Wild Rice Populations Research Articles

Towards a More Efficient In and Ex Situ Conservation of Sri Lankan Wild Rice Species.

Five species of wild Oryza (O. nivara, O. rufipogon, O. eichengeri, O. rhizomatis and O. granulata), including the endemic species O. rhizomatis, have been recorded in Sri Lanka. These species are facing continuous decline in their populations due to natural and anthropogenic processes, with habitat loss being the main threat. This study aimed to provide information on the distribution, the current status of ex situ and in situ conservation, and to identify high-priority species and sites of wild rice in Sri Lanka, in order to improve the effectiveness of conservation efforts. Occurrence records of Sri Lankan wild rice species were collected from literature, gene banks, and field surveys. The distribution of these species was mapped, and areas with high species richness were identified. A gap analysis was conducted to determine the high-priority areas and species for ex situ and in situ conservation. It was found that about 23% of the wild rice populations in Sri Lanka were within protected areas, and by expanding these protected areas by 1 km, an additional 22% of the populations located on the border of these areas could be effectively conserved. Our analysis also revealed that 62% of Sri Lankan wild rice populations were not represented in gene banks. The species-rich areas were found to be in only two districts (Polonnaruwa and Monaragala), and less than 50% of these areas were within protected areas. Based on these findings, O. rhizomatis, O. eichengeri, and O. rufipogon were identified as high-priority species for in situ conservation. Ex situ collections were also deemed necessary for O. granulata and O. rhizomatis to ensure diversity representation in gene banks.

Wild Rice Lakes in Comparison to Mapped Surficial Sands in Minnesota

Several recent studies have considered the distribution of wild rice (Zizania palustris) compared to a variety of physical and watershed parameters. However, the distribution of wild rice has not been systematically compared to the surficial geology. In this study, a relatively comprehensive list of identified wild rice lakes in Minnesota was compared to the mapped areas of surficial sands. Wild rice is significantly more likely to occur on basins which are within or adjacent to mapped surficial sands. Statewide, an odds ratio of 2.1. indicates that a given lake within the mapped surficial sands has more than twice the odds of wild rice occurrence than a lake outside of the mapped surficial sands. The correlation observed here between mapped surficial sands and wild rice presence suggests that a groundwater-surface water interaction may have more widespread importance for sustaining wild rice populations than previously considered.

Wild Rice Lakes in Comparison to Mapped Surficial Sands in Minnesota

Several recent studies have considered the distribution of wild rice (Zizania palustris) compared to a variety of physical and watershed parameters. However, the distribution of wild rice has not been systematically compared to the surficial geology. In this study, a relatively comprehensive list of identified wild rice lakes in Minnesota was compared to the mapped areas of surficial sands. Wild rice is significantly more likely to occur on basins which are within or adjacent to mapped surficial sands. Statewide, an odds ratio of 2.1. indicates that a given lake within the mapped surficial sands has more than twice the odds of wild rice occurrence than a lake outside of the mapped surficial sands. The correlation observed here between mapped surficial sands and wild rice presence suggests that a groundwater-surface water interaction may have more widespread importance for sustaining wild rice populations than previously considered.

Tribally-Led Consultation on the Ethical Use of Sedimentary Ancient DNA for a Culturally Important Plant: Manoomin, Psin, Zizania (Wild Rice)

