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Differential gene expression of Vicia species using a soybean cDNA microarray

ABSTRACT: Hairy vetch (Vicia villosa Roth) is recognized as a beneficial winter cover crop in the Midwestern U.S. DNA microarrays are used for assessing gene expression significance. The objective of the study was to identify a set of genes expressed in hairy vetch, that could be further analyzed for their potential in improving the crop. The RNA of four targets (soybean (Glycine max), hairy vetch, Vicia pannonica PI 170008, and Vicia pannonica PI 515988) were purified, labeled, and hybridized to 142 cDNA clones of biotic stress genes and gene sequences of soybean that were robotically spotted onto aminosilicated slides with duplicate spots and three arrays per slide. The microarray experiments were completed in a reference design experiment incorporating a two-dye system. The data were analyzed using the individual fluorescence intensities to fit two statistical models in a mixed model analysis of variance. In this analysis, systematic error effects were observed to account for 24% of the total variation. The use of a Bonferroni adjusted significance threshold allowed for adequate control over the number of falsely identified significant genes showing expression in the different target comparisons. We observed that 64 of the 142 gene sequences (45%) were differentially expressed in at least one of the target comparisons. Two of these expressed genes in hairy vetch encoded for a cold tolerance indicator, proline, and two other gene sequences encode for stress tolerance indicators, myo-inositol and calmodulin. A soybean cDNA microarray was used effectively to differentiate gene expression in hairy vetch. Keywords: comparative genomic hybridization (cross-species)

ORGANISM(S): Vicia pannonica Vicia villosa Glycine max

PROVIDER: GSE3263 | GEO | 2005/12/01

SECONDARY ACCESSION(S): PRJNA92919

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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Differential gene expression of Vicia species using a soybean cDNA microarray

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