Distribution and Genetic Diversity of Xylella fastidiosa subsp. pauca Associated with Olive Quick Syndrome Symptoms in Southeastern Brazil

In Brazil, the host expansion of Xylella fastidiosa subsp. pauca was recently demonstrated with the report of diseased olive trees (Olea europaea), whose symptoms were associated with olive quick decline syndrome previously described in southern Italy. We employed both polymerase chain reaction-based techniques and culture medium isolation to investigate the geographic distribution of X. fastidiosa as well as the genetic signatures of 21 strains isolated from 11 olive orchards in both São Paulo and Minas Gerais States in Brazil. X. fastidiosa subsp. pauca was detected in 83% of the orchards examined in the region, and was positively diagnosed in 43.7% of all sampled plants with typical scorching symptoms. Of the 21 strains characterized with fast-evolving microsatellite (single sequence repeat [SSR]) markers, 20 different multilocus microsatellite genotypes were observed with the overall allelic diversity of HNei = 0.38. Principal component analysis using the SSR markers clustered all strains, except for three, in one cluster demonstrating a limited range of genetic diversity. Multilocus sequence typing analysis showed the prevalence of a sequence type (ST16) in 75% of the samples; three other novel STs (84, 85, and 86), were detected, all belonging to the X. fastidiosa subsp. pauca cluster. These results show that genetically diverse strains of X. fastidiosa subsp. pauca are widely present in olive orchards in southeastern Brazil, which is consistent with the long history of this bacterium in that region.

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HPLC-MS/MS method applied to an untargeted metabolomics approach for the diagnosis of “olive quick decline syndrome”

Analytical and Bioanalytical Chemistry ◽

10.1007/s00216-021-03279-7 ◽

2021 ◽

Author(s):

Sabrina Di Masi ◽

Giuseppe E. De Benedetto ◽

Cosimino Malitesta ◽

Maria Saponari ◽

Cinzia Citti ◽

...

Keyword(s):

Bacterial Infections ◽

High Performance ◽

High Resolution Mass Spectrometry ◽

Xylella Fastidiosa ◽

Long Chain Fatty Acids ◽

Powerful Approach ◽

Diffusible Signal Factor ◽

Profile Changes ◽

Olive Quick Decline Syndrome ◽

Olive Trees

AbstractOlive quick decline syndrome (OQDS) is a disorder associated with bacterial infections caused by Xylella fastidiosa subsp. pauca ST53 in olive trees. Metabolic profile changes occurring in infected olive trees are still poorly investigated, but have the potential to unravel reliable biomarkers to be exploited for early diagnosis of infections. In this study, an untargeted metabolomic method using high-performance liquid chromatography coupled to quadrupole-time-of-flight high-resolution mass spectrometry (HPLC-ESI-Q-TOF-MS) was used to detect differences in samples (leaves) from healthy (Ctrl) and infected (Xf) olive trees. Both unsupervised and supervised data analysis clearly differentiated the groups. Different metabolites have been identified as potential specific biomarkers, and their characterization strongly suggests that metabolism of flavonoids and long-chain fatty acids is perturbed in Xf samples. In particular, a decrease in the defence capabilities of the host after Xf infection is proposed because of a significant dysregulation of some metabolites belonging to flavonoid family. Moreover, oleic acid is confirmed as a putative diffusible signal factor (DSF). This study provides new insights into the host-pathogen interactions and confirms LC-HRMS-based metabolomics as a powerful approach for disease-associated biomarkers discovery in plants. Graphical abstract

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Genetic diversity and breeding history of Winter Mushroom (Flammulina velutipes) in China uncovered by genomic SSR markers

Gene ◽

10.1016/j.gene.2016.07.009 ◽

2016 ◽

Vol 591 (1) ◽

pp. 227-235 ◽

Cited By ~ 19

Author(s):

Xiao Bin Liu ◽

Bang Feng ◽

Jing Li ◽

Chen Yan ◽

Zhu L. Yang

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Flammulina Velutipes ◽

Genomic Ssr ◽

History Of ◽

Breeding History

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Increase in ring width, vessel number and δ18O in olive trees infected with Xylella fastidiosa

Tree Physiology ◽

10.1093/treephys/tpaa095 ◽

2020 ◽

Vol 40 (11) ◽

pp. 1583-1594

Author(s):

Erika Sabella ◽

Samuele Moretti ◽

Holger Gärtner ◽

Andrea Luvisi ◽

Luigi De Bellis ◽

...

