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A Perfect Marker for Fragrance Genotyping in Rice

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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.

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Abbreviations

2AP:

2-Acetyl-1-pyrroline

ASA:

Allele specific amplification

BAD2:

Betaine aldehyde dehydrogenase 2

SNP:

Single nucleotide polymorphism

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Correspondence to Robert J. Henry.

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Bradbury, L.M.T., Henry, R.J., Jin, Q. et al. A Perfect Marker for Fragrance Genotyping in Rice. Mol Breeding 16, 279–283 (2005). https://doi.org/10.1007/s11032-005-0776-y

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  • DOI: https://doi.org/10.1007/s11032-005-0776-y

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