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Special Issue:
园艺-分子生物合辑Horticulture — Genetics · Breeding
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| QTL-seq analysis of seed size trait in grape provides new molecular insight on seedlessness |
| WANG Li1, 2*, ZHANG Song-lin1, 4*, JIAO Chen1, LI Zhi1, 4, LIU Chong-huai3, WANG Xi-ping1, 4 |
1 State Key Laboratory of Crop Stress Biology in Arid Areas/College of Horticulture, Northwest A&F University,Yangling 712100, P.R.China
2 College of Horticulture, Hebei Agricultural University, Baoding 071001, P.R.China
3 Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450000, P.R.China
4 Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, P.R.China
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摘要 无核是鲜食和制干葡萄市场的重要商品性状。然而众多研究中，葡萄无核关键基因及分子机制仍不明晰。本研究通过对有核葡萄‘红地球’、无核葡萄‘森田尼无核’及二者杂交后代进行基因组重测序，鉴定非同义突变SNP并结合已发表转录组数据开展联合分析。发现非同义突变SNP发生在蛋白激酶、转录因子、细胞色素P450等与种子发育相关基因上，且这些基因在有核和无核葡萄胚珠发育过程中差异表达，参与激素平衡、种皮和胚乳发育、繁殖性器官发育、氧化还原、衰老及细胞死亡等生物学过程。基于SNP-index分析，鉴定到一个潜在的种子大小性状相关QTL区域，并对区域内候选基因开展在多个有核、无核葡萄品种胚珠发育过程中的表达分析。进一步选取3个SNP开展SNaPshot分析，发现G8基因的一个SNP在葡萄子代验证中表现出67.5%的效率。本研究从基因组水平上揭示了有核、无核葡萄子代胚珠发育差异，为后续基因功能研究和葡萄分子育种提供宝贵资源。
Abstract
Seedlessness in grape (Vitis vinifera) is an important commercial trait for both the fresh and drying markets. However, despite numerous studies, the mechanisms and key genes regulating grape seedlessness are mostly unknown. In this study, we sequenced the genomes of the V. vinifera seeded cultivar ‘Red Globe’, the seedless cultivar ‘Centennial Seedless’, and the derived hybrids. Nonsynonymous single nucleotide polymorphisms (SNPs) were identified by genome sequencing and analyzed using published transcriptome data. Nonsynonymous SNPs occurred in genes related to seed development, which were identified as protein kinases, transcription factors, and cytochrome P450s and showed differential expression during ovule development in both seeded and seedless grapes. These nonsynonymous SNP-associated genes were mainly involved in biological processes such as hormone balance, seed coat and endosperm development, reproductive organ development, oxidation and reduction, senescence and cell death. A potential quantitative trait locus (QTL) region associated with seed size was characterized based on the SNP-index, and expression analysis of candidate genes in the QTL region during ovule development in multiple seeded and seedless grape cultivars were conducted. Three SNPs were further subjected to SNaPshot analysis and one SNP in G8 showed 67.5% efficiency in the grape progeny validation. Overall, the data obtained in this study shed light on the differences in seed development between seeded and seedless progeny at the genomic level, which provides valuable resources for future functional studies and grape breeding.
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Received: 30 August 2021
Accepted: 30 March 2022
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This work was supported by the National Natural Science Foundation of China (U1603234), the Program for Innovative Research Team of Grape Germplasm Resources and Breeding of Shaanxi, China (2013KCT-25), the Chinese Universities Scientific Fund (Z109021571 and 2452019170), the Natural Science Foundation of Hebei, China (C2021204146) and the Scientific Research Program of Hebei Educational Commission, China (QN2020232).
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| About author: WANG Li, E-mail: vivi@hebau.edu.cn; ZHANG Song-lin, E-mail: 18821636061@163.com; Correspondence WANG Xi-ping, Fax: +86-29-87082613, E-mail: wangxiping@nwsuaf.edu.cn
* These authors contributed equally to this study. |
Cite this article:
WANG Li, ZHANG Song-lin, JIAO Chen, LI Zhi, LIU Chong-huai, WANG Xi-ping.
2022.
QTL-seq analysis of seed size trait in grape provides new molecular insight on seedlessness. Journal of Integrative Agriculture, 21(10): 2910-2925.
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Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R. 2012. Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnology, 30, 174–178.
