Development, Identification and Validation of a Novel SSR Molecular Marker for Heat Resistance of Grapes Based on miRNA
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Heat Treatments
2.2. DNA, RNA Extraction and cDNA Synthesis
2.3. Mining of SSRs from Pri-miRNAs and Pre-miRNAs of the Grapevine Genome
2.4. RT-qPCR, PCR, and PCR-Sanger Sequencing Analysis
2.5. About the Naming of miRNA-SSR Molecular Marker Sub
2.6. Prediction of Target Genes for miRNAs and Pathway Analyses
2.7. Statistical Analysis
3. Results
3.1. Heat Injury in 40 Grape Varieties’ Leaves Exposed to High-Temperature Stress
3.2. RT-qPCR Analysis of the Pri-miRNA Response to Heat Stress
3.3. MiRNA and Target Genes Mediated Regulatory Networks
3.4. Identification and Frequency Distribution of miRNA-SSRs in the Grape Genome
3.5. Distribution of Pri-miRNA-SSR in Grape Chromosomes
3.6. The Diversity of 13 MIRNA-SSR Loci Was Verified in 8 Grape Germplasm Samples
3.7. Application of VMIRSSRNA Markers in Heat-Resistant and Heat-Sensitive Grape Varieties
3.8. Chromosome Distribution of vvi-miR167 Family Members in Grape
3.9. Phylogenetic Development of the vvi-MIR167s Gene Family of Representative Species
4. Discussion
4.1. Functional Analysis for miRNAs and Their Regulatory Networks
4.2. Development and Application of miRNA-SSR Markers
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Varieties | VMIRSSRNA-Marker | ||||
---|---|---|---|---|---|
NO. | Thermostability | VMIRSSR167c3 (CT)n | VMIRSSR167d1 (TTTTCC)n | VMIRSSR157c2 (AGGG)n | VMIRSSR398b1 (ATAA)n |
1 | Niagara Rosada | (CT)20 | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
2 | Benizuiho | (CT)19 | (TTTTCC)2 | (AGGG)3, 1(AGAG) | (ATAA)5 |
3 | Vitis × Champion | (CT)18, 1(CC) | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
4 | Cuihong | (CT)17, 1(CC) | (TTTTCC)2 | (AGGG)4, 1(AGAG) | (ATAA)5 |
5 | Seibel Blanc | (CT)19 | (TTTTCC)2 | (AGGG)4 | 0 |
6 | Lot Sand | (CT)20, 1(CC) | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
7 | Damubo | (CT)23 | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
8 | Aromatic Rachachi | (CT)24 | (TTTTCC)2 | (AGGG)3, 1(AGAG) | (ATAA)5 |
9 | Pollux | (CT)22, 1(CC) | (TTTTCC)2 | (AGGG)2 | (ATAA)5 |
10 | Anisky | (CT)18, 1(CC) | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
11 | Green beads | (CT)19 | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
12 | Volgarton | (CT)16 | (TTTTCC)2 | (AGGG)3,1(AGAG) | (ATAA)5 |
13 | Augusta | (CT)17, 1(CC) | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
14 | Jifeng | (CT)18, 1(CC) | (TTTTCC)2 | (AGGG)3, 1(AGAG) | (ATAA)5 |
15 | Grand Noir | (CT)23, 1(CC) | (TTTTCC)2 | (AGGG)3, 1(AGAG) | 0 |
16 | Shenmei | (CT)18, 1(CC) | (TTTTCC)2 | (AGGG)4 | 0 |
17 | Jiangsu v. azuLene | (CT)24, 1(CC) | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
