Allele-specific hybridization markers for soybean

V. H. Coryell, H. Jessen, J. M. Schupp, D. Webb, Paul S Keim

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Soybean (Glycine max) is one of the world's most important crop plants due to extensive genetic improvements using traditional breeding approaches. Recently, marker-assisted selection has enhanced the ability of traditional breeding programs to improve soybeans. Most methods of assessing molecular markers involve electrophoretic techniques that constrain the ability to perform high-throughput analyses on breeding populations and germplasm. In order to develop a high-capacity system, we have developed allele-specific hybridization (ASH) markers for soybean. As one example, restriction fragment length polymorphism (RFLP) locus A519-1 (linkage group B) was converted into an ASH marker by (1) sequencing the pA519 cloned insert, (2) designing locus-specific PCR amplification primers, (3) comparative sequencing of A519-1 amplicons from important soybean ancestors, and (4) designing allele-specific oligonucleotide probes around single nucleotide polymorphisms (SNPs) among soybean genotypes. Two SNPs were identified within approximately 400 bp of the sequence. Allele-specific probes generated a 100-fold greater signal to target amplicons than to targets that differed by only a single nucleotide. The A519-1 ASH marker is shown to cosegregate with the A519-1 RFLP locus. In order to determine ASH usefulness, we genotyped 570 soybean lines from the Pioneer Hi-Bred soybean improvement using both A519-1 SNPs. Combined haplotype diversity (D) was 0.43 in this adapted germplasm set. These results demonstrate that ASH markers can allow for high-throughput screening of germplasm and breeding populations, greatly enhancing breeders' capabilities to do marker-assisted selection.

Original languageEnglish (US)
Pages (from-to)690-696
Number of pages7
JournalTheoretical And Applied Genetics
Volume98
Issue number5
DOIs
StatePublished - 1999

Fingerprint

Soybeans
hybridization
Alleles
soybeans
alleles
Breeding
single nucleotide polymorphism
Single Nucleotide Polymorphism
breeding
marker-assisted selection
loci
Restriction Fragment Length Polymorphisms
restriction fragment length polymorphism
germplasm
germplasm screening
oligonucleotide probes
Oligonucleotide Probes
linkage groups
genetic improvement
Glycine max

Keywords

  • Allele-specific hybridization
  • Glycine max
  • Marker-assisted selection
  • PCR
  • Soybean

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Horticulture
  • Plant Science
  • Genetics
  • Genetics(clinical)

Cite this

Allele-specific hybridization markers for soybean. / Coryell, V. H.; Jessen, H.; Schupp, J. M.; Webb, D.; Keim, Paul S.

In: Theoretical And Applied Genetics, Vol. 98, No. 5, 1999, p. 690-696.

Research output: Contribution to journalArticle

Coryell, V. H. ; Jessen, H. ; Schupp, J. M. ; Webb, D. ; Keim, Paul S. / Allele-specific hybridization markers for soybean. In: Theoretical And Applied Genetics. 1999 ; Vol. 98, No. 5. pp. 690-696.
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