Molecular Breeding

, Volume 16, Issue 4, pp 279–283 | Cite as

A Perfect Marker for Fragrance Genotyping in Rice

  • Louis M. T. Bradbury
  • Robert J. Henry
  • Qingsheng Jin
  • Russell F. Reinke
  • Daniel L.E. Waters
Article

Abstract

Allele specific amplification (ASA) is a low-cost, robust technique that can be utilised to discriminate between alleles that differ by SNP's, insertions or deletions, within a single PCR tube. Fragrance in rice, a recessive trait, has been shown to be due to an eight bp deletion and three SNP's in a gene on chromosome 8 which encodes a putative betaine aldehyde dehydrogenase 2 (BAD2). Here we report a single tube ASA assay which allows discrimination between fragrant and non-fragrant rice varieties and identifies homozygous fragrant, homozygous non-fragrant and heterozygous non-fragrant individuals in a population segregating for fragrance. External primers generate a fragment of approximately 580 bp as a positive control for each sample. Internal and corresponding external primers produce a 355 bp fragment from a non-fragrant allele and a 257 bp fragment from a fragrant allele, allowing simple analysis on agarose gels.

Keywords

Aromatic Assay Basmati High-throughput Jasmine Oryza sativa 

Abbreviations

2AP

2-Acetyl-1-pyrroline

ASA

Allele specific amplification

BAD2

Betaine aldehyde dehydrogenase 2

SNP

Single nucleotide polymorphism

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References

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Copyright information

© Springer 2005

Authors and Affiliations

  • Louis M. T. Bradbury
    • 1
    • 2
  • Robert J. Henry
    • 1
    • 2
  • Qingsheng Jin
    • 1
    • 3
  • Russell F. Reinke
    • 4
  • Daniel L.E. Waters
    • 1
  1. 1.Centre for Plant Conservation GeneticsSouthern Cross UniversityLismoreAustralia
  2. 2.Grain Foods CRCSouthern Cross UniversityLismoreAustralia
  3. 3.Crop Research InstituteZhejiang Academy of Agricultural SciencesHangzhouChina
  4. 4.Yanco Agricultural InstituteYancoAustralia

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