Development of recombinant inbred lines and QTL analysis of plant height and fruit shape-related traits in L.

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Zucchini ( subsp. ) stands as an economically vital crop in China. In zucchini breeding, plant architectural patterns and fruit morphological characteristics serve as pivotal traits. In this study, we employed quantitative trait locus (QTL) analysis using recombinant inbred lines (RILs) derived from two distinct inbred lines, JinGL (subsp. ) and HM-S2 (subsp. ), in conjunction with a high-density genetic map. Our investigation focused on ten QTLs associated with six horticulturally significant traits, including hypocotyl length (HL), plant height (PH), and four fruit-related traits: fruit length (FL), fruit diameter (FD), fruit shape index (FSI), and fruit weight (FW). The QTLs governing HL and PH were mapped to Chr03/LG10 and named and , respectively. The candidate gene / for was successfully identified. Additionally, three novel QTLs related to fruit size and shape were discovered. Among them, , demarcated by Marker238258 and Marker240069 on Chromosome 08/Linkage group 17 (Chr08/LG17), is a new major QTL regulating the fruit shape of zucchini. Through genomic insertion-deletion (InDel) and qRT-PCR analyses, we predicted genes within the candidate interval, uncovering and as potential candidate genes. We developed molecular markers tightly linked to and and validated them in 171 and 224 germplasms, achieving accuracy rates of 96% and 100%, respectively. This study deepens our understanding of the genetic basis of key traits and provides valuable references for molecular breeding in .

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11032-025-01592-y.