Adam-Blondon A, Lahogue F, Bouquet A, Boursiquot J, This P. 2001. Usefulness of two SCAR markers for marker-assisted selection of seedless grapevine cultivars. Vitis, 40, 147–155.
Bai Y, Dougherty L, Li M, Fazio G, Cheng L, Xu K. 2012. A natural mutation-led truncation in one of the two aluminum-activated malate transporter-like genes at the Ma locus is associated with low fruit acidity in apple. Molecular Genetics and Genomics, 287, 663–678.
Bolger A M, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120.
Bouakaze C, Keyser C, De Martino S, Sougakoff W, Veziris N, Dabernat H, Ludes B. 2010. Identification and genotyping of Mycobacterium tuberculosis complex species by use of a SNaPshot minisequencing-based assay. Journal of Clinical Microbiology, 48, 1758–1766.
Cabezas J, Cervera M, Ruiz-Garcia L, Carreno J, Martinez-Zapater J. 2006. A genetic analysis of seed and berry weight in grapevine. Genome, 49, 1572–1585.
Claisse G, Charrier B, Kreis M. 2007. The Arabidopsis thaliana GSK3/Shaggy like kinase AtSK3-2 modulates floral cell expansion. Plant Molecular Biology, 64, 113–124.
Doligez A, Bouquet A, Danglot Y, Lahogue F, Riaz S, Meredith P, Edwards J, This P. 2002. Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight. Theoretical and Applied Genetics, 105, 780–795.
Guo C, Guo R, Xu X, Gao M, Li X, Song J, Zheng Y, Wang X. 2014. Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family. Journal of Experimental Botany, 65, 1513–1528.
Hanania U, Velcheva M, Or E, Flaishman M, Sahar N, Perl A. 2007. Silencing of chaperonin 21, that was differentially expressed in inflorescence of seedless and seeded grapes, promoted seed abortion in tobacco and tomato fruits. Transgenic Research, 16, 515–525.
Hill J T, Demarest B L, Bisgrove B W, Gorsi B, Su Y C, Yost H J. 2013. MMAPPR: Mutation mapping analysis pipeline for pooled RNA-seq. Genome Research, 23, 687–697.
Huang J, Chen F, Del Casino C, Autino A, Shen M, Yuan S, Peng J, Shi H, Wang C, Cresti M, Li Y. 2006. An ankyrin repeat-containing protein, characterized as a ubiquitin ligase, is closely associated with membrane-enclosed organelles and required for pollen germination and pollen tube growth in lily. Plant Physiology, 140, 1374–1383.
Jaillon O, Aury J, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463–467.
Jinn T L, Stone J M, Walker J C. 2000. HAESA, an Arabidopsis leucine-rich repeat receptor kinase, controls floral organ abscission. Genes & Development, 14, 108–117.
De Jong M, Woltersarts M, Feron R, Mariani C, Vriezen W H. 2009. The Solanum lycopersicum auxin response factor 7 (SlARF7) regulates auxin signaling during tomato fruit set and development. Plant Journal, 57, 160–170.
Joung J G, Corbett A M, Fellman S M, Tieman D M, Klee H J, Giovannoni J J, Fei Z. 2009. Plant MetGenMAP: an integrative analysis system for plant systems biology. Plant Physiology, 151, 1758–1768.
Lahogue F, This P, Bouquet A. 1998. Identification of a codominant scar marker linked to the seedlessness character in grapevine. Theoretical and Applied Genetics, 97, 950–959.
Ledbetter C, Burgos L. 1994. Inheritance of stenospermocarpic seedlessness in Vitis vinifera L. Journal of Heredity, 85, 157–160.
Ledbetter C, Ramming D. 1989. Seedlessness in grapes. Horticultural Reviews, 11, 159–184.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25, 1754–1760.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. 2009. The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078–2079.
Mackay I J, Caligari P D S. 2000. Efficiencies of F2 and backcross generations for bulked segregant analysis using dominant markers. Crop Science, 40, 626–630.
Mejía N, Hinrichsen P. 2003. A new, highly assertive SCAR marker potentially useful to assist selection for seedlessness in table grape breeding. Acta Horticulturae, 603, 559–564.
Mejía N, Soto B, Guerrero M, Casanueva X, Houel C, Miccono M D, Ramos R, Le Cunff L, Boursiquot J M, Hinrichsen P, Adam-Blondon A F. 2011. Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine. BMC Plant Biology, 11, 57.
