▪ Abstract Host plant resistance has been used extensively for disease control in many crop species; however, the resistance conferred by many sources is not durable as a result of rapid changes in the pathogen. Although many resistance genes have been identified in plant germplasm, there is no easy way to predict the quality or durability of these resistance genes. In this review, we revisit the hypothesis that resistance genes imposing a high penalty to the pathogen for adaptation will likely be durable. By elucidating the molecular changes involved in pathogen adaptation and the associated fitness cost, a proactive approach may be developed to predict the durability of resistance genes available for deployment.

Durability of plant disease resistance ( R ) genes may be predicted if the cost of pathogen adaptation to overcome resistance is understood. Adaptation of the bacterial blight pathogen, Xanthomonas oryzae pv. oryzae ( Xoo ), to virulence in rice is the result of the loss of pathogen avirulence gene function, but little is known about its effect on aggressiveness under field conditions. We evaluated the cost in pathogenic fitness (aggressiveness and persistence) associated with adaptation of Xoo to virulence on near-isogenic rice lines with single R genes ( Xa7 , Xa10 , and Xa4 ) at two field sites endemic for bacterial blight. Disease severity was high in all 3 years on all lines except the line with Xa7 . Of two Xoo lineages (groups of strains inferred to be clonally related based on DNA fingerprinting) detected, one, lineage C, dominated the pathogen population at both sites. All Xoo strains were virulent to Xa4 , whereas only lineage C strains were virulent to Xa10. Only a few strains of lineage C were virulent to Xa7 . Adaptation to virulence on Xa7 occurred through at least four different pathways and was associated with a reduction in aggressiveness. Loss of avirulence and reduced aggressiveness were associated with mutations at the 3′ terminus of the avrXa7 allele. Strains most aggressive to Xa7 were not detected after the second year, suggesting they were less persistent than less aggressive strains. These experiments support the prediction that Xa7 would be a durable R gene because of a fitness penalty in Xoo associated with adaptation to Xa7 .

The diversity of the largest group of plant disease resistance genes, the nucleotide binding site–leucine-rich repeat (NBS–LRR) genes, was examined in cereals following polymerase chain reaction (PCR) cloning and database mining. NBS–LRR genes in rice are a large and diverse class with more than 600 genes, at least three to four times the complement of Arabidopsis. Most occur in small families containing one or a few cross-hybridizing members. Unlike inArabidopsis and other dicots, the class of NBS–LRR genes coding for a Toll and mammalian interleukin-1 receptor (TIR) domain were not amplified during the evolution of the cereals. Genes coding for TIR domains are present in the rice genome, but have diverged from the NBS–LRR genes. Most cereal genes are similar in structure to the members of the non-TIR class of dicots, although many do not code for a coiled-coil domain in their amino termini. One unique class of cereal genes, with ∼50 members, codes for proteins similar to the N-termini and NBS domains of resistance genes but does not code for LRR domains. The resistance gene repertoire of grasses has changed from that of dicots in their independent evolution since the two groups diverged. It is not clear whether this reflects a difference in downstream defense signaling pathways.[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos.AF516886–AF516895.]

Effects of polyploidy in allohexaploid wheat (Triticum aestivum L.) have primarily been ascribed to increases in coding sequence variation and potential to acquire new gene functions through mutation of redundant loci. However, regulatory variation that arises through new promoter and transcription factor combinations or epigenetic events may also contribute to the effects of polyploidization. In this study, gene expression was characterized in a synthetic T. aestivum line and the T. turgidum and Aegilops tauschii parents to establish a timeline for such regulatory changes and estimate the frequency of nonadditive expression of homoeologous transcripts in newly formed T. aestivum. Large-scale analysis of nonadditive gene expression was assayed by microarray expression experiments, where synthetic T. aestivum gene expression was compared to additive model values (mid-parent) calculated from parental T. turgidum and Ae. tauschii expression levels. Approximately 16% of genes were estimated to display nonadditive expression in synthetic T. aestivum. A certain fraction of the genes (2.9%) showed overdominance or underdominance. cDNA–single strand conformation polymorphism analysis was applied to measure expression of homoeologous transcripts and further verify microarray data. The results demonstrate that allopolyploidization, per se, results in rapid initiation of differential expression of homoeologous loci and nonadditive gene expression in T. aestivum.

• Continuous planting of crops containing single disease resistance (R) genes imposes a strong selection for virulence in pathogen populations, often rendering the R gene ineffective. Increasing environmental temperatures may complicate R‐gene‐mediated disease control because high temperatures often promote disease development and reduce R gene effectiveness. Here, performance of one rice bacterial blight disease R gene was assessed in field and growth chamber studies to determine the influence of temperature on R gene effectiveness and durability. • Disease severity and virulence of Xanthomonas oryzae pv. oryzae (Xoo) populations were monitored in field plots planted to rice with and without the bacterial blight R gene Xa7 over 11 yr. The performance of Xa7 was determined in high‐ and low‐temperature regimes in growth chambers. • Rice with Xa7 exhibited less disease than lines without Xa7 over 11 yr, even though virulence of Xoo field populations increased. Xa7 restricted disease more effectively at high than at low temperatures. Other R genes were less effective at high temperatures. • We propose that Xa7 restricts disease and Xoo population size more efficiently in high temperature cropping seasons compared with cool seasons creating fluctuating selection, thereby positively impacting durability of Xa7.