Genetic and molecular analyses of the incompatibility between Lolium isolates of Pyricularia oryzae and wheat

Pyricularia oryzae isolates from Lolium spp. (annual ryegrass and perennial ryegrass) show evidence of recent events in evolution of this fungus. A wheat blast isolate found in Kentucky in 2011 was assumed to originate from annual ryegrass isolates. Genetic analyses revealed that the incompatibility between a Lolium isolate and common wheat cultivars is controlled by two gene pairs, Rmg6–A1 with a strong effect and R2-A2 with a weak effect, implying that this incompatibility is conditioned by simple gene-for-gene interactions. Disruption of the A1 avirulence gene led the Lolium isolate to gain virulence on common wheat. These results suggest a mechanism for host jumping by the blast fungus.     

Effect of inhibitors of melanin biosynthesis on appressorial penetration and reductive reactions in Pyricularia oryzae and Pyricularia grisea

Appressorial penetration of onion epidermal walls by wild-type strains P-2 and O-42 of Pyricularia oryzae was more sensitive to fthalide (4,5,6,7-tetrachlorophthalide) than penetration by wildtype strain 4091-5-8 and black mutant strain BL-3 of Pyricularia grisea. Cerulenin completely blocked appressorial penetration by P. oryzae strain P-2 or P. grisea strain BL-3, but penetration capacity of these appressoria could be largely restored with 0.1 mM scytalone. Fthalide and tricyclazole inhibited the conversion of 1,3,6,8-tetrahydroxynaphthalene (1,3,6,8-THN) to 1,3,8-trihydroxynaphthalene (1,3,8-THN) and 1,8-dihydroxynaphthalene (1,8-DHN) as well as the conversion of scytalone to 1,8-DHN by cell-free extracts of P. oryzae or P. grisea. These inhibitors blocked the NADPH-dependent reductase reactions involved in the conversion of 1,3,6,8-THN to scytalone and the conversion of 1,3,8-THN to vermelone in the melanin biosynthetic pathway to 1,8-DHN. The two reductase reactions in extracts from P. oryzae P-2 were about 10 times as sensitive to fthalide or tricyclazole as those in extracts of P. grisea. Reductase activity with either 1,3,6,8-THN or 1,3,8-THN as substrates was present in only trace amounts in cell-free extracts of the buff mutant, P. oryzae P-2 m-1.     

Identification of a novel locus Rmo2 conditioning resistance in barley to host-specific subgroups of Magnaporthe oryzae

Barley cultivars show various patterns of resistance against isolates of Magnaporthe oryzae and M. grisea. Genetic mechanisms of the resistance of five representative barley cultivars were examined using a highly susceptible barley cultivar, 'Nigrate', as a common parent of genetic crosses. The resistance of the five cultivars against Setaria, Oryza, Eleusine, and Triticum isolates of M. oryzae was all attributed to a single locus, designated as Rmo2. Nevertheless, the Rmo2 locus in each cultivar was effective against a different range of isolates. Genetic analyses of pathogenicity suggested that each cultivar carries an allele at the Rmo2 locus that recognizes a different range of avirulence genes. One allele, Rmo2.a, corresponded to PWT1, which conditioned the avirulence of Setaria and Oryza isolates on wheat, in a gene-for-gene manner. The other alleles, Rmo2.b, Rmo2.c, and Rmo2.d, corresponded to more than one avirulence gene. On the other hand, the resistance of those cultivars to another species, M. grisea, was conditioned by another locus, designated as Rmo3. These results suggest that Rmo2 is effective against a broad range of blast isolates but is specific to M. oryzae. Molecular mapping revealed that Rmo2 is located on the 7H chromosome.     

Expression profiling of rice genes in early defense responses to blast and bacterial blight pathogens using cDNA microarray

In order to understand the defense machinery in the model cereal crop rice, we performed a large-scale analysis of rice gene expression in response to rice blast Magnaporthe grisea (M. grisea) or Magnaporthe oryzae and bacterial blight Xanthomonas oryzae pv. oryzae (Xoo) during the early incompatible and compatible interactions. Using a gene chip containing 10 254 rice cDNAs representing 9240 unique genes, we identified 794 and 612 genes differentially expressed in the incompatible and compatible rice–M. grisea interactions, respectively, with 274 genes co-regulated during both interactions. In the rice–Xoo pathosystem, 454 and 498 differentially expressed genes were identified in the incompatible and compatible interactions, respectively, including 237 co-regulated genes in the both interactions. By clustering differentially regulated genes from all these interactions, we identified 29 co-regulated genes in the all four interactions, and 86 and 74 co-regulated genes in the two incompatible and two compatible interactions, respectively. These differentially expressed genes could be classified into three categories, including M. grisea- and Xoo-regulated, M. grisea-specific, and Xoo-specific. The expression patterns of representative defense-related genes were further confirmed by RT-PCR. The large-scale expression data from our microarray analysis indicated the existence of distinctive as well as shared defense pathways between the rice–M. grisea and rice–Xoo interactions.     

