Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of a breeding program pedigree

ABSTRACT: Transcriptome comparison of 15 lines representing the University of Minnesota six-rowed malting breeding program at two time points of the malting process: 'out of steep' and '3 days of germination'. Three replicates of each genotype and time point were accomplished. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Maria Muñoz-Amatriain. The equivalent experiment is BB91 at PLEXdb.] genotype: Bonanza - time: 0 days(3-replications); genotype: Bonanza - time: 3 days(3-replications); genotype: Cree - time: 0 days(3-replications); genotype: Cree - time: 3 days(3-replications); genotype: Dickson - time: 0 days(3-replications); genotype: Dickson - time: 3 days(3-replications); genotype: Excel - time: 0 days(3-replications); genotype: Excel - time: 3 days(3-replications); genotype: Lacey - time: 0 days(3-replications); genotype: Lacey - time: 3 days(3-replications); genotype: M1 - time: 0 days(3-replications); genotype: M1 - time: 3 days(3-replications); genotype: M44 - time: 0 days(3-replications); genotype: M44 - time: 3 days(3-replications); genotype: M46 - time: 0 days(3-replications); genotype: M46 - time: 3 days(3-replications); genotype: M55 - time: 0 days(3-replications); genotype: M55 - time: 3 days(3-replications); genotype: M66 - time: 0 days(3-replications); genotype: M66 - time: 3 days(3-replications); genotype: M78 - time: 0 days(3-replications); genotype: M78 - time: 3 days(3-replications); genotype: Manker - time: 0 days(3-replications); genotype: Manker - time: 3 days(3-replications); genotype: Morex - time: 0 days(3-replications); genotype: Morex - time: 3 days(3-replications); genotype: Robust - time: 0 days(3-replications); genotype: Robust - time: 3 days(3-replications); genotype: Stander - time: 0 days(3-replications); genotype: Stander - time: 3 days(3-replications)

ORGANISM(S): Hordeum vulgare

SUBMITTER: Maria Muñoz-Amatriain

PROVIDER: E-GEOD-24534 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:TITLE: Transcriptional profiling of Rgene-mediated responses in rice PROJECT DESCRIPTION: The dominant gene Xa7 and the recessive gene xa5 of rice confer resistance to several races of the bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo). To reveal the modes of action and the defense responses these genes initiate, we decided to obtain the global transcriptional profiles of the rice cultivars IRBB7, IRBB5 (which harbor Xa7 and xa5, respectively) and IR24 undergoing early infection by the Xoo Race 2 strain PXO86. Both IRBB7 and IRBB5 are resistant to PXO86 (which carry the corresponding avirulence genes avrXa7 and avrxa5), whereas IR24 is susceptible. We inoculated by vacuum infiltration the three rice cultivars ten days after seed germination (or 2 weeks after sowing) and collected inoculated tissue at 5 different timepoints within the first day after inoculation. The transcriptional profiles obtained will provide valuable insight into the similarities and differences between incompatible interactions mediated by a dominant and a recessive Rgene, in comparison to a compatible interaction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David O Nino-Liu. The equivalent experiment is OS4 at PLEXdb.] genotype: IR24 - time: 0 hai(3-replications); genotype: IR24 - time: 3 hai(3-replications); genotype: IR24 - time: 6 hai(3-replications); genotype: IR24 - time: 12 hai(3-replications); genotype: IR24 - time: 24 hai(3-replications); genotype: IRBB5 - time: 0 hai(3-replications); genotype: IRBB5 - time: 3 hai(3-replications); genotype: IRBB5 - time: 6 hai(3-replications); genotype: IRBB5 - time: 12 hai(3-replications); genotype: IRBB5 - time: 24 hai(3-replications); genotype: IRBB7 - time: 0 hai(3-replications); genotype: IRBB7 - time: 3 hai(3-replications); genotype: IRBB7 - time: 6 hai(3-replications); genotype: IRBB7 - time: 12 hai(3-replications); genotype: IRBB7 - time: 24 hai(3-replications)

