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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Publications at this Location » Publication #381136
Research Project: Grapevine Genetics, Genomics and Molecular Breeding for Disease Resistance, Abiotic Stress Tolerance, and Improved Fruit Quality

Location: Grape Genetics Research Unit (GGRU)

Title: The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine

Author
item WANG, YI - Chinese Academy Of Sciences
item XIN, HAILING - Chinese Academy Of Sciences
item FAN, PEIGE - Chinese Academy Of Sciences
item ZHANG, JISEN - Fujian Agricultural & Forestry University
item LIU, YONGBO - Chinese Research Academy Of Environmental Sciences
item DONG, YANG - Yunnan Agricultural University
item WANG, ZEMIN - Chinese Academy Of Sciences
item Yang, Yingzhen
item ZHANG, QING - Fujian Agricultural & Forestry University
item MING, RAY - Fujian Agricultural & Forestry University
item Zhong, Gan-Yuan
item LI, SHAOHAU - Chinese Academy Of Sciences
item LIANG, ZHENCHANG - Chinese Academy Of Sciences

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/3/2020
Publication Date: 12/10/2020
Citation: Wang, Y., Xin, H., Fan, P., Zhang, J., Liu, Y., Dong, Y., Wang, Z., Yang, Y., Zhang, Q., Ming, R., Zhong, G., Li, S., Liang, Z. 2020. The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine. Plant Journal. https://doi.org/10.1111/tpj.15127.
DOI: https://doi.org/10.1111/tpj.15127

Interpretive Summary: Low winter temperature is a significant abiotic stress for grape production in many areas. Vitis amurensis (Shanputao) is a Chinese grape species and shows extremely cold tolerance. As a first step of understanding the genetic and genomic basis of cold tolerance in Shanputao, we produced a high-quality, chromosome-level genome assembly of the species based on sequence data generated from several cutting-edge sequencing technologies. We found that Shanputao's 604.56 Mb genome contained 32,885 protein coding genes and that gene expansion in Shanputao might contribute to its enhancement of cold tolerance. We also revealed seventeen genes in Shanputao which are likely important to chilling temperature and freezing conditions. Furthermore, we uncovered a phosphoglycerate kinase gene which may contribute to Shanputao's freezing resistance of buds in the winter. This work provides a valuable genomic resource for studying cold tolerance and a genetic resource for breeding future grape cultivars with superior cold tolerance.

Technical Abstract: Vitis amurensis (Shanputao) is the most cold tolerant Vitis species and so is of great interest to grape breeders and producers in areas with low winter temperatures. Here, we report its high-quality, chromosome-level genome assembly based on a combination of sequence data from Illumina and PacBio platforms, BioNano optical mapping and high-throughput chromosome conformation Capture (Hi-C) mapping. The 604.56 Mb genome contains 32,885 protein coding genes. Shanputao was found to share a common ancestor with PN40024 (V. vinifera) approximately 2.17 - 2.91MYA, and gene expansion observed in Shanputao might contribute to the enhancement of cold tolerance. Transcriptome analysis revealed seventeen genes involved in cold signal transduction, suggesting that there were different response mechanism to chilling temperature and freezing conditions. Furthermore, a genome wide association study uncovered a phosphoglycerate kinase gene that may contribute to the freezing resistance of buds in the winter. The Shanputao genome sequence not only represents a valuable resource for grape breeders, but also is important for clarifying the molecular mechanisms involved in cold tolerance.