Keyword(s):

Xylella Fastidiosa ◽

Ring Width ◽

Plant Diseases ◽

Susceptible Cultivar ◽

Water Conductivity ◽

Leaf Transpiration ◽

Leaf Level ◽

Olive Quick Decline Syndrome ◽

Olive Trees ◽

Tree Stem

Abstract Xylella fastidiosa (Xf) Wells, Raju et al., 1986 is a bacterium that causes plant diseases in the Americas. In Europe, it was first detected on the Salento Peninsula (Italy), where it was found to be associated with the olive quick decline syndrome. Here, we present the results of the first tree-ring study of infected and uninfected olive trees (Olea europaea L.) of two different cultivars, one resistant and one susceptible, to establish the effects induced by the spread of the pathogen inside the tree. Changes in wood anatomical characteristics, such as an increase in the number of vessels and in ring width, were observed in the infected plants of both the cultivars Cellina di Nardò (susceptible to Xf infection) and Leccino (resistant to Xf infection). Thus, whether infection affects the mortality of the tree or not, the tree shows a reaction to it. The presence of occlusions was detected in the wood of both 4-year-old branches and the tree stem core. As expected, the percentage of occluded vessels in the Xf-susceptible cultivar Cellina di Nardò was significantly higher than in the Xf-resistant cultivar Leccino. The δ 18O of the 4-year-old branches was significantly higher in infected trees of both cultivars than in noninfected trees, while no variations in δ 13C were observed. This suggests a reduction in leaf transpiration rates during infection and seems to be related to the occlusions observed in rings of the 4-year-old branches. Such occlusions can determine effects at leaf level that could influence stomatal activity. On the other hand, the significant increase in the number of vessels in infected trees could be related to the tree’s attempt to enhance water conductivity in response to the pathogen-induced vessel occlusions.

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The Xylella fastidiosa-Resistant Olive Cultivar “Leccino” Has Stable Endophytic Microbiota during the Olive Quick Decline Syndrome (OQDS)

Pathogens ◽

10.3390/pathogens9010035 ◽

2019 ◽

Vol 9 (1) ◽

pp. 35 ◽

Cited By ~ 7

Author(s):

Marzia Vergine ◽

Joana B. Meyer ◽

Massimiliano Cardinale ◽

Erika Sabella ◽

Martin Hartmann ◽

...

Keyword(s):

Xylella Fastidiosa ◽

Resistance Mechanisms ◽

16S Rrna Genes ◽

Rrna Genes ◽

Olive Cultivar ◽

Olive Quick Decline Syndrome ◽

Olive Trees ◽

Potential Interactions ◽

Highly Virulent

Xylella fastidiosa is a highly virulent pathogen that causes Olive Quick Decline Syndrome (OQDS), which is currently devastating olive plantations in the Salento region (Apulia, Southern Italy). We explored the microbiome associated with X. fastidiosa-infected (Xf-infected) and -uninfected (Xf-uninfected) olive trees in Salento, to assess the level of dysbiosis and to get first insights into the potential role of microbial endophytes in protecting the host from the disease. The resistant cultivar “Leccino” was compared to the susceptible cultivar “Cellina di Nardò”, in order to identify microbial taxa and parameters potentially involved in resistance mechanisms. Metabarcoding of 16S rRNA genes and fungal ITS2 was used to characterize both total and endophytic microbiota in olive branches and leaves. “Cellina di Nardò” showed a drastic dysbiosis after X. fastidiosa infection, while “Leccino” (both infected and uninfected) maintained a similar microbiota. The genus Pseudomonas dominated all “Leccino” and Xf-uninfected “Cellina di Nardò” trees, whereas Ammoniphilus prevailed in Xf-infected “Cellina di Nardò”. Diversity of microbiota in Xf-uninfected “Leccino” was higher than in Xf-uninfected “Cellina di Nardò”. Several bacterial taxa specifically associated with “Leccino” showed potential interactions with X. fastidiosa. The maintenance of a healthy microbiota with higher diversity and the presence of cultivar-specific microbes might support the resistance of “Leccino” to X. fastidiosa. Such beneficial bacteria might be isolated in the future for biological treatment of the OQDS.

