Genetic diversity of Venturia inaequalis isolates (Apple scab) in China and U.K. determined by SSR markers

Analysis of genetic diversity and population structure of Magnaporthe grisea, the causal agent of foxtail millet blast using microsatellites

Foxtail millet blast caused by Magnaporthe grisea is becoming a severe problem in foxtail millet growing regions of India. The genetic diversity and population structure of foxtail millet infecting M. grisea is crucial for developing effective management strategies, such as breeding blast-resistant cultivars. We analyzed thirty-two M. grisea isolates from ten foxtail millet-growing districts in Tamil Nadu, India for genetic diversity using twenty-nine microsatellite or simple sequence repeat (SSR) markers. A total of 103 alleles were identified with a mean of 3.55 alleles/locus. Gene diversity ranged from 0.170 to 0.717, while major allelic frequencies ranged from 0.344 to 0.906. The polymorphism information content (PIC) ranged from 0.155 to 0.680, with a mean value of 0.465. Population structure analysis of the genomic data sets revealed two major populations (SP1 and SP2) with different levels of ancestral admixture among the 32 blast isolates. Phylogenetic analysis classified the isolates into three major clusters. Analysis of molecular variance (AMOVA) showed high genetic variation among individuals and less among populations. Principal Coordinate Analysis (PCoA) revealed 27.16% genetic variation among populations. The present study provides the first report on the genetic diversity and population structure of the foxtail millet-infecting M. grisea population in Tamil Nadu, which could be useful for the development of blast-resistant foxtail millet cultivars.

Genetic footprint of population diversity and genetic structure of Venturia inaequalis infecting apple (Malus × domestica Borkh.)

Apple scab instigated by Venturia inaequalis impels remarkable losses to apple fruit production. In an effort to comprehend the key mechanisms of evolutionary potential defining V. inaequalis population, 132 isolates of V. inaequalis from five commercial apple orchards were collected and assayed using 14 microsatellite markers. The average diversity was observed within the individuals of populations based on the Shannon-Wieners index (I) and observed heterozygosity (Ho) was average but considerably lower than expected heterozygosity (He). The genetic differentiation based on FST values was revealed as an average measure of divergence between populations and had varying proportions of gene flow and migration among themselves. Analysis of Molecular Variance (AMOVA) revealed that variance (94%) was dispersed across individuals with a significant (6%) variation between populations from different regions. To examine host specialization within the V. inaequalis population, the assignment approach based on K-means of clustering (an unsupervised machine learning approach), revealed that the clustering method supported three clusters at (K = 3) and three major clusters were also observed in Principle Component Analysis (PCA). Additionally, Nei's genetic distance values, pairwise estimates of genetic differentiation, dendrogram using the neighbor-joining and PCoA revealed the random distribution of V. Inaequalis isolates that depicted a high proportion of genotypic diversity within populations and population genetic structure.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03672-2.

Secretomic Insights into the Pathophysiology of Venturia inaequalis: The Causative Agent of Scab, a Devastating Apple Tree Disease

Apple scab, caused by Venturia inaequalis, is one of the world's most commercially significant apple diseases. The fungi have a catastrophic impact on apples, causing considerable losses in fruit quality and productivity in many apple-growing locations despite numerous control agents. Fungi secrete various effectors and other virulence-associated proteins that suppress or alter the host's immune system, and several such proteins were discovered in this work. Using state-of-the-art bioinformatics techniques, we examined the V. inaequalis reference genome (EU-B04), resulting in the identification of 647 secreted proteins, of which 328 were classified as small secreted proteins (SSPs), with 76.52% of SSPs identified as anticipated effector proteins. The more prevalent CAZyme proteins were the enzymes engaged in plant cell wall disintegration (targeting pectin and xylanase), adhesion and penetration (Cutinases/acetyl xylan esterase), and reactive oxygen species formation (multicopper oxidases). Furthermore, members of the S9 prolyl oligopeptidase family were identified as the most abundant host defense peptidases. Several known effector proteins were discovered to be expressed during the V. inaequalis infection process on apple leaves. The present study provides valuable data that can be used to develop new strategies for controlling apple scab.

