Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research Unit

Title: QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber

Authors
item Lu, Hongfeng -
item Lin, Tao -
item Klein, Joel -
item Wang, Shenhao -
item Qi, Jianjian -
item Zhou, Qain -
item Sun, Jinjing -
item Zhang, Zhonghua -
item WENG, YIQUN
item Huang, Sanwen -

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 10, 2014
Publication Date: May 21, 2014
Repository URL: http://handle.nal.usda.gov/10113/58983
Citation: Lu, H., Lin, T., Klein, J., Wang, S., Zhou, Q., Sun, J., Weng, Y., Huang, S. 2014. QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber. Theoretical and Applied Genetics. 127(7):1491-1499.

Interpretive Summary: New high throughput next-generation sequencing technologies are making it faster and more efficient to establish the association of agronomic traits with molecular markers or candidate genes, which is the requirement for marker-assisted selection in molecular breeding. Early flowering is an important agronomic trait for cucumber breeding, but the underlying genetic mechanism is unknown. In this study, we identified a candidate gene for early flowering gene Ef1.1 through whole genome resequencing based QTL (quantitative trait loci) analysis (QTL-Seq). Phenotypic analysis in segregating F2 and BC1 populations derived from a cross between an early and late flowering inbred lines suggested quantitative nature of flowering time in cucumber. Genome wide comparison of single nucleotide polymorphism (SNP) profiles between the early and late flowering bulks identified a major QTL (Ef1.1) on cucumber chromosome 1 for early flowering, which was confirmed with microsatellite marker-based classical QTL mapping in the F2 population. Joint QTL-Seq and traditional QTL analysis delimited Ef1.1 to a 930 kb genomic region. A cucumber gene was identified in this region, which is a homolog of the FLOWERING LOCUS T (FT), the main flowering switch gene in Arabidopsis. Quantitative RT-PCR of the expression level of this candidate gene revealed significantly higher expression in early flowering genotypes. Data presented herein support this FT homolog as a possible candidate gene for early flowering in cucumber.

Technical Abstract: Next-generation sequencing (NGS) technologies are making it faster and more efficient to establish the association of agronomic traits with molecular markers or candidate genes, which is the requirement for marker-assisted selection in molecular breeding. Early flowering is an important agronomic trait in cucumber (Cucumis sativus L.), but the underlying genetic mechanism is unknown. In this study, we identified a candidate gene for early flowering QTL, Ef1.1 through QTL-seq. Segregation analysis in F2 and BC1 populations derived from a cross between two inbred lines “Muromskij” (early flowering) and “9930” (late flowering) suggested quantitative nature of flowering time in cucumber. Genome wide comparison of SNP profiles between the early and late flowering bulks constructed from F2 plants identified a major QTL, designated Ef1.1 on cucumber chromosome 1 for early flowering in Muromskij, which was confirmed with microsatellite marker-based classical QTL mapping in the F2 population. Joint QTL-Seq and traditional QTL analysis delimited Ef1.1 to a 930 kb genomic region. A cucumber gene, Csa1G651710, was identified in this region, which is a homolog of the FLOWERING LOCUS T (FT), the main flowering switch gene in Arabidopsis. Quantitative RT-PCR of the expression level of Csa1G651710 revealed significantly higher expression in early flowering genotypes. Data presented herein support Csa1G651710 as a possible candidate gene for early flowering in cucumber.

Last Modified: 9/10/2014
Footer Content Back to Top of Page