Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions
Abstract
:1. Introduction
2. Results and Discussion
2.1. Polymorphism of SCoT Markers
POP | Code | Accession | Origin | Status |
---|---|---|---|---|
QX | 1 | Tongde | Qinghai, China | Cultivar |
QX | 2 | PI504462 | Qinghai, China | Wild |
QX | 3 | Qingmu1 | Qinghai, China | Cultivar |
QX | 4 | PI504463 | Qinghai, China | Wild |
QX | 5 | PI531669 | Qinghai, China | Wild |
QX | 6 | PI639859 | Tibet, China | Wild |
XJ | 7 | PI499468 | Xinjiang, China | Cultivated |
XJ | 8 | PI499462 | Xinjiang, China | Wild |
XJ | 9 | PI619577 | Xinjiang, China | Wild |
XJ | 10 | PI595182 | Xinjiang, China | Wild |
XJ | 11 | PI499614 | Xinjiang, China | Wild |
XJ | 12 | PI499617 | Xinjiang, China | Wild |
XJ | 13 | PI499619 | Xinjiang, China | Wild |
XJ | 14 | PI595180 | Xinjiang, China | Wild |
XJ | 15 | PI655140 | Xinjiang, China | Wild |
XJ | 16 | Y2003 | Xinjiang, China | Wild |
SC | 17 | Y1005 | Sichuan, China | Wild |
SC | 18 | Chuancao2 | Hongyuan, Sichuan, China | Cultivar |
SC | 19 | Hongyuan | Hongyuan, Sichuan, China | Breeding line |
SC | 20 | SAU133 | Aba, Sichuan, China | wild |
SC | 21 | SAU139 | Kangding, Sichuan, China | Wild |
SC | 22 | SAU003 | Kangding, Sichuan, China | wild |
SC | 23 | SAU137 | Aba, Sichuan, China | Wild |
SC | 24 | SC02 | Ruoergai, Sichuan, China | Wild |
SC | 25 | SC03 | Ruoergai, Sichuan, China | Wild |
NM | 26 | PI499457 | Inner Mongolia, China | Cultivated |
NM | 27 | PI499453 | Inner Mongolia, China | Wild |
NM | 28 | PI499456 | Inner Mongolia, China | Cultivated |
NM | 29 | PI499458 | Inner Mongolia, China | Cultivated |
NM | 30 | PI499459 | Inner Mongolia, China | Cultivated |
NM | 31 | W6 614214 | Inner Mongolia, China | Cultivated |
GS | 32 | MQ01 | Maqu, Gansu, China | Wild |
GS | 33 | HZ01 | Hezuo, Gansu, China | Wild |
GS | 34 | HZ02 | Hezuo, Gansu, China | Wild |
GS | 35 | HZ03 | Hezuo, Gansu, China | Wild |
GS | 36 | XH03 | Xiahe, Gansu, China | Wild |
GS | 37 | XH09 | Xiahe, Gansu, China | Wild |
GS | 38 | XH02 | Xiahe, Gansu, China | Wild |
GS | 39 | XH06 | Xiahe, Gansu, China | Wild |
GS | 40 | LT04 | Lintan, Gansu, China | Wild |
GS | 41 | LT02 | Lintan, Gansu, China | Wild |
GS | 42 | LT05 | Lintan, Gansu, China | Wild |
GS | 43 | LT01 | Lintan, Gansu, China | Wild |
GS | 44 | LQ01 | Luqu, Gansu, China | Wild |
GS | 45 | LQ03 | Luqu, Gansu, China | Wild |
GS | 46 | LQ04 | Luqu, Gansu, China | Wild |
GS | 47 | LQ09 | Luqu, Gansu, China | Wild |
GS | 48 | LQ10 | Luqu, Gansu, China | Wild |
GS | 49 | ZHN01 | Zhuoni, Gansu, China | Wild |
GS | 50 | ZHN05 | Zhuoni, Gansu, China | Wild |
GS | 51 | ZHN06 | Zhuoni, Gansu, China | Wild |
GS | 52 | ZHN03 | Zhuoni, Gansu, China | Wild |
