Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Sample Preparation
2.2. Transcriptome Sequencing, Assembly, and Analyses
2.3. Transcriptome Assembly
2.4. EST-SSR Identification and Genotyping
2.5. Genotyping by Sequencing and SNP Identification
2.6. Linkage Map Construction
3. Results
3.1. Transcriptome Analysis and EST-SSR Identification
3.2. EST-SSR Genotyping
3.3. GBS-SNP Discovery
3.4. Construction of Genetic Linkage Maps
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Length | 4 | 5 | 6 | 7 | 8 | 10 | >10 | Total | Distribution Frequency (%) | |
---|---|---|---|---|---|---|---|---|---|---|
Type | ||||||||||
Dinucleotide | 0 | 0 | 1040 | 692 | 861 | 395 | 274 | 3262 | 37.15 | |
Trinucleotide | 2675 | 997 | 434 | 246 | 202 | 60 | 24 | 4638 | 52.82 | |
Tetranucleotide | 226 | 57 | 23 | 15 | 9 | 2 | 0 | 332 | 3.78 | |
Pentanucleotide | 125 | 25 | 6 | 5 | 0 | 0 | 0 | 161 | 1.83 | |
Hexanucleotide | 241 | 93 | 29 | 12 | 6 | 0 | 0 | 381 | 4.34 | |
Other | 6 | 0 | 0 | 0 | 0 | 0 | 0 | 6 | 0.07 |
Linkage Group (LG) | Marker Count (#) | SNP Count (#) | SSR Count (#) | Length (cM) | Average Marker Interval (cM) | Largest Gap (cM) |
---|---|---|---|---|---|---|
1 | 77 | 70 | 7 | 71.0 | 0.9 | 5.9 |
2 | 93 | 83 | 10 | 75.0 | 0.8 | 6.3 |
3 | 120 | 111 | 9 | 74.7 | 0.6 | 6.4 |
4 | 72 | 65 | 7 | 72.7 | 1.0 | 6.2 |
5 | 152 | 138 | 14 | 84.9 | 0.6 | 3.0 |
6 | 49 | 49 | 0 | 45.6 | 0.9 | 4.9 |
7 | 125 | 109 | 16 | 98.1 | 0.8 | 4.8 |
8 | 101 | 98 | 3 | 76.5 | 0.8 | 10.0 |
9 | 68 | 66 | 2 | 39.8 | 0.6 | 3.0 |
10 | 126 | 114 | 12 | 97.9 | 0.8 | 6.6 |
11 | 108 | 98 | 10 | 80.6 | 0.7 | 6.3 |
12 | 92 | 82 | 10 | 99.4 | 1.1 | 11.5 |
13 | 114 | 101 | 13 | 83.2 | 0.7 | 13.5 |
14 | 86 | 77 | 9 | 108.5 | 1.3 | 7.2 |
15 | 83 | 76 | 7 | 75.4 | 0.9 | 6.1 |
16 | 101 | 97 | 4 | 61.7 | 0.6 | 5.2 |
17 | 78 | 78 | 0 | 77.2 | 1.0 | 11.5 |
18 | 122 | 109 | 13 | 61.3 | 0.5 | 6.4 |
Total | 1767 | 1621 | 146 | 1383.4 | 0.8 | 13.5 |
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Wu, X.; Hulse-Kemp, A.M.; Wadl, P.A.; Smith, Z.; Mockaitis, K.; Staton, M.E.; Rinehart, T.A.; Alexander, L.W. Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map. Horticulturae 2021, 7, 25. https://doi.org/10.3390/horticulturae7020025
Wu X, Hulse-Kemp AM, Wadl PA, Smith Z, Mockaitis K, Staton ME, Rinehart TA, Alexander LW. Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map. Horticulturae. 2021; 7(2):25. https://doi.org/10.3390/horticulturae7020025
Chicago/Turabian StyleWu, Xingbo, Amanda M. Hulse-Kemp, Phillip A. Wadl, Zach Smith, Keithanne Mockaitis, Margaret E. Staton, Timothy A. Rinehart, and Lisa W. Alexander. 2021. "Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map" Horticulturae 7, no. 2: 25. https://doi.org/10.3390/horticulturae7020025