Identification of a seed phospholipase D null allele in rice (Oryza sativa L.) and development of SNP markers for phospholipase D deficiency

Abstract

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 F 2 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. © Crop Science Society of America.