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Assessment of Genetic Diversity and Population Genetic Structure of Santalum album L. in India by Genic and Genomic SSR markers

10.1101/2021.05.28.446175 ◽

2021 ◽

Author(s):

Tanzeem Fatima ◽

Ashutosh Srivastava ◽

Vageeshbabu S Hanur ◽

M. Srinivasa Rao

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Ssr Markers ◽

Germplasm Conservation ◽

Principal Component ◽

Santalum Album ◽

High Genetic Diversity ◽

Information Index ◽

Genomic Ssr ◽

Santalum Album L

Sandalwood (Santalum album L.) is highly valued aromatic tropical tree. It is known for its high quality heartwood and oil. In this study 39 genic and genomic SSR markers were used to analyze the genetic diversity and population structure of 177 S. album accessions from 14 populations of three states in India. High genetic diversity was observed in terms of number of alleles 127 expected heterozygosity (He) ranged from 0.63-0.87 and the average PIC was 0.85. The selected population had relatively high genetic diversity with Shannons information index (I) >1.0. 0.02 mean coefficient of genetic differentiation (FST) and 10.55 gene flow were observed. AMOVA revealed that 92% of the variation observed within individuals. Based on cluster and Structure result individuals were not clustered as per their geographical origin. Furthermore the clusters were clearly distinguished by principal component analysis analysis and the result revealed that PC1 reflected the moderate contribution in genetic variation (6%) followed by PC2 (5.5%). From this study, high genetic diversity and genetic differentiation was found in S. album populations. The genetic diversity information of S. album populations can be used for selection of superior genotypes and germplasm conservation to promote the tree improvement of S. album populations.

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Aphrophoridae Role in Xylella fastidiosa subsp. pauca ST53 Invasion in Southern Italy

Pathogens ◽

10.3390/pathogens10081035 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1035

Author(s):

Ugo Picciotti ◽

Nada Lahbib ◽

Valdete Sefa ◽

Francesco Porcelli ◽

Francesca Garganese

Keyword(s):

Pest Management ◽

Plant Pathogen ◽

Southern Italy ◽

Xylella Fastidiosa ◽

Xylem Sap ◽

Disease Spread ◽

Insect Vector ◽

Transmission Control ◽

Olive Quick Decline Syndrome ◽

Olive Trees

The Philaenus spumarius L. (Hemiptera Aphrophoridae) is a xylem-sap feeder vector that acquires Xylella fastidiosa subsp. pauca ST53 during feeding on infected plants. The bacterium is the plant pathogen responsible for olive quick decline syndrome that has decimated olive trees in Southern Italy. Damage originates mainly from the insect vector attitude that multiplies the pathogen potentialities propagating Xf in time and space. The principal action to manage insect-borne pathogens and to contain the disease spread consists in vector and transmission control. The analysis of an innovative and sustainable integrated pest management quantitative strategy that targets the vector and the infection by combining chemical and physical control means demonstrates that it is possible to stop the Xylella invasion. This review updates the available topics addressing vectors’ identification, bionomics, infection management, and induced disease by Xylella invasion to discuss major available tools to mitigate the damage consequent to the disease.

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Ionomic Differences between Susceptible and Resistant Olive Cultivars Infected by Xylella fastidiosa in the Outbreak Area of Salento, Italy

Pathogens ◽

10.3390/pathogens8040272 ◽

2019 ◽

Vol 8 (4) ◽

pp. 272 ◽

Cited By ~ 10

Author(s):

Giusy D’Attoma ◽

Massimiliano Morelli ◽

Pasquale Saldarelli ◽

Maria Saponari ◽

Annalisa Giampetruzzi ◽

...

Keyword(s):

Inductively Coupled Plasma ◽

Xylella Fastidiosa ◽

Optical Emission ◽

Host Genotype ◽

Bacterial Populations ◽

Inductively Coupled ◽

Outbreak Area ◽

Olive Cultivars ◽

Olive Quick Decline Syndrome ◽

Olive Trees

Olive quick decline syndrome (OQDS) is a devastating disease of olive trees in the Salento region, Italy. This disease is caused by the bacterium Xylella fastidiosa, which is widespread in the outbreak area; however, the “Leccino” variety of olives has proven to be resistant with fewer symptoms and lower bacterial populations than the “Ogliarola salentina” variety. We completed an empirical study to determine the mineral and trace element contents (viz; ionome) of leaves from infected trees comparing the two varieties, to develop hypotheses related to the resistance of Leccino trees to X. fastidiosa infection. All samples from both cultivars tested were infected by X. fastidiosa, even if leaves were asymptomatic at the time of collection, due to the high disease pressure in the outbreak area and the long incubation period of this disease. Leaves were binned for the analysis by variety, field location, and infected symptomatic and infected asymptomatic status by visual inspection. The ionome of leaf samples was determined using inductively coupled plasma optical emission spectroscopy (ICP-OES) and compared with each other. These analyses showed that Leccino variety consistently contained higher manganese (Mn) levels compared with Ogliarola salentina, and these levels were higher in both infected asymptomatic and infected symptomatic leaves. Infected asymptomatic and infected symptomatic leaves within a host genotype also showed differences in the ionome, particularly a higher concentration of calcium (Ca) and Mn levels in the Leccino cultivar, and sodium (Na) in both varieties. We hypothesize that the ionome differences in the two varieties contribute to protection against disease caused by X. fastidiosa infection.

