Molecular Markers and Marker-Assisted Selection Provide Genetic Insights for Identifying Key Quantitative Trait Locus for Watermelon Rind Thickness
Abstract
:1. Introduction
2. Results
2.1. Genetic and Phenotypic Characteristics of Watermelon RTs
2.2. Genetic Linkage Analysis Placed the RT Locus into a 12.845 kb Region on Chromosome 2
2.3. Analysis of the Candidate Gene Cla97C02G044120
2.4. Marker-Assisted Selection (MAS) of the RT Trait in a Natural Watermelon Panel
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Genetic Mapping Population
4.2. DNA and RNA Extraction
4.3. Molecular Marker Development and Genetic Mapping
4.4. Candidate Gene Prediction and Analysis with MAS System Verification
4.5. Statistical Analysis
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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Gene ID | Description | Position |
---|---|---|
Cla97C02G043940 | Ethylene-responsive transcription factor 3-like | 32161415 .. 32162074 (+) |
Cla97C02G043950 | Triacylglycerol lipase 2, putative | 32171738 .. 32173760 (+) |
Cla97C02G043960 | Lipase | 32176692 .. 32179249 (+) |
Cla97C02G043970 | Protein disulfide isomerase-like 2-3 | 32182402 .. 32186689 (+) |
Cla97C02G043980 | Centromere/kinetochore protein zw10 homolog | 32188755 .. 32196057 (−) |
Cla97C02G043990 | Lipid-A-disaccharide synthase | 32202021 .. 32205359 (+) |
Cla97C02G044000 | Unknown protein | 32206780 .. 32207294 (+) |
Cla97C02G044010 | Unknown protein | 32208194 .. 32208541 (+) |
Cla97C02G044020 | Ubiquitin and WLM domain-containing protein | 32218483 .. 32221679 (+) |
Cla97C02G044030 | 3-oxoacyl-[acyl-carrier-protein] synthase | 32223103 .. 32229573 (+) |
Cla97C02G044040 | F-box family protein | 32234318 .. 32236622 (−) |
Cla97C02G044050 | Heat stress transcription factor A-4c-like | 32238954 .. 32239963 (−) |
Cla97C02G044060 | Transcription elongation factor B polypeptide 3-like | 32246890 .. 32248741 (+) |
Cla97C02G044070 | Citrate synthase | 32252262 .. 32256301 (−) |
Cla97C02G044080 | Ubiquinone biosynthesis O-methyltransferase, mitochondrial | 32264788 .. 32269245 (−) |
Cla97C02G044090 | Leucine-rich repeat receptor-like protein kinase family protein | 32278703 .. 32280043 (−) |
Cla97C02G044100 | Serine/threonine protein phosphatase 7 long form | 32283295 .. 32286529 (−) |
Cla97C02G044110 | Serine/threonine-protein phosphatase | 32290370 .. 32300164 (−) |
Cla97C02G044120 | Elongation factor 2 | 32305922 .. 32314246 (+) |
Cla97C02G044130 | Protein kinase, putative | 32320831 .. 32328837 (+) |
Cla97C02G044140 | Elongation factor 2 | 32332095 .. 32335291 (+) |
Gene ID | Position | P1 | P2 | Name | Organism | Function |
---|---|---|---|---|---|---|
Cla97C02G043940 | 1112 | A * | T | CAAT-box | Pisum sativum | Common cis-acting element in promoter and enhancer regions |
1112 | A | T * | CAAT-box | Nicotiana giutinosa | - | |
1688 | G | A * | CAAT-box | Nicotiana giutinosa | - | |
Cla97C02G044090 R | 793 | C * | T | TATA-box | Arabidopsis thaliana | Core promoter element around −30 of transcription start |
1724 | G | T * | GARE-motif | Brassica oleracea | Gibberellin-responsive element | |
Cla97C02G044100 R | 141 | G * | A | CAAT-box | Pisum sativum | Common cis-acting element in promoter and enhancer regions |
393 | C * | T | CAAT-box | Nicotiana giutinosa | - | |
391 | C | T * | Box 4 | Petroselinum crispum | Part of a conserved DNA module involved in light responsiveness | |
407 | T * | A | MRE | Petroselinum crispum | MYB binding site involved in light responsiveness | |
410 | T | A * | CAAT-box | Pisum sativum | Common cis-acting element in promoter and enhancer regions | |
Cla97C02G044110 R | 397 | C * | T | CAAT-box | Arabidopsis thaliana | Common cis-acting element in promoter and enhancer regions |
398 | C * | T | CAAT-box | Nicotiana giutinosa | - | |
Cla97C02G044120 | 25 | C * | T | CAAT-box | Petunia hybrida | Common cis-acting element in promoter and enhancer regions |
1083 | C | A * | CTAG-motif | Avena sativa | - | |
Cla97C02G044130 | 151 | C * | G | MYB-binding site | Nicotiana tabacum | - |
151 | A * | T | MYB-binding site | Nicotiana tabacum | - | |
Cla97C02G044140 | 731 | T * | G | CAAT-box | Nicotiana glutinosa | - |
1097 | C * | T | Unnamed__4 | Petroselinum hortense | - | |
1285 | T | C * | CAAT-box | Pisum sativum | Common cis-acting element in promoter and enhancer regions |
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Zhao, Z.; Pei, S.; Song, Y.; Yang, T.; Gao, Y.; Chai, H.; Luan, F.; Zhu, Z.; Wang, X. Molecular Markers and Marker-Assisted Selection Provide Genetic Insights for Identifying Key Quantitative Trait Locus for Watermelon Rind Thickness. Int. J. Mol. Sci. 2024, 25, 10341. https://doi.org/10.3390/ijms251910341
Zhao Z, Pei S, Song Y, Yang T, Gao Y, Chai H, Luan F, Zhu Z, Wang X. Molecular Markers and Marker-Assisted Selection Provide Genetic Insights for Identifying Key Quantitative Trait Locus for Watermelon Rind Thickness. International Journal of Molecular Sciences. 2024; 25(19):10341. https://doi.org/10.3390/ijms251910341
Chicago/Turabian StyleZhao, Zhengxiang, Shuang Pei, Yuying Song, Tiantian Yang, Yuan Gao, Hao Chai, Feishi Luan, Zicheng Zhu, and Xuezheng Wang. 2024. "Molecular Markers and Marker-Assisted Selection Provide Genetic Insights for Identifying Key Quantitative Trait Locus for Watermelon Rind Thickness" International Journal of Molecular Sciences 25, no. 19: 10341. https://doi.org/10.3390/ijms251910341
APA StyleZhao, Z., Pei, S., Song, Y., Yang, T., Gao, Y., Chai, H., Luan, F., Zhu, Z., & Wang, X. (2024). Molecular Markers and Marker-Assisted Selection Provide Genetic Insights for Identifying Key Quantitative Trait Locus for Watermelon Rind Thickness. International Journal of Molecular Sciences, 25(19), 10341. https://doi.org/10.3390/ijms251910341