Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (<i>Rubus idaeus</i> L.)

‘Crumbly’ fruit is a developmental disorder in raspberry that results in malformed and unsaleable fruits. For the first time, we define two distinct crumbly phenotypes as part of this work. A consistent crumbly fruit phenotype affecting the majority of fruits every season, which we refer to as crumb...

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Main Authors: Luca M. Scolari, Robert D. Hancock, Pete E. Hedley, Jenny Morris, Kay Smith, Julie Graham
Format: Article
Language:English
Published: MDPI AG 2021-04-01
Series:Agronomy
Subjects:
Online Access:https://www.mdpi.com/2073-4395/11/4/794
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author Luca M. Scolari
Robert D. Hancock
Pete E. Hedley
Jenny Morris
Kay Smith
Julie Graham
author_facet Luca M. Scolari
Robert D. Hancock
Pete E. Hedley
Jenny Morris
Kay Smith
Julie Graham
author_sort Luca M. Scolari
collection DOAJ
description ‘Crumbly’ fruit is a developmental disorder in raspberry that results in malformed and unsaleable fruits. For the first time, we define two distinct crumbly phenotypes as part of this work. A consistent crumbly fruit phenotype affecting the majority of fruits every season, which we refer to as crumbly fruit disorder (CFD) and a second phenotype where symptoms vary across seasons as malformed fruit disorder (MFD). Here, segregation of crumbly fruit of the MFD phenotype was examined in a full-sib family and three QTL (Quantitative Trait Loci) were identified on a high density GbS (Genotype by Sequencing) linkage map. This included a new QTL and more accurate location of two previously identified QTLs. A microarray experiment using normal and crumbly fruit at three different developmental stages identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within the three QTL. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of crumbly fruit. These candidate genes provided insights regarding the molecular mechanisms involved in the genetic control of crumbly fruit in red raspberry. This study will contribute to new breeding strategies and diagnostics through the selection of molecular markers associated with the crumbly trait.
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spelling doaj.art-24f11da17ac842ecbc309ad3ddc4be092023-11-21T16:01:59ZengMDPI AGAgronomy2073-43952021-04-0111479410.3390/agronomy11040794Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (<i>Rubus idaeus</i> L.)Luca M. Scolari0Robert D. Hancock1Pete E. Hedley2Jenny Morris3Kay Smith4Julie Graham5Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UKCell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UKCell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UKCell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UKCell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UKCell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UK‘Crumbly’ fruit is a developmental disorder in raspberry that results in malformed and unsaleable fruits. For the first time, we define two distinct crumbly phenotypes as part of this work. A consistent crumbly fruit phenotype affecting the majority of fruits every season, which we refer to as crumbly fruit disorder (CFD) and a second phenotype where symptoms vary across seasons as malformed fruit disorder (MFD). Here, segregation of crumbly fruit of the MFD phenotype was examined in a full-sib family and three QTL (Quantitative Trait Loci) were identified on a high density GbS (Genotype by Sequencing) linkage map. This included a new QTL and more accurate location of two previously identified QTLs. A microarray experiment using normal and crumbly fruit at three different developmental stages identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within the three QTL. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of crumbly fruit. These candidate genes provided insights regarding the molecular mechanisms involved in the genetic control of crumbly fruit in red raspberry. This study will contribute to new breeding strategies and diagnostics through the selection of molecular markers associated with the crumbly trait.https://www.mdpi.com/2073-4395/11/4/794crumbly fruitGenotype by Sequencing (GbS)Quantitative Trait Loci (QTL)linkage group (LG)microarrayheatmap and gene ontology (GO)
spellingShingle Luca M. Scolari
Robert D. Hancock
Pete E. Hedley
Jenny Morris
Kay Smith
Julie Graham
Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (<i>Rubus idaeus</i> L.)
Agronomy
crumbly fruit
Genotype by Sequencing (GbS)
Quantitative Trait Loci (QTL)
linkage group (LG)
microarray
heatmap and gene ontology (GO)
title Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (<i>Rubus idaeus</i> L.)
title_full Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (<i>Rubus idaeus</i> L.)
title_fullStr Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (<i>Rubus idaeus</i> L.)
title_full_unstemmed Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (<i>Rubus idaeus</i> L.)
title_short Combining QTL Mapping and Gene Expression Analysis to Elucidate the Genetic Control of ‘Crumbly’ Fruit in Red Raspberry (<i>Rubus idaeus</i> L.)
title_sort combining qtl mapping and gene expression analysis to elucidate the genetic control of crumbly fruit in red raspberry i rubus idaeus i l
topic crumbly fruit
Genotype by Sequencing (GbS)
Quantitative Trait Loci (QTL)
linkage group (LG)
microarray
heatmap and gene ontology (GO)
url https://www.mdpi.com/2073-4395/11/4/794
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