Assessment and modeling using machine learning of resistance to scald (Rhynchosporium commune) in two specific barley genetic resources subsets

Barley production worldwide is limited by several abiotic and biotic stresses and breeding of highly productive and adapted varieties is key to overcome these challenges. Leaf scald, caused by Rhynchosporium commune is a major disease of barley that requires the identification of novel sources of resistance. In this study two subsets of genebank accessions were used: one extracted from the Reference set developed within the Generation Challenge Program (GCP) with 191 accessions, and the other with 101 accessions selected using the filtering approach of the Focused Identification of Germplasm Strategy (FIGS). These subsets were evaluated for resistance to scald at the seedling stage under controlled conditions using two Moroccan isolates, and at the adult plant stage in Ethiopia and Morocco. The results showed that both GCP and FIGS subsets were able to identify sources of resistance to leaf scald at both plant growth stages. In addition, the test of independence and goodness of fit showed that FIGS filtering approach was able to capture higher percentages of resistant accessions compared to GCP subset at the seedling stage against two Moroccan scald isolates, and at the adult plant stage against four field populations of Morocco and Ethiopia, with the exception of Holetta nursery 2017. Furthermore, four machine learning models were tuned on training sets to predict scald reactions on the test sets based on diverse metrics (accuracy, specificity, and Kappa). All models efficiently identified resistant accessions with specificities higher than 0.88 but showed different performances between isolates at the seedling and to field populations at the adult plant stage. The findings of our study will help in fine-tuning FIGS approach using machine learning for the selection of best-bet subsets for resistance to scald disease from the large number of genebank accessions.

Molecular detection and quantification of Xanthomonas albilineans in juice from symptomless sugarcane stalks using a real-time quantitative PCR assay

Leaf scald, a bacterial disease caused by Xanthomonas albilineans (Ashby) Dowson, is a major limiting factor for sugarcane production worldwide. Accurate identification and quantification of X. albilineans is a prerequisite for successful management of this disease. A very sensitive and robust qPCR assay was developed in this study for detection and quantification of X. albilineans using TaqMan probe and primers targeting a putative adenosine triphosphate-binding cassette (ABC) transporter gene (abc). The novel qPCR assay was highly specific to the 43 tested X. albilineans strains belonging to different pulsed-field gel electrophoresis (PFGE) groups. The detection thresholds were 100 copies/µL of plasmid DNA, 100 fg/µL of bacterial genomic DNA, and 100 CFU/ml of bacterial suspension prepared from pure culture. This qPCR assay was 100 times more sensitive than a conventional PCR assay. The pathogen was detected by qPCR in 75.1% (410/546) symptomless stalk samples, whereas only 28.4% (155/546) samples tested positive by conventional PCR. Based on qPCR data, population densities of X. albilineans in symptomless stalks of the same varieties differed between two sugarcane production areas in China, Beihai (Guangxi province) and Zhanjiang (Guangdong province), and no significant correlation between these populations was identified. Furthermore, no relationship was found between these populations of the pathogen in asymptomatic stalks and the resistance level of the sugarcane varieties to leaf scald. The newly developed qPCR assay proved to be highly sensitive and reliable for the detection and quantification of X. albilineans in sugarcane stalks.

Plum leaf scald: characteristics of the causative agent,symptoms, dissemination, control and prevention