Project description:A split-split-plot design with 144 experimental units (3 replications x 4 genotypes x 6 time points x 2 treatment types) was used to profile barley plants containing variants of Mla1 and Mla6 powdery mildew resistance genes in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6). Barley leaves were harvested from inoculated and non-inoculated plants at 6 time points (0,8,16,20,24 and 32 hrs) after Bgh inoculation. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB10 at PLEXdb.] genotype: Mla1 - time: 0 - Treated or untreated: Inoculated (3-replications); genotype: Mla1 - time: 0 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla1 - time: 8 - Treated or untreated: Inoculated (3-replications); genotype: Mla1 - time: 8 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla1 - time: 16 - Treated or untreated: Inoculated (3-replications); genotype: Mla1 - time: 16 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla1 - time: 20 - Treated or untreated: Inoculated (3-replications); genotype: Mla1 - time: 20 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla1 - time: 24 - Treated or untreated: Inoculated (3-replications); genotype: Mla1 - time: 24 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla1 - time: 32 - Treated or untreated: Inoculated (3-replications); genotype: Mla1 - time: 32 - Treated or untreated: Non-inoculated(3-replications); genotype: m508 - time: 0 - Treated or untreated: Inoculated (3-replications); genotype: m508 - time: 0 - Treated or untreated: Non-inoculated(3-replications); genotype: m508 - time: 8 - Treated or untreated: Inoculated (3-replications); genotype: m508 - time: 8 - Treated or untreated: Non-inoculated(3-replications); genotype: m508 - time: 16 - Treated or untreated: Inoculated (3-replications); genotype: m508 - time: 16 - Treated or untreated: Non-inoculated(3-replications); genotype: m508 - time: 20 - Treated or untreated: Inoculated (3-replications); genotype: m508 - time: 20 - Treated or untreated: Non-inoculated(3-replications); genotype: m508 - time: 24 - Treated or untreated: Inoculated (3-replications); genotype: m508 - time: 24 - Treated or untreated: Non-inoculated(3-replications); genotype: m508 - time: 32 - Treated or untreated: Inoculated (3-replications); genotype: m508 - time: 32 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla6 - time: 0 - Treated or untreated: Inoculated (3-replications); genotype: Mla6 - time: 0 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla6 - time: 8 - Treated or untreated: Inoculated (3-replications); genotype: Mla6 - time: 8 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla6 - time: 16 - Treated or untreated: Inoculated (3-replications); genotype: Mla6 - time: 16 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla6 - time: 20 - Treated or untreated: Inoculated (3-replications); genotype: Mla6 - time: 20 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla6 - time: 24 - Treated or untreated: Inoculated (3-replications); genotype: Mla6 - time: 24 - Treated or untreated: Non-inoculated(3-replications); genotype: Mla6 - time: 32 - Treated or untreated: Inoculated (3-replications); genotype: Mla6 - time: 32 - Treated or untreated: Non-inoculated(3-replications); genotype: 9472 - time: 0 - Treated or untreated: Inoculated (3-replications); genotype: 9472 - time: 0 - Treated or untreated: Non-inoculated(3-replications); genotype: 9472 - time: 8 - Treated or untreated: Inoculated (3-replications); genotype: 9472 - time: 8 - Treated or untreated: Non-inoculated(3-replications); genotype: 9472 - time: 16 - Treated or untreated: Inoculated (3-replications); genotype: 9472 - time: 16 - Treated or untreated: Non-inoculated(3-replications); genotype: 9472 - time: 20 - Treated or untreated: Inoculated (3-replications); genotype: 9472 - time: 20 - Treated or untreated: Non-inoculated(3-replications); genotype: 9472 - time: 24 - Treated or untreated: Inoculated (3-replications); genotype: 9472 - time: 24 - Treated or untreated: Non-inoculated(3-replications); genotype: 9472 - time: 32 - Treated or untreated: Inoculated (3-replications); genotype: 9472 - time: 32 - Treated or untreated: Non-inoculated(3-replications)

Project description:A large-scale parallel expression analysis was conducted to elucidate Mla-specified responses to powdery mildew infection using 22K Barley1 GeneChip probe arrays. Our goal was to identify genes differentially expressed in incompatible (resistant) vs. compatible (susceptible) and Mla-specified Rar1-dependent vs. -independent interactions. A split-split-plot design with 108 experimental units (3 replications x 2 isolates x 3 genotypes x 6 time points) was used to profile near-isogenic lines containing the Mla1, Mla6, and Mla13 resistance specificities in response to inoculation with the Blumeria graminis f. sp. hordei (Bgh) isolates 5874 (AvrMla1, AvrMla6) and K1 (AvrMla1, AvrMla13). ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rico Caldo. The equivalent experiment is BB4 at PLEXdb.] genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 0 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 8 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 16 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 20 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 24 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh 5874 - time: 32 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 0 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 8 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 16 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 20 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 24 hai(3-replications); genotype: CI 16137 (Mla1) - pathogen isolates: Bgh K1 - time: 32 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 0 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 8 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 16 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 20 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 24 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh 5874 - time: 32 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 0 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 8 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 16 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 20 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 24 hai(3-replications); genotype: CI 16151 (Mla6) - pathogen isolates: Bgh K1 - time: 32 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 0 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 8 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 16 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 20 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 24 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh 5874 - time: 32 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 0 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 8 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 16 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 20 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 24 hai(3-replications); genotype: CI 16155 (Mla13) - pathogen isolates: Bgh K1 - time: 32 hai(3-replications)

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Transcriptome analysis of a breeding program pedigree

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