Genome wide association studies and whole transcriptomic survey decipher the fruit texture regulation in apple towards the selection of novel superior accessions

M. Di Guardo, A. Tadiello, B. Farneti, N. Busatto, M. Delledonne, W. Guerra, T. Letschka, L. Lozano, R. Velasco, E. Van de Weg, M. Bink, F. Costa

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Fruit quality is represented by a series of genetically controlled features that change throughout the entire ontogenic life. Among the several quality traits, texture plays a crucial role, impacting both consumers’ appreciation and postharvest performance. In order to decipher its regulation a multidisciplinary approach was employed. Initially, the texture performance was measured with a high resolution phenotyping device, represented by a texture analyzer equipped with an acoustic device. In the first attempt to dissect the fruit texture genetic control, two QTL mapping strategies were used. The first approach employed six bi-parental families linked by a common pedigree scheme, known as pedigree based analysis. The joint analysis of the phenotypic and genotypic data set through a Bayesian statistics identified a series of genomic regions related to both mechanical and acoustic signatures. These regions were further validated with a genome wide association study approach, which considered a much larger phenotypic and genotypic variation. To complement the genetic information, a whole transcriptome analysis was also carried out. To this end, two microarray platforms were designed and used to unravel the functional machinery ongoing during the fruit development and ripening phases, especially with regards to the plant hormone ethylene. In this study, the role of this hormone was dissected applying 1-MCP, a molecule competing with ethylene at receptor level. The combination of these resources provides a valuable source of information, essential to step forward in the comprehension of the genetic and physiological regulation of the fruit texture in apple. This knowledge would enable, in a close future, a more accurate and precise selection of the most favourable and valuable new apple accessions distinguished by a superior fruit quality.

Original languageEnglish
Pages (from-to)441-446
Number of pages6
JournalActa Horticulturae
Volume1242
DOIs
Publication statusPublished - 2019

Fingerprint

transcriptomics
apples
texture
fruits
pedigree
fruit quality
acoustics
ethylene
physiological regulation
1-methylcyclopropene
information sources
plant hormones
fruiting
quantitative trait loci
complement
ripening
statistics
hormones
genome-wide association study
genomics

Keywords

  • Ethylene
  • Fruit quality
  • GWAS
  • Marker assisted selection
  • Pedigree based analysis
  • Texture

Cite this

Di Guardo, M. ; Tadiello, A. ; Farneti, B. ; Busatto, N. ; Delledonne, M. ; Guerra, W. ; Letschka, T. ; Lozano, L. ; Velasco, R. ; Van de Weg, E. ; Bink, M. ; Costa, F. / Genome wide association studies and whole transcriptomic survey decipher the fruit texture regulation in apple towards the selection of novel superior accessions. In: Acta Horticulturae. 2019 ; Vol. 1242. pp. 441-446.
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abstract = "Fruit quality is represented by a series of genetically controlled features that change throughout the entire ontogenic life. Among the several quality traits, texture plays a crucial role, impacting both consumers’ appreciation and postharvest performance. In order to decipher its regulation a multidisciplinary approach was employed. Initially, the texture performance was measured with a high resolution phenotyping device, represented by a texture analyzer equipped with an acoustic device. In the first attempt to dissect the fruit texture genetic control, two QTL mapping strategies were used. The first approach employed six bi-parental families linked by a common pedigree scheme, known as pedigree based analysis. The joint analysis of the phenotypic and genotypic data set through a Bayesian statistics identified a series of genomic regions related to both mechanical and acoustic signatures. These regions were further validated with a genome wide association study approach, which considered a much larger phenotypic and genotypic variation. To complement the genetic information, a whole transcriptome analysis was also carried out. To this end, two microarray platforms were designed and used to unravel the functional machinery ongoing during the fruit development and ripening phases, especially with regards to the plant hormone ethylene. In this study, the role of this hormone was dissected applying 1-MCP, a molecule competing with ethylene at receptor level. The combination of these resources provides a valuable source of information, essential to step forward in the comprehension of the genetic and physiological regulation of the fruit texture in apple. This knowledge would enable, in a close future, a more accurate and precise selection of the most favourable and valuable new apple accessions distinguished by a superior fruit quality.",
keywords = "Ethylene, Fruit quality, GWAS, Marker assisted selection, Pedigree based analysis, Texture",
author = "{Di Guardo}, M. and A. Tadiello and B. Farneti and N. Busatto and M. Delledonne and W. Guerra and T. Letschka and L. Lozano and R. Velasco and {Van de Weg}, E. and M. Bink and F. Costa",
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Di Guardo, M, Tadiello, A, Farneti, B, Busatto, N, Delledonne, M, Guerra, W, Letschka, T, Lozano, L, Velasco, R, Van de Weg, E, Bink, M & Costa, F 2019, 'Genome wide association studies and whole transcriptomic survey decipher the fruit texture regulation in apple towards the selection of novel superior accessions', Acta Horticulturae, vol. 1242, pp. 441-446. https://doi.org/10.17660/ActaHortic.2019.1242.63

Genome wide association studies and whole transcriptomic survey decipher the fruit texture regulation in apple towards the selection of novel superior accessions. / Di Guardo, M.; Tadiello, A.; Farneti, B.; Busatto, N.; Delledonne, M.; Guerra, W.; Letschka, T.; Lozano, L.; Velasco, R.; Van de Weg, E.; Bink, M.; Costa, F.

In: Acta Horticulturae, Vol. 1242, 2019, p. 441-446.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Genome wide association studies and whole transcriptomic survey decipher the fruit texture regulation in apple towards the selection of novel superior accessions

AU - Di Guardo, M.

AU - Tadiello, A.

AU - Farneti, B.

AU - Busatto, N.

AU - Delledonne, M.

AU - Guerra, W.

AU - Letschka, T.

AU - Lozano, L.

AU - Velasco, R.

AU - Van de Weg, E.

AU - Bink, M.

AU - Costa, F.

PY - 2019

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N2 - Fruit quality is represented by a series of genetically controlled features that change throughout the entire ontogenic life. Among the several quality traits, texture plays a crucial role, impacting both consumers’ appreciation and postharvest performance. In order to decipher its regulation a multidisciplinary approach was employed. Initially, the texture performance was measured with a high resolution phenotyping device, represented by a texture analyzer equipped with an acoustic device. In the first attempt to dissect the fruit texture genetic control, two QTL mapping strategies were used. The first approach employed six bi-parental families linked by a common pedigree scheme, known as pedigree based analysis. The joint analysis of the phenotypic and genotypic data set through a Bayesian statistics identified a series of genomic regions related to both mechanical and acoustic signatures. These regions were further validated with a genome wide association study approach, which considered a much larger phenotypic and genotypic variation. To complement the genetic information, a whole transcriptome analysis was also carried out. To this end, two microarray platforms were designed and used to unravel the functional machinery ongoing during the fruit development and ripening phases, especially with regards to the plant hormone ethylene. In this study, the role of this hormone was dissected applying 1-MCP, a molecule competing with ethylene at receptor level. The combination of these resources provides a valuable source of information, essential to step forward in the comprehension of the genetic and physiological regulation of the fruit texture in apple. This knowledge would enable, in a close future, a more accurate and precise selection of the most favourable and valuable new apple accessions distinguished by a superior fruit quality.

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KW - Ethylene

KW - Fruit quality

KW - GWAS

KW - Marker assisted selection

KW - Pedigree based analysis

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