Led by Native American resource managers, we have convened a working group across 20+ tribal entities in the north-central United States, with the goal of building consensus around the use of sedimentary ancient DNA (sedaDNA) to detect deep-past and recent populations of wild rice (manoomin in Ojibwe, psiŋ in Dakota, Zizania palustris and Z. aquatica) using lake sediment cores. Wild rice is of extremely high cultural and spiritual importance to many Indigenous people of the Laurentian Great Lakes region, as well as being a valuable traditional food and providing important habitat for waterfowl and other organisms. Because of its importance, any research involving wild rice must be tribally led, and outcomes designed to benefit the tribes (e.g., Matson et al. 2020). Wild rice is threatened by environmental degradation due to industrial processes and agriculture, so its protection can be a contentious regulatory and political issue in Minnesota, Wisconsin, and Michigan, involving tribal, state, and federal agencies. The wild rice paleorecord has tremendous potential for detecting and tracking past changes in wild rice distributions. Until recently, however, proxies for wild rice were either ineffective (pollen, seeds), or low-throughput and thus not scalable to region-wide use (phytoliths). SedaDNA would supplement Indigenous knowledge and Western scientific methods to inform conservation, management, designation for protection, and the enhancement of cultural and historical records. In this presentation, we will describe how we are synthesizing output from facilitated online meetings with and presentations to tribal resource managers into a white paper providing guidance from these sovereign Nations to academic researchers, agencies, and policymakers on restrictions on the utilization of sedaDNA of wild rice, the leadership roles tribal entities should take in all research, and tribal priorities for the application of this technique.

Lost genome segments associate with trait diversity during rice domestication

BackgroundDNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication.ResultsIn this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length.ConclusionsWe provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.

Analysis of Domestication Loci in Wild Rice Populations.

The domestication syndrome is defined as a collection of domestication-related traits that have undergone permanent genetic changes during the domestication of cereals. Australian wild rice populations have not been exposed to gene flow from domesticated rice populations. A high level of natural variation of the sequences at domestication loci (e.g., seed shattering, awn development, and grain size) was found in Australian AA genome wild rice from the primary gene pool of rice. This natural variation is much higher than that found in Asian cultivated rice and wild Asian rice populations. The Australian Oryza meridionalis populations exhibit a high level of homozygous polymorphisms relative to domesticated rice, inferring the fixation of distinct wild and domesticated alleles. Alleles of the seed shattering genes (SH4/SHA1 and OsSh1/SH1) present in the shattering-prone O. meridionalis populations are likely to be functional, while the dysfunctional alleles of these seed shattering genes are found in domesticated rice. This confirms that unlike Asian wild rice populations, Australian wild rice populations have remained genetically isolated from domesticated rice, retaining pre-domestication alleles in their wild populations that uniquely allow the impact of domestication on the rice genome to be characterized. This study also provides key information about the domestication loci in Australian wild rice populations that will be valuable in the utilization of these genetic resources in crop improvement and de novo domestication.

Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome

BackgroundThe assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome.ResultsGeneralized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots.ConclusionWe discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera.92mDw1vveJ8f3-hG51Jkn-Video

Genetic diversity of wild rice accessions (Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection.

Oryza rufipogon Griff. is a valuable germplasm resource for rice genetic improvement. However, natural habitat loss has led to the erosion of the genetic diversity of wild rice populations. Genetic diversity analysis of O. rufipogon accessions and development of the core collection are crucial for conserving natural genetic diversity and providing novel traits for rice breeding. In the present study, we developed 1,592 SNPs by multiplex PCR and next-generation sequencing (NGS) technology and used them to genotype 998 O. rufipogon accessions from 14 agroclimatic zones in Guangdong and Hainan Provinces, China. These SNPs were mapped onto 12 chromosomes, and the average MAF value was 0.128 with a minimum of 0.01 and a maximum of 0.499. The O. rufipogon accessions were classified into ten groups. The mean Nei’s diversity index and Shannon–Wiener index (I) were 0.187 and 0.308, respectively, in all populations, indicating that O. rufipogon accessions had rich genetic diversity. There were also differences in the genetic diversity of O. rufipogon resources in the 14 regions. Hainan populations possessed higher levels of genetic diversity, whereas the Guangzhou population had lower levels of genetic diversity than did the other populations. Phylogenetic analysis revealed that the genetic relationship among the distribution sites of O. rufipogon was closely related to geographical location. Based on genetic distance, a core collection of 299 accessions captured more than 99% of the genetic variation in the germplasm. This study provides insights into O. rufipogon conservation, and the constructed core collection provides valuable resources for future research and genomics-assisted breeding of rice.

