Comparative Metabolome and Transcriptome Analyses of Susceptible Asparagus officinalis and Resistant Wild A. kiusianus Reveal Insights into Stem Blight Disease Resistance.

Phomopsis asparagi is one of the most serious fungal pathogens, which causes stem blight disease in Asparagus officinalis (AO), adversely affecting its production worldwide. Recently, the development of novel asparagus varieties using wild Asparagus genetic resources with natural P. asparagi resistance has become a priority in Japan due to the lack of resistant commercial AO cultivars. In this study, comparative metabolome and transcriptome analyses of susceptible AO and resistant wild Asparagus kiusianus (AK) 24 and 48 h postinoculated (AOI_24 hpi, AOI_48 hpi, AKI_24 hpi and AKI_48 hpi, respectively) with P. asparagi were conducted to gain insights into metabolic and expression changes associated with AK species. Following infection, the resistant wild AK showed rapid metabolic changes with increased levels of flavonoids and steroidal saponins and decreased asparagusic acid glucose ester content, compared with the susceptible AO plants. Transcriptome data revealed a total of 21 differentially expressed genes (DEGs) as the core gene set that displayed upregulation in the resistant AK versus susceptible AO after infection with P. asparagi. Kyoto Encyclopedia of Genes and Genomes pathway analysis of these DEGs identified 11 significantly enriched pathways, including flavonoid biosynthesis and primary metabolite metabolism, in addition to plant signaling and defense-related pathways. In addition, comparative single-nucleotide polymorphism and Indel distributions in susceptible AO and resistant AK plants were evaluated using the latest AO reference genome Aspof.V1. The data generated in this study are important resources for advancing Asparagus breeding programs and for investigations of genetic linkage mapping, phylogenetic diversity and plant defense-related genes.

Differential gene expression analysis and SNP/InDel marker discovery in resistant wild Asparagus kiusianus and susceptible A. officinalis in response to Phomopsis asparagi infection.

This data article reports de novo transcriptome analysis of resistant wild Asparagus kiusianus and susceptible A. officinalis plants 24 and 48 h post-inoculation (24 and 48 hpi) with Phomopsis asparagi. Differential gene expression (DGE) analysis demonstrated that several genes involved in secondary metabolites and plant-pathogen interactions are up-regulated in resistant wild A. kiusianus relative to susceptible A. officinalis. The assembled contig sequences generated in this study were used to search single nucleotide polymorphism (SNP) and insertion/deletion (InDel) distribution in A. kiusianus and A. officinalis plants. SNP and InDel data developed from this transcriptome analysis will be used to generate a high-density linkage map to facilitate further development of molecular marker-assisted selection in A. officinalis.

Comparative de novo transcriptome profiles in Asparagus officinalis and A. kiusianus during the early stage of Phomopsis asparagi infection.

Asparagus kiusianus, an important wild relative of cultivated asparagus (A. officinalis), exhibits resistance to stem blight disease caused by Phomopsis asparagi. However, the mechanisms underlying this resistance are not understood and no transcriptomic or genetic resources are available for this species. De novo transcriptome sequencing of A. officinalis and A. kiusianus stems was performed 24 h after inoculation with P. asparagi. In total, 35,259 and 36,321 transcripts were annotated in A. officinalis and A. kiusianus, respectively. 1,027 up-regulated and 752 down-regulated transcripts were differentially expressed in the two Asparagus species. RNA sequencing data were validated using quantitative real-time reverse transcription PCR. Several defense-related genes including peroxidase 4, cationic peroxidase SPC4-like, pathogenesis-related protein-1-like, and jasmonic acid biosynthesis and signaling-related genes including phospholipase D alpha 1, 12-oxophytodienoate reductase and jasmonate-induced protein 23 KD were up-regulated in A. kiusianus relative to A. officinalis. In addition, infected A. kiusianuns exhibited a substantial increase in jasmonic acid and methyl jasmonate relative to A. officinalis. Peroxidase activity was significantly elevated in infected A. kiusianus compared with infected A. officinalis. Our transcriptomic database provides a resource for identifying novel genes and molecular markers-associated with Phomopsis disease resistance and will facilitate breeding and improvement of cultivated asparagus varieties.

Use of a Nitrate-Nonutilizing Mutant and Selective Media to Examine Population Dynamics of Fusarium oxysporum f. sp. spinaciae in Soil.

ABSTRACT Determining the population density of the spinach wilt pathogen Fusarium oxysporum f. sp. spinaciae in soil with conventional Fusarium-selective media is quite difficult because nonpathogenic strains of F. oxysporum also grow on those media and are indistinguishable from the pathogen. Therefore, a nitrate-nonutilizing (nit) mutant of the pathogen and corresponding selective media were tested in an experimental approach to determine the population density of the pathogen. Colony forming units of the pathogen were countable after soil-dilution plating onto nit mutant-selective media MMCPA, CMP, and CGMBP. Colony forming units of wild-type Fusarium spp. were countable using a wildtype Fusarium-selective medium, GMBP. By combining nit mutant- and wild-type-selective media, the population densities of pathogenic and nonpathogenic F. oxysporum in the same soil could be measured selectively. This method was useful in studying population dynamics of the pathogen after different soil treatments. Soil disinfested with hot water or chloropicrin was amended with the nit mutant pathogen, and subsequent changes in population densities of the pathogen were compared with those in nontreated field soil. The pathogen rapidly proliferated in disinfested soil and wilt developed faster than in nontreated soil. When a nonpathogenic isolate of F. oxysporum was added at high density to sterilized soil prior to the pathogen, growth of the pathogen was greatly suppressed. Nonpathogenic F. oxysporum could not, however, reduce the density of preexisting pathogen.