Development of Genomic SSR for the Subtropical Hardwood Tree Dalbergia hupeana and Assessment of Their Transferability to Other Related Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. De Novo Genome Sequencing
2.3. Genome Survey and Assembly
2.4. Identification and Verification of gSSR Markers
2.5. Transferability to Other Dalbergia Species
2.6. Assessment of Genetic Diversity in Different Species
3. Results
3.1. Genome Survey
3.2. Development and Verification of gSSR Markers
3.3. Transferability of Developed gSSR Markers to Other Dalbergia Species
3.4. Diversity of gSSR Markers in Dalbergia Populations
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Name | Biotype | Location | No. Individuals |
---|---|---|---|
D. balansae | tree | Yingjiang, Yunnan, China | 29 |
D. cultrata | tree | Puer, Yunnan, China | 2 |
D. hupeana | tree | Jiangyou, Sichuan, China (JY) | 30 |
D. hupeana | tree | Xixiang, Shanxi, China (XX) | 30 |
D. hupeana | tree | Dujiangyan, Sichuan, China (DJY) | 30 |
D. mimosoides | vine | Tongren, Guizhou, China | 2 |
D. odorifera | tree | Jiulongling, Fujian, China | 2 |
D. polyadelpha | tree | Longling, Yunnan, China | 29 |
D. sissoo | tree | Yunnan, China | 2 |
D. yunnanensis | shrub | Panzhihua, Sichuan, China | 2 |
D. cochinchinensis | tree | Jiulongling, Fujian, China | 2 |
D. oliveri | tree | Jianfengling, Hainan, China | 2 |
Name | Repeat Motif | Forward Primer Sequence (5′–3′) | Reverse Primer Sequence (5′–3′) | Tm(°C) | Size Range (bp) | Fluorescence Dye |
---|---|---|---|---|---|---|
Dhup14 | (TCT)5 | TCACAAAGGTATGCATTTCCC | TATACGCTTGGCATTTGCAG | 59 | 207~219 | FAM |
Dhup61 | (GGA)11 | GGTCGAAGTGGGAATCGAAG | ATTCTCCCTCCCTTGCTCAT | 60 | 102~120 | FAM |
Dhup64 | (TTA)9 | AGTTAGGTGCACCACAGCCT | TCTATGCCGATGTTTCCCTC | 59 | 158~188 | FAM |
Dhup70 | (TTA)14 | AAGCAACGGAACAATATGAAAAA | TTATTATCACCCACCGCACA | 59 | 203~248 | FAM |
Dhup78 | (ATT)10 | AGTATCCATCCCTGGGTTCC | GTGGGTGGCGTACTGTTTTT | 59 | 257~284 | FAM |
Dhup89 | (TA)20 | TACCGTTGGATGTGATGGTG | ATGCTTCCTGCACCCTAGAA | 59 | 143~177 | FAM |
Dhup90 | (AAT)12 | TCCGATATGCAAACATGAGC | AATCACGTGGCTTTGATTCC | 59 | 222~255 | FAM |
Dhup104 | (AG)14 | TGGACCACCCATGATAGTGA | GGAACAATAGAAACAAAACACGG | 59 | 108~154 | FAM |
Dhup106 | (AT)14 | CATTTGGCATATAACATGTCGG | GCAACAGTGTAACTGATGTTGCT | 59 | 115~165 | FAM |
Dhup108 | (TC)14 | CCCCCTTAAAACTTGCTTCA | CTGATGAGTGGGAAAACGGT | 59 | 117~153 | FAM |
Dhup114 | (GGC)8 | TATTTTTGCGATCGTTGCTG | GCTCGCGGTCATGTAGACTT | 59 | 116~143 | FAM |
Dhup115 | (AAG)10 | TGAAAATGGAGAATGGGGAG | GATACACACGGGAAAATCGG | 59 | 115~142 | FAM |
Dhup116 | (AAT)8 | ATTTCATTCTCTCGCGCTGT | CAAATTTGTGAGCACATGATGA | 59 | 127~157 | FAM |
Dhup118 | (AAG)7 | TTGATCCAAGGGCGAGTAAC | GTGGGCTCTTGTTGTTGTGA | 59 | 128~149 | FAM |
Dhup120 | (AAT)8 | TGAATTTTCTCGGCAAGAGC | TTCCTTCTTTCTCACGGACC | 60 | 124~154 | FAM |
