Genetic variation of wild litchi (<Emphasis Type="Italic">Litchi chinensis</Emphasis> Sonn. subsp. <Emphasis Type="Italic">chinensis</Emphasis>) revealed by microsatellites

Understanding the amount and distribution of genetic diversity in natural populations can inform the conservation strategy for the species in question. In this study, genetic variation at eight nuclear microsatellite loci was used to investigate genetic diversity and population structure of wild litchi (Litchi chinensis Sonn. subsp. chinensis). Totally 215 individuals were sampled, representing nine populations of wild litchi. All eight loci were polymorphic, with a total of 51 alleles. The expected heterozygosity in the nine populations ranged from 0.367 to 0.638 with an average value of 0.526. Inbreeding within wild litchi populations was indicated by a strong heterozygote defect. Significant bottleneck events were detected in the populations from Yunnan and Vietnam, which could be responsible for lower levels of genetic diversity in these populations. Measures of genetic differentiation (F _ST = 0.269) indicated strong differentiation among wild litchi populations. Significant correlation was found between genetic differentiation and geographical distance (r = 0.655, P = 0.002), indicating a strong isolation by distance in these populations. Bayesian clustering suggested genetic separation among three regional groups, namely, the western group, the central group and the eastern group. Some conservation strategies for wild litchi populations were also proposed based on our results.     

Genetic variation in populations of <Emphasis Type="Italic">Allothrombium pulvinum</Emphasis> (Acari: Trombidiidae) from Northern Iran revealed by mitochondrial <Emphasis Type="Italic">cox</Emphasis>I and nuclear rDNA <Emphasis Type="Italic">ITS</Emphasis>2 sequences

Allothrombium pulvinum Ewing is a common natural enemy of aphids and some other arthropods. So far, there are no studies that have addressed genetic variation of this predatory mite. We investigated genetic variation of A. pulvinum across its whole known range in Iran. A 410 bp portion of the mitochondrial cytochrome c oxidase subunit I gene (coxI) and 797–802 bp portion of the internal transcribed spacer 2 of rDNA (ITS2) were sequenced for 55 individuals from 11 populations, resulting in 12 and 26 haplotypes, respectively. In the coxI region, haplotype and nucleotide diversities varied among populations from 0.00 to 0.90 and from 0.0000 to 0.0110, respectively. In the ITS2 region they varied from 0.20 to 0.91 and from 0.0006 to 0.0023, respectively. For both gene regions the highest haplotype and nucleotide diversities were detected in population Mahmoud Abad from northern Iran. Statistically significant population differentiation (F _ST) was detected in most pair-wise population comparisons. The results of population differentiation for both gene regions were generally congruent indicating that A. pulvinum from Iran consists of genetically different populations. This suggests that A. pulvinum comprises at least two geographically distinct populations or even more than one species. This study is an initial step towards understanding genetic variation of A. pulvinum, a taxon for which little molecular information is available. More intensive sampling and analysis of additional DNA regions are necessary for more detailed classification of this taxon.     

The genetic structure of endangered indigenous populations of the amago salmon, <Emphasis Type="Italic">Oncorhynchus</Emphasis><Emphasis Type="Italic">masou</Emphasis><Emphasis Type="Italic">ishikawae</Emphasis>, in Japan

The amago salmon, Oncorhynchus masou ishikawae, is an endemic subspecies of O. masou in Japan. Owing to the extensive stocking of hatchery fish throughout Japan, indigenous populations of O. m. ishikawae are now on the verge of extinction. We examined the genetic effects of stocking hatchery fish on wild populations in the River Koza, Japan, using microsatellite and mitochondrial DNA (mtDNA) markers. For mtDNA, haplotype mt1, which is common in wild populations, was present exclusively in isolated wild populations assumed to be unaffected by previous stocking, while it was never observed in hatchery fish. Genetic diversity was much higher in wild populations in the stocked area, which shared many mtDNA haplotypes with hatchery fish, than in isolated wild populations with haplotype mt1. Pairwise F _ST estimates based on microsatellites showed significant differentiation among the isolated populations with many microsatellite loci monomorphic. Significant deviation from Hardy–Weinberg equilibrium was observed in wild populations in the area subject to stocking, where a Bayesian-based assignment test showed a high level of introgression with hatchery fish. These results suggest that wild populations with haplotype mt1, which became isolated through anthropogenic environmental change in the 1950–1960s, represent indigenous populations of O. m. ishikawae in the River Koza. They have low genetic diversity, most likely caused by genetic bottlenecks following damming and environmental deterioration, while stocking of hatchery fish over the past 30 years apparently had a large impact on the genetic structure of wild populations in the main channel of the River Koza.     

