Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 63

teristics such as salt tolerance in salt cress ( Thellungiella halophila ) and selenium
accumulation in a number of species (De Filippis 2010 ). Full-length cDNA libraries
serve as primary sequence resources for designing microarray probes, and as cloned
resources for genetic engineering to improve crop efficiency (Sakurai et al. 2007 ;
Futamura et al. 2008 ; Ralph et al. 2008b ; Taji et al. 2008 ). Because of the important
function of full-length cDNA resources in 'omics' data and information, it is es-
sential to establish relevant information resources that provide gateways to these
sites, and to integrate this to related data sets derived from other 'omics' field. A
comprehensive computational tool to achieve this total integration is the CLC Biol-
ogy workbench system (Table 2.3 ).
smallRNA(sRNA)Information
In plants, sRNAs, which can include microRNAs (miRNAs), short interfering
RNAs (siRNAs) and trans-acting siRNAs (ta-siRNAs) play important roles in
epigenetic processes, and may control gene activities involved in plant develop-
ment and homeostasis (Ruiz-Ferrer and Voinnet 2009 ). These RNA molecules are
important regulatory resources that should be detailed, and their expression anal-
ysed using the most recent next-generational genomic methods (Nobuta et al. 2007 ;
Chellappan and Jin 2009 ). In maize, sRNAs in the wild type and in the isogenic
mop1-1 loss-of-function mutant were analysed by deep sequencing using Illumina's
sequencing-by-synthesis (SBS) technology to characterise possible regulatory roles
for maize sRNA (Nobuta et al. 2008 ). In poplar, expressed sRNAs from leaves and
vegetative buds were also studied using high throughput Roche 454 pyrosequenc-
ing, and genes in similar families of miRNA identified, including novel new genes
(Barakat et al. 2007 ). Nucleotide sequencing of Brachypodium sRNAs have also
been performed, resulting in the identification of miRNAs involved in low tem-
perature stress tolerance (Zhang et al. 2009a ). The plant miRNA database (PMRD)
is a useful information resource on plant miRNA, and is available on the web site
of PMRD (Zhang et al. 2009b ). The Affymetrix GeneChip miRNA Arrays web site
is also important for such studied. Listed in Table 2.3 are important web-based sites
and URL for databanks often used in regulatory plant micro RNA research.
VariationAnalysisPlatforms
High-throughput polymorphic analyses are important for studying genome-wide ge-
notyping using a hybridization-based SNP molecular marker methods, which have
been used to analyse Arabidopsis ecotypes and rice strains, and the data identified