Somatic cell mutagenesis in Drosophila: recovery of genetic damage in relation to the types of DNA lesions induced in mutationally unstable and stable X-chromosomes

This paper reports the results of a study on the genotoxic activities of 12 mutagens and clastogens of widely differing mode of action in somatic cells in vivo, i.e., in the eye primordia of Drosophila larvae. After emergence, adult flies were monitored for aberrantly colored sectors in the compound eyes of the following genotypes: UZ males and females (zeste) carrying a genetically unstable transposable element, SZ males and females (zeste) carrying a partial duplication of the w+ locus plus a transposon insert, white-coral/white (wco/w) females, w+/w females and w+ males. The UZ and SZ marker sets make it possible to monitor shifts from zeste to red (scored as mosaic red spots, RS) and for loss of the white locus (light spots, LS). wco/w+ females were scored for mosaic twin spots (TS) and LS, w+ genotypes for just LS. The genotoxins analyzed were methyl methanesulfonate (MMS), dimethyl sulfate (DMS) and ethylnitrosourea (ENU) (alkylating), adriamycin (AM) and daunomycin (DM) (intercalating), Trenimon, Thio-TEPA and cisplatin (DDP) (cross-linking), bleomycin (strand-breaking), 7,12-dimethylbenz[a]anthracene (DMBA) and 9,10-dimethylanthracene (DA) (bulky monoadducts) and cytosine arabinofuranoside (inhibition of DNA synthesis). The relative mutabilities with frequencies of mosaic light spots (LS) in w+/w female as the standard (relative mutability = 1) vs. genotypes UZ (RS in male) vs. SZ (RS in male) vs. w+ (LS in male) were 1:0.6:0.2:0.3 for MMS, 1:0.09:0.05:0.7 for DDP, and 1:1.6:0.2:1.0 for ENU, ENU showed exceptional behavior in that it was the only compound for which mutational response, measured by the induction of red spots, was highest with the UZ marker set. Occurrence of large light spots (LS) in male but not in female genotypes was negatively correlated with efficiency of agents for chromosomal damage, suggesting that in the hemizygous condition, as in males, selection of damaged cells and mitotic delay may have played a significant role. In general, the results indicate that there is no association between the ability of an agent to act as a clastogen and the recovery of aberrant (red spots) sectors in either the UZ or the SZ strain, and of single light spots (LS) in w+, UZ and SZ males. The possibility is considered that the process causing the genetic instability in the UZ strain is under genetic control, and that strong point mutagens such as ENU through efficient gene mutation induction can interfere with it.     

DNA Repair Dependence of Somatic Mutagenesis of Transposon-Caused WHITE Alleles in DROSOPHILA MELANOGASTER after Treatment with Alkylating Agents

DNA repair-defective alleles of the mei-9, mei-41, mus-104 and mus-101 loci of Drosophila melanogaster were introduced into stocks bearing the UZ and SZ marker sets. Males with the UZ marker set, z1 (zeste allele) and w+(TE) (genetically unstable white allele presumably caused by a transposable element), or the SZ marker set, z1 and w+R (semistable white allele caused by partial duplication of the w+ locus plus transposon insert), were exposed to EMS at the first instar. After emergence, adult males bearing red spots on lemon-yellow eyes were scored as flies with somatic reversions of w+(TE) or w+R. The relative mutabilities (relative values of reversion frequency at an equal EMS dose) of either w+(TE) or w+R in a repair-proficient strain and in mei-9, mei-41, mus-104 and mus-101 strains were 1: approximately 1.2:0.3:0.3:0.7, despite the fact that w+(TE) reverted two to three times as frequently as w+R under both the repair-proficient and repair-deficient genetic conditions. Similarly, after treatment with MMS, MNNG and ENNG, w+(TE) was somatically more mutable in the mei-9 strain and less mutable in the mei-41 and mus-104 strains than in the repair-proficient strain. From these results, we propose that mutagenic lesions produced in DNA by treatment with these chemicals are converted to mutant DNA sequences via the error-prone repair mechanisms dependent on the products of the genes mei-41+ (mei-41 and mus-104 being alleles of the same locus) and mus-101+, whereas they are eliminated by mei-9+-dependent excision repair. In contrast to the approximately linear responses of induced reversions of w+(TE) with ENNG in the repair-proficient, mei-9, and mei-41 strains, seemingly there were dosage insensitive ranges for induced reversion with MNNG in the repair-proficient and mei-41 strains, but not for reversion in the mei-9 strain; w+(TE) in the mus-104 strain was virtually nonmutable with MNNG and ENNG. These results suggest that O6-methylguanine (O6MeG) produced in DNA with MNNG, but not O6-ethylguanine produced with ENNG, is almost completely repaired in a low dose range by constitutive activity of DNA O6MeG transmethylase. From the distribution of clone sizes of spontaneous revertant spots and other data, we propose that both w+(TE) and w+R have a similar tendency to spontaneously revert more frequently at early rather than at later developmental stages probably reflecting a common property of their inserted transposons.     

