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Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (02): 191-197.doi: 10.3724/SP.J.1006.2014.00191

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

Next-generation Sequencing for Molecular Marker Development in Maize Inbred H99

LÜ Yuan-Da1,**,LI Tan1,**,SHI Li2,ZHANG Xiao-Lin1,ZHAO Han1,*   

  1. 1 Institute of Agricultural Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; 2 College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
  • Received:2013-06-03 Revised:2013-08-30 Online:2014-02-12 Published:2013-11-14
  • Contact: 赵涵, E-mail: zhaohancn@gmail.com

Abstract:

Next Generation Sequencing (NGS) has provided an effective approach to reveal the large scale of DNA polymorphic loci used as molecular markers to distinguish the genetic variations among different genotypes. Maize inbred line H99 is a common transgenic genotype with its desirable regeneration capacity. However, the genome sequence of H99 is unsequenced, which lags the molecular marker development for further maker assisted selection. Here, we used next generation sequencing to resequence H99 whole genome. The contigs assembled with SOAPdenovo2 were further scanned for potential SSR loci by MISA software. Out of 8 268 SSR loci, 4 043 site-specific primers flanking SSR loci were designed and surveyed in silico for locus polymorphism among H99, B73, and Mo17. Around 2 699 SSR loci showed the polymorphism among above three genotypes. Twenty primer pairs from 20 arms of maize chromosomes were selected and validated, and 19 primers amplified the predicted fragments. In addition, we physically mapped and annotated the polymorphic SSR loci, and elucidated the loci distribution in genome. Taken all together, the new developed SSR primers and their information, as a complement to previous ones, were expected to be beneficial to map based cloning and marker-assisted selection.

Key words: Maize inbred line H99, High throughout sequencing, ePCR, Polymorphic SSR

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