Genomic analysis, trajectory tracking, and field surveys reveal sources and long-distance dispersal routes of wheat stripe rust pathogen in China.

Identifying sources of phytopathogen inoculum and determining their contributions to disease outbreaks are essential for predicting disease development and establishing control strategies. Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust, is an airborne fungal pathogen with rapid virulence variation that threatens wheat production through its long-distance migration. Because of wide variation in geographic features, climatic conditions, and wheat production systems, Pst sources and related dispersal routes in China are largely unclear. In the present study, we performed genomic analyses of 154 Pst isolates from all major wheat-growing regions in China to determine Pst population structure and diversity. Through trajectory tracking, historical migration studies, genetic introgression analyses, and field surveys, we investigated Pst sources and their contributions to wheat stripe rust epidemics. We identified Longnan, the Himalayan region, and the Guizhou Plateau, which contain the highest population genetic diversities, as the Pst sources in China. Pst from Longnan disseminates mainly to eastern Liupan Mountain, the Sichuan Basin, and eastern Qinghai; that from the Himalayan region spreads mainly to the Sichuan Basin and eastern Qinghai; and that from the Guizhou Plateau migrates mainly to the Sichuan Basin and the Central Plain. These findings improve our current understanding of wheat stripe rust epidemics in China and emphasize the need for managing stripe rust on a national scale.

Analyses of Wheat Yellow Rust Populations Reveal Sexual Recombination and Seasonal Migration Pattern of Puccinia striiformis f. sp. tritici in Gangu, Northwestern China.

Puccinia striiformis f. sp. tritici is the causal agent of wheat yellow rust with records of regular and severe epidemics in China. This study explored the population dynamics of the yellow rust pathogen in Gangu, northwestern China. In Gangu, the Weihe River runs from west to east and divides Gangu into three regions: North and South mountain, with the valley in between. To study the genetic structure of the pathogen in local populations, samples were collected over 3 years from the three regions at different altitudes both within and between the wheat cropping seasons. A total of 811 P. striiformis f. sp. tritici isolates were successfully genotyped using 16 simple sequence repeat markers. The results suggest that P. striiformis f. sp. tritici can survive year-round in Gangu. The P. striiformis f. sp. tritici populations migrated among the regions, and the migration pattern was not related to altitude. The oversummering populations in the North and South mountain regions were genetically different from each other; and the P. striiformis f. sp. tritici populations collected from the lower altitude in the valley had no relationship with any of the populations collected in the spring or fall, indicating that they too have a different origin. Signatures of random mating were found in the populations collected in both North and South mountain regions, but not in the valley populations.

CoAl-layered double hydroxide nanosheet-based fluorescence assay for fast DNA detection.

In the study, CoAl-layered double hydroxide (CoAl-LDH) was prepared as a fluorescence quenching agent to detect DNA molecules. Because of its simple preparation for a large scale, excellent surface effect, good biocompatibility and high fluorescence quenching capability, the effective, rapid, and sensitive DNA detection was realized. The fluorescence quenching efficiency of LDH to 5(6)-carboxyfluorescein attached to single stranded DNA (FAM-ssDNA) was as high as 88%, and after FAM-ssDNA hybridized with the complementary DNA oligonucleotide, that to FAM-dsDNA was about 33%. The quenching mechanisms of LDH for ssDNA and dsDNA were discussed. Phosphate exposed of ssDNA played an important role in quenching effect. Compared to dsDNA, more exposed phosphate groups in ssDNA resulted in the stronger electrostatic interaction between ssDNA and LDH, and thus the higher quenching efficiency. Under optimal conditions, the linear equation was y = 38.26 + 3.37x in a linear relationship of 1-50 nM, and the correlation coefficient R2 corresponded to 0.999, and the limit of detection was calculated to be 0.79 nM (3σ). Cytotoxicity studies have shown that LDH has good biocompatibility. The study provides an effective, sensitive and safe approach for DNA detection and gives an insight for the design of LDH-based biosensing materials.

Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat (Triticum aestivum).

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated with known resistance genes or quantitative trait loci reported previously, whereas the other six are likely new resistance loci. Annotation of flanking sequences of significantly associated SNPs indicated the presence of three important candidate genes, including E3 ubiquitin-protein ligase, F-box repeat protein, and disease resistance RPP13-like protein. This study increased our knowledge in understanding the genetic architecture for stripe rust resistance and identified wheat varieties with multiple resistance alleles, which are useful for improvement of stripe rust resistance in breeding.

Predicting Overwintering of Wheat Stripe Rust in Central and Northwestern China.

Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), is an important disease of wheat. In China, Pst management has focused on the Gansu region where the pathogen can complete its annual cycle, including oversummering and overwintering. From this region, Pst inoculum is dispersed to the southern Yangtze River region in the late autumn/early winter and then to the main wheat production regions in the following spring. We used historical weather data (1995 to 2016) and field stripe rust assessment data (8 years) in the spring to evaluate the performance of a published model for predicting the potential of Pst overwintering in the Gansu region. Both predicted and observed values of rust overwintering in the Gansu region varied greatly between years and between sites within a single year, indicating the value of predicting rust overwintering for disease management. The model predictions fitted with observed values satisfactorily. All high incidences of rust in the spring were observed in the fields of the monitoring sites where the high potential of overwintering was predicted. Conversely, the predicted rust overwintering potential was also close to zero in the fields where rust was not observed in the spring. There were many false-positive predictions, which may be attributable to the absence of rust in autumn seedlings. This model can be used to target rust management in the spring and its effectiveness will be further improved if autumn rust assessment can be carried out.

Trilocular phenotype in Brassica juncea L. resulted from interruption of CLAVATA1 gene homologue (BjMc1) transcription.

As a desirable agricultural trait, multilocular trait of rapeseed (Brassica rapa; Brassica napus; Brassica juncea), always represents higher yield per plant compared with bilocular plants. We previously isolated a trilocular gene locus, Bjmc1, and identified a set of molecular markers linked to the trilocular gene. With a map-based cloning, we identified that the BjMc1 was located in B genome of Brassica juncea, and it was a CLAVATA1 (CLV1) gene homologue. The insertion of a copia-LTR retrotransposable element 1 (RTE1) into the coding region of BjMc1 interrupted its transcription in rapeseed, leading to the trilocular phenotype. Phylogenetic analysis showed that Mc1 genes were conserved and widespread in land plants. Two amino acid sites had undergone positive selection in the ancestor of Mc1 genes, and then purifying selection was the dominant force after the divergence of dicots and monocots from their common ancestor in the evolutionary process, indicating that Mc1 genes are conserved in modern land plants. Our results provided new insights in molecular regulatory mechanism of multilocularity in rapeseed, and better understanding of molecular mechanism in crop yield improvement.

Application of Geographic Information Systems to Identify the Oversummering Regions of Blumeria graminis f. sp. tritici in China.

Blumeria graminis f. sp. tritici, the pathogen that causes wheat powdery mildew, can oversummer as mycelia or conidia on leaves of volunteer wheat plants in cool mountainous areas in China. In this study, the regions in China where B. graminis f. sp. tritici can oversummer were identified on the basis of the probability that temperature remains below a critical temperature that is lethal to B. graminis f. sp. tritici. Two methods, one describing the relationship between the average temperature (20 to 26°C) in a given continuous 10-day period and wheat powdery mildew severity, the other describing the relationship between the average temperature (26 to 33°C) and the number of lethal days on powdery mildew development, were used to calculate the oversummering probability using weather data for 743 sites across China. Spatial interpolation based on the ordinary kriging method was conducted for the regions without observation. Oversummering probability values were similar for most locations estimated between the two methods. The B. graminis f. sp. tritici oversummering regions in China were identified to be in mountainous or high-elevation areas, including most regions of Yunnan, west and central areas of Guizhou, south and northwest Sichuan, south and east Gansu, south Ningxia, north and west Shaanxi, central-north Shanxi, west Henan and Hubei, and some regions in Qinghai, Tibet, and Xinjiang. When the oversummering sites from this study were compared with observed survey data for some of these sites, about 90% of sites where B. graminis f. sp. tritici oversummering was observed had been found suitable by both methods. The coincidence frequency and the area under the receiver operating characteristic curve for model 2 were higher, albeit only slightly, than those for model 1. Thus, both methods may be used to assist in disease management and further investigation on pathogen oversummering.

Comparative virulence phenotypes and molecular genotypes of Puccinia striiformis f. sp. tritici, the wheat stripe rust pathogen in China and the United States.

Stripe rust (yellow rust) of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the most important diseases in both China and the United States. The Chinese and US populations of the stripe rust fungus were compared for their virulence phenotypes on wheat cultivars used to differentiate races of the pathogen in China and the US and molecular genotypes using simple sequence repeat (SSR) markers. From 86 Chinese isolates, 54 races were identified based on reactions on the 17 Chinese differentials and 52 races were identified based on the 20 US differentials. The selected 51 US isolates, representing 50 races based on the US differentials, were identified as 41 races using the Chinese differentials. A total of 132 virulence phenotypes were identified from the 137 isolates based on reactions on both Chinese and US differentials. None of the isolates from the two countries had identical virulence phenotypes on both sets of differentials. From the 137 isolates, SSR markers identified 102 genotypes, of which 71 from China and 31 from the US. The virulence data clustered the 137 isolates into 20 virulence groups (VGs) and the marker data clustered the isolates into seven molecular groups (MGs). Virulence and SSR data had a low (r = 0.34), but significant (P = 0.01) correlation. Principal component analyses using either the virulence data or the SSR data separated the isolates into three groups: group a consisting of only Chinese isolates, group b consisting of both Chinese and US isolates and group c consisting of mostly US isolates. A neighbour-joining tree generated using the molecular data suggested that the P. striiformis f. sp. tritici populations of China and the US in general evolved independently.