Extreme-phenotype GWAS unravels a complex nexus between apple (Malus domestica) red-flesh colour and internal flesh browning
The genetic link between apple red flesh (RF) coloration and the internal flesh browning disorder (FBD) is a major challenge when breeding high fruit quality RF apple cultivars. A genome-wide association study (GWAS) was conducted in a population of about 900 red-leaved seedlings to identify genomic...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Maximum Academic Press
2022-01-01
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| Series: | Fruit Research |
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| Online Access: | https://www.maxapress.com/article/doi/10.48130/FruRes-2022-0012 |
| _version_ | 1827339854551187456 |
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| author | Satish Kumar Cecilia H. Deng Claire Molloy Chris Kirk Blue Plunkett Kui Lin-Wang Andrew Allan Richard Espley |
| author_facet | Satish Kumar Cecilia H. Deng Claire Molloy Chris Kirk Blue Plunkett Kui Lin-Wang Andrew Allan Richard Espley |
| author_sort | Satish Kumar |
| collection | DOAJ |
| description | The genetic link between apple red flesh (RF) coloration and the internal flesh browning disorder (FBD) is a major challenge when breeding high fruit quality RF apple cultivars. A genome-wide association study (GWAS) was conducted in a population of about 900 red-leaved seedlings to identify genomic regions and putative candidate genes using whole genome sequencing of the pools of extreme phenotypes (XP) for the RF colour coverage (using the weighted cortex index (WCI)) and FBD. This study identified novel genomic regions contributing to WCI and FBD variation in the red-leaved seedlings. The FBD-associated regions were enriched for genes regulating senescence, heat shock proteins, cytochrome P450, ascorbate metabolism and pectin methyl esterases. Although there were no significant regions in common for WCI and FBD, there were several genes (e.g. MYB85, MYB66, ethylene insensitive 3, DNAJ heat shock protein, WRKY7, and NAC42) enriched commonly between the genomic regions associated with these traits, potentially underpinning the genetic connection between WCI and FBD. Some of the differentially expressed genes between the R6:MdMYB10 and white-fleshed ‘control’ apples resided within the GWAS hotspot for WCI (e.g. chalcone synthase, UDP-Glycosyl transferase) and FBD (e.g. Rho GTPase activating protein, lipoxygenase 1, phytoene synthase) – validating the XP-GWAS findings. Paralogs of several genes resided in the trait-associated genomic regions, suggesting that whole genome duplication plays an important role in the regulation of these traits. Adverse genetic correlations between WCI and sensory traits were observed, and strategies to develop FBD-free high fruit quality RF cultivars are discussed. |
| first_indexed | 2024-03-07T20:08:36Z |
| format | Article |
| id | doaj.art-0fc103eecba143d483e14baf7d4482dd |
| institution | Directory Open Access Journal |
| issn | 2769-4615 |
| language | English |
| last_indexed | 2024-03-07T20:08:36Z |
| publishDate | 2022-01-01 |
| publisher | Maximum Academic Press |
| record_format | Article |
| series | Fruit Research |
| spelling | doaj.art-0fc103eecba143d483e14baf7d4482dd2024-02-28T03:19:34ZengMaximum Academic PressFruit Research2769-46152022-01-012111410.48130/FruRes-2022-0012FruRes-2022-0012Extreme-phenotype GWAS unravels a complex nexus between apple (Malus domestica) red-flesh colour and internal flesh browningSatish Kumar0Cecilia H. Deng1Claire Molloy2Chris Kirk3Blue Plunkett4Kui Lin-Wang5Andrew Allan6Richard Espley7The New Zealand Institute for Plant and Food Research Limited, Hawke's Bay Research Centre, Havelock North 4130, New ZealandThe New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1025 , New ZealandThe New Zealand Institute for Plant and Food Research Limited, Hawke's Bay Research Centre, Havelock North 4130, New ZealandThe New Zealand Institute for Plant and Food Research Limited, Palmerston North Research Centre, Palmerston North 4410, New ZealandThe New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1025 , New ZealandThe New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1025 , New ZealandThe New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1025 , New ZealandThe New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland 1025 , New ZealandThe genetic link between apple red flesh (RF) coloration and the internal flesh browning disorder (FBD) is a major challenge when breeding high fruit quality RF apple cultivars. A genome-wide association study (GWAS) was conducted in a population of about 900 red-leaved seedlings to identify genomic regions and putative candidate genes using whole genome sequencing of the pools of extreme phenotypes (XP) for the RF colour coverage (using the weighted cortex index (WCI)) and FBD. This study identified novel genomic regions contributing to WCI and FBD variation in the red-leaved seedlings. The FBD-associated regions were enriched for genes regulating senescence, heat shock proteins, cytochrome P450, ascorbate metabolism and pectin methyl esterases. Although there were no significant regions in common for WCI and FBD, there were several genes (e.g. MYB85, MYB66, ethylene insensitive 3, DNAJ heat shock protein, WRKY7, and NAC42) enriched commonly between the genomic regions associated with these traits, potentially underpinning the genetic connection between WCI and FBD. Some of the differentially expressed genes between the R6:MdMYB10 and white-fleshed ‘control’ apples resided within the GWAS hotspot for WCI (e.g. chalcone synthase, UDP-Glycosyl transferase) and FBD (e.g. Rho GTPase activating protein, lipoxygenase 1, phytoene synthase) – validating the XP-GWAS findings. Paralogs of several genes resided in the trait-associated genomic regions, suggesting that whole genome duplication plays an important role in the regulation of these traits. Adverse genetic correlations between WCI and sensory traits were observed, and strategies to develop FBD-free high fruit quality RF cultivars are discussed.https://www.maxapress.com/article/doi/10.48130/FruRes-2022-0012red-fleshed appleinternal browningfruit qualityxp-gwasgenetic architecture |
| spellingShingle | Satish Kumar Cecilia H. Deng Claire Molloy Chris Kirk Blue Plunkett Kui Lin-Wang Andrew Allan Richard Espley Extreme-phenotype GWAS unravels a complex nexus between apple (Malus domestica) red-flesh colour and internal flesh browning Fruit Research red-fleshed apple internal browning fruit quality xp-gwas genetic architecture |
| title | Extreme-phenotype GWAS unravels a complex nexus between apple (Malus domestica) red-flesh colour and internal flesh browning |
| title_full | Extreme-phenotype GWAS unravels a complex nexus between apple (Malus domestica) red-flesh colour and internal flesh browning |
| title_fullStr | Extreme-phenotype GWAS unravels a complex nexus between apple (Malus domestica) red-flesh colour and internal flesh browning |
| title_full_unstemmed | Extreme-phenotype GWAS unravels a complex nexus between apple (Malus domestica) red-flesh colour and internal flesh browning |
| title_short | Extreme-phenotype GWAS unravels a complex nexus between apple (Malus domestica) red-flesh colour and internal flesh browning |
| title_sort | extreme phenotype gwas unravels a complex nexus between apple malus domestica red flesh colour and internal flesh browning |
| topic | red-fleshed apple internal browning fruit quality xp-gwas genetic architecture |
| url | https://www.maxapress.com/article/doi/10.48130/FruRes-2022-0012 |
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