Bacterial blight and fungal blast diseases ofrice, caused by Xanthomonas oryzae pv. oryzae andPyricularia grisea Sacc., respectively, are two of the mostdevastating diseases in rice worldwide. To study thedefense responses to infection with each of thesepathogens, expression profiling of 12 defense-responsivegenes was performed using near-isogenic rice lines thatare resistant or susceptible to bacterial blight and fungalblast, respectively, and rice cultivars that are resistant orsusceptible to both pathogens. All 12 genes showedconstitutive expression, but expression levels increasedin response to infection. Based on their expression patternsin 12 host-pathogen combinations, these genescould be classified into three types, pathogen non-specific(6), pathogen specific but race non-specific (4) andrace specific (2). Most of the 12 genes were only responsiveduring incompatible interactions. These resultssuggest that bacterial blight and fungal blast resistancesshare common pathway(s), but are also regulated bydifferent defense pathways in rice. Activation of thecorresponding R gene is the key step that initiates theaction of these genes in defense responses. The chromosomallocations and pathogen specificities of seven ofthe 12 genes were consistent with those of previouslyidentified quantitative trait loci for rice disease resistance,which indicates that some of the 12 genes studiedmay have a phenotypic impact on disease resistance inrice.

Degenerated oligonucleotide primerswere used to amplify, clone, and analyze sequence heterogeneity and chromosomaldistribution of 23 PCR fragments corresponding to the reverse transcriptase domain of copia-like retrotransposonsin rice. Of the 23 fragments 22 could be aligned by their deduced amino acid sequences and were dividedinto 6 groups according to the phylogenetic and Southern blot analyses. Amino acid sequence differences among the22 aligned fragments ranged from 1 to 64%. Southern blot analysis of 10 rice accessions including indica, japonicaand common wild rice, using these 23 fragments as probes, showed that copia-like retrotransposons were presentin moderate to high copy numbers in all the rice genome although the exact copy number cannot be determined.The major difference revealed by southern analysis is a differentiation between the four indica varieties as onegroup and the four japonica varieties and the two wild rice accessions as another group. Polymorphisms were alsodetected among the indica and japonica varieties by major bands and repeatable minor bands. Five hybridizationbands were mapped to chromosomes 3, 4, 8, and 9, respectively. All the five bands were inherited in a dominantMendelian fashion and were not allelic with each other, indicating that the same element did not reside on the samelocation in different rice accessions. No transcript of the copia-like reverse transcriptase was detected on northernblot. The results suggest that the sequence heterogeneity and distributional variability of retrotransposons may beone of contributory factors causing genetic diversity in rice.

We used 22 fragments corresponding to thereverse transcriptase domain of copia-like retrotransposonsas representatives to study the organization and distributionof these elements in the rice genome. The loci detected by these22 fragments were assigned to 47 locations in the molecularlinkagemap involving all 12 chromosomes. The distributionalfeatures of copia-like retrotransposons found in the ricegenome indicated that (i) the loci detected were located mainlyin one arm of each chromosome; (ii) one fragment usuallydetected several loci that were mapped to similar locations ofdifferent chromosomes; (iii) retrotransposons sharing highidentity in nucleotide sequences were usually assigned tosimilar locations of the chromosomes; and (iv) concurrencesof multiple loci, detected by different fragments, in similarlocations or stretches of different chromosomes were commonin the rice genome. We also determined that the copy numberof copia-like retrotransposons in rice genome may be as low as'100 per haploid genome. The restricted distribution, alongwith low copy number, suggested that copia-like retrotransposonsin rice were relatively inactive during evolution comparedwith those in other plants. The distributional featuresof the copia-like retrotransposons suggested the existence ofpossible lineages among the rice chromosomes, which in turnsuggested that chromosome duplication and diversificationmay be a mechanism for the origin and evolution of the ricechromosomes. The information provided by fine mapping ofthe retroelements in the genetic linkage map may also beuseful for gene tagging and molecular cloning.

Rice blast disease, caused by the fungalpathogen Pyricularia grisea Sacc., is one of the mostdevastating crop diseases worldwide. Previous studieshave shown that the dominant blast resistance genePi-2(t) confers resistance to a broad spectrum ofpathogenic strains. Using a population of 292 recombinantinbred lines combined with bioinformatic analysis,we mapped Pi-2(t) between the SSR (simple-sequencerepeat) marker SSR140 and the RFLP (restrictionfragment length polymorphism) marker JSH12, 0.9 cMfrom both SSR140 and JSH12. A physical map consistingof six overlapping BAC (bacterial artificialchromosome) clones was anchored to the region containingthe Pi-2(t) locus. By analyzing recombinationevents in this region, the Pi-2(t) locus was localized to aDNA fragment of 118 kb in length. The detailed geneticand physical maps of the Pi-2(t) locus will facilitateboth molecular isolation of the gene and marker-assistedtransfer of the gene in breeding programs.

Comparative genomic analyses have revealed extensive colinearity ingene orders in distantly related taxa in mammals and grasses, whichopened new horizons for evolutionary study. The objective of ourstudy was to assess syntenic relationships of quantitative trait loci(QTL) for disease resistance in cereals by using a model system inwhich rice and barley were used as the hosts and the blast fungusPyricularia grisea Sacc. as the pathogen. In total, 12 QTL against threeisolates were identified in rice; two had effects on all three isolates,and the other 10 had effects on only one or two of the three isolates.Twelve QTL for blast resistance were identified in barley; one hadeffect on all three isolates, and the other 11 had effects on only oneor two of the three isolates. The observed isolate specificity led to ahypothesis about the durability of quantitative resistance commonlyobserved in many plant host-pathogen systems. Four pairs of the QTLshowed corresponding map positions between rice and barley, twoof the four QTL pairs had complete conserved isolate specificity, andanother two QTL pairs had partial conserved isolate specificity. Suchcorresponding locations and conserved specificity suggested a commonorigin and conserved functionality of the genes underlying theQTL for quantitative resistance and may have utility in gene discovery,understanding the function of the genomes, and identifying theevolutionary forces that structured the organization of the grassgenomes.