Rapid Characterization of the Genetic Loci Controlling Commodity Traits of Chinese Hami Melon (Cucumis melo var. Saccharinensis Naud.) through Multiplexed Shotgun Genotyping
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials and DNA Extraction
2.2. Library Preparation and Sequencing
2.3. SNP Identification
2.4. Genotyping and Breakpoint Determination
2.5. Bin Map Construction
2.6. Segregation Distortion and Recombination Rate
2.7. Phenotype Assessment
2.8. QTL Mapping
3. Results
3.1. Sequencing and SNP Identification
3.2. Breakpoint Determination
3.3. Construction of Bin Maps and a High-Resolution Genetic Map
3.4. Mapping the Genetic Loci Controlling the Commodity Traits
4. Discussion
4.1. It Is Time- and Cost-Effective to Use MSG to Achieve Genetic Map Construction and QTL Mapping of an F2 Population in Melon
4.2. Chinese Hami Melon Has a Special Genetic Architecture
4.3. QTLs Identified in This Research Should Facilitate Chinese Hami Melon Breeding
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Availability of Data and Materials
Conflicts of Interest
References
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Total Base (bp) | Mapped Base (bp) | Alignment Rate (%) | Coverage (%) | Depth (X) | ||
---|---|---|---|---|---|---|
K1-7 | 535,301,928 | 368,700,864 | 68.88 | 8.99 | 9.75 | |
K3-92 | 373,295,832 | 217,478,520 | 58.26 | 7.63 | 6.82 | |
F2 population | Average | 202,861,119.2 | 136,117,273.5 | 66.52 | 5.86 | 4.91 |
Max | 443,498,832 | 277,653,180 | 76.82 | 8.20 | 11.78 | |
Min | 49,756,056 | 30,243,360 | 49.01 | 2.59 | 2.31 |
Chromosome | Physical Distance (bp) | Genetic Distance (cM) | #SNPs | Kb/SNP | Recombination Sites | MB/Recombination Sites | Recombination Rate (cM/Mb) |
---|---|---|---|---|---|---|---|
chr01 | 35,476,783 | 141.683 | 2930 | 12.10812 | 253 | 0.14 | 3.99 |
chr02 | 27,452,605 | 197.253 | 3797 | 7.230078 | 213 | 0.128 | 6.57 |
chr03 | 29,387,469 | 115.126 | 5199 | 5.652523 | 274 | 0.107 | 3.92 |
chr04 | 33,172,220 | 134.606 | 3206 | 10.34692 | 224 | 0.147 | 4.06 |
chr05 | 28,337,775 | 183.362 | 3759 | 7.538647 | 260 | 0.109 | 6.47 |
chr06 | 35,939,859 | 141.273 | 6715 | 5.352176 | 321 | 0.112 | 3.93 |
chr07 | 25,560,174 | 110.021 | 5366 | 4.763357 | 226 | 0.113 | 4.3 |
chr08 | 32,847,821 | 103.359 | 3753 | 8.752417 | 178 | 0.184 | 3.14 |
chr09 | 23,991,886 | 105.985 | 3307 | 7.254879 | 216 | 0.111 | 4.17 |
chr10 | 25,362,315 | 82.488 | 3087 | 8.215845 | 143 | 0.176 | 3.25 |
chr11 | 32,125,309 | 168.343 | 3246 | 9.896891 | 235 | 0.136 | 5.24 |
chr12 | 26,635,610 | 89.455 | 3244 | 8.210731 | 186 | 0.142 | 3.35 |
Entire genome | 356,289,826 | 1572.954 | 47,609 | 7.483665 | 2729 | 0.13 | 4.41 |
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Li, S.; Ni, X.; Xia, Q.; Li, Y.; Dong, X.; Hou, J.; Li, Z.; Cheng, S.; Cao, D.; Zhang, Z.; et al. Rapid Characterization of the Genetic Loci Controlling Commodity Traits of Chinese Hami Melon (Cucumis melo var. Saccharinensis Naud.) through Multiplexed Shotgun Genotyping. Agronomy 2019, 9, 430. https://doi.org/10.3390/agronomy9080430
Li S, Ni X, Xia Q, Li Y, Dong X, Hou J, Li Z, Cheng S, Cao D, Zhang Z, et al. Rapid Characterization of the Genetic Loci Controlling Commodity Traits of Chinese Hami Melon (Cucumis melo var. Saccharinensis Naud.) through Multiplexed Shotgun Genotyping. Agronomy. 2019; 9(8):430. https://doi.org/10.3390/agronomy9080430
Chicago/Turabian StyleLi, Shiming, Xuemei Ni, Qiuju Xia, Yunfei Li, Xiao Dong, Junliang Hou, Zehua Li, Shu Cheng, Dong Cao, Zhenyu Zhang, and et al. 2019. "Rapid Characterization of the Genetic Loci Controlling Commodity Traits of Chinese Hami Melon (Cucumis melo var. Saccharinensis Naud.) through Multiplexed Shotgun Genotyping" Agronomy 9, no. 8: 430. https://doi.org/10.3390/agronomy9080430