GS | 53 | ZHN04 | Zhuoni, Gansu, China | Wild |
Primer ID | Primer Sequence (5'–3') | TB | PB | PPB(%) | PIC | Rp |
---|---|---|---|---|---|---|
SCoT 5 | CAACAATGGCTACCACGA | 10 | 9 | 90.00 | 0.45 | 2.65 |
SCoT 7 | CAACAATGGCTACCACGG | 7 | 6 | 85.7 | 0.41 | 2.53 |
SCoT 9 | CAACAATGGCTACCAGCA | 12 | 9 | 75.00 | 0.44 | 3.35 |
SCoT 10 | CAACAATGGCTACCAGCC | 13 | 11 | 84.62 | 0.45 | 2.40 |
SCoT 23 | CACCATGGCTACCACCAG | 18 | 18 | 100.00 | 0.47 | 5.20 |
SCoT 26 | ACCATGGCTACCACCGTC | 10 | 10 | 100.00 | 0.47 | 3.59 |
SCoT 30 | CCATGGCTACCACCGGCG | 6 | 5 | 83.33 | 0.46 | 2.71 |
SCoT 35 | CATGGCTACCACCGGCCC | 7 | 6 | 85.71 | 0.48 | 3.56 |
SCoT 41 | CAATGGCTACCACTGACA | 17 | 16 | 94.12 | 0.50 | 6.49 |
SCoT 42 | CAATGGCTACCATTAGCG | 11 | 10 | 90.91 | 0.50 | 2.56 |
SCoT 44 | CAATGGCTACCATTAGCC | 7 | 7 | 100.00 | 0.47 | 1.94 |
SCoT 45 | ACAATGGCTACCACTGAC | 11 | 7 | 63.64 | 0.45 | 2.14 |
SCoT 54 | ACAATGGCTACCACCAGC | 6 | 4 | 66.67 | 0.20 | 1.40 |
SCoT 60 | ACAATGGCTACCACCACA | 12 | 9 | 75.00 | 0.47 | 3.67 |
SCoT 61 | CAACAATGGCTACCACCG | 10 | 9 | 90.00 | 0.46 | 3.32 |
SCoT 62 | ACCATGGCTACCACGGAG | 16 | 14 | 87.50 | 0.50 | 3.86 |
Mean | 10.8 | 9.4 | 89.60 | 0.45 | --- | |
Total | 173 | 159 | 91.91 | --- | 51.37 |
2.2. Genetic Diversity Analysis
2.2.1. Genetic Diversity among Regions
POP | NPB | PPB (%) | I | H | Na |
---|---|---|---|---|---|
QX | 97 | 56.07 | 0.3002 | 0.2217 | 1.5797 |
XJ | 56 | 32.37 | 0.1662 | 0.1113 | 1.3237 |
SC | 65 | 35.57 | 0.1978 | 0.1327 | 1.3757 |
NM | 52 | 30.06 | 0.1657 | 0.1119 | 1.3006 |
GS | 59 | 34.10 | 0.1615 | 0.1068 | 1.3410 |
Mean | 65.8 | 37.63 | 0.1983 | 0.1369 | 1.3841 |
2.2.2. Genetic Diversity within Regions
Source of Variance | d.f. | Sum of Squares | Variance Component | Total Variation (%) |
---|---|---|---|---|
Among geographic regions | 4 | 408.93 | 9.45 | 49.01 |
Within geographic regions | 48 | 472.09 | 9.83 | 50.99 |
2.3. Population Structure and Cluster Analysis
2.4. Conservation Implications
3. Experimental Section
3.1. Plant Materials
3.2. DNA Extraction
3.3. SCoT-PCR Amplification
3.4. Data Analysis
4. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Zhang, J.; Xie, W.; Wang, Y.; Zhao, X. Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions. Molecules 2015, 20, 5987-6001. https://doi.org/10.3390/molecules20045987
Zhang J, Xie W, Wang Y, Zhao X. Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions. Molecules. 2015; 20(4):5987-6001. https://doi.org/10.3390/molecules20045987
Chicago/Turabian StyleZhang, Junchao, Wengang Xie, Yanrong Wang, and Xuhong Zhao. 2015. "Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions" Molecules 20, no. 4: 5987-6001. https://doi.org/10.3390/molecules20045987