Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 99

cauliflower mosaic virus 35S enhancer (Weigel et al. 2000 ). Transcriptional activa-
tion of genes near the insertion aids in novel phenotype identification and identifies
genes that are redundant and/or essential for survival. AT resources have now been
used to isolate genes from Arabidopsis, rice, petunia and tomato (Kakimoto 1996 ;
Zubko et al. 2002 ; Mathews et al. 2003 ; Mori et al. 2007 ). Recently, AT systems
using transposons of maize En / Spm or Ac/Ds have been developed in Arabidopsis ,
rice and soybean (Weigel et al. 2000 ; An et al. 2005 : Schneider et al. 2005 ; Qu
et al. 2008 ; Kuromori et al. 2009 ). Web-based sites for genotype tagging and mutant
lines, and their purpose and URL are detailed in Table 2.11 .
FoxHunting
The FOX gene hunting system has been developed as an efficient gain-of-function
system that combines a transformation algorithm with large-scale information from
full-length cDNA clones (Ichikawa et al. 2006 ). The system can be applied across
plant species, like the development of a set of full-length rice cDNA clones aimed
at ' in planta ' high-throughput screening of rice functional genes; but with Arabi-
dopsis set as the host reference species (Nakamura et al. 2007 ; Kondou et al. 2009 ).
Similar results (overexpressors using cDNA) have been achieved in tobacco (Lein
et al. 2008 ).
ChemicalandPhysicalMutagenesis
Spontaneous and induced mutations are the major source of most of the existing
genetic variation in plants, and are commonly used in plant breeding. The occur-
rence of spontaneous mutations in nature is relatively rare and difficult to identify
because they can be recessive, or are deleterious and quickly eliminated. Increasing
the rate of mutation (ie induced mutations) can provide additional sources of variant
genotypes important in plant breeding. Mutagenic agents include alkylating agents,
ethyl methanesulfonate (EMS), sodium azide and methylnitrosourea (MNU), or
X-ray and UV-light, fast-neutrons, ion-beam irradiationand nuclear (alpha, beta,
gamma rays) radiation. Alkylating agents that react with DNA to change nucleotide
sequences produce relatively few useful point mutations. However, the absorption
of ionising radiation produces more complex DNA and structural chromosomal
changes, and are considered the mutagenic agents of choice in plant breeding appli-
cations, however most of these mutagenic agents have been used to generate mutant
populations for many years now; these mutant lines have been particularly useful
in forward genetics studies in various plant species (Hoang et al. 2009 ; Uauy et al.
2009 ; Jackson et al. 2011 ).
Mutations can occur in tissue cultured plantlets and the process can be rapid; this
process is sometimes called 'somaclonal variation' and these plants have also found