Isolation and characterization of endophytic taxol-producing fungi from <Emphasis Type="Italic">Taxus chinensis</Emphasis>

This study investigated the endophytic fungi diversity of Taxus chinensis and screened the taxol-producing fungi in the host. A total of 115 endophytic fungi isolates obtained from bark segments of T. chinensis were grouped into 23 genera based on the morphological traits and sequence analysis of the internal transcribed spacers (ITS1-5.8S-ITS2), indicating endophytic fungi in T. chinensis are diverse and abundant. Diaporthe, Phomopsis (anamorph of Diaporthe), Acremonium, and Pezicula were the dominant genera, whereas the remaining genera were infrequent groups. The 13 representative species of the distinct genera were capable of producing taxol verified by reverse-phase high performance liquid chromatography (HPLC). Among the taxol-producing fungi, the yield of taxol produced by the Metarhizium anisopliae, H-27 was 846.1 μg l⁻¹ in reformative potato dextrose liquid medium, and the fungal taxol was further validated by mass spectrometry (MS). The taxol-producing fungi (92.3%) were infrequent communities, suggesting that infrequent fungi associated with T. chinensis might be a fascinating reservoir of taxol-generating fungi.     

Population genetic structure of <Emphasis Type="Italic">Tamarix chinensis</Emphasis> in the Yellow River Delta,China

Tamarix chinensis, with its important ecological significance, is a vital dominant plant in the Yellow River Delta of China. To understand its genetic structure and population dynamics, five populations of T. chinensis, consisting of 140 individuals, were analyzed in this study using inter simple sequence repeat markers. Seventy-eight polymerase chain reaction fragments were scored, of which 62 were polymorphic. The mean percentage of polymorphic loci (P), the mean Nei’s gene diversity (h), and the mean Shannon’s information index (I) were 79.5%, 0.239, and 0.363, respectively. These indexes indicated that a moderate level of genetic diversity existed in T. chinensis populations of the Yellow River Delta. Both analysis of molecular variance (AMOVA) (Φ _st = 0.169) and Popgene (G _st = 0.159) analyses revealed the low level of genetic differences among the five populations of T. chinensis. The results implied that relatively frequent gene flow existed among populations. However, slightly uneven genetic diversity was also found among populations. Unweighted pair group method with arithmetic mean and principal component analysis showed that populations with similar soil salinity had a close relationship, rather than populations with closer geographical distance. A significant negative correlation between genetic diversity and soil salinity of the five populations (r = −0.958, p < 0.01) showed that soil salinity played an important role in shaping the population genetic structure of T. chinensis in the Yellow River Delta, China.     

Genetic variation in island populations of tuatara (<Emphasis Type="Italic">Sphenodon</Emphasis> spp) inferred from microsatellite markers

Tuatara (Sphenodon spp) populations are restricted to 35 offshore islands in the Hauraki Gulf, Bay of Plenty and Cook Strait of New Zealand. Low levels of genetic variation have previously been revealed by allozyme and mtDNA analyses. In this new study, we show that six polymorphic microsatellite loci display high levels of genetic variation in 14 populations across the geographic range of tuatara. These populations are characterised by disjunct allele frequency spectra with high numbers of private alleles. High F _ST (0.26) values indicate marked population structure and assignment tests allocate 96% of all individuals to their source populations. These genetic data confirm that islands support genetically distinct populations. Principal component analysis and allelic sequence data supplied information about genetic relationships between populations. Low numbers of rare alleles and low allelic richness identified populations with reduced genetic diversity. Little Barrier Island has very low numbers of old tuatara which have retained some relictual diversity. North Brother Island’s tuatara population is inbred with fixed alleles at 5 of the 6 loci.     