Elucidation of <Emphasis Type="Italic">veA</Emphasis>-dependent genes associated with aflatoxin and sclerotial production in <Emphasis Type="Italic">Aspergillus flavus</Emphasis> by functional genomics

The aflatoxin-producing fungi, Aspergillus flavus and A. parasiticus, form structures called sclerotia that allow for survival under adverse conditions. Deletion of the veA gene in A. flavus and A. parasiticus blocks production of aflatoxin as well as sclerotial formation. We used microarray technology to identify genes differentially expressed in wild-type veA and veA mutant strains that could be involved in aflatoxin production and sclerotial development in A. flavus. The DNA microarray analysis revealed 684 genes whose expression changed significantly over time; 136 of these were differentially expressed between the two strains including 27 genes that demonstrated a significant difference in expression both between strains and over time. A group of 115 genes showed greater expression in the wild-type than in the veA mutant strain. We identified a subgroup of veA-dependent genes that exhibited time-dependent expression profiles similar to those of known aflatoxin biosynthetic genes or that were candidates for involvement in sclerotial production in the wild type.     

Disruption of the nuclear gene encoding the 20.8-kDa subunit of NADH:ubiquinone reductase ofNeurospora mitochondria

The nuclear gene coding for the 20.8-kDa subunit of the membrane arm of respiratory chain NADH:ubiquinone reductase (Complex I) fromNeurospora crassa, nuo-20.8, was localized on linkage group I of the fungal genome. A genomic DNA fragment containing this gene was cloned and a duplication was created in a strain ofN. crassa by transformation. To generate RIP (repeat-induced point) mutations in the duplicated sequence, the transformant was crossed with another strain carrying an auxotrophic marker on chromosome I. To increase the chance of finding an isolate with a non-functionalnuo-20.8 gene, random progeny from the cross were selected against this auxotrophy since RIP of the target gene will only occur in the nucleus carrying the duplication. Among these, we isolated and characterised a mutant strain that lacks the 20.8 kDa mitochondrial protein, indicating that this cysteine-rich polypeptide is not essential. Nevertheless, the absence of the 20.8-kDa subunit prevents the full assembly of complex I. It appears that the peripheral arm and two intermediates of the membrane arm of the enzyme are still formed in the mutant mitochondria. The NADH:ubiquinone reductase activity of sonicated mitochondria from the mutant is rotenone insensitive. Electron microscopy of mutant mitochondria does not reveal any alteration in the structure or numbers of the organelles.     

The pso4-1 mutation reduces spontaneous mitotic gene conversion and reciprocal recombination in Saccharomyces cerevisiae.

