Comparative transcriptome analysis reveals key genes and pathways in response to Alternaria alternata apple pathotype infection

Apple leaf spot,caused by the Alternaria alternata apple pathotype(AAAP),is an important fungal disease of apple.To understand the molecular basis of resistance and pathogenesis in apple leaf spot,the transcriptomes of two apple cultivars‘Hanfu'(HF)(resistant)and‘Golden Delicious'(GD)(susceptible)were analyzed at 0,6,18,24 and 48 h after AAAP inoculation by RNA-Seq.At each time point,a large number of significantly differentially expressed genes(DEGs)were screened between AAAP-inoculated and uninoculated apple leaves.Analysis of the common DEGs at four time points revealed significant differences in the resistance of‘HF'and‘GD'apple to AAAP infection.RLP,RNL,and JA signal-related genes were upregulated in both cultivars to restrict AAAP development.However,genes encoding CNLs,TNLs,WRKYs,and AP2s were only activated in‘HF'as part of the resistance response,of which,some play major roles in the regulation of ET and SA signal transduction.Further analysis showed that many DEGs with opposite expression trends in the two hosts may play important regulatory roles in response to AAAP infection.Transient expression of one such gene MdERF110 in‘GD'apple leaves improved AAAP resistance.Collectively,this study highlights the reasons for differential resistance to AAAP infection between‘HF'and‘GD'apples which can theoretically assist the molecular breeding of disease-resistant apple crops.

Escherichia coli Pathotypes in Children with Acute Diarrhea in an Informal Settlement in Nairobi, Kenya

Diarrhea is among the leading causes of morbidity and mortality in children aged Escherichia coli (DEC) accounts for 30% - 40% of childhood diarrhea cases. To identify the pathotypes involved in diarrheal outbreaks in Kenya, we analyzed archived E. coli isolates from children E. coli confirmation and antimicrobial susceptibility testing were done using the VITEK®2 instrument. Pathotype identification was performed via conventional polymerase chain reaction. Of 175 E. coli isolates, 48 (27%) were DEC pathotypes, with enteroaggregative E. coli (EAEC) predominating (71%, 34/48). Enterohemorrhagic (EHEC) and enteropathogenic E. coli (EPEC) represented 19% and 10% of isolates, respectively. Enteroinvasive and enterotoxigenic pathotypes were not identified. All DEC isolates were susceptible to amikacin, ertapenem, imipenem, meropenem and tigecycline. Conversely, most (>80%) isolates were resistant to ampicillin, ampicillin-sulbactam and sulfamethoxazole-trimethoprim. Half of all EAEC and EPEC strains were resistant to cefazolin while half of EHEC isolates were resistant to ciprofloxacin and moxifloxacin. In total, 18 resistance phenotypes were identified with “ampicillin-cefazolin-ampicillin/ sulbactam-sulfamethoxazole/trimethoprim” predominating (33%, 16/48). The majority (81%) of DEC isolates were multidrug-resistant, with extended-spectrum beta-lactamase production identified in 8% of these isolates. This study highlights the predominance of Enteroaggregative E. coli and multidrug resistance of DEC pathotypes. Studying the epidemiology of diarrheal disease and antimicrobial resistance surveillance, will aid in identifying dominant etiological agents of diarrhea and newly emerging resistant strains in informal settlements.

A new pathotype characterization of Daxing and Huangyuan populations of cereal cyst nematode(Heterodera avenae) in China

The cereal cyst nematode（CCN, Heteroder aavenae） causes serious yield loss on cereal crops, especially wheat, worldwide. Daxing population in Beijing City and Huangyuan population in Qinghai Province, China, are two CCN populations. In this study, the CCN pathotypes of Daxing and Huangyuan populations were characterized by tests on 23 standard ＂International Test Assortment＂ with the local species Wenmai 19 as the susceptible control. Tested materials were grouped by three nematode populations＇ virulence on resistant genes（Rha1, Rha2, Rha3, Cre1） and nonresistant genes, varieties and lines. Both Daxing and Huangyuan populations were avirulent to Ortolan（Ha1）. Barley cvs. Ortolan, Siri, Morocco, Bajo Aragon 1-1, and Martin 403-2 were all resistant to both populations. Cultivars Herta, Harlan 43 and wheat Iskamish-K-2-light were all susceptible to Huangyuan population, all of them, however, were resistant to Daxing population. The other five oats were all resistant to the two tested CCN populations. Except Iskamisch K-2-light, all the other wheat cultivars（Capa, Loros×Koga, AUS 10894, and Psathias） were susceptible to Daxing population. Because the pathotypes of the two tested CCN populations in Beijing and Qinghai were not identical to any of the 13 pathotypes previously characterized by the test assortment, we classified Daxing and Huangyuan populations as the new pathotypes, named Ha91.