Population cytogenetics of <Emphasis Type="Italic">Chironomus circumdatus</Emphasis> Kieffer, 1921 (Diptera,Chironomidae) from Thailand

The objectives of this study were to explore cytogenetic variation and the role of chromosomal change on local adaptation and genetic differentiation of Chironomus circumdatus Kieffer from Thailand. A total of 1,505 larvae from 24 populations were examined cytologically. Twelve chromosomal inversions were found and most of these (9 of 12) were rare inversions. All populations were in Hardy–Weinberg equilibrium. Significant association (P < 0.001) between the A2 and B5 inversions was detected in one population. Population genetic structure analysis indicated significant genetic differentiation between populations (F _ST = 0.037, P < 0.001). Geographic distance was the principal factor limiting gene flow between populations. Nei’s modified genetic distance (D _A) between populations ranged from 0.001 to 0.011 with an average of 0.003. An UPGMA population phenogram depicting relationship between populations based on D _A values revealed three groups of populations, group I, II and III each characterized by different inversions/inversion frequencies. Significant correlation of inversion C3 and water temperature suggested that this inversion might have a role to play on adaptation to high temperature habitat. However, if detection of significant population subdivision and relationship between genetic and geographic distance are taken into account, relationship between C3 and water temperature will also be due to the effect of migration/drift alone without the effect of selection.     

Population genetic structure of <Emphasis Type="Italic">Sargassum thunbergii</Emphasis> (Fucales,Phaeophyta) detected by RAPD and ISSR markers

Genetic variation of four populations of Sargassum thunbergii (Mert.) O. Kuntze and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China was studied with random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. A total of 28 RAPD primers and 19 ISSR primers were amplified, showing 174 loci and 125 loci, respectively. Calculation of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon’s information index) revealed low or moderate levels of genetic variations within each S. thunbergii population. High genetic differentiations were determined with pairwise Nei’s unbiased genetic distance (D) and fixation index (F _ST ) between the populations. The Mantel test showed that two types of matrices of D and F _ST were highly correlated, whether from RAPD or ISSR data, r = 0.9310 (P  = 0.008) and 0.9313 (P = 0.009) respectively. Analysis of molecular variance (AMOVA) was used to apportion the variations between and within the S. thunbergii populations. It indicated that the variations among populations were higher than those within populations, being 57.57% versus 42.43% by RAPD and 59.52% versus 40.08% by ISSR, respectively. Furthermore, the Mantel test suggested that the genetic differentiations between the four populations were related to the geographical distances (r > 0.5), i.e., they conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. As a whole, the high genetic structuring between the four S. thunbergii populations along distant locations was clearly indicated in the RAPD and ISSR analyses (r > 0.8) in our study.     

Comparative photosynthesis characteristics of <Emphasis Type="Italic">Calycanthus chinensis</Emphasis> and <Emphasis Type="Italic">Chimonanthus praecox</Emphasis>

Calycanthus chinensis is an endangered plant of the national second-grade protection of China restricted in a small area in Zhejiang Province. We studied parameters of photosynthesis, chlorophyll (Chl) contents, and Chl fluorescence (minimum fluorescence, F₀, maximum fluorescence, F_m, variable fluorescence, F_v, and F_v/F_m) of C. chinensis and Chimonanthus praecox. C. chinensis had lower compensation irradiance but higher saturation irradiance than C. praecox. Hence C. chinensis has more advantage in obtaining and utilizing photon energy and higher Chl content, and is more adaptive to higher temperature and propitious to thermal dissipation than C. praecox. In addition, C. chinensis produces abundant, well-preserved seed with a higher germination rate and a wider adaptability to temperature than C. praecox. Thus C. chinensis is prone to survival and viability, and gets rid of the endangered plant species of the national second-grade protection of China.     

Intraspecific genetic polymorphism of Russian sturgeon <Emphasis Type="Italic">Acipenser gueldenstaedtii</Emphasis>

Three populations (Azov, Caspian, and Black Sea) of Russian sturgeon Acipenser queldenstaedtii were tested for polymorphism at nuclear (RAPD and microsatellites) and mitochondrial (PCR identification of two mitotypes) markers. In addition, morphometric analysis of he representatives of Azov population was carried out. According to the morphological characters, the Black Sea population occupied an intermediate position between the Caspian and Azov populations, reflecting the phylogeography of this species. In agreement with the morphometric data, genetic distances (the data of STR analysis) also placed the Black Sea population between the Caspian and Azov populations (F _ST = 0.058 and 0.043). The genetic distance between the Azov and Caspian population was somewhat higher (F _ST = 0.070). The highest allelic polymorphism at four microsatellite loci was found observed in Caspian population, while the lowest polymorphism was in the Sea of Azov. RAPD analysis distinguished high polymorphism within the populations, although it was not feasible for interpopulation analysis. Using the method differentiating the “baerii-like” and typical “gueldenstaedtii” mitotypes, the absence of the “baerii-like” marker in the Black Sea population was demonstrated. The frequency of this marker in Caspian and Azov populations constituted 31.1 and 1.8%, respectively. Possible evolutionary reasons for the interpopulation differences observed are discussed.     

