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Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (03): 397-404.doi: 10.3724/SP.J.1006.2014.00397

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Development and Genetic Mapping of SNP Markers via Genome Complexity Reduction in Tobacco

XIAO Bing-Guang1,*,QIU Jie2,CAO Pei-Jian3,GUI Yi-Jie2,LU Xiu-Ping1,LI Yong-Ping1,FAN Long-Jiang2   

  1. 1 Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China; 2 Department of Agronomy, Zhejiang University, Hangzhou 310058, China;
    3 China Tobacco Gene Research Center, Zhengzhou 450001, China
  • Received:2013-07-11 Revised:2013-11-28 Online:2014-03-12 Published:2014-01-16
  • Contact: 肖炳光, E-mail: xiaobg@263.net E-mail:肖炳光, E-mail: xiaobg@263.net

Abstract:

We proposed an approach for development of the SNP markers via genome complexity reduction in this study. The restriction enzymes were employed to digest target genome and then collect and sequence the fragments flanking the restriction sites by next-generation sequencing platform. A bioinformatics pipeline was developed for the SNP calling. A flue-cured tobacco DH population was used as a case to test the approach. The tobacco representative fragments were collected via a genome complexity reduction method and sequenced by using Illumina GA sequencer. A total of 1015 SNPs were found based on 11.4 Gb Illumina data using the bioinformatics pipeline. Taken available SSR markers (as backbone markers) together, a genetic linkage map with 1 307 molecular markers was constructed. Large-scale inter-chromosomal (linkage group) DNA combinations or exchanges and several homologous pairs among the tobacco 24 chromosomes were detected based on the genetic map and the available genomic sequences of two tobacco (Nicotiana tabacum L.) wild progenitors.

Key words: Flue-cured tobacco, SNP marker, Genome complexity reduction, Restriction enzyme, Genetic map

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