Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 67

SAGE
Serial analysis of gene expression (SAGE) is a method based on sequencing of
short-read cDNA tags. SAGE allows the identification of a large number of tran-
scripts present in tissues, and enables quantitative comparison of transcriptomes
(Velculescu et al. 1995 ). Sequencing of selected clones from the SAGE library al-
lows the efficient collection of transcript sequencetags (TSS). Complete genome
sequencing or large-scale ESTs data are required, and because few plants fall into
this category, very few crop plants have approached the genetics of crop improve-
ment in this manner.
SAGE Derivatives
Some derivatives of the original SAGE protocol (MAGE, SADE, microSAGE,
miniSAGE, longSAGE, superSAGE, deepSAGE, GermSAGE, 5′ SAGE) have
been developed to improve the utility of SAGE (Hashimoto et al. 2004 ; Anisimov
2008 ). For example, superSAGE is an improved version of SAGE, and this method
has been applied to quantitative gene expression of both rice infected host cells and
their pathogen (Matsumura et al. 2003 ). The development of superSAGE tags has
also been used to design probes directly for oligonucleotide based microarrays in
plants (Matsumura et al. 2008 ).
Parallel Signature Sequencing (MPSS)
Massive parallel signature sequencing (MPSS) is uses as an alternate method to
quantify gene expression levels, and generate short sequence tags using a micro-
bead array (Brenner et al. 2000 ). The database of MPSS includes information from
Arabidopsis , rice, grape, soybean, Medicago , maize, Brachypodium and Magna-
porthe grisea (the rice blast fungus) (Nakano et al. 2006 ).
MPSS 2 and Plus ( Arabidopsis profiling)
A new MPSS method has been used to perform genome-scale expression profiling
of sRNAs in Arabidopsis and rice (Lu et al. 2006 ; Nobuta et al. 2007 ). The MPSS2
method has recently been used for quantitative analysis of the 5′ end of transcripts,
which are then coupled to the cap-trap method for full-length cDNA cloning; it is
reported to be applicable to a number of different plants.