Development of a Brassica seed cDNA microarray.
Brassica species represent several important crops including canola (Brassica napus). Understanding of genetic elements that contribute to seed-associated functions will impact future improvements in the canola crop. Brassica species share a very close taxonomic and molecular relationship with Arabidopsis thaliana. However, there are several subtle but distinct seed-associated agronomic characteristics that differ among the oil seed crop species. To address these, we have generated 67,535 ESTs predominately from Brassica seeds, analyzed these sequences, and identified 10,642 unigenes for the preparation of a targeted seed cDNA array. A set of 10,642 PCR primer pairs was designed and corresponding amplicons were produced for spotting, along with relevant controls. Critical quality control tests produced satisfactory results for use of this microarray in biological experiments. The microarray was also tested with specific RNA targets from embryos, germinating seeds, and leaf tissues. The hybridizations, signal intensities, and overall quality of these slides were consistent and reproducible. Additionally, there are 429 ESTs represented on the array that show no homology with any A. thaliana annotated gene or any gene in the Brassica genome databases or other plant databases; however, all of these probes hybridized to B. napus transcripts, indicating that the array also will be useful in defining expression patterns for genes so far unique to Brassica species.
Xiang
Daoquan
D
Plant Biotechnology Institute, National Research Council, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
Datla
Raju
R
Li
Fengling
F
Cutler
Adrian
A
Malik
Meghna R
MR
Krochko
Joan E
JE
Sharma
Nirmala
N
Fobert
Pierre
P
Georges
Fawzy
F
Selvaraj
Gopalan
G
Tsang
Ed
E
Klassen
Darrin
D
Koh
Chushin
C
Deneault
Jean-Sebastien
JS
Nantel
Andre
A
Nowak
Jacek
J
Keller
Wilf
W
Bekkaoui
Faouzi
F
D029688:Brassica napus / Q000145:classification / Q000196:embryology / Q000235:genetics*; D018744:DNA, Plant / Q000378:metabolism; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D017343:Genes, Plant; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010940:Plant Proteins / Q000235:genetics; D015203:Reproducibility of Results; D012639:Seeds / Q000235:genetics*
D018744:DNA, Plant; D010940:Plant Proteins