Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

Claudia Muñoz-Espinoza, Alex Di Genova, José Correa, Romina Silva, Alejandro Maass, Mauricio González-Agüero, Ariel Orellana, Patricio Hinrichsen

Resultado de la investigación: Article

8 Citas (Scopus)

Resumen

Background: Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6-8mm berries (B68) phenological stages. Results: A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions: We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.

Idioma originalEnglish
Número de artículo104
PublicaciónBMC Plant Biology
Volumen16
N.º1
DOI
EstadoPublished - 26 abr 2016

Huella dactilar

transcriptomics
small fruits
table grapes
genes
phenotype
fruits
breeding
selection criteria
quantitative polymerase chain reaction
principal component analysis
RNA
economics

ASJC Scopus subject areas

  • Plant Science

Citar esto

Muñoz-Espinoza, C., Di Genova, A., Correa, J., Silva, R., Maass, A., González-Agüero, M., ... Hinrichsen, P. (2016). Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight. BMC Plant Biology, 16(1), [104]. https://doi.org/10.1186/s12870-016-0789-1
Muñoz-Espinoza, Claudia ; Di Genova, Alex ; Correa, José ; Silva, Romina ; Maass, Alejandro ; González-Agüero, Mauricio ; Orellana, Ariel ; Hinrichsen, Patricio. / Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight. En: BMC Plant Biology. 2016 ; Vol. 16, N.º 1.
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title = "Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight",
abstract = "Background: Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6-8mm berries (B68) phenological stages. Results: A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions: We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.",
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Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight. / Muñoz-Espinoza, Claudia; Di Genova, Alex; Correa, José; Silva, Romina; Maass, Alejandro; González-Agüero, Mauricio; Orellana, Ariel; Hinrichsen, Patricio.

En: BMC Plant Biology, Vol. 16, N.º 1, 104, 26.04.2016.

Resultado de la investigación: Article

TY - JOUR

T1 - Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight

AU - Muñoz-Espinoza, Claudia

AU - Di Genova, Alex

AU - Correa, José

AU - Silva, Romina

AU - Maass, Alejandro

AU - González-Agüero, Mauricio

AU - Orellana, Ariel

AU - Hinrichsen, Patricio

PY - 2016/4/26

Y1 - 2016/4/26

N2 - Background: Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6-8mm berries (B68) phenological stages. Results: A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions: We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.

AB - Background: Berry size is considered as one of the main selection criteria in table grape breeding programs. However, this is a quantitative and polygenic trait, and its genetic determination is still poorly understood. Considering its economic importance, it is relevant to determine its genetic architecture and elucidate the mechanisms involved in its expression. To approach this issue, an RNA-Seq experiment based on Illumina platform was performed (14 libraries), including seedless segregants with contrasting phenotypes for berry weight at fruit setting (FST) and 6-8mm berries (B68) phenological stages. Results: A group of 526 differentially expressed (DE) genes were identified, by comparing seedless segregants with contrasting phenotypes for berry weight: 101 genes from the FST stage and 463 from the B68 stage. Also, we integrated differential expression, principal components analysis (PCA), correlations and network co-expression analyses to characterize the transcriptome profiling observed in segregants with contrasting phenotypes for berry weight. After this, 68 DE genes were selected as candidate genes, and seven candidate genes were validated by real time-PCR, confirming their expression profiles. Conclusions: We have carried out the first transcriptome analysis focused on table grape seedless segregants with contrasting phenotypes for berry weight. Our findings contributed to the understanding of the mechanisms involved in berry weight determination. Also, this comparative transcriptome profiling revealed candidate genes for berry weight which could be evaluated as selection tools in table grape breeding programs.

KW - Berry weight

KW - Candidate genes

KW - Functional genomics

KW - RNA-seq

KW - Table grapes

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