The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants
Abstract
:1. Introduction
2. Results
2.1. Sequencing Outputs and Assembly
2.2. Identification of Polymorphic Genic-SSRs
2.3. Location Prediction and Frequency Analysis of the Polymorphic Genic-SSRs
2.4. Functional Annotation of the Polymorphic SSR-Containing Sequences
2.5. WGCNA Analysis of Polymorphic Genic-SSRs Related Differentially Expressed Genes on Functional Traits
2.6. WGCNA Analysis of Polymorphic Genic-SSRs Related Differentially Expressed Genes on Climate Factors
2.7. Correlation Analysis between SSR Polymorphism and Gene Expression
2.8. Experimental Validation of SSR Polymorphism and Their Effect on Gene Expression
3. Discussion
3.1. Polymorphic Genic-SSRs Provide the Genetic Basis for the Evolution of Ecological Adaptability of Caragana
3.2. Potential Roles of Polymorphic Genic-SSRs in the Formation of Ecological Adaptations in Caragana
4. Materials and Methods
4.1. Plant Materials
4.2. Full-Length Transcriptome Sequencing and Bioinformatics Analysis
4.3. Short-Reads Transcriptome Sequencing and Bioinformatics Analysis
4.4. Identification and Characteristic Analysis of Polymorphic Genic-SSRs
4.5. Weighted Gene Co-Expression Network Analysis and Hub Gene Identifying
4.6. Effect of Genic-SSRs’ Allele Length on Gene Expression
4.7. Validation of SSR Polymorphism and Their Effect on Gene Expression
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Species | Longitude (E) | Latitude (N) | Altitude (m) |
---|---|---|---|
C. tibetica (Inner Mongolia) | 108°19′09.63″ | 41°48′00.61″ | 1411 |
C. korshinskii | 119°50′38.87″ | 45°14′05.92″ | 1149 |
C. microphylla | 115°42′07.48″ | 43°31′48.47″ | 1191 |
C. tibetica (Tibet) | 87°14′02.1″ | 28°36′15.9″ | 4231 |
C. jubata | 105°56′53.12″ | 38°50′09.92″ | 3472 |
C. opulens | 112°00′35.78″ | 40°25′27.07″ | 1906 |
C. roborovskyii | 105°48′00.58″ | 38°40′16.90″ | 2004 |
C. polourensis | 75°04′05.9″ | 39°42′22.1″ | 2130 |
C. intermedia | 112°58′10.87″ | 43°11′22.24″ | 1058 |
C. pygmaea | 112°25′54.79″ | 42°34′1.61″ | 1213 |
C. stenophylla | 110°10′16.62″ | 41°40′41.93″ | 1573 |
C. versicolor | 85°32′48.6″ | 28°45′35.1″ | 4625 |
C. brachypoda | 107°54′59.61″ | 42°02′46.33″ | 1310 |
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Wang, Q.; Chen, X.; Meng, Y.; Niu, M.; Jia, Y.; Huang, L.; Ma, W.; Liang, C.; Li, Z.; Zhao, L.; et al. The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants. Int. J. Mol. Sci. 2024, 25, 2084. https://doi.org/10.3390/ijms25042084
Wang Q, Chen X, Meng Y, Niu M, Jia Y, Huang L, Ma W, Liang C, Li Z, Zhao L, et al. The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants. International Journal of Molecular Sciences. 2024; 25(4):2084. https://doi.org/10.3390/ijms25042084
Chicago/Turabian StyleWang, Qinglang, Xing’er Chen, Yue Meng, Miaomiao Niu, Yuanyuan Jia, Lei Huang, Wenhong Ma, Cunzhu Liang, Zhiyong Li, Liqing Zhao, and et al. 2024. "The Potential Role of Genic-SSRs in Driving Ecological Adaptation Diversity in Caragana Plants" International Journal of Molecular Sciences 25, no. 4: 2084. https://doi.org/10.3390/ijms25042084