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Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

Agronomy ◽

10.3390/agronomy10010068 ◽

2020 ◽

Vol 10 (1) ◽

pp. 68 ◽

Cited By ~ 2

Author(s):

Kyung Jun Lee ◽

Jung-Ro Lee ◽

Raveendar Sebastin ◽

Gyu-Taek Cho ◽

Do Yoon Hyun

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Ssr Markers ◽

Gene Diversity ◽

Research Effort ◽

Molecular Genetic ◽

Allelic Diversity ◽

Perennial Herb ◽

Molecular Evidence ◽

Breeding Lines

Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth habits. In the present study, genetic diversity and population structure of ginseng germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea were analyzed to provide basic data for future preservation and breeding of ginseng genetic resources. Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 1109 ginseng accessions. Among 1109 ginseng accessions, 1042 (94.0%) accessions were landraces and 66 (6.0%) accessions were breeding lines (61 accessions, 5.5%) or cultivars (5 accessions, 0.5%). SSR markers revealed 56 different alleles with an average of 3.29 alleles per locus. The average gene diversity was 0.49. Analysis of molecular variance showed that 91% of allelic diversity was attributed to individual accessions within clusters while only 9% was distributed among clusters. Using discriminant analysis of principal components, 12 clusters were detected in 1109 ginseng accessions. The results of this study provide molecular evidence for the narrow genetic base of ginseng germplasm in NAC. For the broad understanding and efficient use of ginseng germplasm, it is necessary to analyze functional factors and to evaluate morphological traits.

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Diversity, characterization and evaluation in Pummelo (Citrus maxima Merr.) cultivars using SSR markers and quality parameters

Indian Journal of Genetics and Plant Breeding (The) ◽

10.31742/ijgpb.79.3.9 ◽

2019 ◽

Vol 79 (3) ◽

Author(s):

Shahnawaz . Ahmed ◽

H. S. Rattanpal ◽

Gurteg . Singh

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Morphological Variability ◽

Principal Component ◽

Quality Parameters ◽

Average Value ◽

Low Genetic Diversity ◽

Ssr Loci ◽

Citrus Maxima ◽

Maximum Heterozygosity

Fourteen pummelo (Citrus maxima Merr.) fruit varieties were evaluated through morphological and molecular methods to determine the genetic diversity among them. The analysis showed that maximum contribution (60%) towards diversity was due to the number of fruits per tree and rag percentage. Principal component analysis explained 80.26% of the total observed variability. Molecular characterization of pummelo varieties using 60 SSR markers revealed 26 polymorphic SSR loci having 77 amplified alleles and the number of alleles ranged from 1 to 4 with an average of 2.96 alleles per locus. The highest number of alleles per locus recorded was four as amplified by the SSR markers, CAT01, CS05, CCSM70, CIBE5156, AG14, CIBE4728 and CMS26. The PIC value ranged from 0.12 (CIBE5720) to 0.73 (CAT01) with average value of 0.53. Maximum heterozygosity was found in CAT01 (0.73) followed by CS05 (0.72) and AG14 (0.69). Pink Pummelo and White Pummelo showed the highest genetic similarity having coefficient of 89% and were closely related. The present study indicated low genetic diversity in pummelo varieties despite having high morphological variability, which could be elucidated by the fact that much of the phenotypic variation witnessed may be due to somatic mutations.

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Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

BioMed Research International ◽

10.1155/2018/7658032 ◽

2018 ◽

Vol 2018 ◽

pp. 1-11 ◽

Cited By ~ 20

Author(s):

Saba Jasim Aljumaili ◽

M. Y. Rafii ◽

M. A. Latif ◽

Siti Zaharah Sakimin ◽

Ibrahim Wasiu Arolu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Diversity Index ◽

Gene Diversity ◽

Allelic Diversity ◽

Peninsular Malaysia ◽

Breeding Program ◽

Aromatic Rice ◽

Information Index ◽

Rice Germplasm

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon’s information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei’s gene diversity index of 0.36. The dendrogram based on UPGMA and Nei’s genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

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