Dhup122 | (AAT)8 | GAATGAGCTGATGGTGAAGGA | ACATTAATACCTTATTCCTCAATTCTG | 58 | 133~154 | FAM |
Dhup123 | (AAG)7 | TGAGTGAGAGAAAGATAGATCAACG | CCAACGAAACCTGTTTCACA | 59 | 135~168 | FAM |
Dhup125 | (AAG)7 | TGTCTCGTTTCTCTCTCTCATCC | TTTGTGCGCTACCAACAGAG | 60 | 133~157 | FAM |
Dhup129 | (TA)14 | TGTGGTCGATGAAGACTTGG | GCCAGCTATGTGTGAAGTGC | 59 | 174~188 | HEX |
Dhup130 | (GA)13 | AAGCACGAATTAAATTTCTTGGA | AGAGAGTGTTGGTGGTTGGG | 59 | 228~276 | HEX |
Dhup132 | (AT)14 | TTGGGTGCATTGTGATTTGT | ACCATCTGGGCAGTGATAGC | 59 | 195~233 | HEX |
Dhup133 | (AT)14 | CAATACTAATGCAACAAAATTCAAA | CCCGCAATGAGAATAGGAAA | 58 | 199~243 | HEX |
Dhup139 | (AAT)8 | CCCCGGCACTCTCTATATCA | ACTGCGTATCCTTTGCTGCT | 60 | 181~199 | HEX |
Dhup141 | (TTG)8 | CCACCGTGAAAGTAGACCAAG | CCTTCCCTTGAGGACCCTAC | 59 | 187~205 | HEX |
Dhup142 | (CAA)10 | TTTGAGGCCAACCTTCAAAT | ACGAGTGGAGTGAAGTGCAA | 59 | 200~221 | HEX |
Dhup144 | (AAT)8 | AACAAATTCAAACCAAACCGA | TCCAAAGTAGGGCTTGAAAAA | 59 | 184~217 | HEX |
Dhup153 | (AG)14 | ACTTGTGTCACGTTCGTCCA | CTGCTTCCTCTGCTTCTGCT | 60 | 251~293 | ROX |
Dhup159 | (TA)14 | TTTCAGATGCTAGAGTGTGTGTG | CGTGTGCCTAAATTCTTAACCG | 58 | 206~250 | ROX |
Dhup163 | (TTG)8 | ACGAAACCCTAGCCCTTGTT | CAACGAACCTCTTGAAAGGC | 59 | 228~255 | ROX |
Dhup164 | (AAG)7 | AATTGCACAACAATCCAGCA | CGGATTATCTCCGAAAACGA | 60 | 233~254 | ROX |
Dhup167 | (AAT)8 | AAAGGCTGAGAGGAAAAGGC | TCTAAATTAAAGGATTTTTCAGTTGAT | 57 | 232~250 | ROX |
Dhup171 | (GAG)8 | GTTGCCGGTACCTTCATCAT | GTCACGATCAAAGTCGGGTT | 59 | 228~249 | ROX |
Dhup181 | (AT)14 | CCACCAGCAAATAGCTCACA | GGATTCCGAACTTGGAAGAA | 59 | 271~293 | TAMRA |
Dhup183 | (AT)14 | GCAGACATGGTGGTTTCAGA | CGATATTATCACATTTTAAAGACTTGG | 58 | 272~324 | TAMRA |
Dhup185 | (AT)14 | GTGCCAAGTACAACTGCGAA | TCACACTTAGCCACCCTTATGA | 59 | 258~308 | TAMRA |
Dhup191 | (AAT)8 | GTGATGGTCACGTCATTTGC | TTTCTCACCGCCGTTAACTT | 59 | 279~303 | TAMRA |
Dhup194 | (AAT)8 | AACGATTGATCTCTTGGTCATGT | TGTCGGTGTCTATCAATTCCC | 59 | 247~292 | TAMRA |
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Li, C.; Zheng, Y.; Liu, Y.; Lin, F.; Huang, P. Development of Genomic SSR for the Subtropical Hardwood Tree Dalbergia hupeana and Assessment of Their Transferability to Other Related Species. Forests 2021, 12, 804. https://doi.org/10.3390/f12060804
Li C, Zheng Y, Liu Y, Lin F, Huang P. Development of Genomic SSR for the Subtropical Hardwood Tree Dalbergia hupeana and Assessment of Their Transferability to Other Related Species. Forests. 2021; 12(6):804. https://doi.org/10.3390/f12060804
Chicago/Turabian StyleLi, Changhong, Yongqi Zheng, Yu Liu, Furong Lin, and Ping Huang. 2021. "Development of Genomic SSR for the Subtropical Hardwood Tree Dalbergia hupeana and Assessment of Their Transferability to Other Related Species" Forests 12, no. 6: 804. https://doi.org/10.3390/f12060804