Infection by Magnaporthe oryzae chrysovirus 1 strain A triggers reduced virulence and pathogenic race conversion of its host fungus, <Emphasis Type="Italic">Magnaporthe oryzae</Emphasis>

Magnaporthe oryzae chrysovirus 1 strain A (MoCV1-A) is associated with an impaired growth phenotype of its host fungus, Magnaporthe oryzae. In this report, we assayed the virulence and pathogenicity of MoCV1-A-infected and MoCV1-A-free M. oryzae on rice plants. MoCV1-A infection did not affect virulence-associated fungal traits, such as conidial germination and appressorium formation. However, after punch inoculation of leaves on rice plants, MoCV1-A-infected strain formed smaller lesions than the MoCV1-A-free strain did on all rice varieties tested, showing that MoCV1-A infection resulted in reduced virulence of host fungi in rice plants. In contrast, after spray inoculation of rice seedlings, in some cases, MoCV1-A-infected and MoCV1-A-free strains caused different lesion types (resistance to susceptible, or vice versa) on individual international differential rice varieties. However, we did not find any gain/loss of the fungal avirulence genes by PCR, suggesting that MoCV1-A infection can convert the pathogenicity of the host M. oryzae from avirulence to virulence, or from virulence to avirulence, depending on the rice variety. We also confirmed the correlation of these race conversion events and invasive hyphae growth of the fungi in a leaf sheath inoculation assay. These data suggested that MoCV1-A infection generally confers hypovirulence to the fungal host and could be a driving force to generate physiological diversity, including pathogenic races.     

水直播条件下黑龙江省不同稻区稻瘟病菌致病性分析

为明确水直播条件下黑龙江省不同稻区稻瘟病菌Magnaporthe oryzae的致病性分化情况,以24个抗瘟单基因系品种为寄主,来源于2017—2018年黑龙江省水直播稻田的242株稻瘟病菌菌株为接种体,采用离体划伤方法接种,记录病斑反应型,计算有效致病菌株率和抗性频率,并进行聚类分析。结果显示,在水直播条件下,2017年,黑龙江省南部和中东部稻区稻瘟病菌菌株对抗瘟单基因系品种的有效致病菌株率介于8.33%~95.83%和20.83%~95.83%之间,无毒基因出现频率分别为575次和622次;2018年,南部和中东部稻区稻瘟病菌菌株对鉴别体系的有效致病菌株率介于29.17%~95.83%和20.83%~91.67%之间,无毒基因出现频率分别为536次和571次。2017年,黑龙江省南部和中东部稻区稻瘟病菌菌株的致病性相似系数介于0.15~1.00和0.14~1.00之间,以致病性相似系数0.40为阈值,可将菌株分别划分为5个类群和6个类群;2018年,南部和中东部稻区菌株的致病性相似系数介于0.15~0.93和0.26~1.00之间,以致病性相似系数0.40为阈值,可将菌株分别划分为5个类群和4个类群。2017年,抗瘟单基因系品种对黑龙江省南部和中东部稻区稻瘟病菌菌株的抗性频率介于11.29%~88.71%和10.77%~86.15%之间,其中抗瘟单基因系品种IRBL9-W（Pi-9）和IRBLz5-CA（Pi-z5）抗性表现最好;2018年,抗瘟单基因系品种对南部和中东部稻区菌株的抗性频率介于10.34%~82.67%和15.79%~85.96%之间,其中抗瘟单基因系品种IRBL9-W（Pi-9）和IRBLz5-CA（Pi-z5）抗性表现最好。表明水直播条件下黑龙江省稻瘟病菌致病性分化剧烈,稻瘟病菌整体致病力较强,但仍有部分水稻种质抗性较好且相对稳定,基因聚合后抗性会得到进一步提升。     

Identification of avirulence genes in the rice blast fungus corresponding to three resistance genes in Japanese differentials

