Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon
Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait re...
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MDPI AG
2023-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/25/1/65 |
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| author | Ahmed Mahmoud Rui Qi Xiaolu Chi Nanqiao Liao Guy Kateta Malangisha Abid Ali Mohamed Moustafa-Farag Jinghua Yang Mingfang Zhang Zhongyuan Hu |
| author_facet | Ahmed Mahmoud Rui Qi Xiaolu Chi Nanqiao Liao Guy Kateta Malangisha Abid Ali Mohamed Moustafa-Farag Jinghua Yang Mingfang Zhang Zhongyuan Hu |
| author_sort | Ahmed Mahmoud |
| collection | DOAJ |
| description | Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F<sub>2</sub> population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (<i>qNLR_Dr. Chr01</i> and <i>qNLR_Dr. Chr02</i>) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in <i>qNLR_Dr. Chr01</i>) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other <i>Cucurbitacea</i> species. |
| first_indexed | 2024-03-08T15:05:57Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-08T15:05:57Z |
| publishDate | 2023-12-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-0e6f87beba5c4c2d9b516812f5ffe45c2024-01-10T14:58:02ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-12-012516510.3390/ijms25010065Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild WatermelonAhmed Mahmoud0Rui Qi1Xiaolu Chi2Nanqiao Liao3Guy Kateta Malangisha4Abid Ali5Mohamed Moustafa-Farag6Jinghua Yang7Mingfang Zhang8Zhongyuan Hu9Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, ChinaInstitute of Vegetable Science, Zhejiang University, Hangzhou 310058, ChinaInstitute of Vegetable Science, Zhejiang University, Hangzhou 310058, ChinaInstitute of Vegetable Science, Zhejiang University, Hangzhou 310058, ChinaInstitute of Vegetable Science, Zhejiang University, Hangzhou 310058, ChinaInstitute of Vegetable Science, Zhejiang University, Hangzhou 310058, ChinaHorticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, EgyptInstitute of Vegetable Science, Zhejiang University, Hangzhou 310058, ChinaInstitute of Vegetable Science, Zhejiang University, Hangzhou 310058, ChinaInstitute of Vegetable Science, Zhejiang University, Hangzhou 310058, ChinaDrought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F<sub>2</sub> population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (<i>qNLR_Dr. Chr01</i> and <i>qNLR_Dr. Chr02</i>) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in <i>qNLR_Dr. Chr01</i>) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other <i>Cucurbitacea</i> species.https://www.mdpi.com/1422-0067/25/1/65drought tolerancegenetic resourceswild watermelonquantitative trait loci (QTL) mappingtranscriptomegenomics-assisted breeding |
| spellingShingle | Ahmed Mahmoud Rui Qi Xiaolu Chi Nanqiao Liao Guy Kateta Malangisha Abid Ali Mohamed Moustafa-Farag Jinghua Yang Mingfang Zhang Zhongyuan Hu Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon International Journal of Molecular Sciences drought tolerance genetic resources wild watermelon quantitative trait loci (QTL) mapping transcriptome genomics-assisted breeding |
| title | Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon |
| title_full | Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon |
| title_fullStr | Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon |
| title_full_unstemmed | Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon |
| title_short | Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon |
| title_sort | integrated bulk segregant analysis fine mapping and transcriptome revealed qtls and candidate genes associated with drought adaptation in wild watermelon |
| topic | drought tolerance genetic resources wild watermelon quantitative trait loci (QTL) mapping transcriptome genomics-assisted breeding |
| url | https://www.mdpi.com/1422-0067/25/1/65 |
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