Summary Spontaneous mitotic recombination was examined in the haploid pso4-1 mutant of Saccharomyces cerevisiae and in the corresponding wild-type strain. Using a genetic system involving a duplication of the his4 gene it was shown that the pso4-1 mutation decreases at least fourfold the spontaneous rate of mitotic recombination. The frequency of spontaneous recombination was reduced tenfold in pso4-1 strains, as previously observed in the rad52-1 mutant. However, whereas the rad52-1 mutation specifically reduces gene conversion, the pso4-1 mutation reduces both gene conversion and reciprocal recombination. Induced mitotic recombination was also studied in pso4-1 mutant and wild-type strains after treatment with 8-methoxypsoralen plus UVA and 254 nm UV irradiation. Consistent with previous results, the pso4-1 mutation was found strongly to affect recombination induction.     

The isolation and characterization of a mutant allele at a new X-linked locus,mex, affecting NADP+-dependent enzymes inDrosophila melanogaster

The isolation and characterization of mutant alleles in a regulatory gene affecting NADP⁺-dependent enzymes are described. The locus,mex, is at position 26.5 ± 0.74 on the X chromosome ofDrosophila melanogaster. The newly isolated mutant allele,mex ¹, is recessive to either themex allele found in Oregon-R wild-type individuals or that found in thecm v parental stock in which the new mutants were induced. Themex ¹ mutant allele is associated with statistically significant decreases in malic enzyme (ME) specific activity and ME specific immunologically cross-reacting material (ME-CRM) in newly emerged adult males. During this same developmental stage in males, the NADP⁺-dependent isocitrate dehydrogenase specific activity increases to statistically significant levels. Females of themex ¹ mutant strain show statistically significant elevated levels of the pentose phosphate shunt enzymes, glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase. Isoelectric focusing and thermolability comparisons of the active ME from mutant and control organisms indicate that the enzyme is the same. Developmental profiles ofmex ¹ and control strains indicate that this mutant allele differentially modulates the levels of ME enzymatic activity and ME-CRM during development. This work was supported by an Operating Grant from the Natural Sciences and Engineering Research Council of Canada to M.M.B.     

A new yeast gene, HTR1, required for growth at high temperature, is needed for recovery from mating pheromone-induced G1 arrest

A new temperature-sensitive mutant of Saccharomyces cerevisiae was isolated. Arrested cells grown at the nonpermissive temperature were of dumb-bell shape and contained large vacuoles. A DNA fragment was cloned based on its ability to complement this temperature sensitivity. The HTR1 gene encodes a putative protein of 93 kDa without significant homology to any known proteins. The gene was mapped between ade5 and lys5 on the left arm of chromosome VII. The phenotype of the gene disruptant appeared to be strain-specific; disruption of the gene in strain W303 caused the cells to become temperature sensitive. The arrested phenotype here was similar to that of the original is mutant and cells in G2/M phase predominated at high temperature. Another disruptant in a strain YPH background grew slowly at high temperature due to slow progression through G2/M phase, and morphologically abnormal (elongated) cells accumulated. A single-copy suppressor that alleviated the temperature-sensitive defects in both strains was identified as MCS1/SSD1. The wild-type strains W303 and YPH are known to carry defective MCS1/SSD1 alleles; hence HTR1 may function redundantly with MCS1/SSD1 to suppress the temperature-sensitive phenotypes. In addition, based on a halo bioassay, the disruptant strains appeared to be defective in recovery from, or adaptive response to G1 arrest mediated by mating pheromone, even at the permissive temperature. Thus the gene has at least two functions and is designated HTR1 (required for high temperature growth and recovery from G1 arrest induced by mating pheromone).     

