A mutation in the intron splice acceptor site of a GA3ox gene confers dwarf architecture in watermelon (Citrullus lanatus L.)

Abstract

Dwarf architecture is an important trait associated with plant yield, lodging resistance and labor cost. Here, we aimed to identify a gene causing dwarfism in watermelon. The ‘w106’ (dwarf) and ‘Charleston Gray’ (vine) were used as parents to construct F1 and F2 progeny. Dwarf architecture of ‘w106’ was mainly caused by longitudinal cell length reduction and was controlled by a single recessive gene. Whole-genome sequencing of two parents and two bulk DNAs of F2 population localized this gene to a 2.63-Mb region on chromosome 9; this was further narrowed to a 541-kb region. Within this region, Cla015407, encoding a gibberellin 3β-hydroxylase (GA3ox), was the candidate gene. Cla015407 had a SNP mutation (G → A) in the splice acceptor site of the intron, leading to altered splicing event and generating two splicing isoforms in dwarf plants. One splicing isoform retained the intron sequences, while the other had a 13-bp deletion in the second exon of GA3ox transcript, both resulting in truncated proteins and loss of the functional Fe2OG dioxygenase domain in dwarf plants. RNA-Seq analysis indicated that expression of Cla015407 and other GA biosynthetic and metabolic genes were mostly up-regulated in the shoots of dwarf plants compared with vine plants in F2 population. Measurement of endogenous GA levels indicated that bioactive GA4 was significantly decreased in the shoots of dwarf plants. Moreover, the dwarf phenotype can be rescued by exogenous applications of GA3 or GA4+7, with the latter having a more distinct effect than the former. Subcellular localization analyses of GA3ox proteins from two parents revealed their subcellular targeting in nucleus and cytosol. Here, a GA3ox gene controlling dwarf architecture was identified, and loss function of GA3ox leads to GA4 reduction and dwarfism phenotype in watermelon.

Effects of gibberellins on important agronomic traits of horticultural plants

“…Subsequently, related mutation genes ( GA20ox2 and DELLA ) were identified in rice and Triticum aestivum (wheat), and GAs were shown to be involved in the semi-dwarf trait ( Peng et al., 1999 ; Sasaki et al., 2002 ). Similar results were also found in horticultural plants ( Schrager-Lavelle et al., 2019 ; Sun et al., 2020 ).…”

“…By bulked segregant analysis (BSA) and mapping, the gene responsible for ‘w106 (dwarf)’ in Citrullus lanatus (watermelon) was identified as Cla015407 encoding ClGA3ox ( Sun et al., 2020 ). Similar results were found at the same time by Gebremeskel et al.…”

Stability of watermelon phenotype characters (Citrullus lanatus (Thunb.) Matsum. & Nakai) from crossing ♀ ‘Putri Delima’ with ♂ ‘Maduri’

“…Moreover, fruit skin is one of the important qualitative phenotypic characters in watermelon breeding because it determines consumer interest. The green skin color of the watermelon is the wild type and the changes in skin color that occur are caused by evolution, artificial selections, and gene mutations (Yang et al, 2015;Li et al, 2019;Sun et al, 2020). These gene mutations occur on chromosome four with a single gene dominant pattern of inheritance (Guo et al, 2013;Dou et al, 2018).…”

Growth Repressor GmRAV Binds to the GmGA3ox Promoter to Negatively Regulate Plant Height Development in Soybean

“…In recent years, some GA-metabolic-pathway-related genes associated with plant height have been reported in plants [8,28]. For example, a loss function of GA3ox gene led to GA4 reduction and dwarfism phenotype in watermelon [29]. To further analyze the mechanism of GmRAV regulating plant height, based on our previous RNA-seq data that GA4 biosynthetic genes GmGA3ox were repressed in GmRAV-ox soybean [19], the expression levels of the GmGA3ox in the GmRAV-ox and GmRAV-RNAi transgenic soybean plants were further tested.…”