Analysis of Genetic Mechanism
of Grape Distant Hybridization Based on Population Transcriptome

doi:10.16420/j.issn.0513-353x.2024-0115

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (4): 835-845.doi: 10.16420/j.issn.0513-353x.2024-0115

• Genetic & Breeding · Germplasm Resources · Molecular Biology • Previous Articles Next Articles

Analysis of Genetic Mechanism of Grape Distant Hybridization Based on Population Transcriptome

WANG Yi1,2 and LIANG Zhenchang1,2,*(zl249@ibcas.ac.cn)

¹Beijing Key Laboratory of Grape Science and Enology，State Key Laboratory of Plant Diversity and Specialty Crops，Institute of Botany，Chinese Academy of Sciences，Beijing 100093，China ²China National Botanical Garden，Beijing 100093，China

Received:2024-12-17 Revised:2025-02-09 Online:2025-04-25 Published:2025-04-25
Contact: LIANG Zhenchang

Abstract

Abstract: The main grape varieties for wineamking are all belongs to Vitis vinifera，and the genetic background is relative narrow. This study investigated the transcriptome diversity of grape berries in 51 accessions，including wild species，Vitis. vinifera，V. labrusca × V. vinifera and interspecific hybrid at green hard，veraison and ripening stages. The result indicated that the diversity of V. vinifera was extremely low and self-incompatibility was severe. Wild accessions maintained greater diversity，while interspecific hybrids can effectively bring these diversities to the cultivated varieties. Gene expression cluster and phenotypic data analysis also revealed that distant hybridization of cultivated and wild species could obtain good berry quality and strong resistance. In addition，transcriptome based diversity analysis can provide more information，and can serve as a supplement to traditional methods. In summary，wild varieties play an important role in grape breeding，and distant hybridization is an important way to recover grape population diversity.

Key words: grape, breeding, gene expression, diversity, distant hybridization

CLC Number:

S 663.1

WANG Yi, LIANG Zhenchang. Analysis of Genetic Mechanism of Grape Distant Hybridization Based on Population Transcriptome[J]. Acta Horticulturae Sinica, 2025, 52(4): 835-845.