Effects of land use change on population survival of three wild rice species in China since 2001.

Land use change stemming from human activities, particularly cropland expansion, heavily threatens the survival of crop wild relatives that usually occur nearby or scatter in farming systems. Understanding the impacts of land use change on wild populations is critical in forming the conservation decision-making of wild relatives. Based on the investigations on the population survival of three wild rice species (Oryza rufipogon, O. officinalis, and O. granulata) in China over the past 40 years (1978–2019), the effect of land use change during the past 20 years (2001–2019) on the natural populations of the three species was examined using the land use type data of satellite-based Earth observations (data from GlobCover). From 1978 to 2019, the number of populations (distribution sites) of the three wild rice species had decreased by 65–87%, mainly because of the habitat destruction or disappearance caused by human-induced land use change. The three wild rice species display different habitat preferences, resulting in specific land use types surrounding their populations. In the recent 20 years, although the surrounding community composition of the wild rice population has been relatively stable, the surrounding vegetation cover area of the survived populations was significantly more extensive than that of the extinct ones (p < 0.05). These findings suggest that habitat vegetation plays a “biological barrier” role in the survival of wild populations through resisting or mitigating the disturbing impact of land use change on wild populations. This study provides not only direct guidelines for the conservation of wild rice but also new insights into the mechanisms underlying the influence of land use change on wild populations.

Sulfur Geochemistry Destabilizes Population Oscillations of Wild Rice (Zizania palustris)

AbstractElevated inputs of sulfate to freshwater systems can increase sulfide concentrations in anoxic soils and subsequently destabilize aquatic plant populations, but the interactions between sulfate, other geochemical cycles, and interannual plant population cycles are poorly understood. Increased sulfate loading increases mineralization of nitrogen from litter, but the sulfide produced during this process can limit nitrogen uptake by plants. In some cases, iron may mitigate sulfide's impacts on plants by precipitating iron sulfide. We examined the interannual effects of sulfate loading on mesocosm populations of wild rice, an emergent aquatic plant that undergoes population oscillations and is sensitive to sulfide. Using experimental mesocosms with self‐perpetuating populations, we investigated how population dynamics respond to manipulations of surface water sulfate (10 mg L−1 or 300 mg L−1), sediment iron (4.3 mg g−1 or 10.9 mg g−1 dry weight), and shoot litter (present or removed). Populations exposed to constant 10 mg L−1 sulfate concentrations had stable biomass oscillations of approximately 3‐year periods, consistent with previous studies that demonstrated litter‐driven oscillations in nitrogen availability. Populations exposed to 300 mg L−1 sulfate concentrations produced fewer and smaller seeds and declined to extinction in 6 years or less. We did not find a strong effect of iron loading or litter removal on wild rice biomass or seed production. Our observations show the potential of elevated surface water sulfate to rapidly destabilize wild rice populations under varying iron and organic carbon concentrations.

The long-term persistence of transgenic volunteers in wild mustard and rice populations

The undesired presence of GM plants outside of cultivation is one of main concerns for the ecological risk assessment and regulation of GM plants, and how long transgenic volunteers can persist in the nature remains unknown. We conducted two long-term coexistence experiments of Bt-transgenic insect-resistant crops in populations of their wild relatives, using Bt-transgenic oilseed rape (Brassica napus) in wild mustard (B. juncea) populations from 2012 to 2019, and Bt-transgenic rice (Oryza sativa) in wild rice (O. rufipogon and O. minuta) populations from 2013 to 2019. Transgenic oilseed rape volunteers survived only in the 2012 winter, because it is a spring variety and not be resistant to cold climate and competition from weeds. Transgenic rice was not survived because of its low competitive ability compared to wild rice, but survived five years in one population of wild rice O. minuta who could not tolerant to cold temperature. Our results indicated that transgenic volunteers can persist in the wild populations under natural conditions, but the fate of transgenic volunteers in the nature depends on whether the growth environment is favorable, and they could not disperse over its niche or “tolerance zone”.

