An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines

Kazuhiro Sato, Kazuyoshi Takeda

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

An oligo-nucleotide pooled assay (OPA) for high-throughput single nucleotide polymorphism (SNP) genotyping was used for genetic map development in order to coordinate marker information from multiple mapping resources in barley. A doubled haploid (DH) population derived from the cross between barley cultivar "Haruna Nijo" (Hordeum vulgare ssp. vulgare) and wild barley strain "H602" (H. vulgare ssp. spontaneum) was genotyped with 1,448 unigene-derived OPA-SNPs. Of these, 732 markers showed polymorphisms and 384 were cross-referenced with EST markers on our high-density transcript map. The OPA-SNP markers were well distributed on barley chromosomes as follows: 1H (93), 2H (131), 3H (123), 4H (97), 5H (108), 6H (92) and 7H (88). Using a cMAP platform, it was possible to integrate EST marker positions across high-density EST maps. The OPA-SNPs were used to genotype 99 BC3F5 recombinant chromosome substitution lines (RCSLs) from the same cross (Haruna Nijo/H602). These data were used to create graphical genotypes for each line and thus estimate the location, extent, and total number of introgressions from the wild barley parent. The RCSLs sampled most of the wild barley genome, with only a few missing segments. With the resources we have developed, all QTL alleles segregating in this germplasm are now potential targets for map-based cloning.

Original languageEnglish
Pages (from-to)613-619
Number of pages7
JournalTheoretical And Applied Genetics
Volume119
Issue number4
DOIs
Publication statusPublished - Aug 2009

Fingerprint

substitution lines
Chromosome Mapping
Hordeum
genotyping
single nucleotide polymorphism
chromosome mapping
Single Nucleotide Polymorphism
Chromosomes
barley
nucleotides
Expressed Sequence Tags
Nucleotides
assays
Hordeum vulgare subsp. vulgare
Hordeum vulgare subsp. spontaneum
unigenes
genotype
Genotype
doubled haploids
introgression

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Biotechnology

Cite this

@article{466c2f25eb124e94b7b37417f7f70c03,
title = "An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines",
abstract = "An oligo-nucleotide pooled assay (OPA) for high-throughput single nucleotide polymorphism (SNP) genotyping was used for genetic map development in order to coordinate marker information from multiple mapping resources in barley. A doubled haploid (DH) population derived from the cross between barley cultivar {"}Haruna Nijo{"} (Hordeum vulgare ssp. vulgare) and wild barley strain {"}H602{"} (H. vulgare ssp. spontaneum) was genotyped with 1,448 unigene-derived OPA-SNPs. Of these, 732 markers showed polymorphisms and 384 were cross-referenced with EST markers on our high-density transcript map. The OPA-SNP markers were well distributed on barley chromosomes as follows: 1H (93), 2H (131), 3H (123), 4H (97), 5H (108), 6H (92) and 7H (88). Using a cMAP platform, it was possible to integrate EST marker positions across high-density EST maps. The OPA-SNPs were used to genotype 99 BC3F5 recombinant chromosome substitution lines (RCSLs) from the same cross (Haruna Nijo/H602). These data were used to create graphical genotypes for each line and thus estimate the location, extent, and total number of introgressions from the wild barley parent. The RCSLs sampled most of the wild barley genome, with only a few missing segments. With the resources we have developed, all QTL alleles segregating in this germplasm are now potential targets for map-based cloning.",
author = "Kazuhiro Sato and Kazuyoshi Takeda",
year = "2009",
month = "8",
doi = "10.1007/s00122-009-1071-9",
language = "English",
volume = "119",
pages = "613--619",
journal = "Theoretical And Applied Genetics",
issn = "0040-5752",
publisher = "Springer Verlag",
number = "4",

}

TY - JOUR

T1 - An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines

AU - Sato, Kazuhiro

AU - Takeda, Kazuyoshi

PY - 2009/8

Y1 - 2009/8

N2 - An oligo-nucleotide pooled assay (OPA) for high-throughput single nucleotide polymorphism (SNP) genotyping was used for genetic map development in order to coordinate marker information from multiple mapping resources in barley. A doubled haploid (DH) population derived from the cross between barley cultivar "Haruna Nijo" (Hordeum vulgare ssp. vulgare) and wild barley strain "H602" (H. vulgare ssp. spontaneum) was genotyped with 1,448 unigene-derived OPA-SNPs. Of these, 732 markers showed polymorphisms and 384 were cross-referenced with EST markers on our high-density transcript map. The OPA-SNP markers were well distributed on barley chromosomes as follows: 1H (93), 2H (131), 3H (123), 4H (97), 5H (108), 6H (92) and 7H (88). Using a cMAP platform, it was possible to integrate EST marker positions across high-density EST maps. The OPA-SNPs were used to genotype 99 BC3F5 recombinant chromosome substitution lines (RCSLs) from the same cross (Haruna Nijo/H602). These data were used to create graphical genotypes for each line and thus estimate the location, extent, and total number of introgressions from the wild barley parent. The RCSLs sampled most of the wild barley genome, with only a few missing segments. With the resources we have developed, all QTL alleles segregating in this germplasm are now potential targets for map-based cloning.

AB - An oligo-nucleotide pooled assay (OPA) for high-throughput single nucleotide polymorphism (SNP) genotyping was used for genetic map development in order to coordinate marker information from multiple mapping resources in barley. A doubled haploid (DH) population derived from the cross between barley cultivar "Haruna Nijo" (Hordeum vulgare ssp. vulgare) and wild barley strain "H602" (H. vulgare ssp. spontaneum) was genotyped with 1,448 unigene-derived OPA-SNPs. Of these, 732 markers showed polymorphisms and 384 were cross-referenced with EST markers on our high-density transcript map. The OPA-SNP markers were well distributed on barley chromosomes as follows: 1H (93), 2H (131), 3H (123), 4H (97), 5H (108), 6H (92) and 7H (88). Using a cMAP platform, it was possible to integrate EST marker positions across high-density EST maps. The OPA-SNPs were used to genotype 99 BC3F5 recombinant chromosome substitution lines (RCSLs) from the same cross (Haruna Nijo/H602). These data were used to create graphical genotypes for each line and thus estimate the location, extent, and total number of introgressions from the wild barley parent. The RCSLs sampled most of the wild barley genome, with only a few missing segments. With the resources we have developed, all QTL alleles segregating in this germplasm are now potential targets for map-based cloning.

UR - http://www.scopus.com/inward/record.url?scp=68349146530&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=68349146530&partnerID=8YFLogxK

U2 - 10.1007/s00122-009-1071-9

DO - 10.1007/s00122-009-1071-9

M3 - Article

C2 - 19488734

AN - SCOPUS:68349146530

VL - 119

SP - 613

EP - 619

JO - Theoretical And Applied Genetics

JF - Theoretical And Applied Genetics

SN - 0040-5752

IS - 4

ER -