Isolation by distance and a chromosomal cline in the Cayapa cytospecies of <Emphasis Type="Italic">Simulium exiguum</Emphasis>, the vector of human onchocerciasis in Ecuador

The population genetic structure of the Cayapa cytospecies of Simulium exiguum, the vector of onchocerciasis, was analysed using allozyme frequency and chromosomal inversion polymorphism data from 6 and 15 populations respectively, collected in Ecuador. Eight allozyme loci were scored. No unique allozyme markers were found enabling us to identify biting adults of the vector from the non-vector Bucay cytotype. Mannose-phosphate isomerase (Mpi) contributed largely to the significant heterogeneity in gene frequency among populations of the Cayapa cytospecies and also to the overall population structuring (F_ST=0.015 ± 0.014) which fitted the isolation by distance model. However, heterozygote deficits were recorded for Mpi in four of the six populations, which could indicate that selection is acting at this locus but this hypothesis will require further convincing evidence. Furthermore the significant population structuring of allozymes was not evident when Mpi was omitted from the analysis. All inversion polymorphisms (IIS-B, IIS-F, IIL-A and IIL-B) were in Hardy-Weinberg equilibrium, showed significant heterogeneity between populations and revealed the occurrence of an altitudinal cline in inversion IIS-B frequency. The inversion polymorphisms revealed a significant degree of population structuring (F_ST=0.083 ± 0.027), which can be explained by the isolation by distance model. A UPGMA cluster analysis revealed the relatively remote, high altitude Rio Mira populations to be the most genetically distinct.     

Mitochondrial DNA sequence variability in red-legged partridge, <Emphasis Type="Italic">Alectoris rufa</Emphasis>, Spanish populations and the origins of genetic contamination from <Emphasis Type="Italic">A. chukar</Emphasis>

The analysis of 135 mitochondrial D-loop sequences of the Iberian autochthonous red-legged partridge (Alectoris rufa) from wild population hunting bags from various locations and fowl runs in Spain yielded 37 different haplotypes. Among these, three haplotypes correspond to chukar partridges (Alectoris chukar), indicating genetic introgression from birds illegally introduced for restocking: three individuals carrying such haplotypes where found in natural populations, one appeared among those sampled on a mass reproduction farm and the remaining 10 in another fowl-run. The geographical origin of the contaminating chukar haplotypes could be assigned to the most easterly area of the chukar partridge geographical distribution in China. Molecular diversity parameters in the A. rufa samples indicate a considerable amount of genetic variation. Φ_ST showed significant differences among populations that are not explained by geographical distance alone. Particularly, one northern population (Palencia) shows a certain degree of genetic differentiation that could reflect a previously suggested subspecies division. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Genetic structure analysis of natural <Emphasis Type="Italic">Sargassum muticum</Emphasis> (Fucales,Phaeophyta) populations using RAPD and ISSR markers

Sargassum muticum is important in maintaining the structure and function of littoral ecosystems, and is used in aquaculture and alginate production, however, little is known about its population genetic attributes. In this study, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to investigate the genetic structure of four populations of S. muticum and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China. The selected 24 RAPD primers and 19 ISSR primers amplified 164 loci and 122 loci, respectively. Estimates of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon’s information index) revealed low or moderate level of genetic variations within each S. muticum population, and a high level of genetic differentiations were determined with pairwise unbiased genetic distance (D) and fixation index (F _ST ) among the populations. The Mantel test showed that two types of matrices of D and F _ST were highly correlated whether from RAPD (r = 0.9706, P = 0.009) or ISSR data (r = 0.9161, P = 0.009). Analysis of molecular variance (AMOVA) was conducted to apportion the variations among and within the S. muticum populations. It indicated that variations among populations were higher than those within populations, being 55.82% verse 44.18% by RAPD and 55.21% verse 44.79% by ISSR, respectively. Furthermore, the Mantel test suggested that genetic differentiations among populations were related to the geographical distances (r > 0.6), namely, conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. On the whole, the high genetic structuring among the four S. muticum populations along the distant locations was clearly indicated in RAPD and ISSR analyses (r > 0.9, P < 0.05) in our study.     

