| Literature DB >> 29768494 |
Shan Yang1, Xueting Li1, Fei Huang1, Yongji Huang1, Xinlong Liu2, Jiayun Wu3, Qinnan Wang3, Zuhu Deng1,4, Rukai Chen1, Muqing Zhang4.
Abstract
The identification of germplasm resources is an important aspect of sugarcane breeding. The aim of this study was to introduce a new method for identifying Saccharum spontaneum and its progeny. First, we cloned and sequenced nuclear ribosomal DNA internal transcribed spacer (nrDNA-ITS) sequences from 20 Saccharum germplasms. Analysis of these nrDNA-ITS sequences showed a stable mutation at base 89. Primers (FO13, RO13, FI16, and RI16) were then designed for tetra-primer amplification refractory mutation system (ARMS) PCR based on mutations at base 89 of the nrDNA-ITS sequence. An additional 71 Saccharum germplasms were identified using this tetra-primer ARMS PCR method, which confirmed that the method using the described primers successfully identified Saccharum spontaneum and progeny. These results may help improve the efficiency of modern molecular breeding of sugarcane and lay a foundation for identification of sugarcane germplasms and the relationships among them.Entities:
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Year: 2018 PMID: 29768494 PMCID: PMC5955562 DOI: 10.1371/journal.pone.0197458
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Plant materials for cloning and sequencing of nrDNA-ITS sequences.
| No. | Clone name | Species name | Ploidy | Number of chromosomes |
|---|---|---|---|---|
| 1 | Badila | octoploid | 80 | |
| 2 | VN cattle cane | octoploid | 80 | |
| 3 | Loethers | octoploid | 80 | |
| 4 | Crystalina | octoploid | 80 | |
| 5 | S. Cheribon | octoploid | 80 | |
| 6 | 57NG208 | octoploid | 80 | |
| 7 | 51NG63 | octoploid | 80 | |
| 8 | NG77-004 | octoploid | 80 | |
| 9 | 28NG21 | octoploid | 80 | |
| 10 | Daye | octoploid | 80 | |
| 11 | YN75-2-11 | octoploid | 64 | |
| 12 | YN82-110 | octoploid | 64 | |
| 13 | YN83-160 | octoploid | 64 | |
| 14 | FJ89-1-1 | nonuploid | 72 | |
| 15 | YN83-201 | nonuploid | 72 | |
| 16 | YN82-44 | decaploid | 80 | |
| 17 | YN83-171 | decaploid | 80 | |
| 18 | GZ78-2-28 | dodecaploid | 96 | |
| 19 | FJ88-1-13 | dodecaploid | 96 | |
| 20 | FJ89-1-19 | tridecaploid | 104 |
Plant materials used for identifying genetic material from Saccharum spontaneum with tetra-primer ARMS PCR.
| No. | Clone name | Species name | Ploidy | Number of chromosomes |
|---|---|---|---|---|
| 1 | Badila | octoploid | 80 | |
| 2 | VN cattle cane | octoploid | 80 | |
| 3 | Loethers | octoploid | 80 | |
| 4 | Crystalina | octoploid | 80 | |
| 5 | S. Cheribon | octoploid | 80 | |
| 6 | Muckche | F1( | octoploid | 141–143 |
| 7 | Baimeizhe | F1( | octoploid | 104–106 |
| 8 | Cana Blanca | F1( | octoploid | 113–115 |
| 9 | 28NG21 | octoploid | 80 | |
| 10 | 51NG63 | octoploid | 80 | |
| 11 | 51NG3 | octoploid | 80 | |
| 12 | Daye | octoploid | 80 | |
| 13 | 57NG208 | octoploid | 80 | |
| 14 | NG77-004 | octoploid | 80 | |
| 15 | YN75-2-11 | octoploid | 64 | |
| 16 | YN83-160 | octoploid | 64 | |
| 17 | YN83-225 | octoploid | 64 | |
| 18 | YN82-58 | octoploid | 64 | |
| 19 | YN4 | octoploid | 64 | |
| 20 | YN83-238 | octoploid | 64 | |
| 21 | Vietnam-3 | octoploid | 64 | |
| 22 | YN82-9 | octoploid | 64 | |
| 23 | YN-mengzi | octoploid | 64 | |
| 24 | YN84-268 | octoploid | 64 | |
| 25 | YN82-110 | octoploid | 64 | |
| 26 | GZ78-1-11 | nonuploid | 72 | |
| 27 | YN76-1-16 | nonuploid | 72 | |
| 28 | FJ89-1-11 | nonuploid | 72 | |
| 29 | YN82-50 | nonuploid | 72 | |
| 30 | SC92-42 | nonuploid | 72 | |
| 31 | FJ89-1-1 | nonuploid | 72 | |
| 32 | YN83-201 | nonuploid | 72 | |
| 33 | SC88-49 | decaploid | 80 | |
| 34 | FJ89-1-21 | decaploid | 80 | |
| 35 | YN76-1-24 | decaploid | 80 | |
| 36 | YN75-2-35 | decaploid | 80 | |
| 37 | SC79-2-16 | decaploid | 80 | |
| 38 | SC79-1-26 | decaploid | 80 | |
