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Genome-Wide Single-Nucleotide Polymorphisms Discovery and High-Density Genetic Map Construction in Cauliflower Using Specific-Locus Amplified Fragment Sequencing.

Authors
  • Zhao, Zhenqing1
  • Gu, Honghui1
  • Sheng, Xiaoguang1
  • Yu, Huifang1
  • Wang, Jiansheng1
  • Huang, Long2
  • Wang, Dan2
  • 1 Institute of Vegetables, Zhejiang Academy of Agricultural Sciences Hangzhou, China. , (China)
  • 2 Biomarker Technologies Corporation Beijing, China. , (China)
Type
Published Article
Journal
Frontiers in Plant Science
Publisher
Frontiers Media SA
Publication Date
Jan 01, 2016
Volume
7
Pages
334–334
Identifiers
DOI: 10.3389/fpls.2016.00334
PMID: 27047515
Source
Medline
Keywords
License
Unknown

Abstract

Molecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequencing strategy was employed for large-scale single nucleotide polymorphism (SNP) discovery and high-density genetic map construction in a double-haploid, segregating population of cauliflower. A total of 12.47 Gb raw data containing 77.92 M pair-end reads were obtained after processing and 6815 polymorphic SLAFs between the two parents were detected. The average sequencing depths reached 52.66-fold for the female parent and 49.35-fold for the male parent. Subsequently, these polymorphic SLAFs were used to genotype the population and further filtered based on several criteria to construct a genetic linkage map of cauliflower. Finally, 1776 high-quality SLAF markers, including 2741 SNPs, constituted the linkage map with average data integrity of 95.68%. The final map spanned a total genetic length of 890.01 cM with an average marker interval of 0.50 cM, and covered 364.9 Mb of the reference genome. The markers and genetic map developed in this study could provide an important foundation not only for comparative genomics studies within Brassica oleracea species but also for quantitative trait loci identification and molecular breeding of cauliflower.

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