Theoretical and Applied Genetics

, Volume 120, Issue 5, pp 1063–1071 | Cite as

Fine mapping the soybean aphid resistance gene Rag1 in soybean

  • Ki-Seung Kim
  • Stephanie Bellendir
  • Karen A. Hudson
  • Curtis B. Hill
  • Glen L. Hartman
  • David L. Hyten
  • Matthew E. Hudson
  • Brian W. Diers
Original Paper

Abstract

The soybean aphid (Aphis glycines Matsumura) is an important soybean [Glycine max (L.) Merr.] pest in North America. The dominant aphid resistance gene Rag1 was previously mapped from the cultivar ‘Dowling’ to a 12 cM marker interval on soybean chromosome 7 (formerly linkage group M). The development of additional genetic markers mapping closer to Rag1 was needed to accurately position the gene to improve the effectiveness of marker-assisted selection (MAS) and to eventually clone it. The objectives of this study were to identify single nucleotide polymorphisms (SNPs) near Rag1 and to position these SNPs relative to Rag1. To generate a fine map of the Rag1 interval, 824 BC4F2 and 1,000 BC4F3 plants segregating for the gene were screened with markers flanking Rag1. Plants with recombination events close to the gene were tested with SNPs identified in previous studies along with new SNPs identified from the preliminary Williams 82 draft soybean genome shotgun sequence using direct re-sequencing and gene-scanning melt-curve analysis. Progeny of these recombinant plants were evaluated for aphid resistance. These efforts resulted in the mapping of Rag1 between the two SNP markers 46169.7 and 21A, which corresponds to a physical distance on the Williams 82 8× draft assembly (Glyma1.01) of 115 kilobase pair (kb). Several candidate genes for Rag1 are present within the 115-kb interval. The markers identified in this study that are closely linked to Rag1 will be a useful resource in MAS for this important aphid resistance gene.

Abbreviations

bp

Base pair

kb

Kilobase pair

LG

Linkage group

MAS

Marker-assisted selection

MCA

Melting curve assay

PCR

Polymerase chain reaction

SSR

Simple sequence repeat

SNP

Single nucleotide polymorphism

STS

Sequence tagged site

Supplementary material

122_2009_1234_MOESM1_ESM.doc (46 kb)
Supplementary tables (DOC 47 kb)

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Ki-Seung Kim
    • 1
  • Stephanie Bellendir
    • 1
  • Karen A. Hudson
    • 2
  • Curtis B. Hill
    • 1
  • Glen L. Hartman
    • 3
  • David L. Hyten
    • 4
  • Matthew E. Hudson
    • 1
  • Brian W. Diers
    • 1
  1. 1.Department of Crop SciencesUniversity of IllinoisUrbanaUSA
  2. 2.USDA-ARSPurdue UniversityWest LafayetteUSA
  3. 3.USDA-ARSUniversity of IllinoisUrbanaUSA
  4. 4.Soybean Genomics and Improvement LaboratoryUSDA-ARSBeltsvilleUSA

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