18 | Shenyue | (CT)18, 1(CC) | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
19 | Cabernet Sauvignon | (CT)17 | (TTTTCC)2 | (AGGG)3, 1(GAAT) | (ATAA)4 |
20 | Shenhua | (CT)18, 1(CC) | TTTTCCTTGTCC | (AGGG)4, 1(AGAG) | (ATAA)5 |
Varieties | VMIRSSRNA-Marker | ||||
---|---|---|---|---|---|
NO. | Heat-Sensitive | VMIRSSR167c3 (CT) | VMIRSSR167d1 (TTTTCC) | VMIRSSR157c2 (AGGG) | VMIRSSR398b1 (ATAA) |
21 | Ruiduxiangyu | (CT)24, 1(CC) | (TTTTCC)2 | (GA)3, 1(TA) | (ATAA)4 |
22 | Shenbao | (CT)19 | (TTTTCC)2 | (AGGG)4 | (ATAA)4 |
23 | Hakuho | (CT)16, 1(GT) | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
24 | Xinya | (CT)17 | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
25 | Beta | (CT)21 | (TTTTCC)2 | (AGGG)4 | (ATAA)4 |
26 | Beichun | (CT)13, 1(CC) | (TTTTCC)2 | (AGGG)4 | (ATAA)4 |
27 | Molixiang | (CT)16, 1(CC) | TTTTCCTTTTTC | (AGGG)4 | (ATAA)5 |
28 | Yan 74 | (CT)12, 1(CC) | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
29 | Μgni Blanc | (CT)19 | (TTTTCC)2 | (AGGG)4, 1(AGAG) | (ATAA)5 |
30 | Shine Muscat | (CT)14 | (TTTTCC)2 | (AGGG)4, 1(AGAG) | (ATAA)5 |
31 | Fujiminori | (CT)14 | (TTTTCC)2 | (AGGG)3, 1(AGAG) | (ATAA)5 |
32 | Italy grape | (CT)17 | (TTTTCC)2 | (AGGG)3, 1(AGAG) | (ATAA)5 |
33 | SO4 | (CT)14 | (TTTTCC)2 | (AGGG)4 | 3(ATAA), 1(ATTA) |
34 | Wuhecuibao | (CT)14 | (TTTTCC)2 | (AGGG)3, 1(AGAG) | (ATAA)5 |
35 | Jumeigui | (CT)14 | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
36 | Kyoho | (CT)17 | (TTTTCC)2 | (AGGG)4 | (ATAA)5 |
37 | MuscatHamburgh | (CT)17 | (TTTTCC)2 | (AGGG)3, 1(AGAG) | (ATAA)5 |
38 | Thompson Seedless | (CT)17 | (TTTTCC)2 | (AGGG)3, 1(AGAG) | (ATAA)4 |
39 | Shuanghong | (CT)15 | TTTTCCTTGTCC | (AGGG)4, 1(AGAG) | (ATAA)5 |
40 | 1103P | (CT)14 | (TTTTCC)2 | (AGGG)4 | 3(ATAA), 1(ATTA) |
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Zhang, L.; Song, Y.; Li, J.; Liu, J.; Zhang, Z.; Xu, Y.; Fan, D.; Liu, M.; Ren, Y.; Xi, X.; et al. Development, Identification and Validation of a Novel SSR Molecular Marker for Heat Resistance of Grapes Based on miRNA. Horticulturae 2023, 9, 931. https://doi.org/10.3390/horticulturae9080931
Zhang L, Song Y, Li J, Liu J, Zhang Z, Xu Y, Fan D, Liu M, Ren Y, Xi X, et al. Development, Identification and Validation of a Novel SSR Molecular Marker for Heat Resistance of Grapes Based on miRNA. Horticulturae. 2023; 9(8):931. https://doi.org/10.3390/horticulturae9080931
Chicago/Turabian StyleZhang, Lipeng, Yue Song, Junpeng Li, Jingjing Liu, Zhen Zhang, Yuanyuan Xu, Dongying Fan, Mingying Liu, Yi Ren, Xiaojun Xi, and et al. 2023. "Development, Identification and Validation of a Novel SSR Molecular Marker for Heat Resistance of Grapes Based on miRNA" Horticulturae 9, no. 8: 931. https://doi.org/10.3390/horticulturae9080931