Genetic diversity of Venturia inaequalis isolates from the scabs in apple trees in Gansu Province, China, using AFLP markers

Apple scab is a serious disease that restricts the growth of cultivated apples. The objective of this study is to investigate the genetic variations and genetic structure of Venturia inaequalis in Gansu Province, China. 108 isolates of the pathogen V. inaequalis from the Jingning, Lingtai, Jingchuan, Xifeng, Ning and Maiji regions were collected, and their genetic diversity was analyzed using AFLP molecular marker technique. The results showed that genetic diversity was present among the isolates but was not statistically significant. Genetic distance values ranged from 0.0095 to 0.0762. Cluster analysis results showed that the 108 isolates could be divided into two clusters using a similarity coefficient of 0.69. A total of 104 isolates were contained in cluster I while four isolates were contained in Cluster II. From the AMOVA analysis, 98% of variations were observed within the same region, while 2% were observed across different regions. The analysis of population structure showed that 108 isolates had two common ancestors, with the Jingning isolates mainly being derived from the red ancestor. PCoA analysis showed that the Jingning isolates were independent to a certain extent. The different geographical location caused the genetic difference of the isolates. The genetic diversity of apple scab in Gansu Province is greatly aided by this work, which also offers a theoretical foundation for the use of molecular markers in assisted breeding to create novel resistant types.

Strong Genetic Differentiation between Generalist Populations of Venturia inaequalis and Populations from Partially Resistant Apple Cultivars Carrying Rvi3 or Rvi5

The ascomycete fungus Venturia inaequalis causes scab disease, a major problem in apple production. The utilization of resistant cultivars is hindered by emerging new pathogen races, which erode their resistance. Increasing our knowledge on the population genetic processes of the fungus can contribute to the development of resistance gene deployment strategies and more durable resistance. We investigated the effect of four scab race indicator cultivars, ‘Gala’ (no R-gene), ‘Golden Delicious’ (Rvi1), ‘Geneva’ (Rvi3, complex), and OR45t132 (Rvi5), on the V. inaequalis population genetic structure and diversity. Sixty-six monosporic fungal isolates from the four cultivars were genotyped with seven simple sequence repeat primers. Furthermore, the partial resistance of the indicators and the pathogenicity profile of the conidia from each host were assessed. The genetic diversity and structure of the investigated V. inaequalis subpopulations correspond to the partial resistance of the original hosts as well as the subpopulations’ pathogenicity profiles. Indicators carrying Rvi3 and Rvi5 had strongly diverged and specialized V. inaequalis populations on them and fewer symptoms on the field. In line with the complete breakdown of the Rvi1 gene, the population from ‘Golden Delicious’ did not segregate from the susceptible ‘Gala’, and virulence towards Rvi1 was present in all subpopulations.

Genetic Diversity of Venturia inaequalis in Latvia Revealed by Microsatellite Markers

Apple scab caused by the ascomycete Venturia inaequalis is an economically significant disease worldwide. The annual sexual reproduction of V. inaequalis leads to high variation, changes in the population's genetic structure and adaptations to the changing environment, including overcoming the host's resistance. The objective of this study is to characterise and assess the genetic diversity of V. inaequalis populations in two main apple-growing regions in Latvia. In total, 143 V. inaequalis isolates were collected from Latvia, six reference strains with known virulence were obtained from other countries, and all strains were genotyped by 12 SSR markers. The SSR markers were highly variable and informative, identifying 158 alleles that ranged from two to 29 per locus. The Bayesian clustering identified three genetic lineages among the Latvian isolates that did not correlate to the geographic origin, host genotype, organ (leaves or fruits) from which the pathogen was isolated, time of collection, and type of isolation (single conidium or ascospore). The possible relatedness to virulence was detected when reference strains with known virulence were included in the analysis. Our findings correspond with previous studies demonstrating that V. inaequalis in Europe has a high genetic diversity within populations, but low diversity among the populations.

Population Genetic Characteristics and Mating Type Frequency of Venturia effusa from Pecan in South America

Scab, caused by the plant-pathogenic fungus Venturia effusa, is a major disease of pecan in South America, resulting in loss of quantity and quality of nut yield. Characteristics of the populations of V. effusa in South America are unknown. We used microsatellites to describe the genetic diversity and population structure of V. effusa in South America, and determined the mating type status of the pathogen. The four hierarchically sampled orchard populations from Argentina (AR), Brazil (BRC and BRS), and Uruguay (UR) had moderate to high genotypic and gene diversity. There was evidence of population differentiation (F_st = 0.196) but the correlation between geographic distance and genetic distance was not statistically significant. Genetic differentiation was minimal between the UR, BRC, and BRS populations, and these populations were more clearly differentiated from the AR population. The MAT1-1 and MAT1-2 mating types occurred in all four orchards and their frequencies did not deviate from the 1:1 ratio expected under random mating; however, multilocus linkage equilibrium was rejected in three of the four populations. The population genetics of South American populations of V. effusa has many similarities to the population genetics of V. effusa previously described in the United States. Characterizing the populations genetics and reproductive systems of V. effusa are important to establish the evolutionary potential of the pathogen and, thus, its adaptability-and can provide a basis for informed approaches to utilizing available host resistance and determining phytosanitary needs.