| 39 | YN83-171 | decaploid | 80 | |
| 40 | Wenshan cane | Unknown | Unknown | |
| 41 | Uba | Unknown | 116–118 | |
| 42 | GD-sinense | Unknown | Unknown | |
| 43 | Nagans | Unknown | Unknown | |
| 44 | Pansahi | Unknown | Unknown | |
| 45 | Saretha | Unknown | 91–92 | |
| 46 | ROC10 | Cultivars | Unknown | Unknown |
| 47 | ROC22 | Cultivars | Unknown | Unknown |
| 48 | CP84-1198 | Cultivars | Unknown | Unknown |
| 49 | FJ92-1-11 | decaploid | 80 | |
| 50 | Heqing | decaploid | 80 | |
| 51 | YN75-2-35 | decaploid | 80 | |
| 52 | GD-16 | decaploid | 80 | |
| 53 | GD-60 | decaploid | 80 | |
| 54 | GD-71 | decaploid | 80 | |
| 55 | YN82-44 | decaploid | 80 | |
| 56 | Ledong-1 | decaploid | 80 | |
| 57 | Xundian | decaploid | 80 | |
| 58 | GZ78-1-5 | decaploid | 80 | |
| 59 | GZ79-1-4 | decaploid | 80 | |
| 60 | FJ88-1-13 | dodecaploid | 96 | |
| 61 | GZ78-2-28 | dodecaploid | 96 | |
| 62 | FJ-HuiAn | dodecaploid | 96 | |
| 63 | FJ89-1-16 | dodecaploid | 96 | |
| 64 | GD-30 | dodecaploid | 96 | |
| 65 | FJ89-1-18 | dodecaploid | 96 | |
| 66 | FJ89-1-19 | tridecaploid | 104 | |
| 67 | RL12-38-1 | F1( | Unknown | Unknown |
| 68 | RL12-38-5 | F1( | Unknown | Unknown |
| 69 | RL12-38-76 | F1( | Unknown | Unknown |
| 70 | RL12-38-81 | F1( | Unknown | Unknown |
| 71 | RL12-38-84 | F1( | Unknown | Unknown |
nrDNA-ITS PCR reaction mixture.
| Components | Volume (μL) |
|---|---|
| ddH2O | 13.9 |
| 10× LA buffer (Mg2+ plus) | 2.0 |
| dNTP (2.5 mM each) | 1.6 |
| ITS1 (10 μM) | 0.8 |
| ITS4 (10 μM) | 0.8 |
| Template (gDNA; 50 ng/μL) | 0.8 |
| LA Taq (5 U/μL) | 0.1 |
| Total volume | 20.0 |
Tetra-primer ARMS PCR mixtures.
| Components | Volume (μL) |
|---|---|
| ddH2O | 1.4 |
| 2×GC buffer | 10.0 |
| dNTP (2.5 mM each) | 2.4 |
| Dimethylsulphoxide | 0.8 |
| FO13 (5 μM) | 1.6 |
| RO13 (5 μM) | 1.2 |
| FI16 (5 μM) | 0.4 |
| RI16 (5 μM) | 1.6 |
| Template (gDNA; 50 ng/μL) | 0.4 |
| Ex Taq (5 U/μL) | 0.2 |
| Total volume | 20.0 |
Fig 1Electrophoretogram of nrDNA-ITS PCR products.
M: 100 bp DNA ladder marker. Lanes 1–5: Badila, VN cattle cane, Loethers, Crystalina, Cheribon, respectively, belong to S. officinarum. Lanes 6–10: 57NG208, 51NG63, NG77-004, 28NG21, Daye, respectively, belong to S. robustum. Lanes 11–20: YN75-2-11, YN82-110, YN83-160, FJ89-1-1, YN83-201, YN82-44, YN83-171, GZ78-2-28, FJ88-1-13, FJ89-1-19, respectively, belong to S. spontaneum.
Fig 2Analysis of nrDNA-ITS sequences.
“······” represents sequences that are identical to that of Badila. Only base mutations are shown.
Fig 3Electrophoretogram of tetra-primer ARMS PCR products.
M: 100 bp DNA ladder marker. Lanes 1–5: Badila, VN cattle cane, Loethers, Crystalina, and S. Cheribon, respectively, are S. officinarum. Lanes 6–8: Muckche, Baimeizhe, and Canablanca, respectively, are F1 generations produced between S. officinarum and S. spontaneum. Lanes 9–14: 28NG21, 51NG63, 51NG3, Daye, 57NG208, and NG77-004, respectively, are S. robustum. Lanes 15–39: YN75-2-11, YN83-160, YN83-225, YN82-58, YN4, YN83-238, Vietnam-3, YN82-9, YN-mengzi, YN84-268, YN82-110, GZ78-1-11, YN76-1-16, FJ89-1-11, YN82-50, SC92-42, FJ89-1-1, YN83-201, SC88-49, FJ89-1-21, YN76-1-24, YN75-2-35, SC79-2-16, SC79-1-26, and YN83-171, respectively, are S. spontaneum. Lanes 40–42: Wenshan cane, Uba, and GD-sinense, respectively, are S. sinense. Lanes 43–45: Nagans, Pansahi, and Saretha, respectively, are S. barberi. 46–48: ROC10, ROC22, and CP84-1196, respectively, are cultivars. Lanes 49–66: FJ92-1-11, Heqing, YN75-2-35, GD-16, GD-60, GD-71, YN82-44, Ledong-1, Xundian, GZ78-1-5, GZ79-1-4, FJ88-1-13, GZ78-2-28, FJ-HuiAn, FJ89-1-16, GD-30, FJ89-1-18, and FJ89-1-19, respectively, are S. spontaneum. Lanes 67–71: RL12-38-1, RL12-38-5, RL12-38-76, RL12-38-81, and RL12-38-84, respectively, are F1 generations produced between S. officinarum and S. robustum. Lane 72: H2O.