The pathogenicity of progeny from crosses among three Chinese isolates of Magnaporthe grisea collected from rice was tested on three Japanese differentials (Ishikarishiroke, Aichiasahi, K 59) having the blast resistance genes Pii, Pia, and Pit, respectively. Monogenic control was demonstrated for avirulence to the differentials. To identify resistance genes corresponding to the avirulence genes, the resistance and susceptibility in F₃ lines of the cultivars in response to the parents of the crosses were analyzed genetically. The three avirulence genes identified, designated Avr-Pii, Avr-Pia, and Avr-Pit, appear to correspond to resistance genes Pii, Pia, and Pit, respectively. The monogenic control of avirulence in the fungus and monogenic dominant resistance in rice cultivars supports a gene-for-gene relation in the Pii-, Pia-, or Pit-dependent resistance to the rice blast fungus in rice cultivars.     

Reaction of <Emphasis Type="Italic">Leersia</Emphasis> grasses to <Emphasis Type="Italic">Xanthomonas oryzae</Emphasis> pv. <Emphasis Type="Italic">oryzae</Emphasis> collected from Japan and Asian countries

The present study was conducted to determine if there is specificity in the host-pathogen relationship between the isolates of Xanthomonas oryzae pv. oryzae, the causal bacterium for rice blight and Leersia grasses, the alternative weed hosts of the disease. Plants of three species of Leersia, namely, L. sayanuka, L. oryzoides and L. japonica, were collected from various parts of Japan and were inoculated with the X. oryzae pv. oryzae isolates obtained from various locations in Japan and from 11 Asian countries. Four L. sayanuka plants were found susceptible to all Race II isolates and some Race I isolates, but were resistant to all Race III isolates. Race III is known to have a wider range pathogenicity to rice cultivar groups compared with Race I and II. Although the reactions of two L. oryzoides plants to Race I and II isolates were similar to that of L. sayanuka, the L. oryzoides plant collected from Niigata Prefecture showed a susceptible reaction to some Race III isolates. On the other hand, L. japonica plants gave reactions different those of L. sayanuka and L. oryzoides, with two plants of L. japonica found to be resistant to all test isolates collected from Japan. The Asian isolates exhibited a wide host range against the international differential rice cultivars, but almost all of them were avirulent to Leersia plants. These results indicate that the relationship between the pathogenicity of the causal bacterium and the resistance of host plants is very complex, and suggest that pathogenic diversity of X. oryzae pv. oryzae might be related to the resistance of Leersia spp.     

Experimental evidence of a pathogenic change caused by homologous recombination between endogenous and introduced dysfunctional Avr-Pita genes in Pyricularia oryzae

To provide experimental evidence that somatic homologous recombination (HR) is involved in the instability and diversification of the avirulence gene Avr-Pita in Pyricularia oryzae, we generated a dysfunctional Avr-Pita homolog and integrated it into strain Hoku-1 containing Avr-Pita. In the transformants, the occurrence of somatic HR events between Avr-Pita and the dysfunctional homolog was confirmed by PCR–RFLP. Germlings from conidia from the HR-positive transformants had lost the avirulence function, which enabled it to infect rice cultivar Yashiromochi containing the corresponding resistant gene Pi-ta. These results suggested that genetic mutation caused by somatic HR is one of the mechanisms responsible for virulence diversity.     

Selection and mutation of the avirulence gene AVR-Pii of the rice blast fungus Magnaporthe oryzae

Magnaporthe oryzae avirulence (AVR) genes are predicted to be involved in pathogen invasion and their virulence functions are restricted by the presence of the cognate resistance (R) genes. In this study, the distribution and variation of the avirulence (AVR-Pii) gene of M. oryzae in Yunnan province, China were analysed to understand haplotype diversity of AVR-Pii under field conditions. The presence of AVR-Pii in 454 field isolates of M. oryzae collected in Yunnan province was examined using gene-specific PCR markers. The results showed that 82 M. oryzae isolates carried AVR-Pii. Among them, 39 (35.5%), 5 (15.2%), 4 (14.3%), 2 (13.3%), 25 (12.8%) and 7 (9.7%) of the M. oryzae isolates carried AVR-Pii from central, southeastern, southwestern, northwestern, western and northeastern Yunnan province, respectively. Of these isolates, 55 were sequenced, while the remaining 27 isolates were not suitable for PCR-based sequencing and were not used for further analysis. Moreover, three AVR-Pii haplotypes were identified among the 55 isolates, in which H1 was identical with a previous sequence in GenBank (accession no. AB498874 ) and H2 and H3 were novel variants. All DNA sequence variations were found to occur in the protein-coding region resulting in amino acid substitutions. One virulent haplotype of AVR-Pii to Pii was identified among 55 field isolates, suggesting that the AVR-Pii gene has lost avirulence function through base substitution. These findings suggest that AVR-Pii is under positive selection and AVR-Pii mutations are responsible for overcoming race-specific resistance in nature.     

