Transcriptome profiling of grapevine seedless segregants during berry development reveals candidate genes associated with berry weight.
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 6-8 mm 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.
Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile.|Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. Repúbica 217, Santiago, Chile.|Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.
Claudia
C
Muñoz-Espinoza
Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, University of Chile, Av. Blanco Encalada 2120, 7th Floor, Santiago, Chile.|Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.
Alex
A
Di Genova
Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile.
José
J
Correa
Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile.
Romina
R
Silva
Center for Mathematical Modeling (UMI2807-CNRS) and Department of Mathematical Engineering, Faculty of Mathematical and Physical Sciences, University of Chile, Av. Blanco Encalada 2120, 7th Floor, Santiago, Chile.|Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.
Alejandro
A
Maass
Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile.
Mauricio
M
González-Agüero
Centro de Biotecnología Vegetal, Universidad Andrés Bello, Av. Repúbica 217, Santiago, Chile.|Center for Genome Regulation, Av. Blanco Encalada 2085, 3rd floor, Santiago, Chile.
Ariel
A
Orellana
Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11, 610, Santiago, Chile. phinrichsen@inia.cl.
Patricio
P
Hinrichsen
D016000:Cluster Analysis; D005638:Fruit / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics; D005838:Genotype; D010641:Phenotype; D000069600:Plant Breeding / Q000379:methods; D025341:Principal Component Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000235:genetics / Q000254:growth & development / Q000502:physiology; D017423:Sequence Analysis, RNA / Q000379:methods; D027843:Vitis / Q000235:genetics* / Q000254:growth & development / Q000502:physiology
Berry weight; Candidate genes; Functional genomics; RNA-seq; Table grapes