Transcriptomics,Genomics

Dataset Information

35

Zea mays Transcriptome or Gene expression


ABSTRACT: In the current study a microarray (46k, University of Arizona, USA) analysis of 21 European maize (Zea mays L.) parental inbred lines (14 dent and 7 flint) was applied. The aim was the identification of parental genes which expression levels are correlated to heterosis and/or hybrid performance for grain yield (GY) and grain dry matter content (GDMC) in the hybrid progeny (F1). Therefore gene expression profiles of differentially expressed genes of the parental inbred lines at the seedling stage were correlated with GY- and GDMC-field data of 98 flint x dent factorial crosses gained at six different locations in Germany. The identification of heterosis-correlated genes is an approach for the characterization and also for the prediction of this phenomenon. For the analyses total RNA of seven days old seedlings was extracted and aminoallyl-labeled RNA probes were synthesized. RNA labeling (Cy3, Cy5) and hybridizations were performed according to the protocol of the maize oligonucleotide array project (http://www.maizearray.org). The microarrays were scanned (AppliedPrecision ArrayWorx Scanner, Applied Precision Inc., USA) and data were evaluated using the Software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, USA). An experimental interwoven loop design was developed aiming to yield in a preferably low average variance among the hybridizations, especially between intergroup (dent lines vs. flint lines) hybridizations. As a result 12288 (28.3%) of the genes showed differential expression between any combination of inbred lines. These differentially expressed genes were used for subsequent field data correlation analyses. Overall design: Five plants of each of the 21 inbred lines (7 flint lines: F037, F039, F043, F047, L024, L035, L043; 14 dent lines: P033, P040, P046, P048, P063, P066, S028, S036, S044, S046, S049, S050, S058, S067) were grown for seven days in a climate chamber (Percival Scientific Inc., Perry, USA) under regulated growth conditions (25℃ 16h-day, 21℃ 8h-night, 70% air humidity). Since we aimed for the identification of genotype-dependent expression differences in inbred lines and for diminishing individual expression variations, the five biological replicates were pooled before target labeling and hybridization. Whole tissue of 7-days old seedlings was used. The pooled tissue was frozen in liquid nitrogen and finely pounded. The complete RNA was isolated and used to synthesize aminoallyl-labeled RNA (aaRNA) following the "Amino Allyl MessageAmp II aRNA Amplification Kit" protocol (Applied Biosystems/Ambion, Austin, USA). Synthesised aaRNA was coupled with fluorescence dyes Cy3 or Cy5. In total 63 hybridizations were realized in an interwoven loop design, in which the dye used for each genotype was alternated to reduce systematic bias. The loop was designed in a way that each dent line was sampled 5 times and each flint line 8 times. In addition to every direct connection between dent and flint lines, multiple indirect connections of three or more hybridizations were realized.

INSTRUMENT(S): Maize oligonucleotide array 46K version

SUBMITTER: Stefan Scholten  

PROVIDER: GSE17754 | GEO | 2010-08-21

SECONDARY ACCESSION(S): PRJNA118397

REPOSITORIES: GEO

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Publications

Correlation between parental transcriptome and field data for the characterization of heterosis in Zea mays L.

Thiemann Alexander A   Fu Junjie J   Schrag Tobias A TA   Melchinger Albrecht E AE   Frisch Matthias M   Scholten Stefan S  

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 20091104 2


Heterosis is widely exploited in plant breeding, although its molecular basis is still not fully understood. For the characterization of this phenomenon and the development of transcriptome-based methods to predict hybrid performance (HP), we applied a microarray (46k) analysis of 21 European maize (Zea mays L.), 14 dent and 7 flint parental inbred lines. Expression profiles of the parental inbreds at the seedling stage were correlated with grain yield (GY) and grain dry matter content (GDMC) of  ...[more]

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