Dataset Information

Comparison of foliage of diploid potato clones 07506-01 and 12120-03

ABSTRACT: Verticillium dahliae Kleb., a soil-borne fungus that colonizes vascular tissues, induces wilting, chlorosis and early senescence in potato. Difference in senescence timing found in two diploid potato clones, 07506-01 and 12120-03, was studied and genetic variation in response to V. dahliae infection was identified as a causal factor. The clone, 07506-01, was infected with V. dahliae but did not develop symptoms, indicating tolerance to the pathogen. The other diploid clone, 12120-03 had low levels of pathogen with infection and moderate symptoms indicating partial resistance. 07506-01 was found to carry two susceptible alleles of the Ve2 gene and 12120-03 carried one Ve2 resistant and one susceptible allele. Infected leaves of the two clones were compared using gene expression profiling with the Potato Oligonucleotide Chip Initiative (POCI) microrarray. The results provide further evidence for differences in response of the two clones to infection with V. dahliae. Chlorophyll biosynthesis was higher in the tolerant 07506-01 compared to partially resistant 12120-03. On the other hand, expression of fungal defense genes, Ve resistance genes and defense phytohormone biosynthetic enzyme genes was decreased in 07506-01 compared to 12120-03 suggesting defense responses were suppressed in tolerance compared to resistance. Transcription factor gene expression differences pointed to the WRKY family as potential regulators of V. dahliae responses in potato.

ORGANISM(S): Solanum tuberosum

PROVIDER: GSE48881 | GEO | 2013/07/15

SECONDARY ACCESSION(S): PRJNA212119

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Purpose: Verticillium dahliae is a fungal plant pathogen. The goals of the study are to examine gene networks involved in controlling resistance to V. dahliae in potato using expression quantitative trait loci (eQTL) mapping. Methods: 91 clones from a diploid potato mapping population 15143 and the parental lines 07506-01 and 12120-03 from the Agriculture and Agri-Food Canada in Fredericton, New Brunswick, Canada were propagated in a V. dahliae-infested field in triplicate plots of five plants in a randomized complete block design. Tetraploid varieties Shepody, Hindenburg, Kennebec, Russet Burbank, Atlantic and Green Mountain were planted similarly and included in the analysis. Green Mountain was also planted in additional plots and used a guard row clone. Leaf samples were taken at 70 days after planting. Two µg of total RNA per sample was used to construct DeepSAGE tag libraries using a modification to facilitate direct sequencing of the amplicons by Illumina sequencing. The samples from 91 clones were bar-coded with a different identification key. Samples were diluted to a final concentration of 10 nM and were pooled. Each of the three biological replicates was done in a separate pool. Final pool concentrations were estimated using Quant-iT-PicoGreen prior to template DNA hybridization and sequencing on an Illumina Genome Analyzer II according to the manufacturer's instructions. Results: Tag count data were transformed to the relative unit of counts per million. Tags included in the analysis had to be present in at least one biological replicate. Clonal variation between samples was detected (p-value ≤ 0.05) using the exact test for a negative binomial distribution . Tags that did not have significant clonal variation were removed, leaving 6248 tags. The LS mean of tag count was calculated for each tag for each clone. The 21-nt tag sequences were aligned against PGSC S. tuberosum group Phureja DM1-3 transcripts (v3.4) using blastn. Hits with E-value ≤ 0.5 were filtered in. Where there were multiple blast hits meeting E-value criteria, only the one with the longest alignment was included. 4198 tags were assigned single-hit annotations in this manner and were used for eQTL analysis. Conclusions: The results indicated that for most genes the eQTL controlling expression was mapped near the gene (cis-eQTL). There were also many trans-eQTLs, where were eQTLs for a gene that were found on another chromosome particularly on chromosome 5.

Dataset Information

Comparison of foliage of diploid potato clones 07506-01 and 12120-03

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets