Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]
Significant differences in softening rate have been reported between melting flesh in peach and nectarine varieties. This trait seems to be controlled by several genes. We aimed to identify candidate genes involved in fruit softening rate by integrating quantitative trait loci (QTL) and expression Q...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2019.01581/full |
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| author | Tomás Carrasco-Valenzuela Claudia Muñoz-Espinoza Aníbal Riveros Romina Pedreschi Pere Arús Reinaldo Campos-Vargas Claudio Meneses Claudio Meneses |
| author_facet | Tomás Carrasco-Valenzuela Claudia Muñoz-Espinoza Aníbal Riveros Romina Pedreschi Pere Arús Reinaldo Campos-Vargas Claudio Meneses Claudio Meneses |
| author_sort | Tomás Carrasco-Valenzuela |
| collection | DOAJ |
| description | Significant differences in softening rate have been reported between melting flesh in peach and nectarine varieties. This trait seems to be controlled by several genes. We aimed to identify candidate genes involved in fruit softening rate by integrating quantitative trait loci (QTL) and expression QTL (eQTL) analyses, comparing siblings with contrasting softening rates. We used a segregating population derived from nectarine cv. ‘Venus’ selfing, which was phenotyped for softening rate during three seasons. Six siblings with high (HSR) and six with low softening rate (LSR) were sequenced using RNA-Seq. A group of 5,041 differentially expressed genes was identified. Also, we found a QTL with a LOD (logarithm of odds) score of 9.7 on LG4 in all analyzed seasons. Furthermore, we detected 1,062 eQTLs, of which 133 were found co-localizing with the identified QTL. Gene Ontology (GO) analysis showed ‘Response to auxin’ as one the main over-represented categories. Our findings suggest over-expression of auxin biosynthetic related genes in the HSR group, which implies a higher expression and/or accumulation of auxin, thereby triggering fast softening. Conversely, the LSR phenotype might be explained by an altered auxin-homeostasis associated with low auxin levels. This work will contribute to unraveling the genetic mechanisms responsible for the softening rate in peaches and nectarines and lead to the development of molecular markers. |
| first_indexed | 2024-12-10T21:29:38Z |
| format | Article |
| id | doaj.art-a57522e9ced14668af0cf386d15d22bc |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-10T21:29:38Z |
| publishDate | 2019-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-a57522e9ced14668af0cf386d15d22bc2022-12-22T01:32:52ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2019-12-011010.3389/fpls.2019.01581463598Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch]Tomás Carrasco-Valenzuela0Claudia Muñoz-Espinoza1Aníbal Riveros2Romina Pedreschi3Pere Arús4Reinaldo Campos-Vargas5Claudio Meneses6Claudio Meneses7Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, ChileCentro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, ChileCentro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, ChileEscuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Quillota, ChileIRTA, Centre de Recerca en Agrigenòmica (CSIC-IRTA-UAB-UB), Barcelona, SpainCentro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, ChileCentro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, ChileFONDAP Center for Genome Regulation, Santiago, ChileSignificant differences in softening rate have been reported between melting flesh in peach and nectarine varieties. This trait seems to be controlled by several genes. We aimed to identify candidate genes involved in fruit softening rate by integrating quantitative trait loci (QTL) and expression QTL (eQTL) analyses, comparing siblings with contrasting softening rates. We used a segregating population derived from nectarine cv. ‘Venus’ selfing, which was phenotyped for softening rate during three seasons. Six siblings with high (HSR) and six with low softening rate (LSR) were sequenced using RNA-Seq. A group of 5,041 differentially expressed genes was identified. Also, we found a QTL with a LOD (logarithm of odds) score of 9.7 on LG4 in all analyzed seasons. Furthermore, we detected 1,062 eQTLs, of which 133 were found co-localizing with the identified QTL. Gene Ontology (GO) analysis showed ‘Response to auxin’ as one the main over-represented categories. Our findings suggest over-expression of auxin biosynthetic related genes in the HSR group, which implies a higher expression and/or accumulation of auxin, thereby triggering fast softening. Conversely, the LSR phenotype might be explained by an altered auxin-homeostasis associated with low auxin levels. This work will contribute to unraveling the genetic mechanisms responsible for the softening rate in peaches and nectarines and lead to the development of molecular markers.https://www.frontiersin.org/article/10.3389/fpls.2019.01581/fullexpression quantitative trait lociPrunus persicasoftening rateflesh firmnessRNA-seq |
| spellingShingle | Tomás Carrasco-Valenzuela Claudia Muñoz-Espinoza Aníbal Riveros Romina Pedreschi Pere Arús Reinaldo Campos-Vargas Claudio Meneses Claudio Meneses Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch] Frontiers in Plant Science expression quantitative trait loci Prunus persica softening rate flesh firmness RNA-seq |
| title | Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch] |
| title_full | Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch] |
| title_fullStr | Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch] |
| title_full_unstemmed | Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch] |
| title_short | Expression QTL (eQTLs) Analyses Reveal Candidate Genes Associated With Fruit Flesh Softening Rate in Peach [Prunus persica (L.) Batsch] |
| title_sort | expression qtl eqtls analyses reveal candidate genes associated with fruit flesh softening rate in peach prunus persica l batsch |
| topic | expression quantitative trait loci Prunus persica softening rate flesh firmness RNA-seq |
| url | https://www.frontiersin.org/article/10.3389/fpls.2019.01581/full |
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