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Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae

ABSTRACT: Phytophthora root and stem rot (PRR) of soybean, caused by Phytophthora sojae, is effectively controlled by Rps genes in soybean. Rps genes are race-specific, yet the mechanism of resistance, as well as susceptibility, remains largely unclear. Taking advantage of RNA-seq technology, we sequenced the transcriptomes of 10 near isogenic lines (NIL), each with a unique Rps gene, and the recurrent susceptible parent ‘Williams’. A total of 4330 differentially expressed genes (DEGs) were identified in ‘Williams’ while 2075 to 5499 DEGs were identified in each NIL. Comparisons between the NILs and ‘Williams’ allowed classification of two major groups of DEGs of interest: incompatible reaction associated genes (IRAGs) and compatible reaction associated genes (CRAGs). Hierarchical cluster analysis divided NILs into three clusters: Cluster I (Rps1-a), Cluster II (Rps1-b, 1-c and 1-k) and Cluster III (Rps3-a, 3-b, 3-c, 4, 5, and 6). Heatmap analysis, along with GO analysis suggested that the diversity of clusters for NILs were likely due to variation of the number of DEGs and the intensity of gene expression, rather than functional differentiation. Further analysis suggested that transcription factors might play pivotal role in determination of the cluster pattern, and that WRKY family were strongly associated with incompatible reactions. Analysis of IRAGs and CRAGs with putative functions suggested that the regulation of many phytohormone signaling pathways were associated with incompatible or compatible interactions with potential crosstalk between each other. As such, our study provides an in depth view of both incompatible and compatible interactions between soybean and P. sojae, which provides further insight into the mechanisms involved in host-pathogen interactions.

ORGANISM(S): Glycine max

PROVIDER: GSE48524 | GEO | 2014/04/16

SECONDARY ACCESSION(S): PRJNA210431

REPOSITORIES: GEO

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Project description:Phytophthora root and stem rot caused by the oomycete pathogen Phytophthora sojae, is one of the most destructive diseases of soybean. Deploying soybean cultivars carrying race-specific resistance conferred by Rps genes is the most practicalapproach to managing this disease. Previously, two Rps genes, RpsUN1 and RpsUN2 conferring broad spectra of resistance to P. sojae isolates, were identified in a landrace PI 567139B and mapped to a 6.5-cM region on chromosome 3 and a 3.0-cM region on chromosome 16, corresponding to 840 kb and 600 kb of sequences, respectively,of the soybean reference genome. By analyzing ten and nine recombinants defined by genotypic and phenotypic screening of the 826 F2:3 families derived from two reciprocal crosses between the two parental lines of the mapping populations, RpsUN1 and RpsUN2 were further narrowed to a 151-kb region that harbors five genes including three NBS-LRR genes, and a 36-kb region that contains four genes including five NBS-LRR genes, respectively, according to the reference genome. Analysis of expressional changes of these nine genes before and after inoculation with the pathogen suggest that the counterparts of Glyma.03g034600 in the RpsUN1 region and the counterparts of Glyma.16g215200 and Glyma.16g214900 in the RpsUN2 region of PI 567139B may be associated with the resistance to P. sojae. It is also suggested that unequal recombination between different NBS-LRR genes in the mapped regions may have occurred, resulting in the formation of two recombinants with inconsistent genotypes and phenotypes detected by molecular markers within the fine-mapped regions. The haplotypes of genomic regions surrounding RpsUN1 and RpsUN2 in the entire soybean germplasm deposited in the US soybean germplasm collection were analyzed towards a better understanding of the origins of these two novel sources of resistance and screening of effective markers for marker-assisted selectionof these two resistance genes for soybean breeding.

Project description:Fusarium oxysporum is one of the most common species causing soybean root rot and seedling blight in the U.S. In a recent study, significant variation in aggressiveness was observed among isolates of F. oxysporum collected from roots in Iowa, ranging from highly pathogenic to weakly or non-pathogenic isolates. In the present work, a RNA-seq-based analysis was used for the first time to investigate the molecular aspect of the interaction of a partially resistant soybean genotype with non-pathogenic/pathogenic isolates of F. oxysporum at 72 and 96 hours post inoculation (hpi). Markedly different gene expression profiles were observed in compatible and incompatible host-pathogen combinations. A peak of differentially expressed genes (DEGs) was observed at 72 hpi in soybean roots in response to both isolates, although the number of DEGs was about eight times higher for the pathogenic isolate compared to the non-pathogenic one (1,659 vs. 203 DEGs, respectively). Furthermore, not only the number of genes, but also the magnitude of induction was much greater in response to the pathogenic isolate. This response included a stronger activation of many well-known defense-related genes, and several genes involved in ethylene biosynthesis and signalling, transcription factors, secondary and sugar metabolism. In addition, 1130 fungal genes were differentially expressed between the F. oxysporum isolates in planta during the infection process. Interestingly, 10% of these genes encode plant cell-wall degrading enzymes, reactive oxygen species-related enzymes and fungal proteins involved in primary metabolic pathways. Such information may be useful in the development of new methods of broadening resistance of soybean to F. oxysporum, including the silencing of important fungal genes, and also to understand the molecular basis of soybean-F. oxysporum interactions. Soybean seedlings mRNA profiles inoculated with a non-pathogenic and pathogenic isolates of F. oxysporum and collected at 72 and 96 hpi, were generated using Illumina HiSeq 2500. Control seedlings were also included for each time of inoculation. Three biological replicates were considered for each condition, 18 samples in total.

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Comparative Transcriptomics of Soybean Near Isogenic Lines in Response to Phytophthora Sojae

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