The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa)
Octoploid strawberry (Fragaria ×ananassa) is a major specialty crop under intense annual selection for traits relating to plant vigor and fruit quality. Most functional validation experiments rely on transgenic or transient gene expression assays in the mature receptacle. These findings are not typi...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.01317/full |
| _version_ | 1828826107265155072 |
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| author | Christopher Barbey Max Hogshead Anne E. Schwartz Nadia Mourad Sujeet Verma Seonghee Lee Vance M. Whitaker Kevin M. Folta |
| author_facet | Christopher Barbey Max Hogshead Anne E. Schwartz Nadia Mourad Sujeet Verma Seonghee Lee Vance M. Whitaker Kevin M. Folta |
| author_sort | Christopher Barbey |
| collection | DOAJ |
| description | Octoploid strawberry (Fragaria ×ananassa) is a major specialty crop under intense annual selection for traits relating to plant vigor and fruit quality. Most functional validation experiments rely on transgenic or transient gene expression assays in the mature receptacle. These findings are not typically translatable to breeding without identifying a natural genetic source of transcript level variation, and developing reliable markers for selection in octoploids. Expression QTL (eQTL) analysis is a genetic/transcriptomic association approach for identifying sequence variants predicting differential expression. This eQTL study analyzed a wide array of mature receptacle-expressed genes, encompassing the majority of total mature receptacle transcript accumulation and almost all strawberry genes described in the literature. These results identified segregating genetic variants associated with the differential expression of hundreds of strawberry genes, many with known interest to breeders. Several of these eQTL pertain to published genes whose expression levels have been demonstrated to influence mature receptacle phenotypes. Many include key genes of the phenylpropanoid pathway, vitamin C, carotenoid, pectin, and receptacle carbohydrate/sugar metabolism. These subgenome-specific genetic markers may allow breeders to select for desired ranges of target gene expression. These results may also guide basic research efforts and facilitate the identification of causal genes underlying trait QTL. |
| first_indexed | 2024-12-12T14:31:51Z |
| format | Article |
| id | doaj.art-79bc2d8c0dec43d8bcace41f3a6dcf52 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-12T14:31:51Z |
| publishDate | 2020-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-79bc2d8c0dec43d8bcace41f3a6dcf522022-12-22T00:21:28ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-02-011010.3389/fgene.2019.01317490125The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa)Christopher Barbey0Max Hogshead1Anne E. Schwartz2Nadia Mourad3Sujeet Verma4Seonghee Lee5Vance M. Whitaker6Kevin M. Folta7Horticultural Sciences Department, IFAS, University of Florida, Gainesville, FL, United StatesHorticultural Sciences Department, IFAS, University of Florida, Gainesville, FL, United StatesHorticultural Sciences Department, IFAS, University of Florida, Gainesville, FL, United StatesHorticultural Sciences Department, IFAS, University of Florida, Gainesville, FL, United StatesGulf Coast Research and Education Center, IFAS, University of Florida, Wimauma, FL, United StatesGulf Coast Research and Education Center, IFAS, University of Florida, Wimauma, FL, United StatesGulf Coast Research and Education Center, IFAS, University of Florida, Wimauma, FL, United StatesHorticultural Sciences Department, IFAS, University of Florida, Gainesville, FL, United StatesOctoploid strawberry (Fragaria ×ananassa) is a major specialty crop under intense annual selection for traits relating to plant vigor and fruit quality. Most functional validation experiments rely on transgenic or transient gene expression assays in the mature receptacle. These findings are not typically translatable to breeding without identifying a natural genetic source of transcript level variation, and developing reliable markers for selection in octoploids. Expression QTL (eQTL) analysis is a genetic/transcriptomic association approach for identifying sequence variants predicting differential expression. This eQTL study analyzed a wide array of mature receptacle-expressed genes, encompassing the majority of total mature receptacle transcript accumulation and almost all strawberry genes described in the literature. These results identified segregating genetic variants associated with the differential expression of hundreds of strawberry genes, many with known interest to breeders. Several of these eQTL pertain to published genes whose expression levels have been demonstrated to influence mature receptacle phenotypes. Many include key genes of the phenylpropanoid pathway, vitamin C, carotenoid, pectin, and receptacle carbohydrate/sugar metabolism. These subgenome-specific genetic markers may allow breeders to select for desired ranges of target gene expression. These results may also guide basic research efforts and facilitate the identification of causal genes underlying trait QTL.https://www.frontiersin.org/article/10.3389/fgene.2019.01317/fulleQTL analysispathway analysisanthocyaninspectintranscriptomicsstrawberry (Fragaria ×ananassa Duch.) |
| spellingShingle | Christopher Barbey Max Hogshead Anne E. Schwartz Nadia Mourad Sujeet Verma Seonghee Lee Vance M. Whitaker Kevin M. Folta The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa) Frontiers in Genetics eQTL analysis pathway analysis anthocyanins pectin transcriptomics strawberry (Fragaria ×ananassa Duch.) |
| title | The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa) |
| title_full | The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa) |
| title_fullStr | The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa) |
| title_full_unstemmed | The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa) |
| title_short | The Genetics of Differential Gene Expression Related to Fruit Traits in Strawberry (Fragaria ×ananassa) |
| title_sort | genetics of differential gene expression related to fruit traits in strawberry fragaria ananassa |
| topic | eQTL analysis pathway analysis anthocyanins pectin transcriptomics strawberry (Fragaria ×ananassa Duch.) |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.01317/full |
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