Characterization of nicking of the nontoxic-nonhemagglutinin components of Clostridium botulinum types C and D progenitor toxin

Clostridium botulinum C and D strains produce two types of progenitor toxins, M and L. Previously we reported that a 130-kDa nontoxic-nonhemagglutinin (NTNHA) component of the M toxin produced by type D strain CB16 was nicked at a unique site, leading to a 15-kDa N-terminal fragment and a 115-kDa C-terminal fragment. In this study, we identified the amino acid sequences around the nicking sites in the NTNHAs of the M toxins produced by C. botulinum type C and D strains by analysis of their C-terminal and N-terminal sequences and mass spectrometry. The C-terminus of the 15-kDa fragments was identified as Lys127 from these strains, indicating that a bacterial trypsin-like protease is responsible for the nicking. The 115-kDa fragment had mixtures of three different N-terminal amino acid sequences beginning with Leu135, Val139, and Ser141, indicating that 7–13 amino acid residues were deleted from the nicking site. The sequence beginning with Leu135 would also suggest cleavage by a trypsin-like protease, while the other two N-terminal amino acid sequences beginning with Val139 and Ser141 would imply proteolysis by an unknown protease. The nicked NTNHA forms a binary complex of two fragments that could not be separated without sodium dodecyl sulfate.     

Effect of lacZY-marking of the 2,4-diacetyl-phloroglucinol producing Pseudomonas fluorescens-strain 5-2/4 on its physiological performance and root colonization ability

Transgenic Pseudomonas fluorescens 5-2/4 with reinforced 2,4-diacetyl phloroglucinol (phl) production had shown increased biocontrol ability towards Pythium ultimum (Pu), but inferior root colonization ability compared to its wild type 5.014. Therefore, enhanced root colonization ability of the transgenic strain by repeated inoculation and reisolation on tomato plants was suggested. As a preparation for repeated inoculation and reisolation cycles, the construction of a negative control of the transgenic strain 5-2/4 by marking with lacZY and screening for a mutant possessing qualities comparable to 5-2/4 was performed. Morphologically, colonies of all of the 11 selected mutants were similar on MLXgal medium. The root colonization ability of two of the lacZY-marked strains (mutants 1 and 10) was comparable to the parental strain. These were also able to compete with the resident microflora of tomato seedlings to the same extent as the parental strain. Five mutants were excluded due to lower growth rates on Yeast Malt, King's B Medium (KB) and 0.1 Tryptic Soy Agar (mutant 4, 5 and 8), excessive growth and higher siderophore production on KB (mutant 10) and increased protease production (mutant 2). With respect to in vitro-antagonism of Pu, no differences could be found between the target strain and mutants 1, 3, 6, 7 and 9. Examination of sole carbon source utilization of these five lacZY-marked strains revealed a significantly higher utilization of alpha-D-lactose and lactulose compared to 5-2/4. However, significant differences could be found for 51% of the utilized carbon sources. Cluster analysis showed a high degree of similarity between 5-2/4 and mutant 1 both when analyzed with and without alpha-D-lactose. As mutant 1 also represented the colonization pattern most similar to the parental strain 5-2/4, it presents a presumptive subject for a negative control in the following inoculation and reisolation studies on tomato.     

Reassessment of the effect of biological rhythm mutations on learning in Drosophila melanogaster

A link between learning deficits and circadian period-lengthening mutations in Drosophila melanogaster previously has been reported. Mutant long-period males performed poorly in two learning assays involving experience-dependent courtship inhibition. In one, normal males that have courted fertilized females subsequently show courtship inhibition with virgin females. In the other, normal males that have courted sexually immature males subsequently fail to court other immature males. Those results have been reassessed in an extended study of genetic variants involving the period gene. 1. Long-period perL1 males demonstrated poor conditioned courtship inhibition when exposed to fertilized females; they showed normal courtship conditioning when exposed to immature males. This could be due to a perL1-associated olfactory deficit with fertilized females, since perL1 males were unable to discriminate behaviorally between fertilized and virgin females. 2. Other long-period males, including perL2 males and transgenic perL1 males bearing a truncated form of the per+ gene, were conditioned normally by fertilized females. Thus, the courtship inhibition defect is specific to the perL1 mutant strain. 3. perL1 (and other per mutant) flies showed normal acquisition and retention of a classically conditioned olfactory avoidance response. 4. Results from a new conditioned courtship inhibition experiment are presented; males exposed to fertilized females during training showed further courtship inhibition during subsequent exposure to fertilized females. From the perspective of learning theory, this can be viewed as a savings experiment.     

