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

Hongfeng Lu, Tao Lin, Joel Klein, Shenhao Wang, Jianjiam Qi, Qian Zhou, Jinjing Sun, Zhonghua Zhang, Yiqun Weng, Sanwen Huang
Theoretical and applied genetics 2014 v.127 pp. 1491-1499
Arabidopsis, Cucumis sativus, agronomic traits, cucumbers, early development, flowering, gene segregation, genes, genetic markers, genotype, inbred lines, loci, marker-assisted selection, microsatellite repeats, phenology, quantitative trait loci, reverse transcriptase polymerase chain reaction, single nucleotide polymorphism
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.