Potential of Waxy gene microsatellite and single-nucleotide polymorphisms to develop japonica varieties with desired amylose levels in rice (Oryza sativa L.)

P. Jayamani, S. Negrão, C. Brites, M. M. Oliveira*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

The Waxy (Wx) gene is responsible for the synthesis of amylose, a key determinant of the cooking and processing qualities of rice. Polymorphisms of CT-microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene and their relationship to amylose content (Ac) were explored using 178 non-waxy rice genotypes. Nine Wx microsatellite alleles, namely (CT)10 and 11, and (CT)14-20 were identified and 11 haplotypes were recognised by different combinations of CT-microsatellite and G-T SNP. Amylose content analysed in a random set of 39 genotypes was correlated with different microsatellite alleles/haplotypes. The highest Ac levels (>30%) correlated with (CT)10 and 16, high (26-30%) with (CT)11, 15 and 20, and intermediate (21-25%) with (CT)14, in all cases with G at the G-T SNP. The CT-classes (CT)17 and 18 (mean Ac value of 21%), could be subdivided into low amylose haplotypes (16-20%) for 17T and 18T and intermediate amylose haplotypes (21-25%) for 17G and 18G. The use of haplotypes proved to discriminate between intermediate and low amylose accessions within the same microsatellite class. Analyses of a segregating population of a cross between low and high Ac parents showed that CT-microsatellite may help to classify breeding lines and identify pollen contamination. We suggest that CT-microsatellite together with G-T SNP may be used as molecular marker by breeders to develop varieties with desired amylose levels.

Original languageEnglish (US)
Pages (from-to)178-186
Number of pages9
JournalJournal of Cereal Science
Volume46
Issue number2
DOIs
StatePublished - Sep 2007
Externally publishedYes

Keywords

  • Amylose content
  • Microsatellite
  • Rice
  • Single-nucleotide polymorphism
  • Waxy gene

ASJC Scopus subject areas

  • Food Science
  • Biochemistry

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