Endopolyploidy in Chlorella

A mutant of Dunaliella tertiolecta produced by treatment with methyl nitrosoguanidine and designated HL25/8, grew more slowly than the parent strain under all experimental conditions and was conspicuously less tolerant of NaCl. Total photosynthetic activity (C-fixation and O₂ evolution) was less in HL25/8 than in the parent strain and was affected differently by [NaCl] in the two strains. Various growth characteristics indicated that the mutant had a greater need than the parent strain for CO₂ as distinct from HCO ₃ ^– as a source of carbon. Gaseous CO₂ extended the range of salt tolerance of the mutant. For example, HL25/8 could not sustain growth at 1.02 M NaCl in a conventional buffered medium containing bicarbonate as the sole carbon source but could do so if the medium were sparged with a CO₂/air mixture. The mutant strain has a lower activity of carbonic anhydrase on the cell surface than the parent D. tertiolecta. Moreover, the two strains differ sharply in the responses of their surface carbonic anhydrase activity to salinity of the growth medium. Increasing sodium chloride concentration above 0.17 M raised activity of the enzyme in the parent strain but decreased it in HL25/8. We conclude that the low activity of carbonic anhydrase and its response to salinity can largely, but perhaps not fully, explain the diminished salt tolerance of the mutant. A plate counting method applicable to Dunaliella is described.     

Towards a male-only release system for SIT with the Queensland fruit fly,Bactrocera tryoni,using a genetic sexing strain with a temperature-sensitive lethal mutation

Flies that are homozygous for the recessive autosomal mutation bent wingshave a limited ability to fly and are less tolerant of high temperatures than normal flies in both the egg and puparial stages. The differences between the mutant and normal flies were found sufficient to be the basis of a genetic sexing strain. Genetic sexing strains were created using translocations of the autosome bearing the wild-type allele of bent wings(chromosome 2) to the Y chromosome, and crossing male flies carrying the translocation to mutant bent wingsfemales. In the resulting strain, the females were homozygous for the bent wingsmutation and the males were phenotypically normal for wing characters. Several translocations were recovered after irradiation, but only one translocation involving chromosome 2 was both stable and expressed in a stock that was vigorous enough for long-term viability. Unfortunately, all stocks containing the translocation showed high levels of temperature-dependent lethality, including, inexplicably, both males and females. Translocation stocks showing this effect included bent wings, another second chromosome mutation, white marks, and an otherwise normal stock. This phenomenon is probably rare, as it has not been reported before. It is likely that bent wingscould be suitably used with another translocation.     

Involvement of the PS03 gene of Saccharomyces cerevisiae in intrachromosomal mitotic recombination and gene amplification

Using a genetic system of haploid strains of Saccharomyces cerevisiae carrying a duplication of the his4 region on chromosome III, the pso3-1 mutation was shown to decrease the rate of spontaneous mitotic intrachromosomal recombination 2- to 13-fold. As previously found for the rad52-1 mutant, the pso3-1 mutant is specifically affected in mitotic gene conversion. Moreover, both mutations reduce the frequency of spontaneous recombination. However, the two mutations differ in the extent to which they affect recombination between either proximally or distally located markers on the two his4 heteroalleles. In addition, amplifications of the his4 region were detected in the pso3-1 mutant. We suggest that the appearance of these amplifications is a consequence of the inability of the pso3-1 mutant to perform mitotic gene conversion.     

