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Molecular Breeding

, Volume 32, Issue 4, pp 977–980 | Cite as

Cot-based sampling of genomes for polymorphic low-copy DNA

  • Junkang Rong
  • Jon S. Robertson
  • Stefan R. Schulze
  • Andrew H. Paterson
Short communication
  • 173 Downloads

Abstract

DNA polymorphisms are powerful tools for many evolutionary and genomic studies in plants including molecular breeding. Single nucleotide polymorphisms (SNPs) are the most elemental DNA marker for genomic studies, but even with advances in DNA sequencing technology, SNP discovery remains costly and computationally demanding, especially in large genomes that are rich in repetitive DNA such as those of many plants. Here we report a method using DNA renaturation kinetics (Cot techniques), sequencing, and BLAST-based screening to identify low-copy, non-coding DNA sequences that were subsequently found to be relatively rich in polymorphisms. A total of of 63 such fragments isolated from a diploid D genome cotton species (Gossypium raimondii) revealed a higher frequency of polymorphisms than that observed for cotton expressed sequence tags or hypomethylated (PstI-susceptible) genomic DNA. While microsatellite-derived loci show still higher polymorphism rates, they often fall in repetitive elements and their sequence analysis is often complicated by alignment difficulties. The potential applications of Cot-filtered noncoding (CFNC) DNA in development of DNA markers are discussed.

Keywords

Cotton SNP Cot DNA Marker 

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Junkang Rong
    • 1
    • 2
  • Jon S. Robertson
    • 1
  • Stefan R. Schulze
    • 1
  • Andrew H. Paterson
    • 1
  1. 1.Plant Genome Mapping LaboratoryUniversity of GeorgiaAthensUSA
  2. 2.School of Agriculture and Food ScienceZhejiang A and F UniversityZhejiangPeople’s Republic of China

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