Pathotypes and Genetic Diversity of Blumeria graminis f.sp.hordei in the Winter Barley Regions in China

Barley powdery mildew caused by Blumeria graminis f. sp. hordei （Bgh） is one of the most destructive foliar diseases of barley in the winter barley region of China. The evaluation and assessment of the virulence and diversity of Bgh populations help to determine effective sources of resistance to the pathogen. 515 isolates were collected from seven populations of Bgh on cultivated barley in seven geographically distant locations in 2006. Their virulence was determined by inoculation onto 26 differential host lines. All of the isolates belonged to 58 pathotypes and 13 of which included 81% of these isolates. The most abundant pathotype was pathotype 0047 （18.3%）, the second most abundant was pathotype 0045 （11.8%） and the third most abundant was pathotype 0057 （7.8%）. Most of virulent genes investigated in this study showed similar frequencies in the seven different areas. These indicate that the seven locations may be in a uniform epidemiological region and barley cultivars in these areas may have similar genetic background. Diversities within these populations and distances between these populations measured by KOIND package were different. Correlations were not found between the genetic distance and the geographical distances between different locations. This suggested that long distance spread and local epidemics existed in the major winter barley growing regions in China.

Pathotypes and Genetic Diversity of Chinese Collections of Elsinoě fawcettii Causing Citrus Scab

Two scab diseases are currently recognized on citrus：citrus scab, caused by Elsino？ fawcettii, and sweet orange scab, caused by E. australis. Although these pathogens are economically important, there is no molecular data on these species in China. Here we use internal transcribed spacer sequence data to report on host-speciifcity and genetic relationships among 46 isolates collected from the main citrus varieties grown across China. All strains isolated were E. fawcettii. Based on pathogenicity testing on 9 different citrus species, isolates were divided into 11 pathotypes （SM, FBHR, SJCR, SPOJCR, SR, SOJG, SPOJC, SRGC, Lemon and two unnamed pathotypes）. SM is a new pathotype, and two isolates did not ift into any of the known pathotypes of E. fawcettii. Inter-simple sequence repeat （ISSR-PCR） assays separated the E. fawcettii isolates into 10 subgroups;the groupings basically corresponded to the pathogenicity test.

Differential Detection and Analysis of Pathotypes and Differentiation against Xanthomonas oryzae pv. oryzae in Southern China

Pathogenic isolates were collected from different rice-cropping regions in southern China to dissect the pathogenic disintegration and variation of Xanthornonas oryzae pv. oryzae （Xoo）. Two sets of rice-Xoo differential hosts, including Chinese system with such five euhivars as IR26, Java14, Nangeng15, Tetep and Jingang 30 and international system with a series of nearisogenic lines （NILs） including IRBB5, IRBB13, IRBB3, IRBB14, IRBB2 and IR24 carrying different known resistance genes,were used to detect pathogenic disintegration for the reaction between host and pathogen with leaf-clippingmethod at the rice booting stage. The results showed the type of the pathogen were divided intosix pathotypes, i.e. , Ⅰ, Ⅱ, Ⅲ, Ⅳ, Ⅴ and Ⅸ based on the Chinese differential system, and seven pathogenicraces including RI, R2, R3, R4, R5, R8 and R10 based on the international differential system. The pathogenicity frequency of Xoo pathotypes V and IV and pathogenic races R8 and R5 were 27.40% , 19.30% and 44.67% , 15.34%, which were considered to be the prevailing races in southern China. Pathogenic rates of pathotypes Ⅳ, Ⅴ, Ⅸ and races R8, R5 against 500 varieties derived from southernChina were 96.40% , 95.00% , 50.40% , 62.00% , and 42.60%, respectively. Among which pathotype Ⅸ was the most virulent pathotype. The pathotype Ⅴ became preponderant pathotype and the new pathotype Ⅸ grew up quickly.

