Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 52

tions through available databases in crop plants, and where improvement in crop
production has been described.
Bioinformatics and web addresses for plant genomics and proteomics have been
reviewed by a number of authors (Rose et al. 2004 ; Sterck et al. 2007 ; Takeda and
Matsuoka 2008 ; Zhang 2008 ; Baginsky 2009 ; Varshney et al. 2009 ; Mochida and
Shinozaki 2010 ; Jackson et al. 2011 ; Memon 2012 ), and this review will basically
cover some new areas in population (breeding) genetics, and topics which require
more detail explanation and are updated in crop plants. The excellent review by
Mochida and Shinozaki ( 2010 ) has provided the framework for this review, and we
intend to concentrate on more recent developments, and focus on bioinformation
and implications in crop improvement; although the technology, instrumentation
and molecular biology achieved in other plants must also be covered.
DNA Based Sequence Resources
GenomeSequencingProjects
Initially, the publication and accumulation of nucleotide sequences for model plants
only provided fundamental information, however now these base sequences form
the fundamentals of research in functional plant genetics in applied species such as
crops and domestic animals. Furthermore, DNA sequence data continues to be cen-
tral in providing the genomic basis for accelerating molecular level understanding
of basic biological mechanisms, and the application of such information to crops.
In this section, we describe recently developed plant sequencing advancements.
Species-specific nucleotide sequences are now providing information related to
phenotypic characters, even when based on genome comparative analyses from the
few model plants available (Cogburn et al. 2007 ; Flicek et al. 2008 ; Paterson 2008 ;
Tanaka et al. 2008 ).
The genome sequence of Arabidopsis thaliana is now used as a model species
in plant molecular biology mainly because of its small size, short generation time
and high efficiency of transformation. The genome sequence of rice ( Oryza sativa ),
including japonica and indica (an important staple food and a model monocotyle-
don) has also been used for comparative studies. These two plants still provide the
only model plant systems to date, however several genome sequencing projects
involving other plants have been completed, and many others are in progress; these
are detailed in Table 2.1 . Listed below are six of the most important web-based sites
for DNA based genome sequencing and annotation projects, their purpose and their
URL are detailed in Table 2.2 .
NCBI—BioProject
The NCBI site provides genome sequences and information for many plant spe-