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Small RNA mediated immune responses: insights from analyses of nine soybean R-gene near-isogenic lines and their susceptible parent

ABSTRACT: Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are negative regulators to target endogenous genes and repetitive sequences in plants. Although miRNAs and trans-acting or phased siRNAs (tasiRNAs or phasiRNAs) were found to target hundreds of disease related genes in Medicago, their role in plant-pathogen interactions in the legumes, particularly the R genes mediated interaction of soybean and the pathogen Phytophthora sojae is poorly understood. A deep sequencing was performed on nine soybean near isogenic lines (NILs) each carrying an Rps (Resistance to Phytophthora sojae) gene and their recurrent parent “Williams”, with sampling performed both pre- and post-inoculation with P. sojae. From these data, 44 known MIRNA loci with new miRNA variants, 78 novel miRNAs corresponding to 108 precursors, and 208 phasiRNA-producing (PHAS) loci were identified. Our data showed that overall the expression levels of miRNAs, phasiRNAs and siRNAs were extensively down-regulated after pathogen-inoculation. Moreover, the down-regulation levels in the nine resistant NILs were significantly higher than that detected in the susceptible Williams, and variations of small RNA expression within the resistant NILs were also observed, suggesting the molecular responses of different Rps lines are distinct. Surprisingly, the expression level changes of 21-nt phasiRNAs were significantly positively correlated with that of the corresponding mRNA level of the PHAS genes, suggesting the cascade effects of miRNA triggers on the downstream PHAS genes and phasiRNAs. Our data provided a comprehensive picture regarding small RNA based regulation of target genes, particularly NB-LRRs, involved in the responses to the pathogen.

ORGANISM(S): Glycine max

PROVIDER: GSE56859 | GEO | 2015/04/15

SECONDARY ACCESSION(S): PRJNA244779

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.

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Small RNA mediated immune responses: insights from analyses of nine soybean R-gene near-isogenic lines and their susceptible parent

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