Molecular evolution of the Pi-d2 gene conferring resistance to rice blast in Oryza

Abstract

The exploitation of plant disease resistance (R) genes in breeding programs is an effective strategy for coping with pathogens. An understanding of R gene variation is the basis for this strategy. Rice blast disease, caused by the Magnaporthe oryzae fungus, is a destructive disease of rice. The rice blast resistance gene Pi-d2 represents a new class of plant R gene because of its novel extracellular domain. We investigated the nucleotide polymorphism, phylogenetic topology and evolution patterns of the Pi-d2 gene among 67 cultivated and wild rice relatives. The Pi-d2 gene originated early in the basal Poales and has remained as a single gene without expansion. The striking finding is that susceptible Pi-d2 alleles might be derived from a single nucleotide substitution of the resistant alleles after the split of Oryza subspecies. Functional pleiotropy and linkage effects are proposed for the evolution and retention of the disease-susceptible alleles in rice populations. One set of DNA primers was developed from the polymorphic position to detect the functional nucleotide polymorphism for disease resistance of the Pi-d2 gene based on conventional Polymerase Chain Reaction. The nucleotide diversity level varied between different domains of the Pi-d2 gene, which might be related to distinct functions of each domain in the disease defense response. Directional (or purifying) selection appears dominant in the molecular evolution of the Pi-d2 gene and has shaped its conserved variation pattern.

Chromosome-level genome assembly of Hippophae tibetana provides insights into high-altitude adaptation and flavonoid biosynthesis

“…The Arabidopsis LRR-RLK IOS1 plays a critical role in pattern-triggered immunity triggered by BAK1 [29]. For rice, Pi-d2 encodes a G-type RLK protein that provides resistance to Magnaporthe grisea [30]. Two RLP genes, which encode receptorlike proteins, are also involved in contracted genes.…”

“…The average length of genes and coding sequences were 4387 bp and 1176 bp, respectively (Additional file 2: Table S2). According to mapping results, 96.8% (30,345) of the predicted genes have a corresponding function (Additional file 1: Fig. S2).…”