Abstract
The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes.
Highlights
Cucumber, Cucumis sativus L. (2n = 2x = 14), originates from the southern Himalayas and has been cultivated in India for at least 3000 years
Given the complex genetic basis of quantitative traits plus influences caused by different mapping population and environments, additional efforts are still needed to screen for reliable QTL regions and identify candidate genes
The results indicate that factors regulating fruit length are largely determined pre-anthesis and that ovary length (OvL) is a good predictor for FL and MFL
Summary
Using RIL populations developed from North China type ×semi-wild cucumber inbred lines, Bo et al.[10] detected 5 QTLs for MFL (fl1.1, fl3.1, fl4.1, fl6.1, and fl7.1). Weng et al.[2] performed QTL analysis with three QTL models and multiple populations, detecting 29 consistent and distinct QTLs for fruit size/shape in different developing stages. Given the complex genetic basis of quantitative traits plus influences caused by different mapping population and environments, additional efforts are still needed to screen for reliable QTL regions and identify candidate genes. QTL-seq is proposed as an efficient strategy for rapid identification of QTLs, which takes advantage of bulked-segregant analysis and high-throughput genotyping using next-generation sequencing (NGS) This approach has been applied to detecting QTLs in rice, cucumber, tomato, and chickpea[15,16,17,18,19]. The expression levels of candidate genes localized in a consensus QTL region on chromosome 3 were analysed by quantitative RT-PCR
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