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Crop Science Abstract - Genomics, Molecular Genetics & Biotechnology

Identification of a Seed Phospholipase D Null Allele in Rice (Oryza sativa L.) and Development of SNP Markers for Phospholipase D Deficiency


This article in CS

  1. Vol. 51 No. 5, p. 2113-2118
    unlockOPEN ACCESS
    Received: Dec 20, 2010

    * Corresponding author(s): suzuyasu@affrc.go.jp
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  1. Yasuhiro Suzuki *a,
  2. Yoshinobu Takeuchia and
  3. Kenta Shirasawaab
  1. a National Agriculture and Food Research Organization (NARO), Institute of Crop Science (NICS), Kannondai, Tsukuba, Ibaraki 305-8518, Japan
    b current address: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan


Rice (Oryza sativa L.) bran usage is severely limited by the rapid degradation of rice bran oil and rapid development of hydrolytic rancidity. Because phospholipase D (PLD) disintegrates phospholipid membranes of oil bodies to deteriorate bran quality, we isolated a PLD-null rice mutant, ‘03-s108’, whose PLD-null phenotype is inherited as a single recessive trait. To develop a convenient DNA marker-assisted selection method for the PLD-null trait, we first performed a linkage analysis between the PLD-null phenotype and simple sequence repeat (SSR) markers by using F2 progeny from 03-s108 × ‘Koshihikari’ crosses, and we mapped the PLD-null genotype to chromosome 1 near a putative PLD gene sequence, PLDα1. DNA sequencing of the 03-s108 allele of PLDα1 revealed a transition mutation (G to A) in the third exon. This change resulted in a stop codon, indicating the presence of a nonsense mutation in the 03-s108 allele. Using this DNA sequence information, we then developed methods of cleaved amplified polymorphic sequence (CAPS) and dot-blot single-nucleotide polymorphism (SNP) detection for this mutation, and we confirmed that the sequence polymorphism was predictive of the presence or absence of the seed PLD-null phenotype. These CAPS and dot-blot-SNP methods are easy and cost-effective means for identifying seed PLD-null strains, to enable screening and breeding of PLD-null rice varieties.

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