Meyer S, Scholzstarke J, De Angeli A, Kovermann P, Burla B, Gambale F, Martinoia E. 2011. Malate transport by the vacuolar AtALMT6 channel in guard cells is subject to multiple regulation. Plant Journal, 67, 247–257.
Mu J, Lee H, Kao T. 1994. Characterization of a pollen-expressed receptor-like kinase gene of Petunia inflata and the activity of its encoded kinase. The Plant Cell, 6, 709–721.
Nicolas P, Lecourieux D, Gomes E, Delrot S, Lecourieux F. 2013. The grape berry-specific basic helix-loop-helix transcription factor VvCEB1 affects cell size. Journal of Experimental Botany, 64, 991–1003.
Niu B X, He F R, He M, Ren D, Chen L T, Liu Y G. 2013. The ATP-binding cassette transporter OsABCG15 is required for anther development and pollen fertility in rice. Journal of Integrative Plant Biology, 55, 710–720.
Pandolfini T, Molesini B, Spena A. 2007. Molecular dissection of the role of auxin in fruit initiation. Trends in Plant Science, 12, 327–329.
Royo C, Carbonell-Bejerano P, Torres-Perez R, Nebish A, Martinez O, Rey M, Aroutiounian R, Ibanez J, Martinez-Zapater J M. 2015. Developmental, transcriptome, and genetic alterations associated with parthenocarpy in the grapevine seedless somatic variant Corinto bianco. Journal of Experimental Botany, 67, 259–273.
Royo C, Torres-Pérez R, Mauri N, Diestro N, Cabezas J A, Marchal C, Lacombe T, Ibáñez J, Tornel M, Carreño J. 2018. The major origin of seedless grapes is associated with a missense mutation in the MADS-box gene VviAGL11. Plant Physiologyogy, 177, 1234–1253.
Schruff M C, Spielman M, Tiwari S, Adams S, Fenby N, Scott R J. 2005. The AUXIN RESPONSE FACTOR 2 gene of Arabidopsis links auxin signalling, cell division, and the size of seeds and other organs. Development, 133, 251–261.
Striem M, Ben-Hayyim G, Spiegel-Roy P. 1996. Identifying molecular genetic markers associated with seedlessness in grape. Journal of the American Society for Horticultural Science, 121, 758–763.
Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S. 2013. QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant Journal, 74, 174–183.
Trick M, Adamski N M, Mugford S G, Jiang C, Febrer M, Uauy C. 2012. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biology, 12, 14.
Wang C, Luan F, Liu H, Angela R D, Zhang Q, Dai Z, Liu S. 2021. Mapping and predicting a candidate gene for flesh color in watermelon. Journal of Integrative Agriculture, 20, 2100–2111.
Wang L, Hu X, Jiao C, Li Z, Fei Z, Yan X, Liu C, Wang Y, Wang X. 2016. Transcriptome analyses of seed development in grape hybrids reveals a possible mechanism influencing seed size. BMC Genomics, 17, 898.
Wang L, Yin X, Cheng C, Wang H, Guo R, Xu X, Zhao J, Zheng Y, Wang X. 2015. Evolutionary and expression analysis of a MADS-box gene superfamily involved in ovule development of seeded and seedless grapevines. Molecular Genetics and Genomics, 290, 825–846.
Wang R, Sun L, Bao L, Zhang J, Jiang Y, Yao J, Song L, Feng J, Liu S, Liu Z. 2013. Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish. BMC Genomics, 14, 1–18.
Wang S, Yu Y, Zhang C, Xu W, Wang Y. 2011. Molecular cloning and characterization of a novel gene encoding an EF-hand calcium-binding protein related to fruit seedlessness of grapevine. Scientia Horticulturae, 130, 708–714.
Wang Y. 1997. Analysis of sequencing the RAPD marker linked to seedless genes in grapes. Acta Universitatis Agriculturae Boreali-Occidentalis, 25, 1–5.
Yuan Y, Sagawa J M, Stilio V S D, Bradshaw H D. 2013. Bulk segregant analysis of an induced floral mutant identifies a MIXTA-like R2R3 MYB controlling nectar guide formation in Mimulus lewisii. Genetics, 194, 523–528.
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