基于群体转录组的葡萄远缘杂交遗传机制分析

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

摘要/Abstract

摘要：

目前主要酿酒葡萄品种均为欧亚种，遗传背景单一。本研究中系统分析了51份葡萄核心种质（包括野生种、欧亚种、欧美杂交种品种和种间杂交种4类）绿果期、转色期以及成熟期的果实转录组数据，并从多个角度对不同类型种质进行多样性评估。结果表明欧亚种的多样性极低且自交衰退严重，而野生葡萄保持了较高的多样性，通过远缘杂交可以有效地将野生种的多样性引入栽培种。表达聚类分析和表型分析也表明利用远缘杂交和人工选择可以快速获得具有良好果实品质和较高抗性的新品种。基于转录组的多样性分析可以提供更多DNA水平多样性分析所不具备的信息，可以作为传统多样性研究方法的一种补充。综上，野生种对葡萄育种具有重要作用，远缘杂交是恢复葡萄种群多样性的重要手段。

关键词: 葡萄, 育种, 基因表达, 多样性, 远缘杂交

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

王毅, 梁振昌. 基于群体转录组的葡萄远缘杂交遗传机制分析[J]. 园艺学报, 2025, 52(4): 835-845.

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.

图/表 8

图1 4种葡萄3个时期的表达量变异系数分布 W：野生种；H：其他种间杂交种；V：欧亚种；L：欧美杂交种。下同

Fig. 1 Coefficient of variation distribution of four grapes in green hard，veraison，and ripening developmental stages W：Wild species；H：Interspecific hybrids；V：Vitis. vinifera；L：Vitis. labrusca × Vitis. vinifera. The same below

图2 4种葡萄种质的遗传多样性和近交系数分析 A：基于表达区域SNP的葡萄群体遗传多样性（π）分析。B：葡萄不同类群的杂合SNP比例。C：葡萄种质资源近交系数分析。不同小写字母表示在不同类群间差异显著（P < 0.05）

Fig. 2 Genetics diversity and inbreeding coefficient analysis of four grape groups A：Genetics diversity（π）analysis based on SNP information in expression region of four groups. B：Heterozygous SNP rate of four groups. C：Inbreeding coefficient comparison of all the four groups. Different lowercase letters indicate significant differences between different groups（P < 0.05）

图3 基因组中新注释到的编码及非编码转录本的分布情况 GH：绿果期；VE：转色期；R：成熟期。下同

Fig. 3 The distribution of new annotated coding and non-coding RNAs on the genome GH：Green hard；VE：Veraison；R：Ripening. The same below

图4 4个类型葡萄3个时期新注释的转录本的数目

Fig. 4 The number of new-transcripts of the four grape groups in three berry development stages

图5 不同类型葡萄转录本的特异性以及相似性分析

Fig. 5 The shared and the similar rate of the new annotated genes based on different types of grape transcripts

图6 4个类群葡萄中特有基因和共有基因分析

Fig. 6 The shared and specific gene families of the four grape groups based on the transcripts assemble

图7 葡萄果实发育关键基因的表达量（Z-score）聚类和不同群体相关性分析

Fig. 7 Gene expression（Z-score）cluster and correlation analysis among wild and cultivated grape accessions

图8 4种葡萄种质的糖酸含量分布不同小写字母表示在不同类群中的糖酸含量差异显著（P < 0.05）

Fig. 8 Sugar and acid content in four grape groups Different lowercase letters indicate significant differences of sugar or acid content among different groups（P < 0.05）

参考文献 32

[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.