Microarray Related Studies in Rice

What is Microarray?

A microarray is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate (usually a glass slide or silicon thin-film cell) that assays large amounts of biological material using high-throughput screening miniaturized, multiplexed and parallel processing and detection methods. The concept and methodology of microarrays was first introduced and illustrated in antibody microarrays (also referred to as antibody matrix) by Tse Wen Chang in 1983 in a scientific publication[1] and a series of patents^[1]^[2].
Microarray is also the method of choice as it gives detailed information on a genome- wide scale while processing tens of thousands of genes at a time which surpasses any other technology in its speed, accuracy and comprehensiveness (Brandl and Anderson 2015). This can be done by comparing the gene expression at a specific time and place to a particular phenotype or by comparing the co-expression and co- regulation of known to unknown genes (Mingzhu et al. 2015).^[2]

Figure 1 describes the details of cDNA fragment-based microarray technology. Target-DNAs are prepared by PCR amplifying inserts from cDNA clones. The amplicons are spotted onto microscope slides at indexed locations using high speed arraying machines. Usually probes from two independent samples are prepared and labelled with fluorescent nucleotides. Two ̄fluorescent tags with different excitation and emission optima can be used to differently label the two probes. Both probes are mixed together and allowed to hybridize to the same microarray under a coverslip. After washing off the unbound probe, the ̄uorescent DNA molecules that have hybridized to DNA fragments on the microarray are excited by light and the fluorescence signal associated with each element of the microarray is read with an array scanner. The intensity of the ̄florescence signal ranges from about 1000 (background) to 35 000 ̄uorescence intensity units. For each element of the microarray, the ratio of ̄florescence emission at the two wavelengths reflects the ratio of the abundance of that sequence in the two probes. The result is often displayed as a false-colour image. Thus, in the diagram red may indicate that the corresponding RNAs were more abundant in probe 1 than in probe 2, yellow may indicate that they were present at similar concentrations in both probes and green that the RNAs associated with these array elements were more abundant in probe 2 than in probe 1.^[2]

Figure 1.cDNA fragment-based microarray technology.^[2]

Figure 2 shows some Visualization tools for microarray analysis. (a) Heatmaps consist of small cells, each consisting of a colour, which represent relative expression values. Heatmaps are often generated from hierarchical cluster analyses of both samples and genes. (b) Box plots present various statistics for a given data set. The plots consist of boxes with a central line and two tails. (c)MA plots are used to detect artefacts in the array that are intensity dependent. They are often used as an aid when normalizing two-colour cDNA microarrays. (d) Volcano plots are used to look at fold change and statistical significance simultaneously. Cartesian plots typically show – log 10 (p-values) or log odds on the ordinate and fold-change values on the abscissa for all genes in a data set. (e) p-value histograms have abscissae that range from 0 to 1 and contain the p-values for a test of differential expression for each gene.

Figure 2. Visualization tools for microarray analysis.

Project Title	Species	Published years	RiceWiki Project ID
Distinct Gene Expression Profiles in Egg and Synergid Cells of Rice as Revealed by Cell Type-Specific Microarrays	Oryza sativa L. ssp. Japnoica	2011	IC4R001-Microarray-2011-221106719
Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa)	Oryza sativa cultivars	2011	IC4R002-Microarray-2011-21915109
Genome-Wide Analyses of Changes in Translation State Caused by Elevated Temperature in Oryza sativa	Oryza sativa L. ssp. Japnoica	2012	IC4R003-Microarray-2012-22722767
Microarray analysis reveals overlapping and specific transcriptional responses to different plant hormones in rice	Oryza sativa L. ssp. indica	2012	IC4R004-Microarray-2012-22827941
Efficacy of Microarray Profiling Data Combined with QTL Mapping for the Identification of a QTL Gene Controlling the Initial Growth Rate in Rice	Oryza sativa L. ssp. Japnoica & Oryza sativa L. ssp. indica	2012	IC4R005-Microarray-2012-22419825
Microarray analysis of laser-microdissected tissues indicates the biosynthesis of suberin in the outer part of roots during formation of a barrier to radial oxygen loss in rice (Oryza sativa)	Oryza sativa L. ssp. Japnoica	2014	IC4R006-Microarray-2014-24913626

↑ https://en.wikipedia.org/wiki/Microarray
↑ ^2.0 ^2.1 ^2.2 ^2.3 Kuhn, Ekkehard. "From library screening to microarray technology: strategies to determine gene expression profiles and to identify differentially regulated genes in plants." Annals of Botany 87.2 (2001): 139-155.