黑龙江省水稻种质抗瘟性及稻瘟病菌致病性分析

为明确黑龙江省水稻种质抗性及稻瘟病菌的致病性,以黑龙江省8个水稻品种、24个单基因系作为供试材料,120株稻瘟病菌株作为接种体,采用喷雾接种法测定了各供试水稻的抗瘟性及稻瘟病菌的致病性。结果表明,水稻品种对2010年和2011年菌株的抗性频率分别在31.67%~68.33%和21.67%~55.00%之间,2010年最好的抗性品种为松粳12,2011年最好的抗性品种为五优稻4和东农425;松粳12东农425组合联合抗病性最好。水稻单基因系对2010年和2011年菌株的抗性频率分别在10.00%~90.00%和5.00%~86.67%之间,抗性最好的单基因系分别为IRBLzt-T(Pi-zt)和IRBLz5-CA(Pi-z5);松粳12、东农425和龙粳22的基因聚合效果最好。2010年和2011年菌株对抗瘟基因群的致病率分别在8.33%~95.83%和25.00%~95.83%之间;无毒基因总出现频率分别为461和412次。研究表明,水稻种质抗性受菌株致病性影响较大,但高抗种质相对稳定,基因聚合方式更适宜当地品种抗性改良。     

侵染优质稻美香占2号的稻瘟病菌生理小种鉴定及无毒基因分析

为明确优质稻种美香占2号的抗瘟性,并为其合理布局以及与不同品种的轮换种植提供科学依据,利用7个中国鉴别品种和11个抗稻瘟病单基因系,对2013—2017年自广东省美香占2号品种上分离获得的50株稻瘟病菌Magnaporthe oryzae菌株进行生理小种鉴定和无毒基因型分析。结果显示,50株稻瘟病菌菌株被鉴定为11个生理小种,其中优势小种分别为C13、B13、B01、B05和C05;50株稻瘟病菌菌株对IRBLkh-K3(仅含Pik-h基因)、NIL-e1(仅含Pi50基因)、IRBL9-W(仅含Pi9基因)和IRBLzt-T(仅含Piz-t基因)4个抗稻瘟病单基因系表现出极低的毒性,频率分别为4%、6%、6%和8%;对IRBLz-Fu(仅含Piz基因)、IRBLkp-K60(仅含Pik-p基因)和IRBLi-F5(仅含Pii基因)3个抗稻瘟病单基因系表现出相对较高的毒性,频率分别为88%、86%和80%;自美香占2号以及其它4个主栽品种上获得的70株稻瘟病菌菌株被聚为不同类群;2003—2007年供试菌株中无毒基因AvrPi9、AvrPiz-t、AvrPi50和AvrPik-h的出现频率较高,无毒基因AvrPi1、AvrPita2、AvrPi2和AvrPish的出现频率中等,无毒基因AvrPii、AvrPik-p和AvrPiz的出现频率较低。     

Management of rice blast (Pyricularia oryzae): implications of alternative hosts

Rice blast (Pyricularia oryzae) has become a serious disease on commercial rice (Oryza sativa) crops in northern Australia and is present there on wild rice (O. australiensis). Characterisation of the host range of P. oryzae is fundamental to both reducing disease spread and to preventing development of epidemics via better management of Poaceae inoculum reservoirs in Australia. Studies on response of three different wild O. australiensis sources toward four isolates of P. oryzae showed all genotypes very susceptible to three isolates [WAC13466 (race IA-1), BRIP53376 (race IB-3), NT2014a (race unknown)], but resistant to isolate BRIP39772 (race IA-3). Studies to investigate levels of blast disease development following inoculation on a range of Poaceae hosts showed both P. oryzae isolates (WAC13466, BRIP53376) were highly virulent on barley (disease index, DI?=?100%), and on Phalaris and O. australiensis (DI?=?70%). However, isolate BRIP53376 showed a significantly higher level of aggressiveness (DI ~80%) on ryegrass, wild oat and rice. Of the two wheat cultivars tested, only one cultivar showed disease and only from WAC13466 (DI ~30%). Sweet corn and goosegrass were also susceptible to both blast isolates, but DI was <50%. That P. oryzae was virulent across these diverse Poaceae hosts, highlights, for Australia, the possibility for these species in, first, harbouring P. oryzae isolates highly virulent to commercial rice, second, fostering spread of rice-attacking P. oryzae strains into regions currently free of rice blast, and third, potential for these alternative host species to encourage development of more virulent host-specific strains of P. oryzae. The current study is an important step towards facilitating improved crop protection in the medium and long term from reducing P. oryzae disease epidemics via a better understanding and management of inoculum reservoirs in Australia.

