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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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