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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #313651
Title: A sequencing-based linkage map of cucumber

Author
item ZHOU, QIAN - Xuzhou Normal University
item MIAO, HAN - Xuzhou Normal University
item LI, SHUAI - Xuzhou Normal University
item ZHANG, SHENGPING - Xuzhou Normal University
item WANG, YE - Xuzhou Normal University
item Weng, Yiqun
item ZHANG, ZHOUGHUA - Xuzhou Normal University
item HUANG, SANWEN - Xuzhou Normal University
item GU, XINGFANG - Xuzhou Normal University

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/7/2015
Publication Date: 3/10/2015
Publication URL: http://handle.nal.usda.gov/10113/60967
Citation: Zhou, Q., Miao, H., Li, S., Zhang, S., Wang, Y., Weng, Y., Zhang, Z., Huang, S., Gu, X. 2015. A sequencing-based linkage map of cucumber. Molecular Plant. 8(6):961-963.

Interpretive Summary: Genetic map is an important tool for molecular breeding, genetic mapping, gene cloning, and study of meiotic recombinations. In cucumber, the marker density, resolution and genome coverage of previously developed maps using PCR-based markers are relatively low. In the present study we developed an ultra-high density linkage map by conducting low-coverage next-generation sequencing of 147 recombinant inbred lines derived from two cultivated cucumber inbred lines. This map spanned 1,384 cM in length and consisted of 115,933 SNPs that could be grouped into 759 bins. Comparison of this genetic map and the 9930 draft genome assembly revealed more than 98% genome coverage, 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 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.

Technical Abstract: 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.