High resolution agarose-based system for single-tube genotvping of fgr and Waxy genes in rice

MAGE to displace PAGE?

Acga Cheng, Festo Massawe, Ismanizan Ismail, Mohamad Osman, Habibuddin Hashim

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Aroma and amylose content are the key determinants of grain quality and commercial value in rice (Oryza sativa L.). Here, we report a novel agarose-based multiplex polymerase chain reaction (PCR)-assay for the unambiguous identification of genes controlling aroma (fgr) and amylose content (Wx) traits in rice. The multiplex assay was developed following the validation of two previously reported gene-specific primers, namely, the fgr-SNP and Wx-SSR. Twenty aromatic and non-aromatic rice genotypes with a wide range of variation in amylose content were used in this study. Optimization of primer concentration and critical parameters for thermal cycling, inclusive of cycle number and annealing temperature, were performed to obtain optimal results for the multiplex amplification. The resulting amplification products displayed well-differentiated allelic variants of both fgr and Wx genes on a 3% MetaPhor agarose gel, at the cost of less than $0.15 per sample. MetaPhor agarose gel electrophoresis (MAGE) was effectively employed as a genotyping method which offers an alternative to polyacrylamide gel electrophoresis (PAGE); a system, commonly used in rice research, that can be technically challenging and time-consuming. Without the need of expensive probes or specialized equipment, this newly developed multiplex assay is suitable for researchers, whose studies are dependent on mass genotyping, and in molecular laboratories with limited resources.

Original languageEnglish
Pages (from-to)348-352
Number of pages5
JournalPlant OMICS
Volume8
Issue number4
Publication statusPublished - 2015

Fingerprint

agarose
gel electrophoresis
polyacrylamide gel electrophoresis
amylose
rice
genotyping
assays
genes
odors
annealing
probes (equipment)
aromatic compounds
Oryza sativa
researchers
polymerase chain reaction
gels
heat
genotype
temperature
sampling

Keywords

  • Amylose content
  • Aroma
  • Fgr gene
  • Metaphor agarose gel electrophoresis
  • Multiplex PCR
  • Rice
  • Waxy gene

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science

Cite this

High resolution agarose-based system for single-tube genotvping of fgr and Waxy genes in rice : MAGE to displace PAGE? / Cheng, Acga; Massawe, Festo; Ismail, Ismanizan; Osman, Mohamad; Hashim, Habibuddin.

In: Plant OMICS, Vol. 8, No. 4, 2015, p. 348-352.

Research output: Contribution to journalArticle

Cheng, Acga ; Massawe, Festo ; Ismail, Ismanizan ; Osman, Mohamad ; Hashim, Habibuddin. / High resolution agarose-based system for single-tube genotvping of fgr and Waxy genes in rice : MAGE to displace PAGE?. In: Plant OMICS. 2015 ; Vol. 8, No. 4. pp. 348-352.
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