References

[1]	Arnold C，Schnitzler A，Parisot C，Maurin A. 2010. Historical reconstruction of a relictual population of wild grapevines（Vitis vinifera ssp sylvestris，Gmelin，Hegi）in a floodplain forest of the upper Seine valley，France. River Research & Applications，26：904–914.
[2]	Ban Y，Mitani N，Sato A，Kono A，Hayashi T. 2016. Genetic dissection of quantitative trait loci for berry traits in interspecific hybrid grape（Vitis labruscana × Vitis vinifera）. Euphytica，211 (3)：295–310.
[3]	Bolger A M，Usadel B，Lohse M. 2014. Trimmomatic：a flexible trimmer for Illumina sequence data. Bioinformatics，30 (15)：2114–2120.
[4]	Camacho C，Coulouris G，Avagyan V，Ma N，Papadopoulos J，Bealer K，Madden TL. 2009. BLAST+：architecture and applications. Bmc Bioinformatics，10：421.
[5]	Cindric P，Korac N. 2015. Frost resistance of grapevine cultivars of different origin. Vitis，79：340–351.
[6]	Duan N，Bai Y，Sun H，Wang N，Ma Y，Li M，Wang X，Jiao C，Legall N，Mao L，Wan S，Wang K，He T，Feng S，Zhang Z，Mao Z，Shen X，Chen X，Jiang Y，Wu S，Yin C，Ge S，Yang L，Jiang S，Xu H，Liu J，Wang D，Qu C，Wang Y，Zuo W，Xiang L，Liu C，Zhang D，Gao Y，Xu Y，Xu K，Chao T，Fazio G，Shu H，Zhong GY，Cheng L，Fei Z，Chen X. 2017. Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nat Communications，8：249.
[7]	Emanuelli F，Silvia L，Lukasz G，Valentina C，Marco S，Michela T，Sean M，José M M，Eva Z，Flavia M M. 2013. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biology，13：39.
[8]	Fan Zhiyuan，Xi Xueliang，Fang Wenliang，Zhang Yu，Zhao Tingsong. 2005. Breeding of three early fruiting walnut varieties through interspecific hybridization. Journal of Zhejiang Forestry College，(5)：581–523. (in Chinese)
	范志远，习学良，方文亮，张雨，赵廷松. 2005. 种间杂交3个优良早实核桃新品种的选育. 浙江林学院学报，(5)：518–523.
[9]	Grabherr M G，Brian J H，Moran Y，Joshua Z. Levin，Dawn A T，Amit I，Xian A，Fan L，Raktima R，Zeng Q D，Chen Z H，Evan M，Nir H，Andreas G，Nicholas R，Federica D P，Bruce W B，Chad N，Kerstin L，Nir F，Aviv R. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology，29：644–652.
[10]	Ishikawa R，Ohnishi T，Kinoshita Y，Eiguchi M，Kurata N，Kinoshita T. 2011. Rice interspecies hybrids show precocious or delayed developmental transitions in the endosperm without change to the rate of syncytial nuclear division. Plant Journal，65：798–806.
[11]	Jia Libang，Feng Meiqing，Ding Lihua. 1984. Preliminary analysis on several fruit traits in pear interspecific hybrid cold resistance breeding. Chinese Fruits，(2)：16–21. (in Chinese)
	贾立邦，冯美琦，丁立华. 1984. 梨种间杂交抗寒育种的若干果实性状遗传的初步分析. 中国果树，(2)：16–21.
[12]	Kim D，Pertea G，Trapnell C，Pimentel H，Kelley R，Salzberg S L. 2013. TopHat2： accurate alignment of transcriptomes in the presence of insertions，deletions and gene fusions. Genome Biology，14：1.
[13]	Klein L L，Miller A J，Ciotir C，Hyma K，Uribe-Convers S，Londo J. 2018. High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections. American Journal of Botany，105：215–226.
[14]	Krivanek A F，Famula T R，Tenscher A， Walker M A. 2005. Inheritance of resistance to Xylella fastidiosa within a Vitis rupestris × Vitis arizonica hybrid population. Theoretical and Applied Genetics，111 (1)：110–119.
[15]	Migicovsky Z，Sawler J，Money D，Eibach R，Miller A J，Luby J J，Jamieson A R，Velasco D，Kintzel S，Warner J，Wuhrer W，Brown P J，Myles S，von Kimtzel S. 2016. Genomic ancestry estimation quantifies use of wild species in grape breeding. BMC Genomics，17：478.
[16]	Mu X Y，Shen X L，Wu Y M，Zhu Y X，Dong S B，Xia X F，Lin Q W，Fan P G，Liu Y L，Zhang Z X. 2018. Plastid phylogenomic study of grape species and its implications for evolutionary study and conservation of Vitis. Phytotaxa，364：71–80.
[17]	Myles S. 2013. Improving fruit and wine：what does genomics have to offer? Trends in Genetics，29：190–196.
[18]	Myles S，Boyko A R，Owens C L，Brown P J，Grassi F，Aradhya M K，Prins B，Reynolds A，Chia J M，Ware D，Bustamante C D，Buckler E S. 2011. Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences of the United States of America，108：3530–3535.