     

Investigation of rice blast development in susceptible and resistant rice cultivars using a gfp‐expressing Magnaporthe oryzae isolate

In this study, an isolate of Magnaporthe oryzae expressing the green fluorescent protein gene (gfp) was used to monitor early events in the interaction of M. oryzae with resistant rice cultivars harbouring a blast resistance (R) gene. In the resistant cultivars Saber and TeQing (Pib gene), M. oryzae spores germinated normally on the leaf surface but produced morphologically abnormal germ tubes. Germling growth and development were markedly and adversely affected in leaves of these resistant cultivars. Penetration of host cells was never seen, supporting the idea that disruption of germling development on the leaf surface might be one of the resistance mechanisms associated with Pib function. Thus, this particular R gene appeared to function in the absence of host penetration by the fungal pathogen. Confocal laser scanning microscopy of M. oryzae‐infected susceptible rice cultivars showed the dimorphic growth pattern that is typically observed during the biotrophic and necrotrophic stages of leaf colonization in susceptible cultivars. The suitability of the gfp‐expressing M. oryzae isolate for further research on R‐gene function and identification of resistant genotypes in rice germplasm collections is discussed.     

Taxonomic characterization of Pyricularia isolates from green foxtail and giant foxtail, wild foxtails in Japan

Twenty-eight Pyricularia isolates from two wild foxtails—green foxtail (Setaria viridis) and giant foxtail (S. faberii)—in Japan were taxonomically characterized by DNA analyses, mating tests, and pathogenicity assays. Although most of the isolates failed to produce perithecia in mating tests with Magnaporthe oryzae, a diagnostic polymerase chain reaction-restriction fragment length polymorphism phenotype of M. oryzae was detected in the beta-tubulin genomic region in all isolates. The pathogenicity assays revealed that host ranges of the isolates were similar to those of isolates from foxtail millet (S. italica), which were exclusively pathogenic on foxtail millet. In addition to the 28 isolates from wild foxtails, 22 Pyricularia isolates from 11 other grasses were analyzed by RFLP using single-copy sequences as probes. In a dendrogram constructed from the RFLP data, isolates that were previously identified as M. oryzae formed a single cluster. All the wild foxtail isolates formed a subcluster with foxtail millet isolates within the M. oryzae cluster. From these results, we conclude that Pyricularia isolates from the wild foxtails are closely related to isolates from foxtail millet and should be classified into the Setaria pathotype of M. oryzae.     

Generation and characterisation of Tn5-tagged <Emphasis Type="Italic">Xanthomonas oryzae</Emphasis> pv. <Emphasis Type="Italic">oryzae</Emphasis> mutants that overcome <Emphasis Type="Italic">Xa23</Emphasis>-mediated resistance to bacterial blight of rice

Xanthomonas oryzae pv. oryzae causes bacterial blight of rice. Xa23, a bacterial blight resistance gene identified originally in wild rice, Oryza rufipogon, is dominant and resistant to all X. oryzae pv. oryzae field isolates tested. The corresponding avirulence gene avrXa23 is unknown. Here we report the generation of a random insertion mutant library of X. oryzae pv. oryzae strain PXO99 using a Tn5-derived transposon tagging system, and identification of mutant strains that are virulent on CBB23, a near-isogenic rice line containing Xa23. A total of 24,192 Tn5 inserted clones was screened on CBB23 by leaf-cutting inoculation and at least eight of them caused lesions on CBB23 comparable to those on JG30, the susceptible recurrent parent of CBB23. Polymerase chain reaction and Southern blot analysis showed that all the eight mutants, designated as P99M1, P99M2, P99M3, P99M4, P99M5, P99M6, P99M7 and P99M8, have a single Tn5-insertion in their genomes. The flanking DNA sequences of the Tn5-insertion sites were isolated by PCR-walking and sequenced. Bioinformatic analysis of the flanking sequences, by aligning them with the whole genome sequences of X. oryzae pv. oryzae strains PXO99, KACC10331 and MAFF311018 through NCBI, revealed that the Tn5-insertions disrupted genes that encode TAL effector AvrBs3/PthA, ISXo1 transposase, Type II secretion system protein-like protein or outer membrane protein, glycogen synthase, cytochrome C5 and conserved hypothetical protein. Further identification of these mutants will facilitate the molecular cloning of avirulence gene avrXa23. The authors C.-L. Wang, A.-B. Xu contributed equally to this work; Y. Gao and Y.-L. Fan contributed equally to this work.     

