Agriculture Reference
In-Depth Information
becoming easier and cheaper to obtain, which promises increased availability of
'transciptome' information in all plants
Functional proteomics, including quantitative proteomics, subcellular pro-
teomics and various modifications of proteins and polypeptides, and protein-protein
and protein-DNA interactions are new and essential technologies to develop in crop
plants. The MALDI or ESI MS methods are still popular and important, but more
recent MS procedures must be considered and used in crop plants to obtain high res-
olution, high sensitivity, high dynamic range and high mass measurement accuracy.
Difference gel electrophoresis (DIGE), isotope-coded affinity tags (ICATs) and
isobaric tags for relative and absolute quantitation (iTRAQ) of proteins will enable
a better insight into basic regulation of proteins and polypeptides. Stable isotope
labelling with amino acids in cell culture (SILAC) combined with MS-MS Analysis
(using differential isotope analysis) are further improvements in protein determina-
tion important to crop plant proteomics.
Cell organelle analysis of their proteome and metabolite contents are essential
for understanding the various enzymatic activities within cell organelles, the com-
partmentalisation of metabolic pathways, protein targeting, trafficking and regula-
tion, and polypeptide dynamics for many of the crop plants still to be investigated.
Modificon research can be aimed to identify modified proteins, through protein
phosphorylation and ubiquitination, and although these important studies are just
beginning they are becoming more and more important to our understanding of
plant metabolism.
Systematic collection of metabolite profiles and advances in instrumentation like
NMR analysis will create new information in metabolomics. Chemical phenotype
identification are important to develop in crop plants, which can be used to identify
genes involved in particular metabolic pathways and cellular processes. This type of
information is important to integrate with other 'omics' research, such as profiles of
the transcriptome and proteome, now mainly available in Arabidopsis.
It is essential in crop breeding to associate and determine molecular, metabolic,
genomic and proteomic diversity of species, cultivars and breeding lines in those
plants. This will increase our knowledge and identify many of the genes involved in
phenotypic changes, and would also aid in the identification of genetic associations,
providing a strong basis for better utilisation of marker assisted selection (MAS),
and the use of more stable and informative molecular markers in plant breeding.
T-DNA-tagged lines have emerged as a popular mutant resource, due to the
rapid generation of large-scale mutant populations, but are not readily available in
many crop plants. Activation tagging (AT) is a popular method for generating gain-
of-function mutants important in breeding, and a better knowledge across related
breeding stocks and species in terms of comparative genomics. Computer assembly
into gene families can verify gene content and elucidates gene duplication (poly-
ploidy).
Chemical mutagenic agents and physical mutagens should be utilised more often
to obtain a comprehensive set of crop mutant lines, and then employ these to target
induced local lesions in genomes (ie TILLING) as a tool for general reverse-genet-
ics, and RNA interference (RNAi) to screen for gene silencing and gene inactiva-
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