McATL43 encoding a RING-H2 finger E3 ubiquitin ligase is responsible for Shark teeth (St) fruit wart in bitter gourd (Momordica charantia L.).

Abstract

Key message: Fine mapping and cloning identified a 2-bp deletion within the McATL43 gene, which encodes a RING-H2 finger E3 ubiquitin ligase, resulting in a loss-of-function mutation and smooth fruit wart phenotype in bitter gourd. Fruit wart morphology, defined by the size and arrangement of ridges and tubercles, significantly affects the commercial value of bitter gourd (Momordica charantia L.). Through QTL mapping using accessions that differ in fruit wart feature, we previously identified two major loci, fwf4.1 and fwf6.1, which together explain most of the phenotypic variation. Here, we show that fwf6.1 dominantly controls a tooth-shaped wart pattern, and therefore is named Shark teeth (St). Using a segregating BC₁F₂ population, we narrowed the St locus to a 19.23-kb interval containing six annotated genes. Among them, McATL43, encoding a RING-H2 finger E3 ubiquitin ligase, emerged as the best candidate. A 2-bp deletion in the single exon of the smooth-wart allele causes a frameshift and premature stop codon, likely disrupting the C-terminal substrate recognition domain. A diagnostic marker based on this deletion accurately distinguishes St and smooth-wart (wild-type, WT) alleles across 40 diverse accessions, indicating its potential use for marker-assisted selection. Subcellular localization showed that McATL43 is present in both the plasma membrane and cytosol. Phylogenic analysis also revealed that its homologs in cucurbits contain a cucurbit-specific signal peptide. Transcriptome profiling of homozygous BC₁F₃ plants indicated that McATL43-associated networks are involved in stimulus responses, auxin signaling, and transcriptional regulation. These findings provide a molecular basis for the genetic control of fruit wart morphology in bitter gourd and offer a valuable tool for breeding programs targeting improved fruit appearance.