Functional & Integrative Genomics

, Volume 8, Issue 3, pp 223–233

EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome

  • R. Kota
  • R. K. Varshney
  • M. Prasad
  • H. Zhang
  • N. Stein
  • A. Graner
Original Paper

DOI: 10.1007/s10142-007-0060-9

Cite this article as:
Kota, R., Varshney, R.K., Prasad, M. et al. Funct Integr Genomics (2008) 8: 223. doi:10.1007/s10142-007-0060-9

Abstract

In a panel of seven genotypes, 437 expressed sequence tag (EST)-derived DNA fragments were sequenced. Single nucleotide polymorphisms (SNPs) that were polymorphic between the parents of three mapping populations were mapped by heteroduplex analysis and a genome-wide consensus map comprising 216 EST-derived SNPs and 4 InDel (insertion/deletion) markers was constructed. The average frequency of SNPs amounted to 1/130 bp and 1/107.8 bp for a set of randomly selected and a set of mapped ESTs, respectively. The calculated nucleotide diversities (π) ranged from 0 to 40.0 × 10−3 (average 3.1 × 10−3) and 0.52 × 10−3 to 39.51 × 10–3 (average 4.37 × 10−3) for random and mapped ESTs, respectively. The polymorphism information content value for mapped SNPs ranged from 0.24 to 0.50 with an average of 0.34. As expected, combination of SNPs present in an amplicon (haplotype) exhibited a higher information content ranging from 0.24 to 0.85 with an average of 0.50. Cleaved amplified polymorphic sequence assays (including InDels) were designed for a total of 87 (39.5%) SNP markers. The high abundance of SNPs in the barley genome provides avenues for the systematic development of saturated genetic maps and their integration with physical maps.

Keywords

Molecular markersSNPsHaplotype diversityNucleotide diversityGenetic map

Supplementary material

10142_2007_60_MOESM1_ESM.html.
Table ESM 1Details on development and characterization of SNP markers (HTML 360 kb)
10142_2007_60_MOESM2_ESM.doc (83 kb)
Table ESM 2Informative set of SNP markers for haplotype analysis and CAPS assays (DOC 83 kb)

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • R. Kota
    • 1
    • 5
  • R. K. Varshney
    • 2
    • 5
  • M. Prasad
    • 3
    • 5
  • H. Zhang
    • 4
    • 5
  • N. Stein
    • 5
  • A. Graner
    • 5
  1. 1.Plant Disease Resistance GroupCSIRO–Plant IndustryCanberraAustralia
  2. 2.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)PatancheruIndia
  3. 3.National Institute for Plant Genome Research (NIPGR)New DelhiIndia
  4. 4.Laboratory of Molecular Plant PhysiologyUniversity of FloridaGainesvilleUSA
  5. 5.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany