Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. DNA Extraction
2.3. SSR Markers and PCR Reactions
2.4. Marker Scoring
2.5. Structure and Genetic Diversity Analysis
2.6. Species-Specific and Species-Associated SSR Allele
2.7. Phylogenetic Analysis of the Sugarcane Accessions Using Species Associated SSR Alleles
3. Results
3.1. SSR Alleles
3.2. Population Structure
3.3. Phylogenetic Analysis
3.4. Principal Component Analysis
3.5. Species-Specific and Species-Associated SSR Alleles
3.6. Phylogenetic Analysis of the Sugarcane Accessions Using Species-Specific or Species-Associated SSR Alleles
4. Discussion
4.1. Profile of the SSR Alleles
4.2. Population Structure and Phylogenetic Analysis
4.3. Species-Specific and Species-Associated SSR Alleles
4.4. Summary
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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No. | SSR Markers | Size Range (bp) | Number of Detected Peaks (Alleles) | Number of Original Alleles | Number of New Alleles | New SSR Alleles (bp) Detected in This Study |
---|---|---|---|---|---|---|
1 | SMC119CG | 80~239 | 32 | 6 | 26 | 80, 92, 95, 99, 109, 115, 121, 125, 136, 138, 141, 143, 145, 149, 152, 155, 168, 172, 187, 190, 195, 204, 210, 229, 231, 239 |
2 | SMC1604SA | 91~140 | 26 | 19 | 7 | 92, 97, 104, 107, 126, 129, 140 |
3 | SMC1751CL | 122~169 | 26 | 23 | 3 | 156, 168, 169 |
4 | SMC18SA | 127~165 | 14 | 13 | 1 | 128 |
5 | SMC22DUQ | 123~177 | 21 | 20 | 1 | 141 |
6 | SMC24DUQ | 119~144 | 17 | 15 | 2 | 119, 126 |
7 | SMC278CS | 110~238 | 32 | 30 | 2 | 112, 144 |
8 | SMC319CG | 79~189 | 26 | 0 | 26 | 79, 123, 143, 144, 145, 147, 149, 151, 153, 155, 158, 160, 162, 163, 164, 166, 168, 170, 172, 175, 179, 181, 183, 185, 187, 189 |
9 | SMC31CUQ | 108~234 | 30 | 29 | 1 | 151 |
10 | SMC334BS | 130~170 | 30 | 27 | 3 | 130, 141, 169 |
11 | SMC336BS | 112~239 | 31 | 30 | 1 | 152 |
12 | SMC36BUQ | 82~338 | 35 | 27 | 8 | 102, 124, 137, 147, 192, 258, 277, 338 |
13 | SMC486CG | 222~247 | 15 | 14 | 1 | 229 |
14 | SMC569CS | 165~238 | 38 | 36 | 2 | 177, 211 |
15 | SMC597CS | 128~188 | 46 | 45 | 1 | 177 |
16 | SMC703BS | 181~237 | 33 | 31 | 2 | 181, 184 |
17 | SMC7CUQ | 144~171 | 16 | 13 | 3 | 144, 147, 150 |
18 | SMC851MS | 127~158 | 31 | 31 | 0 | N/A |
19 | CIR3 | 148~467 | 34 | 26 | 8 | 166, 401, 424, 440, 442, 462, 464, 467 |
20 | CIR43 | 162~256 | 37 | 31 | 6 | 162, 164, 203, 222, 249, 251 |
21 | CIR66 | 102~154 | 27 | 27 | 0 | N/A |
22 | CIR74 | 118~245 | 27 | 22 | 5 | 118, 175, 200, 202, 245 |
Total | N/A | N/A | 624 | 515 | 109 | 109 |
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Xiong, H.; Chen, Y.; Gao, S.-J.; Pan, Y.-B.; Shi, A. Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species. Agronomy 2022, 12, 412. https://doi.org/10.3390/agronomy12020412
Xiong H, Chen Y, Gao S-J, Pan Y-B, Shi A. Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species. Agronomy. 2022; 12(2):412. https://doi.org/10.3390/agronomy12020412
Chicago/Turabian StyleXiong, Haizheng, Yilin Chen, San-Ji Gao, Yong-Bao Pan, and Ainong Shi. 2022. "Population Structure and Genetic Diversity Analysis in Sugarcane (Saccharum spp. hybrids) and Six Related Saccharum Species" Agronomy 12, no. 2: 412. https://doi.org/10.3390/agronomy12020412