黑龙江省稻瘟病菌育性及其交配型分析

为明确黑龙江省采集自不同年份、不同地区的稻瘟病菌Magnaporthe oryzae的育性能力和交配型分布,采用2株标准菌株GUY11(MAT1-2)和KA3(MAT1-1)对2016—2017年黑龙江省西部、东部、中部3个地区经单孢分离的241株稻瘟病菌进行育性测定,并利用PCR技术对其交配型进行检测。结果表明,黑龙江省西部、东部、中部的241株稻瘟病菌中可育性菌株比例为11.62%,其中雌性菌株、雄性菌株、两性菌株分别占1.66%、4.56%和1.25%,不能判断其性别的未知菌株占4.15%。采集自不同地区、不同年份的稻瘟病菌可育性差异均较大,西部、东部、中部地区可育性菌株出现频率分别为13.25%、7.27%和12.62%;2016年采集的稻瘟病菌可育性较高,可育性菌株出现频率为25.30%。黑龙江省稻瘟病菌群体中同时存在MAT1-1和MAT1-2两种交配型,主要以交配型MAT1-1占优势,出现频率为58.92%,交配型为MAT1-2的菌株出现频率为8.30%。不同地区稻瘟病菌的交配型亦有差异,交配型为MAT1-1的菌株在黑龙江省东部地区出现频率最高,为72.73%,在中部、西部地区的出现频率次之,分别为61.17%和46.99%。表明黑龙江省水稻种植区的稻瘟病菌同时存在2种交配型菌株,其交配型存在丰富的多态性,但其可育性及交配型分布不均衡。     

三份重要水稻资源的稻瘟病抗性鉴定及不同评价指标间的相关性分析

为明确杂交水稻育种骨干亲本93-11、纹枯病重要抗源YSBR1及水稻重要基础研究的遗传转化材料Kitaake共3份重要水稻资源的稻瘟病抗谱及不同评价指标间的相关性,通过喷雾接种法,采用国际水稻稻瘟病抗性评价分级标准、致病率、病斑数量和病斑长度4个评价指标,分析了这3份重要水稻资源对36个稻瘟病菌生理小种的抗性。结果表明这3份水稻资源材料的病情指数主要集中于4和5级,但针对不同的生理小种其致病率存在较大差异。同时,93-11、YSBR1和Kitaake产生的病斑平均长度分别为0.56、0.54和0.66 cm,病斑平均数量分别为6.50、4.10和4.80个。Spearman相关性分析证明所采用的4个稻瘟病抗性评价指标之间均呈极显著正相关。表明93-11、YSBR1和Kitaake均对多数稻瘟病生理小种表现出抗性,但抗谱各不相同,且采用的4个评价指标间无显著差异。     

Molecular characterization of the avrXa7 locus from Xanthomonas oryzae pv. oryzae field isolates

The effector gene avrXa7 from Xanthomonas oryzae pv. oryzae has avirulence function in rice with the Xa7 resistance gene and confers pathogenic fitness (aggressiveness). Field strains of X. oryzae pv. oryzae displayed a diversity of phenotypes on rice ranging from complete to partial loss of these functions. To understand the molecular basis for variation in avrXa7 function, we sequenced the alleles from seven field strains. The avrXa7 gene is an avrBs3/pthA family member and contains nuclear localization signal sequences and an acidic activation domain (AAD) in the 3′ end and a central region containing repeated sequences, all of which are important for avirulence and aggressiveness. Sequence analysis revealed changes in the avrXa7 alleles ranging from a point mutation to multiple mutations spread throughout the alleles. Some strains with identical mutant alleles exhibited different levels of aggressiveness to rice, suggesting the presence of second mutations. A point mutation found at the beginning of the AAD of one avrXa7 allele was reconstructed in the wild type gene; this mutant exhibited partial loss of avirulence and aggressiveness. Our data suggest that adaptation of X. oryzae pv. oryzae to Xa7 rice fields involves not only alterations in avrXa7, but may include changes in other gene family members resulting from recombination between family members.