 02 Oct 2024 Accepted: 11 Oct 2025 Published online: 20 Oct 2025
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.
, Ling Tian5 ,