Genomic Analysis Provides Insights Into the Plant Architecture Variations in in situ Conserved Chinese Wild Rice (Oryza rufipogon Griff.).

In situ conserved wild rice (Oryza rufipogon Griff.) is a promising source of alleles for improving rice production worldwide. In this study, we conducted a genomic analysis of an in situ conserved wild rice population (Guiping wild rice) growing at the center of wild rice genetic diversity in South China. Differences in the plant architecture in this population were investigated. An analysis using molecular markers revealed the substantial genetic diversity in this population, which was divided into subgroups according to the plant architecture. After resequencing representative individuals, the Guiping wild rice population was compared with other O. rufipogon and Oryza sativa populations. The results indicated that this in situ conserved wild rice population has a unique genetic structure, with genes that were introgressed from aromatic and O. sativa ssp. indica and japonica populations. The QTLs associated with plant architecture in this population were detected via a pair-wise comparison analysis of the sequencing data for multiple DNA pools. The results suggested that a heading date-related gene (DHD1) might be associated with variations in plant architecture and may have originated in cultivated rice. Our findings provide researchers with useful insights for future genomic analyses of in situ conserved wild rice populations.

Genotype calling and haplotype inference from low coverage sequence data in heterozygous plant genome using HetMap.

This study developed a new genotyping method that can accurately infer heterozygous genotype information from the complex plant genome sequence data, which helped discover new alleles in the association studies. Many software packages and pipelines had been developed to handle the sequence data of the model species. However, Genotyping from complex heterozygous plant genome needs further improvement on the previous methods. Here we present a new pipeline available at https://github.com/Ncgrhg/HetMapv1 ) for variant calling and missing genotype imputation from low coverage sequence data for heterozygous plant genomes. To check the performance of the HetMap on the real sequence data, HetMap was applied to both the F1 hybrid rice population, which consists of 1495 samples and the wild rice population with 446 samples. The high coverage sequence data of four hybrid rice accessions and two wild rice accessions, which were also included in low coverage sequence data, were used to validate the accuracy of genotype inference. The validation results showed that HetMap archieved significant improvement in heterozygous genotype inference accuracy (13.65% for hybrid rice, 26.05% for wild rice) and total accuracy compared with similar software packages. The application of the new genotype with the genome-wide association study also showed improvement of association power in wild rice awn length phenotype. It could archive high genotype inference accuracy in low sequence coverage in a small population with both the natural and constructed recombination population. HetMap provided a powerful tool for the heterozygous plant genome sequence data analysis, which may help to discover new phenotype regions for the plant species with the complex heterozygous genome.

Potential of Genome Editing to Capture Diversity From Australian Wild Rice Relatives.

Rice, a staple food worldwide and a model crop, could benefit from the introduction of novel genetics from wild relatives. Wild rice in the AA genome group closely related to domesticated rice is found across the tropical world. Due to their locality outside the range of domesticated rice, Australian wild rice populations are a potential source of unique traits for rice breeding. These rice species provide a diverse gene pool for improvement that could be utilized for desirable traits such as stress resistance, disease tolerance, and nutritional qualities. However, they remain poorly characterized. The CRISPR/Cas system has revolutionized gene editing and has improved our understanding of gene functions. Coupled with the increasing availability of genomic information on the species, genes in Australian wild rice could be modified through genome editing technologies to produce new domesticates. Alternatively, beneficial alleles from these rice species could be incorporated into cultivated rice to improve critical traits. Here, we summarize the beneficial traits in Australian wild rice, the available genomic information and the potential of gene editing to discover and understand the functions of novel alleles. Moreover, we discuss the potential domestication of these wild rice species for health and economic benefits to rice production globally.