Evaluation of the Pathotypes of Xanthomonas oryzae pv. oryzae and Preliminary Analysis of the Resistant Reactions of Main Japonica Rice in the Yunnan Plateau, China

The pathogenicity of 36 isolates of Xanthomonas oryzae pv. oryzae （Xoo）, which were collected from japonica rice varieties in the Yunnan Plateau, China, was evaluated. It was evaluated on 29 rice varieties including a set of seven varieties to identify pathogenicity, i.e., Haonuoyang, TN1, Kogyoku, Zhenzhu＇ai, IR26, Nanjing 33, and Kinmaze, which may be considered as a set of differential varieties for Xoo races from Yunnan japonica rice. The efficiency of the seven varieties was further confirmed. The results showed reversible and specific interactions between isolates and varieties. The isolates were classified into nine pathotypes from pathotyp Ⅰ to Ⅸ according to their pathogenic reactions on the seven rice varieties. The pathotype V was the epidemic, whereas pathogen Ⅶ was the most pathogenic. Most japonica varieties grown in the Yunnan Plateau were susceptible to Xoo. The rice lines IRBB21 （Xa-21）, Zhachanglong （Xa-22,, Xa- 24,）, and IR1545-339 （xa-5）, which were resistant to all the isolates tested, can be used as donors of resistant genes for bacterial blight in japonica rice breeding in the Yunnan Plateau.

Response of Sorghum Accessions against Newly Documented Pathotypes 5 and 6 of Head Smut Pathogen, <i>Sporisorium reilianum</i>

This study was conducted to identify resistance sources against the newly documented pathotypes (P5 and P6) of Sporisorium reilianum, causing sorghum head smut. A subset of 67 sorghum association panel (SAP) accessions, 29 in 2017 and 38 in 2018 along with checks BTx635 (resistant) and BTx643 (susceptible) were screened in the greenhouse against P5 and P6 pathotypes in two separate experiments in both years. At 18 to 20 days after planting, accessions were inoculated by injecting the seedlings below the apical meristem with sporidial suspensions following an established inoculation procedure. Three accessions (PI656091, PI533919, and PI533821) in 2017 and 17 accessions (PI597961, PI656071, PI656048, PI576435, PI534075, PI534145, PI656057, PI576437, PI651492, PI656014, PI656025, PI655999, PI656010, PI656082, PI534123, PI533927, PI656100) in 2018 were identified as potential resistant sources to both P5 and P6 pathotypes of S. reilianum. These SAP accessions are new sources that can be further used to develop new breeding parental lines and hybrids and mapping populations for quantitative trait loci markers closely linked to head smut resistance.

Utilization Situation and Prospect of Gene xa5 Against Pathotype Ⅴ of Rice Bacterial Blight

In recent years,the strong virulence pathotype Ⅴ of rice bacterial blight grew up quickly in Southern China,which has become a major population and spread to the rice regions of Jiangsu and Zhejiang provinces in Southern China.Since pathotype Ⅴ caused serious bacterial blight disease in rice production regions,it is urgent to breed and promote resistant varieties against pathotype Ⅴ.The most economic and effective measure to control rice bacterial blight is to breed resistant cultivars for widely planting using resistance genes.The Institute of Plant Protection,Guangdong Academy of Agricultural Sciences,and Agricultural Science Research Institute of Panyu District of Guangzhou used IRBB5 carrying the recessive xa5 gene from IRRI that is resistant to pathotype Ⅴ to breed resistant varieties with rice blast resistance source,through hybridization,multiple cross,pedigree selection and synchronous resistance evaluation.We successfully bred series of new resistant rice varieties such as Baijiangzhan,Baijingzhan and Baisizhan,which showed resistance to strong virulence pathotype Ⅴ(grade 1-3)of bacterial blight and rice blast(mediate to high resistance),good grain quality(level 3 of rice quality of Guangdong),and yield equivalent to major cultivars(compared with region trial control cultivars of Guangdong).These new resistant varieties were promoted and planted in the strong virulence pathotype Ⅴ region along the west coast of Guangdong,which showed favorable superiority and wide application prospect in controlling rice bacterial blight with resistance varieties.

Impact of Crop Rotation on Pathotype and Genetic Structure of Phythophthora sojae in Fields

To estimate the impact of crop rotation on the pathotype and genetic structure of Phythophthora sojae in fields, 372 isolates of P. sojae were obtained from long-term localisation experimental fields in Heilongjiang Province of China. The hypocotyl inoculation method was used to characterize the virulence of P. sojae on 13 differential cultivars, and the amplified fragment length polymorphism（AFLP） technique was used to analyze difference in the genetic structure of P. sojae. The results indicated that an abundant diversity of genetic structures and pathotypes of P. sojae, a more uniform distribution of pathotypes and less dominance of pathotypes occurred in corn-soybean and wheat-soybean rotation fields than in a continuous soybean mono-cropping field. These findings suggested that P. sojae did not easily become the dominant race in rotation fields, which maintain disease resistance in soybean varieties. Therefore, the results of this study suggested that Phytophthora stem and root rot of soybeans could be effectively controlled by rotating soybeans with non-host crops of corn and wheat.

