A novel pathogen Fusarium cuneirostrum causing common bean(Phaseolus vulgaris)root rot in China

Several fungal pathogens cause root rot of common bean,among which Fusarium spp.are the most common pathogens causing Fusarium root rot(FRR)worldwide.FRR has been becoming an increasingly severe disease of common bean in China,but the species of Fusarium spp.have remained unclear.Thus,this study was performed to identify the pathogen causing common bean root rot in Liangcheng County,Inner Mongolia,China.Nineteen Fusarium-like isolates were obtained after pathogen isolation and purification.The pathogenicity test indicated that eight isolates caused severe disease symptoms on common bean,while 11 other isolates were not pathogenic.The eight pathogenic isolates,FCL1–FCL8,were identified as Fusarium cuneirostrum by morphological characterization and phylogenetic analysis using partial sequences of EF-1α,ITS,28S,and IGS regions.Host range test showed that the representative F.cuneirostrum isolate FCL3 was also pathogenic to mung bean,while not pathogenic to adzuki bean,chickpea,cowpea,faba bean,pea,and soybean.Moreover,50 common bean and 50 mung bean cultivars were screened for resistance to FRR,and seven highly resistant or resistant cultivars of common bean were identified,while no resistant cultivars of mung bean were screened.This study revealed that F.cuneirostrum was one of common bean FRR pathogens in Inner Mongolia and it could induce mung bean root rot as well.To our knowledge,this is the first report of F.cuneirostrum causing FRR of common bean in China.

Changes in concentrations and transcripts of plant hormones in wheat seedling roots in response to Fusarium crown rot

Fusarium crown rot(FCR) is a soilborne disease causing severe yield losses in many wheat-growing areas of the world. Diseased plants show browning and necrosis of roots and stems causing white heads at maturity. Little is known about the molecular processes employed by wheat roots to respond to the disease. We characterized morphological, transcriptional and hormonal changes in wheat seedling roots following challenge with Fusarium pseudograminearum(Fp), the main pathogen of FCR. The pathogen inhibited root development to various extents depending on plants' resistance level. Many genes responsive to FCR infection in wheat roots were enriched in plant hormone pathways. The contents of compounds involved in biosynthesis and metabolism of jasmonic acid, salicylic acid, cytokinin and auxin were drastically changed in roots at five days post-inoculation. Presoaking seeds in methyl jasmonate for 24 h promoted FCR resistance, whereas presoaking with cytokinin 6-benzylaminopurine made plants more susceptible. Overexpression of TaOPR3, a gene involved in jasmonic acid biosynthesis, enhanced plant resistance as well as root and shoot growth during infection.

Elimination of the yellow pigment gene PSY-E2 tightly linked to the Fusarium head blight resistance gene Fhb7 from Thinopyrum ponticum

Fhb7 is a major gene that was transferred from Thinopyrum ponticum to chromosome 7D of wheat(Triticum aestivum)and confers resistance to both Fusarium head blight(FHB)and Fusarium crown rot(FCR).However,Fhb7 is tightly linked to the PSY-E2 gene,which causes yellow flour,limiting its application in breeding.To break this linkage,marker K-PSY was developed for tagging PSY-E2 and used with Fhb7 markers to identify recombination between the two genes.Screening 21,000 BC1F2 backcross progeny(Chinese Spring ph1bph1b*2/SDAU 2028)revealed two Fhb7^(+)wheat-Tp7el_(2)L lines,Shannong 2–16and Shannong 16–1,that carry a desired truncated Fhb7^(+)translocation segment without PSY-E2.The two lines show levels of resistance to FHB and FCR similar to those of the original translocation line SDAU 2028,but have white flour.To facilitate Fhb7 use in wheat breeding,STS markers were developed and used to isolate Fhb7 on a truncated Tp7el_(2) translocation segment.Near-isogenic lines carrying the Fhb7^(+)segment were generated in the backgrounds of three commercial cultivars,and Fhb7^(+)lines showed increased FHB and FCR resistance without yield penalty.The breakage of the tight linkage between Fhb7 and PSY-E2 via homoeologous recombination provides genetic resources for improvement of wheat resistance to FHB and FCR and permit the large-scale deployment of Fhb7 in breeding using marker-assisted selection.

Genome-wide association study and genomic prediction of Fusarium ear rot resistance in tropical maize germplasm

Fusarium ear rot(FER)is a destructive maize fungal disease worldwide.In this study,three tropical maize populations consisting of 874 inbred lines were used to perform genomewide association study(GWAS)and genomic prediction(GP)analyses of FER resistance.Broad phenotypic variation and high heritability for FER were observed,although it was highly influenced by large genotype-by-environment interactions.In the 874 inbred lines,GWAS with general linear model(GLM)identified 3034 single-nucleotide polymorphisms(SNPs)significantly associated with FER resistance at the P-value threshold of 1×10^(-5),the average phenotypic variation explained(PVE)by these associations was 3%with a range from 2.33%to 6.92%,and 49 of these associations had PVE values greater than 5%.The GWAS analysis with mixed linear model(MLM)identified 19 significantly associated SNPs at the P-value threshold of 1×10^(-4),the average PVE of these associations was 1.60%with a range from 1.39%to 2.04%.Within each of the three populations,the number of significantly associated SNPs identified by GLM and MLM ranged from 25 to 41,and from 5 to 22,respectively.Overlapping SNP associations across populations were rare.A few stable genomic regions conferring FER resistance were identified,which located in bins 3.04/05,7.02/04,9.00/01,9.04,9.06/07,and 10.03/04.The genomic regions in bins 9.00/01 and 9.04 are new.GP produced moderate accuracies with genome-wide markers,and relatively high accuracies with SNP associations detected from GWAS.Moderate prediction accuracies were observed when the training and validation sets were closely related.These results implied that FER resistance in maize is controlled by minor QTL with small effects,and highly influenced by the genetic background of the populations studied.Genomic selection(GS)by incorporating SNP associations detected from GWAS is a promising tool for improving FER resistance in maize.

Integrated transcriptome and metabolite profiling highlights the role of benzoxazinoids in wheat resistance against Fusarium crown rot

Fusarium crown rot(FCR), caused by Fusarium spp., is a chronic and severe plant disease worldwide. In the last years, the incidence and severity of FCR in China has increased to the point that it is now considered a threat to local wheat crops. In this study, for the first time, the metabolites and transcripts responsive to FCR infection in the partial resistant wheat cultivar 04 Zhong 36(04 z36) and susceptible cultivar Xinmai 26(XM) were investigated and compared at 20 and 25 days post inoculation(dpi). A total of 443 metabolites were detected, of which 102 were significantly changed because of pathogen colonization.Most of these 102 metabolites belonged to the flavonoid, phenolic acid, amino acid and derivative classes.Some metabolites, such as proline betaine, lauric acid, ribitol, and arabitol, were stably induced by Fusarium pseudograminearum(Fp) infection at two time points and may have important roles in FCR resistance. In line with the reduced seedling height of 04 z36 and XM plants, RNA-seq analysis revealed that FCR infection significantly affected the photosynthesis activities in two cultivars. Furthermore, 15 jasmonate ZIM-domain genes(JAZ) in the significantly enriched ‘regulation of jasmonic acid mediated signaling pathway’ in 04 z36 were down-regulated. The down-regulation of these JAZ genes in 04 z36 may cause a strong activation of the jasmonate signaling pathway. Based on combined data from gene expression and metabolite profiles, two metabolites, benzoxazolin-2-one(BOA) and 6-methoxy-benzoxazolin-2-one(MBOA), involved in the benzoxazinoid-biosynthesis pathway, were tested for their effects on FCR resistance. Both BOA and MBOA significantly reduced fungal growth in vitro and in vivo, and, thus, a higher content of BOA and MBOA in 04 z36 may contribute to FCR resistance. Above all, the current analysis extends our understanding of the molecular mechanisms of FCR resistance/susceptibility in wheat and will benefit further efforts for the genetic improvement of disease resistance.

Identification of proteins associated with Fusarium crown rot resistance in wheat using label-free quantification analysis

Fusarium crown rot(FCR),typically caused by Fusarium pseudograminearum,is a severe soil-borne disease that,in recent years,has become an emerging threat to Chinese wheat crops.For the first time in this study,we investigated and compared the proteomic characteristics of two Chinese wheat varieties(04 Zhong 36 and Xinmai 26)at 24,48,and 72 h post-inoculation using label-free quantitative proteomic analysis.A total of 9234 proteins were successfully quantified,of which 783 were differentially expressed after inoculation.These proteins were mainly involved in metabolic,single-organism,and cellular processes.Thirty-three proteins associated with defense,cell wall formation,photosynthesis,etc.,showed consistently different expression between the two genotypes at multiple time points.In particular,chitinase,which degrades chitin in the fungal cell wall and limits fungal growth,was exclusively and consistently upregulated in 04 Zhong 36 across the three time points.Other proteins such as flavonoid O-methyltransferase,glycosyltransferase,and peroxidase were only upregulated in 04 Zhong 36,and proteins,including the berberine bridge enzyme and rubisco large subunit-binding protein,were specifically downregulated in Xinmai 26.The expression of transcripts encoding eight selected proteins through qRT-PCR analysis supported the proteomic profiles.Overall,the results of this study allow us to understand FCR resistance in wheat at the protein level.Some proteins and their corresponding genes may be useful resources for the genetic improvement of FCR resistance in wheat.

