Phenotypic Characterization and Fine Mapping of a Major-Effect Fruit Shape QTL FS5.2 in Cucumber, Cucumis sativus L., with Near-Isogenic Line-Derived Segregating Populations

Abstract

Cucumber (<i>Cucumis sativus</i> L.) fruit size/shape (FS) is an important yield and quality trait that is quantitatively inherited. Many quantitative trait loci (QTLs) for fruit size/shape have been identified, but very few have been fine-mapped or cloned. In this study, through marker-assisted foreground and background selections, we developed near-isogenic lines (NILs) for a major-effect fruit size/shape QTL <i>FS5.2</i> in cucumber. Morphological and microscopic characterization of NILs suggests that the allele of <i>fs5.2</i> from the semi-wild Xishuangbanna (XIS) cucumber (<i>C</i>. <i>s</i>. var. <i>xishuangbannesis</i>) reduces fruit elongation but promotes radial growth resulting in shorter but wider fruit, which seems to be due to reduced cell length, but increased cellular layers. Consistent with this, the NIL carrying the homozygous XIS allele (<i>fs5.2</i>) had lower auxin/IAA contents in both the ovary and the developing fruit. Fine genetic mapping with NIL-derived segregating populations placed <i>FS5.2</i> into a 95.5 kb region with 15 predicted genes, and a homolog of the Arabidopsis <i>CRABS CLAW</i> (<i>CsCRC</i>) appeared to be the most possible candidate for <i>FS5.2</i>. Transcriptome profiling of NIL fruits at anthesis identified differentially expressed genes enriched in the auxin biosynthesis and signaling pathways, as well as genes involved in cell cycle, division, and cell wall processes. We conclude that the major-effect QTL <i>FS5.2</i> controls cucumber fruit size/shape through regulating auxin-mediated cell division and expansion for the lateral and longitudinal fruit growth, respectively. The gibberellic acid (GA) signaling pathway also plays a role in <i>FS5.2</i>-mediated fruit elongation.