Evaluation of the Genetic Diversity and Differentiation of Black Locust (Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats
Abstract
:1. Introduction
2. Results
2.1. Polymorphism and Determination of SSR Markers
2.2. Characteristics of EST-SSRs and G-SSRs
2.3. Genetic Diversity Analysis
2.4. Provenance Differentiation Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. DNA Extraction
4.3. SSR Marker Screening
4.4. Comparison of EST-SSR and G-SSR outcomes
4.5. SSR Amplification of Provenances
4.6. Genetic Diversity and Differentiation Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Repeat Type | EST-SSR Polymorphic Number | Remaining Number after Screening | Percentage | G-SSR Polymorphic Number | Remaining Number after Screening | Percentage |
---|---|---|---|---|---|---|
Di- | 4 | 2 | 7.143 | 11 | 7 | 100 |
Tri- | 14 | 10 | 35.714 | - | 0 | 0 |
Tetra- | 3 | 3 | 10.714 | - | 0 | 0 |
Penta- | 7 | 5 | 17.857 | - | 0 | 0 |
Hexa- | 9 | 8 | 28.571 | - | 0 | 0 |
Total | 37 | 28 | 100 | 11 | 7 | 100 |
SSR Marker Type | Genotype Number | Allele Number (N) | Gene Diversity (H) | Polymorphism Information Content (PIC) |
---|---|---|---|---|
EST-SSR | 24.286 | 10.464 | 0.535 | 0.503 |
G-SSR | 65.429 | 20.857 | 0.835 | 0.817 |
Species | EST-SSR Number of Loci | Percentage | G-SSR Noumber of Loci | Percentage |
---|---|---|---|---|
Gleditsia sinensis | 20 | 57.143 | 8 | 61.538 |
Cercis chinensis | 20 | 57.143 | 6 | 46.154 |
Wisteria sinensis (Sims) Sweet | 21 | 60.000 | 8 | 61.538 |
Trifolium repens | 17 | 48.571 | 0 | 0.000 |
Amorpha fruticosa | 19 | 54.286 | 8 | 61.538 |
Sophora japonica | 21 | 60.000 | 9 | 69.231 |
Sophora japonica var. pendula | 21 | 60.000 | 7 | 53.846 |
Robinia pseudoacacia ‘Frisia’ | 34 | 97.143 | 7 | 53.846 |
Robinia pseu-doacacia var. decaisneana | 32 | 91.429 | 9 | 69.231 |
Mean | 22.778 | 65.079 | 6.889 | 52.99 |
Source of Variation | Degree of Freedom | Sum of Squares | Mean Square | Percentage Variation | Percentage Variation (%) | p-Value |
---|---|---|---|---|---|---|
Among Provenances | 18 | 686.448 | 38.136 | 0.715 | 3% | <0.01 |
Within Provenances | 348 | 8565.051 | 24.612 | 24.612 | 97% | <0.01 |
Total | 366 | 9251.499 | 25.327 | 100% |
Provenance Name | Source Sites | Sample Number | Latitude (N) | Longitude (W) | |
---|---|---|---|---|---|
VA | Black Burg | 12 | 37°26′ | 80°45′ | |
Independence | 12 | 36°37′ | 81°07′ | ||
Washington DC | 14 | 38°27′ | 76°28′ | ||
WV | New River Gorge | 14 | 38°04′ | 81°03′ | |
Morgantown | 11 | 39°36′ | 79°57′ | ||
West Huntington | 14 | 38°23′ | 82°29′ | ||
NC | Huntersville | 12 | 39°08′ | 90°45′ | |
GA | Blue Ridge Lake | 13 | 34°51′ | 84°19′ | |
MD | Old National Pike | 9 | 39°42′ | 78°18′ | |
PA | Big Beaver Blvd | 13 | 40°32′ | 80°18′ | |
Bedford | 15 | 40°08′ | 78°30′ | ||
OH | Cadiz piedmont | 12 | 40°07′ | 81°13′ | |
Cincinnati | 10 | 39°03′ | 84°31′ | ||
IN | Fisher | 12 | 39°56′ | 85°53′ | |
Georgetwon | 13 | 38°17′ | 85°55′ | ||
Elberfeld | 8 | 38°10′ | 87°26′ | ||
IL | Bloomington | 12 | 40°28′ | 89°01′ | |
Toe Exit | 12 | 39°03′ | 88°40′ | ||
KY | Mt Sterling | 11 | 38°03′ | 84°02′ | |
Bowling Green | 14 | 37°00′ | 86°17′ | ||
Kentucky Lake | 6 | 36°59′′ | 88°08′ | ||
Wickliffe | 10 | 37°01′ | 89°03′ | ||
TN | Knoxville | 13 | 35°52′ | 83°57′ | |
Waverly | 14 | 35°53′ | 87°39′ | ||
MS | Sardis | 8 | 34°26′ | 89°53′ | |
AL | Upper Elkton RD | 11 | 34°56′ | 86°53′ | |
MS/AL | Ms/AL Border | 13 | 34°11′ | 88°06′ | |
IA | Brulington | 10 | 40°50′ | 91°08′ | |
MO | Hannidal | 8 | 39°43′ | 91°21′ | |
ST James | 14 | 37°56′ | 91°08′ | ||
KS | Riverton | 4 | 37°06′ | 94°42′ | |
OK | Pryor | 8 | 36°19′ | 95°18′ | |
AR | Colt | 5 | 35°21′ | 80°51′ | |
Total Number | 19 | 33 | 367 | - | - |
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Guo, Q.; Li, X.; Yang, S.; Yang, Z.; Sun, Y.; Zhang, J.; Cao, S.; Dong, L.; Uddin, S.; Li, Y. Evaluation of the Genetic Diversity and Differentiation of Black Locust (Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats. Int. J. Mol. Sci. 2018, 19, 2492. https://doi.org/10.3390/ijms19092492
Guo Q, Li X, Yang S, Yang Z, Sun Y, Zhang J, Cao S, Dong L, Uddin S, Li Y. Evaluation of the Genetic Diversity and Differentiation of Black Locust (Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats. International Journal of Molecular Sciences. 2018; 19(9):2492. https://doi.org/10.3390/ijms19092492
Chicago/Turabian StyleGuo, Qi, Xiuyu Li, Shuhong Yang, Zhiheng Yang, Yuhan Sun, Jiangtao Zhang, Sen Cao, Li Dong, Saleem Uddin, and Yun Li. 2018. "Evaluation of the Genetic Diversity and Differentiation of Black Locust (Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats" International Journal of Molecular Sciences 19, no. 9: 2492. https://doi.org/10.3390/ijms19092492
APA StyleGuo, Q., Li, X., Yang, S., Yang, Z., Sun, Y., Zhang, J., Cao, S., Dong, L., Uddin, S., & Li, Y. (2018). Evaluation of the Genetic Diversity and Differentiation of Black Locust (Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats. International Journal of Molecular Sciences, 19(9), 2492. https://doi.org/10.3390/ijms19092492