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Genome-wide identification, phylogenetic analysis, and expression profiling of glycine-rich RNA-binding protein (GRPs) genes in seeded and seedless grapes (Vitis vinifera)

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Abstract

Glycine-rich RNA-binding proteins (GRPs) are essential for many physiological and biochemical processes in plants, especially the response to environmental stresses. GRPs exist widely in angiosperms and gymnosperms plant species; however, their roles in Vitis vinifera are still poorly understood. To characterize VviGRP gene family, we performed a genomic survey, bioinformatics and expression analysis of VviGRPs in grape. We identified nineteen VviGRPs gene family members. The result of bioinformatics analysis showed their motif distribution, gene structure characteristics and chromosomal locations. Then we carried out synteny and phylogenetic analysis to study the origin and evolutionary relationship of GRPs. Tissue-specific expression analysis showed that VviGRPs have different expression patterns. Meanwhile, we studied expression profiles of seventeen ovule-expressed genes during seed development of stenospermocarpic seedless and seeded grapes, and the result showed that most of them have much higher relative expression levels in stenospermocarpic seedless grapes than that of seeded one before 25 days after full bloom (DAFB). It is suggested that VviGRPs may involve in the seed development process. Taken together, our research indicated that VviGRPs are related to seed development and will be beneficial for further investigations into the seed abortion mechanism under stenospermocarpic grapes.

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Acknowledgements

This work was supported by the National Key R&D Program of China [2019YFD1001405]; the Modern Agro-industry Technology Research System [No. CARS-30-yz-7]; and the Natural Science Foundation of China [No. 32072554].

Funding

National Key R&D Program of China [2019YFD1001405]; the Modern Agro-industry Technology Research System [No. CARS-30-yz-7]; and the Natural Science Foundation of China [No. 32072554].

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Authors and Affiliations

  1. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China

    Yujin Tang, Congbo Huang, Yuejin Wang & Chaohong Zhang

  2. Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100, Shaanxi, China

    Yujin Tang, Congbo Huang, Yuejin Wang & Chaohong Zhang

  3. College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China

    Yan Li

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  1. Yujin Tang
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  3. Yan Li
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Contributions

All authors contributed to the study conception and design. CZ and YL conceived and designed the whole experiments; YT and CH performed the experiments; YT analysed the data; CZ, YW contributed reagents/materials/analysis tools; YT and CH wrote the manuscript; YL reviewed and edited the manuscript. All authors read and approved the final manuscript.

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Correspondence to Chaohong Zhang.

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12298_2021_1082_MOESM1_ESM.tif

ESM_1 RNA extraction of six tissues or organs and ovules at different development stages from ‘Pinot Noir’ and ‘Thompson Seedless’. (a) RNA extraction of six tissues or organs from ‘Pinot Noir’. Line 1, RNA of leaf; Line 2, RNA of stem; Line 3, RNA of flower; Line 4, RNA of flower bud; Line 5, RNA of ovule; Line 6, RNA of tendril. (b) RNA extract from ‘Pinot Noir’ ovules at different development stages. Line 1, RNA of ‘Pinot Noir’ ovules in 10 day after full-bloom (DAFB); Line 2, RNA of ‘Pinot Noir’ ovules in 15 DAFB; Line 3, RNA of ‘Pinot Noir’ ovules in 20 DAFB; Line 4, RNA of ‘Pinot Noir’ ovules in 25 DAFB; Line 5, RNA of ‘Pinot Noir’ ovules in 30 DAFB; Line 6, RNA of ‘Pinot Noir’ ovules in 35 DAFB. (c) RNA extract from ‘Pinot Noir’ and ‘Thompson Seedless’ovules at different development stages. Line 1, RNA of ‘Pinot Noir’ ovules in 40 DAFB; Line 2, RNA of ‘Pinot Noir’ ovules in 45 DAFB; Line 3, RNA of ‘Thompson Seedless’ ovules in 10 DAFB; Line 4, RNA of ‘Thompson Seedless’ ovules in 15 DAFB; Line 5, RNA of ‘Thompson Seedless’ ovules in 20 DAFB; Line 6, RNA of ‘Thompson Seedless’ ovules in 25 DAFB; Line 7, RNA of ‘Thompson Seedless’ ovules in 30 DAFB; Line 8, RNA of ‘Thompson Seedless’ ovules in 35 DAFB. (d) RNA extract from ‘Thompson Seedless’ovules at different development stages. Line 1, RNA of ‘Thompson Seedless’ ovules in 40 DAFB; Line 2, RNA of ‘Thompson Seedless’ ovules in 45 DAFB (TIF 12504 KB)

Supplementary file2 (XLSX 11 KB)

Supplementary file3 (XLSX 12 KB)

Supplementary file4 (XLSX 12 KB)

12298_2021_1082_MOESM5_ESM.tif

ESM_5. RT-qPCR primers location and dissolution curve of VviGRP5Lh. (a) RT-qPCR primers location of VviGRP5Lh. (a) Dissolution curve of VviGRP5Lh. (TIF 14309 KB)

12298_2021_1082_MOESM6_ESM.tif

ESM_6 Dissolution curve of VviGRP in RT-qPCR. (a) Dissolution curve of VviACTIN. (a) Dissolution curve of VviACTIN. (b) Dissolution curve of VviGADPH. (c) Dissolution curve of VviRZ-1A. (d) Dissolution curve of VviGRP5Le. (e) Dissolution curve of VviGRP5Lg. (f) Dissolution curve of VviGRP5Lh. (g) Dissolution curve of VviGRP4L. (h) Dissolution curve of VviGRP5Ld. (i) Dissolution curve of VviGRP5Lf. (j) Dissolution curve of VviGRP5Lc. (k) Dissolution curve of VviGRP3. (l) Dissolution curve of VviRZ-1B. (m) Dissolution curve of VviGRP7. (n) Dissolution curve of VviGRP2. (o) Dissolution curve of VviRZ-1C. (p) Dissolution curve of VviGRP5Li. (q) Dissolution curve of VviGRP5Lb. (r) Dissolution curve of VviGRP5. (s) Dissolution curve of VviSUA. (TIF 27180 KB)

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Tang, Y., Huang, C., Li, Y. et al. Genome-wide identification, phylogenetic analysis, and expression profiling of glycine-rich RNA-binding protein (GRPs) genes in seeded and seedless grapes (Vitis vinifera). Physiol Mol Biol Plants 27, 2231–2243 (2021). https://doi.org/10.1007/s12298-021-01082-3

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