The very slow-growing gram-negative bacterium, Xylella fastidiosa, inhabits the xylem and is vector-borne. It causes several diseases in plants, including plum leaf scald (PLS), which is the main limiting factor over the years for the crop expansion, both in productivity and in cultivation areas in Brazil. There is little information about the management and control of the disease. Brazilian breeding programs of plum trees have launched few resistant cultivars. The aim of this work was to carry out a systematic review with current information regarding PLS, characteristics of the causative agent, symptoms, transmission/dissemination, control and prevention. The use of certified propagation material, free from bacteria and the elimination of infected plants are the main measures used in Brazil. The vast majority of commercial cultivars are highly susceptible to bacteria and only few cultivars of interest have any resistance. In 2017 the Agricultural Research and Rural Extension Company of Santa Catarina launched the ‘Zafira’ plum cultivar, the first cultivar for commercial purposes that is not naturally infected; however, it was observed that the transmission of the bacteria occurs by grafting. The Institute of Rural Development of Paraná IAPAR-EMATER evaluated different plum crosses and concluded that the ‘PR-1095’ genotype was the most resistant and did not show any foliar symptoms of the disease. However, the PCR test revealed the presence of the bacteria, indicating that the genotype is probably tolerant. In contrast, ‘PR 1142’, ‘PR 1149’ and ‘PR 1260’ genotypes do not show symptoms or the presence of the bacteria by PCR, resulting in resistance to the disease. These genotypes have not been released, and further studies are still needed.

Selection of plum genotypes for resistance to leaf scald

ABSTRACT Plum (Prunus salicina Lindl.) cultivation is seriously compromised in Brazil due to the occurrence of leaf scald, a disease caused by the bacterium Xylella fastidiosa subsp. multiplex. The objective of this study was to evaluate plum genotypes agronomically promising for resistance to leaf scald, under natural conditions of occurrence of the disease. Ten out of 50 plum genotypes belonging to the germplasm bank of “Instituto Agronômico do Paraná (IAPAR)” were selected. Five evaluations of leaf scald severity were carried out from January to February (2017 and 2018). Polymerase chain reaction (PCR) was also performed for samples of these genotypes to determine the presence of the bacterium X. fastidiosa subsp. multiplex. The genotypes differed in relation to their susceptibility to leaf scald. PR-1095 was the most resistant genotype and did not show any leaf symptom of the disease. In contrast, genotypes PR-1126 and PR-1137 had the greatest susceptibility to the disease, showing severe scald symptoms. However, PCR revealed the presence of the bacterium even in the most resistant genotypes, indicating, for example, that PR-1095, which had no symptoms of the disease, is probably tolerant to leaf scald.

Pyrenophora teres and Rhynchosporium secalis Establishment in a Mediterranean Malt Barley Field: Assessing Spatial, Temporal and Management Effects

Malt barley is one of the promising crops in Greece, mainly due to high yields and contract farming, which have led to an increase in malt barley acreage. Net form net blotch (NFNB), caused by Pyrenophora teres f. teres, and barley leaf scald, caused by Rhynchosporium secalis, are among the most important barley diseases worldwide and particularly in Greece. Their occurrence in malt barley can exert a significant negative effect on malt barley grain yield and quality. An experimental trial across two growing seasons was implemented in Greece in order (i) to estimate the epidemiology of NFNB and leaf scald in a barley disease-free area when the initial inoculation of the field occurs through infected seeds, (ii) to explore the spatial dynamics of disease spread under the interaction of the nitrogen rate and genotype when there are limited sources of infected host residues in the soil and (iii) to assess the relationship among the nitrogen rate, grain yield, quality variables (i.e., grain protein content and grain size) and disease severity. It was confirmed that both NFNB and leaf scald can be carried over from one season to the next on infected seed under Mediterranean conditions. However, the disease severity was more pronounced after the barley tillering phase when the soil had been successfully inoculated, which supports the hypothesis that the most important source of primary inoculum for NFNB comes from infected host residue. Increasing the rate of nitrogen application, when malt barley was cultivated in the same field for a second year in a row, caused a non-significant increase in disease severity for both pathogens from anthesis onwards. However, hotspot and commonality analyses revealed that spatial and genotypic effects were mainly responsible for hiding this effect. In addition, it was found that the effect of disease infections on yield, grain size and grain protein content varied in relation to the genotype, pathogen and stage of crop development. The importance of crop residues in the evolution of both diseases was also highlighted.