Phenotypic Characterization of Oryza nivara (Sharma et Shastry) Collected from Different Ecological Niches of Sri Lanka

Information on the genetic diversity of wild rice species in Sri Lanka is relatively meagre, though it plays a key role in crop improvement programs of cultivated rice (Oryza sativa L.). The present study was carried out to identify the morphological variation pattern of the wild populations of O. nivara in Sri Lanka. Seven populations (P1 to P7) collected from different agro-ecological regions were characterized in a common garden based on nine morphological traits. The findings revealed a high level of phenotypic variation between populations when compared to within a population. The most variable traits were the flag leaf panicle neck length (FLPNL) and flag leaf angle (FLA), whereas the least variable trait was the flag leaf length (FLL). Box plots clearly illustrated the large differentiation of phenotypic traits in the entire distribution of wild rice populations. The cumulative values of the two principal components, i.e., FLPNL and FLA, explained 58.7% of the total variance. Populations from similar natural habitats clustered together. The P7 was adapted to intercept more sunlight by increasing flag leaf width (FLW) and FLA to compete with weeds and other shrubs. P2 and P5 were the most closely related populations representing approximately similar ecological conditions of the dry zone. The P3 population from the intermediate zone showed a vigorous plant growth with the highest plant height, culm girth and awn length (P < 0.05). Knowledge of such morphological diversity would facilitate designing conservation strategies and basic information for the proper utilization of wild resources in rice genetic improvement.

Wild rice research: Advancing plant science and food security

Wild rice research: Advancing plant science and food security

Compensation of Wild Plants Weakens the Effects of Crop-Wild Gene Flow on Wild Rice Populations.

Crop-wild gene flow may alter the fitness of the recipient i.e., crop-wild hybrids, then potentially impact wild populations, especially for the gene flow carrying selective advantageous crop alleles, such as transgenes conferring insect resistance. Given the continuous crop-wild gene flow since crop domestication and the occasionally stressful environments, the extant wild populations of most crops are still “wild.” One interpretation for this phenomenon is that wild populations have the mechanism buffered for the effects of crop alleles. However, solid evidence for this has been scarce. We used wild rice (Oryza rufipogon) and transgenic (Bt/CpTI) rice (O. sativa) as a crop-wild gene flow model and established cultivated, wild, and F7 hybrid rice populations under four levels of insect (Chilo suppressalis) pressure. Then, we measured the trait performance of the plants and estimated fitness to test the compensatory response of relatively high fitness compared to the level of insect damage. The performance of all plants varied with the insect pressure level; wild plants had higher insect-tolerance that was expressed as over- or equal-compensatory responses to insect damage, whereas crop and hybrids exhibited under-compensatory responses. The higher compensation resulted in a better performance of wild rice under insect pressure where transgenes conferring insect resistance had a somewhat beneficial effect. Remarkable hybrid vigour and the benefit effect of transgenes increased the fitness of hybrids together, but this joint effect was weakened by the compensation of wild plants. These results suggest that compensation to environmental stress may reduce the potential impacts of crop alleles on wild plants, thereby it is a mechanism maintaining the “wild” characteristics of wild populations under the scenario of continuous crop-wild gene flow.

Genomic basis of geographical adaptation to soil nitrogen in rice.

The intensive application of inorganic nitrogen underlies marked increases in crop production, but imposes detrimental effects on ecosystems1,2: it is therefore crucial for future sustainable agriculture to improve the nitrogen-use efficiency of crop plants. Here we report the genetic basis of nitrogen-use efficiency associated with adaptation to local soils in rice (Oryza sativa L.). Using a panel of diverse rice germplasm collected from different ecogeographical regions, we performed a genome-wide association study on the tillering response to nitrogen-the trait that is most closely correlated with nitrogen-use efficiency in rice-and identified OsTCP19 as a modulator of this tillering response through its transcriptional response to nitrogen and its targeting to the tiller-promoting gene DWARF AND LOW-TILLERING (DLT)3,4. A 29-bp insertion and/or deletion in the OsTCP19 promoter confers a differential transcriptional response and variation in the tillering response to nitrogen among rice varieties. The allele of OsTCP19 associated with a high tillering response to nitrogen is prevalent in wild rice populations, but has largely been lost in modern cultivars: this loss correlates with increased local soil nitrogen content, which suggests that it might have contributed to geographical adaptation in rice. Introgression of the allele associated with a high tillering response into modern rice cultivars boosts grain yield and nitrogen-use efficiency under low or moderate levels of nitrogen, which demonstrates substantial potential for rice breeding and the amelioration of negative environment effects by reducing the application of nitrogen to crops.