Landscape genetic structure of <Emphasis Type="Italic">Betula maximowicziana</Emphasis> in the Chichibu mountain range,central Japan

We evaluated the genetic structure of 16 Betula maximowicziana populations in the Chichibu mountain range, central Japan, located within a 25-km radius; all but two populations were at altitudes of 1,100–1,400 m. The results indicate the effects of geographic topology on the landscape genetic structure of the populations and should facilitate the development of local-scale strategies to conserve and manage them. Analyses involving 11 nuclear simple sequence repeat loci showed that most populations had similar intrapopulation genetic diversity parameters. Population differentiation (F _ST = 0.021, G′_ST = 0.033) parameters for the populations examined were low but were relatively high compared to those obtained in a previous study covering populations in a much larger area with a radius of approximately 1,000 km (F _ST = 0.062, G′_ST = 0.102). Three populations (Iriyama, Kanayamasawa, and Nishizawa) were differentiated from the other populations by Monmonier’s and spatial analysis of molecular variance algorithms or by STRUCTURE analysis. Since a high mountain ridge (nearly 2,000 m) separates the Kanayamasawa and Nishizawa populations from the other 14 populations and the Kanayamasawa and Nishizawa populations are themselves separated by another mountain ridge, the genetic structure appears to be partly due to mountain ridges acting as genetic barriers and restricting gene flow. However, the Iriyama population is genetically different but not separated by any clear geographic barrier. These results show that the landscape genetic structure is complex in the mountain range and we need to pay attention, within landscape genetic studies and conservation programs, to geographic barriers and local population differentiation.     

Genetic consequences of habitat fragmentation and loss: the case of the Florida black bear (<Emphasis Type="Italic">Ursus americanus floridanus</Emphasis>)

Habitat loss and fragmentation can influence the genetic structure of biological populations. We studied the genetic consequences of habitat fragmentation in Florida black bear (Ursus americanus floridanus) populations. Genetic samples were collected from 339 bears, representing nine populations. Bears were genotyped for 12 microsatellite loci to estimate genetic variation and to characterize genetic structure. None of the nine study populations deviated from Hardy–Weinberg equilibrium. Genetic variation, quantified by mean expected heterozygosity (H _E), ranged from 0.27 to 0.71 and was substantially lower in smaller and less connected populations. High levels of genetic differentiation among populations (global F _ST = 0.224; global R _ST = 0.245) suggest that fragmentation of once contiguous habitat has resulted in genetically distinct populations. There was no isolation-by-distance relationship among Florida black bear populations, likely because of barriers to gene flow created by habitat fragmentation and other anthropogenic disturbances. These factors resulted in genetic differentiation among populations, even those that were geographically close. Population assignment tests indicated that most individuals were genetically assigned to the population where they were sampled. Habitat fragmentation and anthropogenic barriers to movement appear to have limited the dispersal capabilities of the Florida black bear, thereby reducing gene flow among populations. Regional corridors or translocation of bears may be needed to restore historical levels of genetic variation. Our results suggest that management actions to mitigate genetic consequences of habitat fragmentation are needed to ensure long-term persistence of the Florida black bear.     

Genetic diversity and population structure of two important medicinal plant species <Emphasis Type="Italic">Schisandra chinensis</Emphasis> and <Emphasis Type="Italic">Schisandra sphenanthera</Emphasis> revealed by nuclear microsatellites

Seven polymorphic and transferable nuclear microsatellites were used to investigate the population structure of genetic diversity of Schisandra chinensis and Schisandra sphenanthera for facilitating their conservation and sustainable utilization. High levels of gene diversity were revealed in these two medicinal species, the majority of genetic diversity was harbored within populations, and population structure was might due to restricted gene flow among populations. Isolation by distance was close to significance in S. chinensis but not in S. sphenanthera. In S. chinensis, null alleles were identified as a cause for excess of homozygotes at loci G24 and WGA60, but inbreeding might also be partly responsible for the positive F _IS values in this species. In contrast, null allele frequencies were high at all the seven loci in S. sphenanthera and resulted in overestimation of fixation index. The strategy for ex situ conservation of these two medicinal species is discussed based on the genetic results.     