Reactivation of the ATCase domain of the URA2 gene complex: a positive selection method for Ty insertions and chromosomal rearrangements in Saccharomyces cerevisiae

Genetic rearrangements such as deletions or duplications of DNA sequences are rarely detected in the yeast Saccharomyces cerevisiae. We have developed a screening system using the URA2 gene coding for the bi-functional CPSase-ATCase (carbamyl phosphate synthetase — aspartate transcarbamylase) to select positively for these kinds of events. Nonsense mutations in the CPSase region cause a complete loss of the ATCase activity because of their strong polar effect. Thirty-seven ATCase⁺ revertants were isolated from a strain containing three nonsense mutations in the proximal CPSase region. Genetic and structural analysis of the URA2 locus in these strains allowed us to characterize two major classes of revertants. In the first, an entire copy of a Ty transposon was found to be inserted in the CPSase coding domain. This event, which represents a new form of Ty-mediated gene activation was further analysed by mapping the Ty integration site in 26 strains. In a second class of revertants, we observed chromosomal rearrangements and, in particular, duplication of the ATCase region and its integration in a new chromosomal environment in which this sequence becomes active.     

Improved electrotransformation frequencies of Corynebacterium glutamicum using cell-surface mutants

The electrotransformation efficiency for homologously- and heterologously-derived plasmid DNA was determined for two families of Corynebacterium glutamicum strains derived from ATCC13059 (AS019 and auxotrophic, cell surface mutants MLB133 and MLB194) and ATCC13032 (parent strain and restriction-minus mutants RM3 and RM4), following their growth in LBG supplemented with glycine plus isonicotinic acid hydrazide (INH). Electrotransformation efficiencies of MLB133 were up to 100-fold higher than for strain ASO19 and, when using heterologously-derived plasmid DNA, MLB133 showed efficiencies comparable to or better than strains RM3 and RM4, demonstrating the relative importance of cell surface structures in impeding DNA uptake in C. glutamicum. Transmission electron microscopy analysis of cell surface structures showed that strain MLB133 has a thin cell wall relative to AS019 and growth in either glycine or INH further diminished its thickness. Both RM3 and RM4 were more sensitive to INH than ATCC13032 and growth in glycine plus INH further improved transformation efficiency. The mycolic acid composition of these strains is described and the impact of glycine and INH on this is reported.     

Identification of compatibility between ooplasmic factor and sperm gene in the intersubspecific crosses involving DDK and PWK mice strains

The DDK strain (Mus musculus domesticus) of inbred mouse has a unique peculiarity known as DDK syndrome.The DDK females are mostly infertile when crossed with males of other inbred strains,while DDK males exhibit normal fertility in the reciprocal crosses,as intrastrain matings.This DDK syndrome has been demonstrated to be caused by an incompatibility system between DDK ooplasmic factor and the sperm gene of other strains owing to the ovum mutant (Om) locus on mouse Chromosome 11.Recently,it was reported that DDK females are fully fertile when crossed to males of MOM (M.m.molossinus) and CASP (M.m.castaneus) strains,indicating that no incompatibilities exist between DDK ooplasmic factor and sperm gene of MOM or CASP males.In the present study,DDK females were found to be also fully fertile when crossed to the males of PWK wild-derived inbred strain (originated from Czech Republic wild mice,M.m.musculus).The crosses of DDK females × F1 (DDK♀ × PWK♂) males also resulted in normal fertility.Furthermore,the transmission ratios of Om alleles from these F1 males to their backcross N2 offspring are 50％∶50％ as genotyped by microsatellite markers closely linked to Om locus.Moreover,it was demonstrated that PWK females are also fully fertile when crossed to DDK males.All above results indicated that no incompatibility exists between ooplasmic factor and sperm gene in the intersubspecific crosses with DDK and PWK strains.PWK strain would also be useful for further investigations on the DDK syndrome,and DDK strain can be used more widely for various studies in the mouse.     