Assessment of Genetic Diversity of the Wild Rice (Oryza longistaminata) Populations in Tanzania Using Microsatellite Markers

The genetic diversity of 132 samples of the perennial wild rice (Oryza longistaminata) populations from selected districts (Bagamoyo, Kibaha, Kilombero and Mbarali) in Tanzania was evaluated using twenty eight microsatellite markers. Genomic DNA was extracted using standard protocols. Polymerase Chain Reaction (PCR) was carried out in a total reaction volume of 10 μL, using Touchdown protocol. It was found that all 28 microsatellite markers generated polymorphic patterns, with average Polymorphic Information Content (PIC) value of 0.631. Moreover, a total of 243 alleles were detected by the 28 markers, with average of 8.68 alleles per marker. The percentages of genetic variations among and within populations were 10% and 90%, respectively, implying that there was more gene flow among populations than within populations. Furthermore, the O. longistaminata population from Kilombero had highest genetic diversity followed by population from Mbarali, while the lowest genetic diversity was recorded in the population from Kibaha. Generally the populations from Kilombero, Mbarali and Bagamoyo were found to have relatively high genetic diversity, hence have potential to be used in rice breeding. In situ conservation of this species is recommended, and it can be achieved by conserving all areas which harbour populations with high levels of genetic diversity.&#x0D; Keywords: Genetic diversity; Microsatellites; SSR Markers; Oryza longistaminata; Wild rice;

Diversity of resistance to bacterial blight and geographical distribution of 29 populations of wild rice [Oryza meyeriana (Zoll. &amp; Moritzi) Baill.] in Yunnan, China

Oryza meyeriana (Zoll. & Moritzi) Baill. is a wild relative of cultivated rice. O. meyeriana is reported to exhibit high resistance or immunity to bacterial blight (BB), a disease caused by Xanthomonas oryzae pv. Oryzae (Xoo). To fully understand the BB resistance of O. meyeriana across multiple distribution sites in Yunnan, China, 87 accessions of 29 O. meyeriana populations were inoculated by artificial leaf cutting with the Xoo virulent strain CX28-3 isolated from rice in Yunnan. The diversity of resistance and habitat of each accession were then analysed. The results showed that resistance was variable. Among the 87 accessions, only 20.7% were resistant (12 resistant and 6 highly resistant), 37.9% were susceptible (9 highly susceptible and 24 susceptible), and the remaining 41.4% (36 accessions) were moderately resistant; no accession tested displayed immunity to CX28-3. The variation of resistance among populations is higher than within a population. The 29 populations of O. meyeriana were divided into categories according to administrative region, river system, longitude, latitude, altitude and climate factors. The resistance distribution and diversity index of the 29 O. meyeriana populations were calculated. The resistance of O. meyeriana accessions was shown to be quite different among the five administrative regions. The resistance from Xishuangbanna was the strongest, followed by Pu’er, Dehong, and Lincang, while that from Baoshan was the weakest. The diversity index of resistance is highest in Pu’er (1.13), followed by Dehong (0.95), Baoshan (0.69), Lincang (0.67), and Xishuangbanna (0.64). Correlation analysis showed that geographical and climatic factors impacted the resistance of O. meyeriana. There is a highly significant positive correlation between latitude and disease index. There is also a significant positive correlation between altitude and disease index. These results indicate that accessions of O. meyeriana at greater latitude or altitude are more susceptible to BB. By cluster analysis of the geographical and climatic factors of the O. meyeriana distribution sites, the 29 populations were classified into five groups with differences in resistance. O. meyeriana is considered nearly immune to BB, but susceptible accessions were found for the first time in Yunnan Province, China.