Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet Potato
Sweet potato is a hexaploid heterozygote with a complex genetic background, self-pollination infertility, and cross incompatibility, which makes genetic linkage analysis quite difficult. Genome-wide association studies (GWAS) provide a new strategy for gene mapping and cloning in sweet potato. Stora...
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| Format: | Article |
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MDPI AG
2022-04-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/12/5/991 |
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| author | Yi Liu Rui Pan Wenying Zhang Jian Lei Lianjun Wang Shasha Chai Xiaojie Jin Chunhai Jiao Xinsun Yang |
| author_facet | Yi Liu Rui Pan Wenying Zhang Jian Lei Lianjun Wang Shasha Chai Xiaojie Jin Chunhai Jiao Xinsun Yang |
| author_sort | Yi Liu |
| collection | DOAJ |
| description | Sweet potato is a hexaploid heterozygote with a complex genetic background, self-pollination infertility, and cross incompatibility, which makes genetic linkage analysis quite difficult. Genome-wide association studies (GWAS) provide a new strategy for gene mapping and cloning in sweet potato. Storage root flesh color (SRFC) is an important sensory evaluation, which correlates with storage root flesh composition, such as starch, anthocyanin, and carotenoid. We performed GWAS using SRFC data of 300 accessions and 567,828 single nucleotide polymorphism (SNP) markers. Furthermore, we analyzed transcriptome data of different SRFC varieties, and conducted real-time quantitative PCR (qRT-PCR) to measure the expression level of the candidate gene in purple and non-purple fleshed sweet potato genotypes. The results showed that five unique SNPs were significantly (−log<sub>10</sub><i>P</i> > 7) associated with SRFC. Based on these trait-associated SNPs, four candidate genes, g55964 (<i>IbF3′H</i>), g17506 (<i>IbBAG2-like</i>), g25206 (<i>IbUGT-73D1-like</i>), and g58377 (<i>IbVQ25-isoform X2</i>) were identified. Expression profiles derived from transcriptome data and qRT-PCR analyses showed that the expression of g55964 in purple-fleshed sweet potato was significantly (<i>p</i> < 0.01) higher than that of non-purple fleshed sweet potato. By combining the GWAS, transcriptomic analysis and qRT-PCR, we inferred that <i>g55964</i> is the key gene related to purple formation of storage root in sweet potato. Our results lay the foundation for accelerating sweet potato genetic improvement of anthocyanin through marker-assisted selection. |
| first_indexed | 2024-03-10T03:31:31Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-10T03:31:31Z |
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| series | Agronomy |
| spelling | doaj.art-adb0c586dc284036a6a3d93f44e537c32023-11-23T09:41:10ZengMDPI AGAgronomy2073-43952022-04-0112599110.3390/agronomy12050991Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet PotatoYi Liu0Rui Pan1Wenying Zhang2Jian Lei3Lianjun Wang4Shasha Chai5Xiaojie Jin6Chunhai Jiao7Xinsun Yang8Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, ChinaResearch Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou 434025, ChinaResearch Center of Crop Stresses Resistance Technologies/Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou 434025, ChinaFood Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, ChinaFood Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, ChinaFood Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, ChinaFood Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, ChinaFood Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, ChinaFood Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, ChinaSweet potato is a hexaploid heterozygote with a complex genetic background, self-pollination infertility, and cross incompatibility, which makes genetic linkage analysis quite difficult. Genome-wide association studies (GWAS) provide a new strategy for gene mapping and cloning in sweet potato. Storage root flesh color (SRFC) is an important sensory evaluation, which correlates with storage root flesh composition, such as starch, anthocyanin, and carotenoid. We performed GWAS using SRFC data of 300 accessions and 567,828 single nucleotide polymorphism (SNP) markers. Furthermore, we analyzed transcriptome data of different SRFC varieties, and conducted real-time quantitative PCR (qRT-PCR) to measure the expression level of the candidate gene in purple and non-purple fleshed sweet potato genotypes. The results showed that five unique SNPs were significantly (−log<sub>10</sub><i>P</i> > 7) associated with SRFC. Based on these trait-associated SNPs, four candidate genes, g55964 (<i>IbF3′H</i>), g17506 (<i>IbBAG2-like</i>), g25206 (<i>IbUGT-73D1-like</i>), and g58377 (<i>IbVQ25-isoform X2</i>) were identified. Expression profiles derived from transcriptome data and qRT-PCR analyses showed that the expression of g55964 in purple-fleshed sweet potato was significantly (<i>p</i> < 0.01) higher than that of non-purple fleshed sweet potato. By combining the GWAS, transcriptomic analysis and qRT-PCR, we inferred that <i>g55964</i> is the key gene related to purple formation of storage root in sweet potato. Our results lay the foundation for accelerating sweet potato genetic improvement of anthocyanin through marker-assisted selection.https://www.mdpi.com/2073-4395/12/5/991sweet potatogenome-wide association studiesstorage root flesh colortranscriptomic analysis |
| spellingShingle | Yi Liu Rui Pan Wenying Zhang Jian Lei Lianjun Wang Shasha Chai Xiaojie Jin Chunhai Jiao Xinsun Yang Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet Potato Agronomy sweet potato genome-wide association studies storage root flesh color transcriptomic analysis |
| title | Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet Potato |
| title_full | Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet Potato |
| title_fullStr | Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet Potato |
| title_full_unstemmed | Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet Potato |
| title_short | Integrating Genome-Wide Association Study with Transcriptomic Analysis to Predict Candidate Genes Controlling Storage Root Flesh Color in Sweet Potato |
| title_sort | integrating genome wide association study with transcriptomic analysis to predict candidate genes controlling storage root flesh color in sweet potato |
| topic | sweet potato genome-wide association studies storage root flesh color transcriptomic analysis |
| url | https://www.mdpi.com/2073-4395/12/5/991 |
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