Bacteriophage λ-mediated transposon mutagenesis of phytopathogenic and epiphytic Erwinia species is strain dependent

Summary Using transformation and conjugal mobilization, plasmids carrying the lamB gene of Escherichia coli were transferred to a range of Erwinia strains. The resultant strains were infected with 467, and kanamycin resistant transductants were screened for various mutant phenotypes including auxotrophy and altered extracellular enzyme activities. Reversion analysis suggested that most mutant phenotypes were due to Tn5 insertion. The applicability of the techniques was highly strain dependent. However a rapid and simple route to mutant isolation was obtained, which could allow the use of other -related genetic techniques in several important species which, to date, have not been genetically manipulated.     

Insecticide resistance and malathion carboxylesterase in the sheep blowfly,Lucilia cuprina

Resistance to the organophosphorus insecticide malathion in genetically related strains of the Australian sheep blowflyLucilia curprina was examined. Separate lines of blowflies were established by homozygosis of the fourth chromosome of the parental RM strain. Both the RM and the derived resistant (der-R) strains are approximately 100 times more resistant to malathion than the related susceptible der-S strain, resistance being correlated with a 45- to 50-fold increase in a malathion carboxylesterase (MCE) activity. MCE has a pH optimum ranging between 6.6 and 8.0 and is strongly inhibited by the carboxylesterase inhibitors triphenyl phosphate, paraoxon, and diiospropylfluorophosphate. Subcellular fractionation revealed that MCE was localized predominantly to the cytosol and mitochondria in both resistant and susceptible blowflies. A single MCE was purified to homogeneity from RM blowflies. It has a pI of 5.5, is a monomer of 60.5 kDa, and hydrolyzes malathion with aV _max of 755 nmol/min/mg protein and aK _m of 11.0 µM. L. cuprina have thus evolved a remarkable MCE which is faster and more efficient at hydrolyzing a specific insecticide than any other insect esterase yet described.     

Identification and fine mapping of <Emphasis Type="Italic">Pi39</Emphasis>(t), a major gene conferring the broad-spectrum resistance to <Emphasis Type="Italic">Magnaporthe oryzae</Emphasis>

Blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most devastating diseases of rice worldwide. The Chinese native cultivar (cv.) Q15 expresses the broad-spectrum resistance to most of the isolates collected from China. To effectively utilize the resistance, three rounds of linkage analysis were performed in an F₂ population derived from a cross of Q15 and a susceptible cv. Tsuyuake, which segregated into 3:1 (resistant/susceptible) ratio. The first round of linkage analysis employing simple sequence repeat (SSR) markers was carried out in the F₂ population through bulked-segregant assay. A total of 180 SSR markers selected from each chromosome equally were surveyed. The results revealed that only two polymorphic markers, RM247 and RM463, located on chromosome 12, were linked to the resistance (R) gene. To further define the chromosomal location of the R gene locus, the second round of linkage analysis was performed using additional five SSR markers, which located in the region anchored by markers RM247 and RM463. The locus was further mapped to a 0.27 cM region bounded by markers RM27933 and RM27940 in the pericentromeric region towards the short arm. For fine mapping of the R locus, seven new markers were developed in the smaller region for the third round of linkage analysis, based on the reference sequences. The R locus was further mapped to a 0.18 cM region flanked by marker clusters 39M11 and 39M22, which is closest to, but away from the Pita/Pita ² locus by 0.09 cM. To physically map the locus, all the linked markers were landed on the respective bacterial artificial chromosome clones of the reference cv. Nipponbare. Sequence information of these clones was used to construct a physical map of the locus, in silico, by bioinformatics analysis. The locus was physically defined to an interval of ≈37 kb. To further characterize the R gene, five R genes mapped near the locus, as well as 10 main R genes those might be exploited in the resistance breeding programs, were selected for differential tests with 475 Chinese isolates. The R gene carrier Q15 conveys resistances distinct from those conditioned by the carriers of the 15 R genes. Together, this valuable R gene was, therefore, designated as Pi39(t). The sequence information of the R gene locus could be used for further marker-based selection and cloning. Xinqiong Liu and Qinzhong Yang contributed equally to this work.