Morphological characterization of fungi associated with the ascochyta blight complex and pathogenic variability of Mycosphaerella pinodes on field pea crops in central Alberta

Field pea crops in central Alberta were surveyed for ascochyta blight from 2011 to 2012 and fungal isolates were recovered from foliar lesions on selected plants. Cultural and microscopic characterization of the 275 isolates obtained revealed that 272 were of Mycosphaerella pinodes and three were of Phoma medicaginis var. pinodella. Ascochyta pisi or Phoma koolunga were not identified. Isolates of M. pinodes were divided into two groups,GI and GII, based on visual assessment of culture characteristics. GI isolates(light to dark, mostly gray colony color; pycnidial distribution radial and concentric; conidia10.5–14.5 × 4.2–6.2 μm most with one septum, occasionally two, constricted at the septum;spore mass light buff to flesh color) were predominant(83%), while GII isolates(dark to gray colony color; pycnidia abundant; conidia 8–16 × 3.5–6.2 μm most with 1 septum, constricted at the septum; spore mass light buff to flesh color) were less common(17%). The cultures of GII isolates were similar to recent descriptions of A. pisi, but they differed in spore color. In a host differential study, 13 pathotypes of M. pinodes were identified from 110 single-spore isolates. Pathotype I was predominant(88 isolates) and virulent on all nine differential genotypes. The other pathotypes(pathotypes II–XIII) were rare(1–6 isolates of each).Comparison of the present results with earlier studies suggests that pathotype I has been prevalent for many years, and that its aggressiveness on the host differentials has increased over time. Emphasis should be placed on breeding for resistance to M. pinodes in field pea cultivars intended for deployment in central Alberta.

The Effects of Host Diversity in Anthracnose Management and Race Composition of Colletotrichum sublineolum in Sorghum Lineage Mixtures

Alternative strategies of management of sorghum diseases were implemented using field experiments conducted in Embrapa Maize and Sorghum Research Center,Brazil in 2001 until 2003 to evaluate the efficacy of lineage mixtures of Sorghum bicolor for the control of anthracnose(caused by Colletotrichum sublineolum).The calculated values for disease severity considered the area under the disease progress curve(AUDPC)observed for the nine susceptible and resistant elite strains of sorghum planted in 30 stands randomly.Each stand was drawn in mixtures of three genotypes each,in the same proportions per plant.This design was compared with the severity of the disease measured in AUDPC calculated for each of the same nine strains of sorghum in pure stands.In most of the cases,the disease severity on the susceptible cultivars was decreased;and in some cases,reached 85%of disease reduction compared with disease progress in pure stand of correspondent plant.The implication and effect of these sorghum mixtures on the populations of C.sublineolum on each treatment were evaluated and revealed that there was an increase of frequency of complex races in most of these mixtures and a highest phenotypic diversity for virulence to pathogen populations from pure stands,than the characterized on populations collected from the mixtures,despite of the effectiveness on decrease of the anthracnose severity.

Genetic sources and loci for wheat head blast resistance identified by genome-wide association analysis

The emergence and spread of wheat blast caused by fungal pathogen Magnaporthe oryzae pathotype Triticum is a threat to global wheat production.The resistance level and genetic loci for blast resistance in Chinese germplasm remain unknown.A panel of 266 bread wheat accessions from China,CIMMYTMexico and other countries was screened for head blast resistance under 12 field experiments in Bolivia and Bangladesh.Subsequently,a genome-wide association study was performed to understand the genetic basis of wheat blast resistance.The average blast index of all the accessions was 53.7%±12.7%,and 10 accessions including Chinese accessions Yumai 10 and Yu 02321 showed moderate to high levels of blast resistance,accounting for only 3.8%in the panel.Fifty-eight significant SNPs clustered in a 28.9 Mb interval on the 2 AS/2 NS translocation region,explaining phenotypic variation between10.0%and 35.0%.The frequency of the 2 AS/2 NS translocation in the Chinese accessions was as low as4.5%.These results indicated that the 2 NS fragment was the only major locus conferring resistance to wheat blast in this panel,and the resistant and moderately resistant lines identified could be deployed in breeding.

