Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 107

Pyrosequencing procedures, massive parallel DNA sequencing and single mol-
ecule sequencing are now becoming normal and readily available to scientists. Ad-
ditionally, these new technologies have provided researchers with new avenues to
addressed web information at the entire genome level in the fields of inter-species
and intra-species comparative genomics and evolutionary genetics. In evolution-
ary and population genetics, knowledge of genetic diversity, natural and induced
variations and population structure are not only important in ecology, but are also
important to the breeding and biodiversity of crop plants in agriculture.
New and efficient procedures for whole-genome de novo sequencing in crop
plants is perhaps one of the most anticipated innovations for next-generation se-
quencing and related applications. Although, to date, this approach has been real-
ized only in bacteria, a number of tentative attempts are being made to realise this
advancement in higher plants, and this must be developed further in crop species.
Breeding crop plants for QTL and traits with low heritability can be the most
interesting and the most difficult to work with in breeding programs, but marker as-
sisted selection (MAS) is improving all the time and stable, specific more informa-
tive molecular markers must be developed for crop plants. In crop plants especially
these traits with low heritability can be important in improving yield, quality and
production, and despite being difficult to master must be addressed.
Expressed Sequence Tags (ESTs) derived from different and specific tissues,
including tissues from organisms in a range of developmental stages or under biotic
and abiotic stress could significantly facilitate gene discovery, and this information
is vital in the design of molecular markers and probes for microarrays and gene-chip
studies. Full-length cDNA libraries have contributed to function alanalysis by creat-
ing overexpressors used in reverse genetics, and this approach is only beginning to
be applied in crop plants. However for results to be easily interpreted, reverse genet-
ics must be used in conjunction with comparative analyses of 'modificon' events
among plants.
RNA interference, includingsRNAs, microRNAs (miRNAs), short interfering
RNAs (siRNAs) and trans-acting siRNAs (ta-siRNAs) are playing important roles
as crucial components of epigenetic processes, and gene networks involved in plant
development and homeostasis. More information on identification and expression
of interfering RNA molecules is necessary, especially by using next-generational
genomic technologies in crop plants.
Measurement in abundance of transcripts expressed in cells, tissues and organs
can now be estimated from sequence clusters. These methodological principle have
been applied in human and mouse, in the form of a type of 'tissue or organ map' to
derive the transcriptome in organs; and such 'plant tissue and organ' mapping could
be instrumental as reference material for increased crop production.
Differential display methods are now cost effective and produce large amounts
of data. Serial analysis of gene expression (SAGE) and derivatives of this method
can genetically define host cells and their pathogens simultaneously in crop plants,
and additionally superSAGE tags have been used to design probes directly for oligo
microarrays in plants and pathogen alike. Microarray and DNA chip-related tech-
nologies have advanced rapidly and their application has expanded to a wide variety
of crop science disciplines. Today commercially available DNA microarrays are