Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 50

age of more than two persons every second; and over 95 % of these will live in
developing countries (De Filippis 2012 ). It will be difficult satisfying the needs of
this growing population and avoid serious food shortages or even famine from the
limited arable land and natural resources available. These factors combined have
already resulted in food deficiency and malnutrition, which have become serious
health problems. Additionally, recent increased demand for biofuel crops has cre-
ated a new market for agricultural commodities, causing even more stress on food
security (Ozturk et al. 2006 ; Ozturk 2010 ; Hakeem et al. 2012 ). In order to try to re-
solve these problems and increase crop yields, breeding plants based on a better mo-
lecular understanding of gene function, and on the regulatory mechanisms involved
in crop production (Pinstrup-Andersen and Cohen 2000 ; Takeda and Matsuoka
2008 ) appears to be necessary. Plant molecular biology continues to progress, and
important gene sequences and their function have been described; many of which
are related to crop yields (production), crop quality (protein and carbohydrate), and
tolerance to biotic and abiotic stresses (De Filippis 2012 ). There are legal, social
and political barriers to the full potential use of crop biotechnology and transgenic
plants, nevertheless advances in these fields have lead to improvements in agricul-
ture and human life. One vital tool of biotechnology is 'bioinformatics', which is
commonly used to genetically type and identify genotypic and phenotypic changes
in plants, and this information is important for improvement in performance of crop
plants (Ahmad et al. 2011 ).
The complete genome sequence of the mustard plant Arabidopsis thaliana has
been available to scientists since 2000 (International Arabidopsis Genome Initia-
tive 2000 ; Somerville and Dangl 2000 ). Similarly, the rice ( Oryza sativun cv. ja-
ponica ) complete genome sequence has been documented since 2005 (International
Rice Genome Sequencing Project 2005 ; Itoh et al. 2007 ; Hakeem et al. 2012 ). The
rice genome sequencing project in particular with its molecular methods and DNA
markers on chromosomes, introduced important developments in mapping popula-
tions and chromosome marker resources, which accelerated the isolation of agro-
nomically important quantitative trait loci (QTLs) in crop breeding programs (Ashi-
kari et al. 2005 ; Konishi et al. 2006 ; Ma et al. 2006 ; Kurakawa et al. 2007 ; Ma et al.
2007 ; Zhang et al. 2007).
Each biological element that can been measured, can also be represented in a
typical plant cell, tissue and organ at various molecular and/or morphological lev-
els, or in other words a conceptual model with layers ranging from the 'genome'
to the 'phenome'; a model called 'omic space' (Fig. 2.1 ) (Toyoda and Wada 2004 ).
Advances in each 'omics' research area have become essential for investigations of
gene function and structure, and the type of phenotypic changes present in plants.
A schematic presentation of relevant 'omics' resource is shown in Fig. 2.1 , together
with the current status of available areas of research from Arabidopsis, rice, soy-
bean, corn and Brassica ; just to cite a few examples. Some of these advances have
included improved methods for gene expression, gene modifications, molecular
breeding, plant genome and proteome interactions, and metabolite profiling. Large
volumes of information in biological resources, mass identification of mutant lines
and full-length cDNAs, and the publication of this information in web-based data