[19]	Pertea G，Huang X，Liang F，Antonescu V，Sultana R，Karamycheva S，Lee Y，White J，Cheung F，Parvizi B，Tsai J，Quackenbush J. 2003. TIGR Gene Indices clustering tools（TGICL）：a software system for fast clustering of large EST datasets. Bioinformatics，19：651–652.
[20]	Pertea M，Kim D，Pertea G M，Leek J T，Salzberg S L. 2016. Transcript-level expression analysis of RNA-seq experiments with HISAT，StringTie and Ballgown. Nature Protocols，11：1650.
[21]	Riaz S，Boursiquot J M，Dangl G S，Lacombe T，Laucou V，Tenscher A C，Walker M A. 2013. Identification of mildew resistance in wild and cultivated Central Asian grape germplasm. BMC Plant Biology，13：149.
[22]	Shirasawa K，Hirakawa H，Azuma A，Taniguchi F，Yamamoto T，Sato A，Hirakawa H，Isobe S. 2022. De novo whole-genome assembly in an interspecific hybrid table grape，‘Shine Muscat’. DNA Research，29. Doi：10.1101/730762.
[23]	Song Rungang，Lu Wenpeng，Li Changyu，Lin Xinggui，Shen Yujie，Li Xiaohong. 2005. Heredity analysis of fruit mature period in progenies from and intraspecific and interspecific hibridization of Vitis amurensis Rupr. Acta Horticulturae Sinica，32 (2)：212–217. (in Chinese)
	宋润刚，路文鹏，李昌禹，林兴桂，沈玉杰，李晓红. 2005. 山葡萄种内和种间杂交后代果实成熟期遗传分析. 园艺学报，32 (2)：212–217.
[24]	Song Rungang，Zheng Yongchun，Lu Wenpeng，Li Changyu，Shen Yujie，Li Xiaohong，Zhang Baoxiang，Lin Xinggui. 2007. Hereditary analysis of total fruit acid content and sugar content of progenies（F₁–F₄）of Vitis amurensis Rupr. via intraspecific or interspecific hybridization. Acta Horticulturae Sinica，34 (4)：813–822. (in Chinese)
	宋润刚，郑永春，路文鹏，李昌禹，沈育杰，李晓红，张宝香，林兴桂. 2007. 山葡萄种内和种间杂交F₁ ~ F₄代果实酸和糖含量的遗传分析. 园艺学报，34 (4)：813–822.
[25]	Sun L，Luo H，Bu D，Zhao G，Yu K，Zhang C，Liu Y，Chen R，Zhao Y. 2013. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Research，41：e166.
[26]	Tang Qilin，Yang Kecheng，Zheng Zuping，Rong Tingzhao. 2006. Cross-compatibility between maize and maize relatives. Acta Agronomica Sinica，32 (1)：144–146. (in Chinese)
	唐祈林，杨克诚，郑祖平，荣廷昭. 2006. 玉米与玉米近缘种可杂交性研究. 作物学报，32 (1)：144–146.
[27]	Trapnell C，Roberts A，Goff L，Pertea G，Kim D，Kelley D R，Pimentel H，Salzberg S L，Rinn J L，Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protocols，9 (10)：2513.
[28]	Viana A P，Riaz S，Walker M A. 2011. Evaluating genetic diversity and optimizing parental selections in a segregating table-grape population. American Journal of Enology & Viticulture，62：285–290.
[29]	Wang Y，Xin H，Fan P，Zhang J，Liu Y，Dong Y，Wang Z，Yang Y，Zhang Q，Ming R，Zhong G Y，Li S，Liang Z. 2021. The genome of Shanputao （Vitis amurensis）provides a new insight into cold tolerance of grapevine. Plant Journal，105：1495–1506.
[30]	Wu G A，Prochnik S，Jenkins J，Salse J，Hellsten U，Murat F，Perrier X，Ruiz M，Scalabrin S，Terol J，Takita M A，Labadie K，Poulain J，Couloux A，Jabbari K，Cattonaro F，Del Fabbro C，Pinosio S，Zuccolo A，Chapman J，Grimwood J，Tadeo F R，Estornell L H，Munoz-Sanz J V，Ibanez V，Herrero-Ortega A，Aleza P，Perez-Perez J，Ramon D，Brunel D，Luro F，Chen C，Farmerie W G，Desany B，Kodira C， Mohiuddin M，Harkins T，Fredrikson K，Burns P，Lomsadze A，Borodovsky M，Reforgiato G，Freitas-Astua J，Quetier F，Navarro L，Roose M，Wincker P，Schmutz J，Morgante M，Machado M A，Talon M，Jaillon O，Ollitrault P，Gmitter F，Rokhsar D. 2014. Sequencing of diverse mandarin，pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nature Biotechnology，32：656–662.
[31]	Wu J，Wang Y，Xu J，Korban S S，Fei Z，Tao S，Ming R，Tai S，Khan A M，Postman J D，Gu C，Yin H，Zheng D，Qi K，Li Y，Wang R，Deng C H，Kumar S，Chagne D，Li X，Wu J，Huang X，Zhang H，Xie Z，Li X，Zhang M，Li Y，Yue Z，Fang X，Li J，Li L，Jin C，Qin M，Zhang J，Wu X，Ke Y，Wang J，Yang H，Zhang S. 2018. Diversification and independent domestication of Asian and European pears. Genome Biology，19：77.
[32]	Zhou Y，Massonnet M，Sanjak J S，Cantu D，Gaut B S. 2017. Evolutionary genomics of grape（Vitis vinifera ssp. vinifera）domestication. Proceedings of the National Academy of Sciences of the United States of America，114：11715–11720.

