Genome-Wide Development of MicroRNA-Based SSR Markers in Medicago truncatula with Their Transferability Analysis and Utilization in Related Legume Species
Abstract
:1. Introduction
2. Results and Discussion
2.1. The Frequency, Distribution and Characterization of miRNA-SSRs in the M. truncatula Genome
2.2. Development of Mt-miRNA-SSR Markers
2.3. Functional Classification of SSR-Containing miRNA Genes
2.4. Transferability of Mt-mi-RNA-SSR Markers in Leguminous Species
2.5. Genetic Diversity Analysis of 20 Alfalfa Accessions
3. Materials and Methods
3.1. Plant Material and DNA Isolation
3.2. Identification of SSRs and Primer Design
3.3. Prediction of miRNA Targets and Functional Gene Ontology (GO) Analysis
3.4. PCR Amplification
3.5. Genetic Diversity Analysis
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Search Items | Numbers |
---|---|
Total number of pri_miRNA sequence examined | 356 |
Total number of identified SSRs | 189 |
Number of SSR containing sequences | 137 |
Number of pri-miRNA containing more than 1 SSR | 46 |
Number of SSRs present in compound formation | 21 |
Repeat type | |
Mononucleotide | 133 |
Dinucleotide | 27 |
Trinucleotide | 8 |
Total length of sequences searched (kb) | 407.9 |
Frequency of SSRs | One per 0.5 kb |
Species | Transferability |
---|---|
Medicago truncatula | 157 (92.90%) |
Medicago sativa | 126 (74.56%) |
Glycine max | 131 (77.51%) |
Vicia sativa | 151 (89.35%) |
Melilotus | 150 (88.76%) |
Lotus corniculatus | 153 (90.53%) |
Sophora alopecuroides | 151 (89.35%) |
No. | Primer Name | Primer Sequence (5′–3′) | No. of Alleles | He | PIC Value |
---|---|---|---|---|---|
1 | Mt-miRNA-SSR-7 | F: CGCAACCAACATAGAAGCAA | 11 | 0.84 | 0.82 |
R: CGCGGTCTTATTAGGGATCA | |||||
2 | Mt-miRNA-SSR-10 | F: GCATCGCCGTTATTAACAAAA | 3 | 0.56 | 0.47 |
R: CGGCTTCATACACAGGGAAT | |||||
3 | Mt-miRNA-SSR-26 | F: TTGCAAACCAAACACACACA | 5 | 0.78 | 0.74 |
R: GCGACATACAATTTGGGCTT | |||||
4 | Mt-miRNA-SSR-28 | F: CAAACGTTTTCTCAATTTCTAATCG | 7 | 0.71 | 0.66 |
R: CCAAGGTTGTTCCAAGGTGT | |||||
5 | Mt-miRNA-SSR-29 | F: AGCCTCTCATTTAATTGGTGC | 4 | 0.69 | 0.62 |
R: GCAGGTGCAAATGCAGATAA | |||||
6 | Mt-miRNA-SSR-37 | F: TCCTTTGCTCTTCCAACTCTTT | 18 | 0.90 | 0.89 |
R: CCCCCTTTGTTAGCAGATGA | |||||
7 | Mt-miRNA-SSR-38 | F: AATGTATGGAGAGGATGAGCTTT | 6 | 0.68 | 0.65 |
R: AACCAGATTACCTTCATCATTCG | |||||
8 | Mt-miRNA-SSR-41 | F: TGGTTCAGAAACGGTTAGGG | 5 | 0.76 | 0.72 |
R: CAGAAAGGTCCAGAAGCCAA | |||||
9 | Mt-miRNA-SSR-45 | F: GTGAAGCAATGGTGCCTTTT | 10 | 0.75 | 0.71 |
R: TCACGGCTCAAAGGTATGTG | |||||
10 | Mt-miRNA-SSR-47 | F: TCAATCAGAAAAATTGCACCC | 13 | 0.87 | 0.86 |