Delineating a locus conferring Fusarium crown rot resistance on chromosome arm 1HL in barley by developing and analysing a large population derived from near isogenic lines

Fusarium crown rot(FCR),a chronic and severe disease caused by various Fusarium species,is prevalent in semi-arid cropping regions worldwide.One of the major QTL conferring FCR resistance was detected on chromosome arm 1 HL(Qcrs.cpi-1 H)in barley.To develop markers that can be reliably used to incorporate the resistance locus into breeding programs,we developed and assessed a near-isogenic line-derived population consisting of1180 recombinant inbred lines targeting the locus.Using this population,we delineated Qcrs.cpi-1 H into an interval of 0.4 c M covering a physical length of about 487 kb.Six markers co-segregating with this locus were generated.Co-linearity for genes located in this interval between the genome of barley and those of either rice or Brachypodium distachyon is poor.Three genes with non-synonymous variations between the resistant and susceptible lines were identified within the interval.The results reported in this study not only provide markers for integrating Qcrs.cpi-1 H into breeding programs,but also form a solid foundation for cloning the causal gene(s)underlying this locus.

A cell wall invertase modulates resistance to fusarium crown rot and sharp eyespot in common wheat

Fusarium crown rot(FCR) and sharp eyespot(SE)are serious soil-borne diseases in wheat and its relatives that have been reported to cause wheat yield losses in many areas. In this study, the expression of a cell wall invertase gene, TaCWI-B1,was identified to be associated with FCR resistance through a combination of bulk segregant RNA sequencing and genome resequencing in a recombinant inbred line population. Two biparental populations were developed to further verify TaCWI-B1 association with FCR resistance.Overexpression lines and ethyl methanesulfonate(EMS) mutants revealed TaCWI-B1 positively regulating FCR resistance. Determination of cell wall thickness and components showed that the TaCWI-B1-overexpression lines exhibited considerably increased thickness and pectin and cellulose contents. Furthermore, we found that TaCWI-B1 directly interacted with an alphagalactosidase(TaGAL). EMS mutants showed that TaGAL negatively modulated FCR resistance. The expression of TaGAL is negatively correlated with TaCWI-B1 levels, thus may reduce mannan degradation in the cell wall, consequently leading to thickening of the cell wall. Additionally, TaCWI-B1-overexpression lines and TaGAL mutants showed higher resistance to SE;however, TaCWI-B1 mutants were more susceptible to SE than controls.This study provides insights into a FCR and SE resistance gene to combat soil-borne diseases in common wheat.

MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot

Fusarium ear rot(FER)caused by Fusarium verticillioides is one of the most common diseases affecting maize production worldwide.FER results in severe yield losses and grain contamination with health-threatening mycotoxins.Although most studies to date have focused on comprehensive analysis of gene regulation in maize during defense responses against F.verticillioides infection,less is known about the role of micro RNAs(mi RNAs)in this process.We used deep sequencing to compare small RNA libraries from the maize kernels of susceptible(N6)or resistant(BT-1)inbred lines from uninfected plants and upon F.verticillioides infection.We found that pathogen exposure was accompanied by dynamic alterations in expression levels of multiple mi RNAs,including new members of previously annotated mi RNA families.A combination of transcriptomic,degradomic,and bioinformatics analyses revealed that F.verticillioides-responsive mi RNAs and their potential target genes displayed opposite expression patterns in the susceptible and resistant genotypes.Functional category analysis uncovered preferential enrichment of the pathogen-responsive mi RNAs and their targets in the phenylpropanoid metabolic processes,plant–pathogen interactions,and plant phytohormone signal transduction pathways.Furthermore,transgenic maize plants overexpressing mi R408 b exhibited reduced resistance to F.verticillioides infection in a susceptible maize line.These findings provide new insights into the regulatory roles of mi RNAs in maize immunity against FER and new resources for breeding disease resistance into maize.