Comparisons of microsatellite variability and population genetic structure of two endangered wild rice species, <Emphasis Type="Italic">Oryza rufipogon</Emphasis> and <Emphasis Type="Italic">O. officinalis</Emphasis>, and their conservation implications

Conserving endangered wild rice species requires a thorough understanding of their population genetic structure and appropriate approaches. We applied six and seven microsatellite loci to study the genetic structure of six populations throughout the range of Chinese Oryza rufipogon and Oryza officinalis, respectively. The results showed that O. rufipogon possesses higher levels of genetic diversity but lower differentiation (R_S = 3.2713, P = 100.0%, H_O = 0.1401, H_S = 0.5800, F_ST = 0.271) than O. officinalis (R_S = 2.0545, P = 57.14%, H_O = 0.0470, H_S = 0.2830, F_ST = 0.554). Mean population F_IS was slightly larger for O. officinalis (F_IS = 0.844) than that for O. rufipogon (F_IS = 0.755), indicating that O. officinalis has slightly higher departures from Hardy–Weinberg expectations and heterozygosity deficits than O. rufipogon. In addition to different origins and evolutionary histories, O. officinalis has restricted gene flow, high inbreeding, isolated small populations and fewer opportunities of hybridization with other taxa, which may determine major differences in population genetic structure from O. rufipogon. Our results suggest the adoption of a plan of involving fewer populations but more individuals within populations for O. rufipogon, while both the number of populations and the individuals for a sampled population should be almost equally considered for O. officinalis. The known high degree of inbreeding in the populations of both species implies that conservation and restoration genetics should particularly focus on the maintenance of historically significant processes such as high levels of outbreeding, gene flow and large effective population sizes. We finally proposed to further estimate the role of rice gene flow in the conservation of O. rufipogon, and to perform detailed analysis of mating systems in both species for better conservation perspectives of their ecological and evolutionary processes.     

Extreme isolation by distance in a montane frog <Emphasis Type="Italic">Rana cascadae</Emphasis>

Given the recent interest in declining amphibian populations, it is surprising that there are so few data on genetic drift and gene flow in anuran species. We used seven microsatellite loci to investigate genetic structure and diversity at both large and small geographic scales, and to estimate gene flow in the Cascades frog, Rana cascadae. We sampled 18 sites in a hierarchical design (inter-population distances ranging from 1–670 km) to test for isolation by distance and to determine the geographic scale over which substantial gene flow occurs. Eleven of these sites were sampled as three fine-scale clusters of three, three, and five sites separated by pairwise distances of 1–23 km to estimate number of migrants exchanged per generation via F _ST and by a coalescent approach. We found R. cascadae exhibits a strong pattern of isolation by distance over the entire species range, and that there is a sharp drop in migrants exchanged between sites separated by greater than 10 km. These data, in conjunction with results of other recent studies, suggest that montane habitats promote unusually strong genetic isolation among frog populations. We discuss our results in light of future management and conservation of R. cascadae.     

High-resolution mapping and gene prediction of <Emphasis Type="Italic">Xanthomonas Oryzae</Emphasis> pv. <Emphasis Type="Italic">Oryzae</Emphasis> resistance gene <Emphasis Type="Italic">Xa7</Emphasis>

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a devastating disease in rice worldwide. The resistance gene Xa7, which provides dominant resistance against the pathogen with avirulence (Avr) gene AvrXa7, has proved to be durably resistant to BB. A set of SSR markers were selected from the “gramene” database based on the Xa7 gene initial mapping region on chromosome 6. These markers were used to construct a high-resolution genetic map of the chromosomal region surrounding the Xa7 gene. An F₂ mapping population with 721 highly susceptible individuals derived from a cross between the near isogenic lines (NILs) IRBB7 and IR24 were constructed to localize the Xa7 gene. In a primary analysis with eleven polymorphic SSR markers, Xa7 was located in approximately the 0.28-cM region. To walk closer to the target gene, recombinant F₂ individuals were tested using newly developed STMS (sequence tagged microsatellite) markers. Finally, the Xa7 gene was mapped to a 0.21-cM interval between the markers GDSSR02 and RM20593. The Xa7-linked markers were landed on the reference sequence of cv. Nipponbare through bioinformatics analysis. A contig map corresponding to the Xa7 gene was constructed. The target gene was assumed to span an interval of approximately 118.5-kb which contained a total of fourteen genes released by the TIGR Genome Annotation Version 5.0. Candidate-gene analysis of Xa7 revealed that the fourteen genes encode novel domains that have no amino acid sequence similar to other cloned Xa(xa) genes. Shen Chen and Zhanghui Huang are contributed equally to this work.