Rapid and Reliable Identification of Cucumber Fruit Length Loci by QTL-seq

Cucumber，Cucumis sativus L.(2n = 2x = 14), is a globally cultivated vegetable crop of economic importance. Fruit length is an important agronomic and domesticated trait in cucumber, which is controlled by multiple quantitative trait loci (QTL), nonetheless the underlying genetic mechanism remains unclear. In the present study, QTL-seq, a rapid identification method of plant QTLs via whole-genome resequencing was employed to explore the fruit length QTL loci based on a population of 135 F₇ recombinant inbred lines (RILs). A major QTL fl3.1 on cucumber chromosome 3 was detected through genome-wide comparison of SNP profiles between the extreme long and short fruit bulks. Four candidate genes, Csa3M180400.1 Csa3M778360.1 Csa3M778370.1 Csa3M823020.1 were discovered, of which quantitative RT-PCR results revealed significantly higher expression in long fruit genotypes. In combination with our previous QTL analysis using specific-length amplified sequencing (SLAF-seq), several minor QTLs (QTL fl1.1, fl1.2, fl1.3, fl2.1, and fl6.1) were also identified. We also demonstrate that mature fruit length is largely determined during early embryo development. Results from this study shows the benefits of QTL-seq method in rapid QTL detection and potential application in marker-assistant selection, as well as fine mapping of fruit-length related loci.

Key words: QTL-seq, whole genome re-sequencing, fruit length, Cucumis sativus L.