Mutations in the miR396 binding site of the growth‐regulating factor gene VvGRF4 modulate inflorescence architecture in grapevine

• Published in: The Plant journal : for cell and molecular biology Vol. 101; no. 5; pp. 1234 - 1248
• Main Authors: Rossmann, Susanne, Richter, Robert, Sun, Hequan, Schneeberger, Korbinian, Töpfer, Reinhard, Zyprian, Eva, Theres, Klaus
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.03.2020
• Subjects: Alleles; Architecture; Binding Sites; Biodegradation; Botrytis - physiology; Botrytis cinerea; bunch compactness; Cloning; Clusters; CRISPR; Cultivars; Cultivation; Developmental stages; Elongation; Fruit; Fruit cultivation; Fruits; Fungicides; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene sequencing; Genomes; Grapevines; growth‐regulating factor (GRF); Inflorescence - genetics; Inflorescence - immunology; Inflorescence - microbiology; MicroRNAs - genetics; miR396; Mutation; pedicel length; Phenotype; Pinot noir; Plant breeding; Plant Diseases - immunology; Plant Diseases - microbiology; Plants, Genetically Modified; rachis length; Rot; Vitaceae; Vitis - genetics; Vitis - immunology; Vitis - microbiology; Vitis vinifera (grapevine); VvGRF4; Whole genome sequencing; pedicel length; Pinot noir; bunch compactness; rachis length; Vitis vinifera (grapevine); miR396; VvGRF4; growth-regulating factor (GRF)
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.14588

Summary Bunch rot caused by Botrytis cinerea infections is a notorious problem in grapevine cultivation. To produce high quality fruits, grapevine plants are treated with fungicides, which is cost intensive and harmful to the environment. Conversely, loose cluster bunches show a considerably enhanced physical resilience to bunch diseases. With the aim to identify genetic determinants that modulate the development of bunch architecture, we have compared loose and compact 'Pinot noir' clones. Loose cluster architecture was found to be correlated with increased berry size, elongated rachis and elongated pedicels. Using transcriptome analysis in combination with whole genome sequencing, we have identified a growth‐regulating factor gene, VvGRF4, upregulated and harbours heterozygous mutations in the loose cluster clones. At late stages of inflorescence development, the mRNA pools of loose cluster clones contain predominantly mRNAs derived from the mutated alleles, which are resistant to miR396 degradation. Expression of the VvGRF4 gene and its mutated variants in Arabidopsis demonstrates that it promotes pedicel elongation. Taken together, VvGRF4 modulates bunch architecture in grapevine 'Pinot noir' clones. This trait can be introduced into other cultivars using marker‐assisted breeding or CRISPR‐Cas9 technology. Related growth‐regulating factors or other genes of the same pathway may have similar functions. Significance Statement In grapevine, clones with loose cluster architecture show an enhanced physical resilience to Botrytis cinerea infections, however the genetic basis of this phenotype was not known. A combination of RNA‐seq and DNA‐seq analysis of 'Pinot noir' clones revealed that heterozygous mutations in the growth‐regulating factor gene VvGRF4 are associated with the loose cluster phenotype, which can be introduced into other cultivars using marker‐assisted breeding or CRISPR‐Cas9 technology.