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Diurnal expression data from developing barley caryopses

ABSTRACT: Caryopses of barley (Hordeum vulgare), like all other cereal seeds, are complex sink organs optimized for storage starch accumulation and embryo development. Their development from early stages after pollination to late stages of seed ripening has been studied in great detail. However, information on the caryopsesâ?? diurnal adaptation to changes in light, temperature and alterations in phloem-supplied carbon and nitrogen remained unknown. In this study, we applied the 22K Barley1 GeneChip microarray to investigate diurnal gene regulation events of barley caryopses at 11 to 12 days post anthesis. Developing barley caryopses were harvested at different time-points of a day (at 7:00 AM, 2:00 PM, 5:00 PM and 8:00 PM) including dark samples (6:00 AM and 10:00 PM). Pooled caryopses (form 3 Plants) from the respective time points were used for RNA extraction and hybridization on Affymetrix microarrays (Barley1 GeneChip; GEO accsession GPL1340). Biological replicates were performed.

ORGANISM(S): Hordeum vulgare

SUBMITTER: Elke Mangelsen

PROVIDER: E-GEOD-20034 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Significance of light, sugar, and amino acid supply for diurnal gene regulation in developing barley caryopses.

Mangelsen Elke E Wanke Dierk D Kilian Joachim J Sundberg Eva E Harter Klaus K Jansson Christer C

Plant physiology 20100319 1

The caryopses of barley (Hordeum vulgare), as of all cereals, are complex sink organs optimized for starch accumulation and embryo development. While their early to late development has been studied in great detail, processes underlying the caryopses' diurnal adaptation to changes in light, temperature, and the fluctuations in phloem-supplied carbon and nitrogen have remained unknown. In an attempt to identify diurnally affected processes in developing caryopses at the early maturation phase, we ...[more]

PMID: 20304969

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Project description:We combined heritability analysis of larval development rate with a global expression analysis of this phenotype to investigate genotype by environment interactions across three ecologically relevant temperatures in the Glanville fritillary butterfly (Melitaea cinxia). We focused upon the development of final instar caterpillars which is greatly affected by temperature, and during this stage the caterpillars build up most of the resources for adult life. Second generation, lab reared larvae, initially collected from the M-CM-^Eland metapopulation, were reared in standard lab condition until 6th larval instar. At the beginning of the final (7th) instar stage the larvae were separated into of three temperature conditions: Cold treatment (temperature profile: 8M-BM-0C 18:00-9:59, 14M-BM-0C 10:00-11:59, 20M-BM-0C 12:00-15:59 and 14M-BM-0C 16:00-17:59) Standard treatment (temperature profile: 15M-BM-0C 17:00-6:59, 18M-BM-0C 7:00-8:59, 22M-BM-0C 9:00-10:59 and 26M-BM-0C 11:00-16:59) Hot treatment (temperature profile: 8M-BM-0C 20:00-7:59, 15M-BM-0C 8:00-9:59, 35M-BM-0C 10:00-17:59 and 15M-BM-0C 18:00-19:59) The temperature profiles mimic the diurnal thermal variation of the natural habitat (M-CM-^Eland islands) of samples. Cold treatment mimics a cool and cloudy summer, Standard represents an average temperature profile in the M-CM-^Eland islands and Hot treatment mimics an exceptionally hot and sunny summer, with cold night-time temperatures. The experiment contained several larval families (full-sib) of which three were selected for gene expression analysis. Samples were snap-frozen in liquid nitrogen during mid-development (after 6, 5 and 4 days, for Cold, Standard and Hot respectively). Additional larvae from the same treatments were assayed for survival and growth. Gene expression was analyzed using a mixed model approach to identify genes with potential heritable expression variation (variation among families), genes with plastic expression responses (treatment induced changes) and genes with treatment dependent expression that varies among families (family by treatment interactions). Full-sib larvae from three families (N170, N74 and O171) were exposed to three temperature treatments (Cold, Standard and Hot) during final (7th) instar stage. A total of 35 samples were used to analyze family, treatment and family by treatment interactions in gene expression, using a mixed model approach. This included 3 biological replicates in Cold and Hot treatments from each family and 5-6 biological replicates in Standard (5 in O171) per family. Techinal replicates from each family and additional techical replicates in family O171 (including dye swap replicates) were used to assess robustness of the findings.

Dataset Information

Diurnal expression data from developing barley caryopses

Publications

Significance of light, sugar, and amino acid supply for diurnal gene regulation in developing barley caryopses.

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