R: AAAGTTTTTGTTGGGAAAGATGA | |||||
11 | Mt-miRNA-SSR-52 | F: ATTTTGTGTGCCATCGTGAA | 14 | 0.85 | 0.83 |
R: GGGACCGGTTATCTTTTGGT | |||||
12 | Mt-miRNA-SSR-63 | F: GCCATGTTTTGCATGACTGT | 13 | 0.90 | 0.89 |
R: TGCAGGTCCAAATTCAACAA | |||||
13 | Mt-miRNA-SSR-87 | F: TGAAATGCCTTTTTCTTCCC | 7 | 0.83 | 0.81 |
R: TTCCCAAACACCATCATCAA | |||||
14 | Mt-miRNA-SSR-99 | F: GAGGACGGATCAATAGGCAA | 4 | 0.69 | 0.62 |
R: TGTCTGGAAAGTGCTTCACAA | |||||
15 | Mt-miRNA-SSR-102 | F: CCACGATGCTACACACGTTC | 4 | 0.44 | 0.39 |
R: CTTCCACGTCCAGACCAACT | |||||
16 | Mt-miRNA-SSR-125 | F: TAGCCCTGCCAGCCTATTTA | 15 | 0.81 | 0.79 |
R: AAGGTGTCATCTCTCCTGCG | |||||
17 | Mt-miRNA-SSR-126 | F: TTCTCCAGCAGTGCTATTCTGA | 7 | 0.83 | 0.81 |
R: TGCTGTTCCTTTGTTTTCAATG | |||||
18 | Mt-miRNA-SSR-130 | F: TCCATGTTTTTGGCATCAGA | 4 | 0.60 | 0.52 |
R: AATTGGGGAAATAAGGGGTG | |||||
19 | Mt-miRNA-SSR-142 | F: CCAAAAAGATTTGGCCCTTT | 6 | 0.81 | 0.78 |
F: GCATGGTTGTCCCTTGCTAT | |||||
20 | Mt-miRNA-SSR-144 | R: TGCTTGTTCAATTTCGAATG | 4 | 0.69 | 0.62 |
F: CTTAAGTTACCTGTCCGGCG | |||||
21 | Mt-miRNA-SSR-148 | R: TGCTCATGTTGATTCCCAGA | 5 | 0.58 | 0.50 |
F: AGCATTAGTTGTCATGCCCC | |||||
22 | Mt-miRNA-SSR-151 | R: AAACATGTGGGGTTTGGTGT | 10 | 0.89 | 0.88 |
F: AGCCAAGTTTGGACCATCAG | |||||
23 | Mt-miRNA-SSR-163 | R: GGGGAGGAAAGGTTGAATTT | 12 | 0.87 | 0.86 |
F: GCTGCAGTTAACTACCGAGGA | |||||
24 | Mt-miRNA-SSR-164 | R: GGGGAGGAAAGGTTGAATTT | 6 | 0.78 | 0.74 |
F: GCTGCAGTTAACTACCGAGGA | |||||
25 | Mt-miRNA-SSR-166 | R: GCACCATTAGTGTGGTGTGAG | 4 | 0.70 | 0.64 |
F: GCCAACATTCCCCTCAAATA | |||||
Average | 7.88 | 0.75 | 0.71 |
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Min, X.; Zhang, Z.; Liu, Y.; Wei, X.; Liu, Z.; Wang, Y.; Liu, W. Genome-Wide Development of MicroRNA-Based SSR Markers in Medicago truncatula with Their Transferability Analysis and Utilization in Related Legume Species. Int. J. Mol. Sci. 2017, 18, 2440. https://doi.org/10.3390/ijms18112440
Min X, Zhang Z, Liu Y, Wei X, Liu Z, Wang Y, Liu W. Genome-Wide Development of MicroRNA-Based SSR Markers in Medicago truncatula with Their Transferability Analysis and Utilization in Related Legume Species. International Journal of Molecular Sciences. 2017; 18(11):2440. https://doi.org/10.3390/ijms18112440
Chicago/Turabian StyleMin, Xueyang, Zhengshe Zhang, Yisong Liu, Xingyi Wei, Zhipeng Liu, Yanrong Wang, and Wenxian Liu. 2017. "Genome-Wide Development of MicroRNA-Based SSR Markers in Medicago truncatula with Their Transferability Analysis and Utilization in Related Legume Species" International Journal of Molecular Sciences 18, no. 11: 2440. https://doi.org/10.3390/ijms18112440