Development of EST-SSR Markers Linked to Flowering Candidate Genes in Elymus sibiricus L. Based on RNA Sequencing
Abstract
:1. Introduction
2. Results
2.1. Transcriptome Sequencing, Unigenes Annotation, and Differentially Expressed Genes Analysis
2.2. Frequency and Distribution of EST-SSR Markers
2.3. Development of Candidate Gene-Based EST-SSR Markers
2.4. Validation of Candidate Gene-Based Specific Primers Authenticity
2.5. Genetic Diversity Analysis Using Candidate Gene-Based EST-SSR Markers
3. Discussion
3.1. Candidate Gene-Based EST-SSR Markers with Flowering Time for Marker-Assisted Selection
3.2. Genetic Diversity of Candidate Gene-Based EST-SSR Markers
4. Materials and Methods
4.1. Plant Materials
4.2. Development of Candidate Gene-Based EST-SSR Markers Based on RNA-Seq in E. sibiricus
4.3. DNA Extraction, Genotyping and Primer Validation
4.4. Allele Scoring and Polymorphism Detection
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Searching Item | Number |
---|---|
Total number of sequences examined | 40,639 |
Total size of examined sequences (bp) | 78,157,064 |
Total number of identified SSRs | 13,052 |
Number of SSR containing sequences | 10,286 |
Number of sequences containing more than 1 SSR | 2176 |
Number of SSRs present in compound formation | 742 |
Mono-nucleotide | 5471 |
Di-nucleotide | 2642 |
Tri-nucleotide | 4551 |
Tetra-nucleotide | 314 |
Penta-nucleotide | 48 |
Hexa-nucleotide | 26 |
Primer Code | Flowering Genes | Flowering Pathways/Functions | He | Ho | PIC |
---|---|---|---|---|---|
Primer 46865 | FPF1 | Flowering | 0.6592 | 0.9231 | 0.4767 |
Primer 33680 | FPF1 | Flowering | 0.2268 | 0.1500 | 0.1275 |
Primer 43088 | ELF3 | Flowering | 0.7966 | 0.9412 | 0.4210 |
Primer 41496 | GID1 | Gibberellin | 0.4911 | 0.5000 | 0.2367 |
Primer 40505 | GA2OX6 | Gibberellin | 0.6655 | 0.7000 | 0.2513 |
Primer 37852 | CIGR | Gibberellin | 0.1975 | 0.0588 | 0.2500 |
Primer 34975 | XCT | Circadian Clock | 0.5170 | 0.8000 | 0.1567 |
Primer 48198 | GIGANTEA | Circadian Clock | 0.6584 | 1.0000 | 0.1400 |
Primer 34500 | MBD9 | CONSTANS-Like | 0.8731 | 1.0000 | 0.2606 |
Primer 31670 | NFYC4 | CONSTANS-Like | 0.3200 | 0.5946 | 0.1875 |
Primer 43287 | COL4 | CONSTANS-Like | 0.7138 | 0.9730 | 0.3325 |
Primer 36067 | COL13 | CONSTANS-Like | 0.8117 | 0.9730 | 0.3025 |
Primer 36927 | FLC | Central Integrator | 0.8147 | 1.0000 | 0.1500 |
Primer 34261 | HD3 | Central Integrator | 0.7794 | 1.0000 | 0.2590 |
Primer 28366 | HD3a | Central Integrator | 0.6509 | 1.0000 | 0.1600 |
Mean | 0.6117 | 0.7742 | 0.2475 |
Code | Accession Number | Sample ID | Origins | Longitude/Latitude | Altitude (m) |
---|---|---|---|---|---|
1 | PI598781 | Z1 | Baikal, Buryat, Russia | - | - |
2 | PI610876 | Z2 | - | - | - |
3 | PI610994 | Z3 | Siberia, Russia | - | 1250 |
4 | PI636676 | Z4 | Xiahe, Gansu, China | 35.19 N, 102.65 E | 2720 |
5 | PI655199 | Z5 | Hongyuan, Sichuan, China | 32.08 N, 102.57 E | 3280 |
6 | W610305 | Z6 | Siberia, Russia | - | - |
7 | W630476 | Z7 | Kyrgyzstan | - | - |
8 | HZ03 | Z8 | Hezuo, Gansu, China | - | - |
9 | LT05 | Z9 | Lintan, Gansu, China | - | - |
10 | LQ02 | Z10 | Luqu, Gansu, China | - | - |
11 | PI435088 | W1 | Ninshan, Xinjiang, China | - | - |
12 | PI504462 | W2 | Xining, Qinghai, China | - | - |
13 | PI531665 | W3 | Beijing, China | - | - |
14 | PI531669 | W4 | Xining, Qinghai, China | - | 2400 |
15 | PI595149 | W5 | Xinjiang, China | 44.17 N, 84.57 E | 1500 |
16 | PI595156 | W6 | Xinjiang, China | 45.03 N, 81.12 E | 1300 |
17 | PI595162 | W7 | Xinjiang, China | 44.12 N, 87.97 E | 1680 |
18 | PI595169 | W8 | Xinjiang, China | 43.77 N, 89.45 E | 1300 |
19 | PI595174 | W9 | Xinjiang, China | 43.68 N, 89.30 E | 1870 |
20 | PI655092 | W10 | Mongolia | 49.80 N, 94.96 E | 1370 |
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Zheng, Y.; Zhang, Z.; Wan, Y.; Tian, J.; Xie, W. Development of EST-SSR Markers Linked to Flowering Candidate Genes in Elymus sibiricus L. Based on RNA Sequencing. Plants 2020, 9, 1371. https://doi.org/10.3390/plants9101371
Zheng Y, Zhang Z, Wan Y, Tian J, Xie W. Development of EST-SSR Markers Linked to Flowering Candidate Genes in Elymus sibiricus L. Based on RNA Sequencing. Plants. 2020; 9(10):1371. https://doi.org/10.3390/plants9101371
Chicago/Turabian StyleZheng, Yuying, Zongyu Zhang, Yiyang Wan, Jiaoyang Tian, and Wengang Xie. 2020. "Development of EST-SSR Markers Linked to Flowering Candidate Genes in Elymus sibiricus L. Based on RNA Sequencing" Plants 9, no. 10: 1371. https://doi.org/10.3390/plants9101371