Single nucleotide polymorphism mapping and alignment of recombinant chromosome substitution lines in barley

Kazuhiro Sato, Timothy J. Close, Prasanna Bhat, María Muñoz-Amatriaín, Gary J. Muehlbauer

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Single nucleotide polymorphism (SNP) genotyping is useful for assessing genetic variation in germplasm collections, genetic map development and detection of alien chromosome substitutions. In this study, a diversity analysis using 1,301 SNPs on a set of 37 barley accessions was conducted. This analysis showed a high polymorphism rate between the malting barley cultivar 'Haruna Nijo' and the food barley cultivar 'Akashinriki'. Haruna Nijo and Akashinriki are donors of the barley expressed sequence tag (EST) collections. A doubled haploid (DH) population derived from the cross between Haruna Nijo and Akashinriki was genotyped with 1,448 SNPs. Of these 1,448 SNPs, 734 were polymorphic and distributed on barley linkage groups (chromosomes) as follows: 1H (86), 2H (125), 3H (120), 4H (100), 5H (127), 6H (88) and 7H (88). By using cMAP, we integrated the SNP markers across high-density maps. The SNPs were also used to genotype 98 BC3F4 recombinant chromosome substitution lines (RCSLs) developed from the same cross (Haruna Nijo/Akashinriki). These data were used to create graphical genotypes for each line and thus estimate the location, extent and total number of introgressions from Akashinriki in the Haruna Nijo background. The 35 selected RCSLs sample most of the Akashinriki food barley genome, with only a few missing segments. These resources bring new alleles into the malting barley gene pool from food barley.

Original languageEnglish
Pages (from-to)728-737
Number of pages10
JournalPlant and Cell Physiology
Volume52
Issue number5
DOIs
Publication statusPublished - May 2011

Fingerprint

Nucleotide Mapping
substitution lines
Hordeum
single nucleotide polymorphism
Single Nucleotide Polymorphism
Chromosomes
barley
malting barley
chromosome substitution
Food
genotype
Genotype
doubled haploids
cultivars
germplasm conservation
expressed sequence tags
linkage groups
Gene Pool
introgression
genotyping

Keywords

  • Barley
  • Expressed sequence tag
  • Hordeum vulgare
  • Mapping
  • Single nucleotide polymorphism

ASJC Scopus subject areas

  • Plant Science
  • Physiology
  • Cell Biology

Cite this

Single nucleotide polymorphism mapping and alignment of recombinant chromosome substitution lines in barley. / Sato, Kazuhiro; Close, Timothy J.; Bhat, Prasanna; Muñoz-Amatriaín, María; Muehlbauer, Gary J.

In: Plant and Cell Physiology, Vol. 52, No. 5, 05.2011, p. 728-737.

Research output: Contribution to journalArticle

Sato, Kazuhiro ; Close, Timothy J. ; Bhat, Prasanna ; Muñoz-Amatriaín, María ; Muehlbauer, Gary J. / Single nucleotide polymorphism mapping and alignment of recombinant chromosome substitution lines in barley. In: Plant and Cell Physiology. 2011 ; Vol. 52, No. 5. pp. 728-737.
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