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A Sequencing-Based Linkage Map of Cucumber

Qian Zhou, Han Miao, Shuai Li, Shengping Zhang, Ye Wang, Yiqun Weng, Zhonghua Zhang, Sanwen Huang, Xingfang Gu
Molecular plant 2015 v.8 no.6 pp. 961-963
Cucumis sativus, chromosome mapping, cucumbers, genes, genetic markers, genome assembly, inbred lines, loci, molecular cloning, plant breeding, polymerase chain reaction, quantitative trait loci, segregation distortion, single nucleotide polymorphism
Genetic maps are important tools for molecular breeding, gene cloning, and study of meiotic recombination. In cucumber (Cucumis sativus L.), the marker density, resolution and genome coverage of previously developed genetic maps using PCR-based molecular markers are relatively low. In this study we generated an ultra-high density linkage map by conducting low-coverage sequencing of 147 recombinant inbred lines (RILs) derived from two cultivated cucumber inbred lines. This map spanned 1384.4 cM in length and consisted of 115,933 SNPs that were grouped into 759 bins. Comparison of the genetic map and the 9930 draft genome assembly revealed more than 98% genome coverage of this map, and a high degree of concordance between marker orders and their physical locations. An assembly error of nine scaffolds in chromosome 5 was detected. Genomic regions with high recombination frequency and segregation distortion were also identified. The quality of the map was authenticated by refining the map locations of several horticulturally important genes or quantitative loci (QTLs) of cucumber that were previously mapped including a cluster of genes in chromosome 5 for fruit epidermal features. This high-density genetic map should be a valuable tool for molecular breeding in cucumber and facilitate our understanding of cucumber genetics.