Analysis of Genetic Mechanism of Grape Distant Hybridization Based on Population Transcriptome

PDF

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	ZHANG Ruifen, ZHANG Cuiling, LIU Zhizhou, WANG Zhengxin, LIU Fangxin, YIN Tao, WANG Nannan, JIANG Lin. A New Cultivar of Prunus sogdiana‘Huazhen 1’Used as Peach Rootstock [J]. Acta Horticulturae Sinica, 2025, 52(S1): 33-34.
[2]	WANG Hao, WANG Yan, LIU Zhenshan, TU Hongxia, ZHANG Jing, HE Wen, WU Zhiwei, FU Xiaoke, CHEN Qing, WANG Xiaorong. A New Extremely Early Ripening Chinese Cherry Cultivar‘Shuzaomei’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 35-36.
[3]	HAN Jiayu, GUO Rongrong, ZHANG Ying, SHI Xiaofang, CAO Xiongjun, HUANG Guiyuan, BAI xianjin, XIE Taili, YU Huan, XIE Shuyu, LIN Ling. Low Chilling Requirement Grape New Cultivar‘Guipu 9’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 45-46.
[4]	SHU Nan, LU Wenpeng, YANG Yiming, XU Peilei, LI Jiaqi, LIU Tao, QU Bingzhang. A New Wine Grape Cultivar‘Zijinglu’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 47-48.
[5]	ZHANG Liwei, DAI Zhongren, CHEN Qingqi, LEI Na, HUANG Jun, Hu Haijiang, MEN Wanjie. A New Tomato Cultivar‘Hayan Zhongfenguo 1’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 111-112.
[6]	WANG Yue, JI Shujuan, WANG Zihao, YANG Wenduo, LU Zhu, WANG Yuwei, YU Yanshen, REN Ziming, WANG Guozhong. A New Auricularia heimuer Cultivar‘Jiyaner 1’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 139-140.
[7]	KONG Danrui, ZHANG Wei, ZHENG Xiaoyue, WANG Meixian, ZHAO Huien. A New Ground-Cover Chrysanthemum Cultivar‘Damo Qiuxue’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 169-170.
[8]	ZHANG Wei, KONG Danrui, QIU Yue, ZHENG Xiaoyue, ZHAO Huien. A New Cold-Resistant Groundcover Chrysanthemum Cultivar‘Yinghuo’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 171-172.
[9]	CHEN Ziqi, WANG Zhiling, HUANG Hongfeng, ZHAO Xin, GU Zhaoyu, XU Yanjie, HONG Bo. A New Chrysanthemum morifolium Cultivar‘Baichongxiang 1’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 173-174.
[10]	JIANG Xiuna, GUO Yingduo, CHEN Junsheng, ZHENG Yunhuang, WEI Xiaolian, TANG Kai, LIN Hanrui, CHEN Chunlai, ZHENG Danhong, CHEN Li, HUANG Jinchao. A New Phalaenopsis Cultivar‘Shannong Yunü’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 187-188.
[11]	SHEN Zhen, HUANG Surong, ZHANG Dongxue, ZHU Tianlong, YANG Guangsui. A New Waterlily Cultivar‘Chunqiu’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 205-206.
[12]	SHEN Zhen, ZHANG Dongxue, YANG Guangsui, HUANG Surong, ZHU Tianlong, YIN Junmei. A New Waterlily Cultivar‘Xiari Tiankong’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 207-208.
[13]	ZHAO Guochun, LIAO Yangmei, GAO Shilun, XU Yuanyuan, LIU Jiming, ZHENG Yulin, WENG Xuehuang, CHEN Zhong, JIA Liming. A New Male Sterility Soapberry Cultivar‘Qirui’ [J]. Acta Horticulturae Sinica, 2025, 52(S1): 243-244.
[14]	CHEN Shanbo, WANG Lihua, WANG Sha, LUO Dezhi, JIN Yinchun, YANG Zhiwu, FENG Shijing, ZHANG Chenghao, CHEN Liu, LIU Mao, ZHANG Zhiqing, WU Bin. A New Cultivar‘Chuanjiao’of Zanthoxylum armatum [J]. Acta Horticulturae Sinica, 2025, 52(S1): 265-266.
[15]	LIANG Jing, ZENG Baozhen, LIANG Guoping, MAO Juan, CHEN Baihong. Grapevine VvARF18 Regulates Fruit Expansion and Screening of its Interacting Proteins [J]. Acta Horticulturae Sinica, 2025, 52(4): 821-834.