Vegetative Compatibility and Virulence Diversity of Verticillium dahliae from Okra (Abelmoschus esculentus) Plantations in Turkey and Evaluation of Okra Landraces for Resistance to V. dahliae

Forty-four V.dahliae isolates were collected from symptomatic vascular tissues of okra plants each from a different field in eight provinces located in the eastern Mediterranean and western Anatolia regions of Turkey during 2006-2009.Nitrate-nonutilizing(nit)mutants of V.dahliae from okra were used to determine heterokaryosis and genetic relatedness among isolates.All isolates from okra plants were grouped into two vegetative compatibility groups(VCGs)(1 and 2)and three subgroups as 1A(13.6%,6/44),2A(20.5%,9/44)and 2B(65.9%,29/44)according to international criteria.Pathogenicity tests were performed on a susceptible local okra(A.esculentus)landrace in greenhouse conditions.All isolates from VCG1A and VCG2B induced defoliation(D)and partial defoliation(PD)symptoms,respectively.Other isolates from VCG2A gave rise to typical leaf chlorosis symptoms without defoliation.The obtained data showed that the virulence level of V.dahliae isolates from okra was related to their VCG belongings.Eighteen okra landraces from diverse geographical origins were screened for resistance to VCG2B and VCG1A of V.dahliae.The results indicated that all landraces were more susceptible to highly virulent VCG1A-D pathotype displaying D or PD symptoms depending on their susceptibility levels with a mean disease severity index of 3.52 than to less virulent VCG2B-PD pathotype of V.dahliae displaying PD and ND symptoms with a mean disease severity index of 2.52.Significant differences were observed among the landraces;however,none of them exhibited a level of resistance.Okra landraces;Çorum,Hatay Has and Sanlıurfa displayed the lowest level of susceptibility or little tolerance to both D and PD pathotypes.VCG2B of PD was prevailing in the surveyed areas and VCG1A of D was the most virulent of the VCGs identified.Introduction of resistant genotypes to Turkish okra germplasm from different sources and breeding new resistant okra cultivars are critical for the sustainability of okra production.

Pathogenic and Genetic Diversity of Magneporthe oryzae Populations from Sri Lanka

The present study was undertaken to determine the pathogenic and the genetic diversity of the isolates of M.oryzae collected from the wet,intermediate and dry zones of Sri Lanka with a view to develop rice varieties conferring durable resistance to rice blast.No significant morphological or growth variations existed amongst the isolates studied.The genetic diversity of isolates determined by carrying out Pot2 transposable element based on repetitive-PCR revealed that the majority of isolates （92%） clustered into a single group with 45.4% similarity.The existence of nine pathotypes was identified by observing the reaction type of isolates on 16 different rice lines.Pathotype 1 which was distributed in all zones affected only one differential line.Pathotype 2 which was able to infect six lines was restricted only to the dry zone of Sri Lanka.Of the 16 rice lines,seven lines,K3 （Pik-h）,C101A51 （Piz5）,K1 （Pita）,C105TTP2L9 （Pita）,K59 （Pit）,Shin （Pish） and WHD-1S-75-1-127 （Pi9） had highly effective blast resistance.None of the isolates of the fungus showed any virulence against the seven lines.These seven blast resistant lines can be used in the breeding programmes in Sri Lanka for development of lines conferring durable resistance to rice blast.

Water Consumption and Vegetative Growth Progress in Resistant and Susceptible Olive Cultivars Infected by Verticillium dahliae

Purpose: Water consumption and vegetative growth in resistant (“Frantoio”) and susceptible (“Picual”) olive cultivars infected with Verticillium dahliae were assessed. Methods: Plants were inoculated with the pathogen and disease evaluated in growth chamber. Mean daily water consumption and vegetative growth were recorded during 13 weeks. Results: Water consumption significantly decreased in inoculated plants compared to non-inoculated plants during the 3rd - 6th weeks after inoculation period. From the 9th week, a significantly lower consumption occurred in infected “Picual” plants compared with “Frantoio” plants. Vegetative growth was reduced in inoculated plants of both cultivars, although the reduction of the fresh weight was remarkably higher in “Picual” compared with controls due to defoliation and tissue desiccation, impeding the production of new shoots and leaves. Conversely, in “Frantoio”, defoliation was significantly reduced to low levels. Conclusions: Water consumption and vegetative growth in plants of resistant (“Frantoio”) and susceptible (“Picual”) olive cultivars inoculated by Verticillium dahliae were consistently associated with the progress of the wilt symptoms and the level of resistance of the cultivar. Growth and water consumption reductions in “Picual” were irreversible in almost all plants, while “Frantoio” plants were able to maintain water translocation, overcome the infection and avoid vascular occlusion, and restart vegetative growth.