Agriculture Reference
In-Depth Information
repeatable, and be performed in environments
representative of the target environment. Among
the various marker types available, Diversity
Array Technology markers (DArTs) show good
potential as an inexpensive high-throughput
marker tool and provide opportunity toward
whole-genome mapping (Gupta et al., 2008).
Finally, methods are being developed aimed at
effi cient marker implementation strategies in
breeding programs. These strategies may vary
depending on breeding program structure and
goals, genetic complexity of traits, and cost and
type of markers (Wang et al., 2007).
signal transduction and gene expression
(Umezawa et al., 2006). The fi rst group of genes
includes osmoprotectants, chaperones, reactive
oxygen species (ROS) scavengers, turnover
transport proteins, membrane modifi ers, and
detoxifi cation proteins. The second group of
genes includes signaling molecules and tran-
scription factors.
Transcriptomics enables high-throughput
investigation of changes in mRNA expression
levels, for example in response to drought. Pro-
teomic and metabolomic profi ling enable investi-
gation of the effects of post-transcriptional and
post-translational regulation, which complements
information generated by mRNA profi ling and
provides further insight into the response of
plants to water stress. For example, proteomic
studies in wild watermelon (
Citrullus lanatus
)
(Yoshimura et al., 2008) suggest that proteins
produced early in drought stress are involved in
root morphogenesis and carbon-nitrogen metab-
olism, while proteins involved in lignin and cell
wall synthesis are switched on later. Proteomic
and metabolomic studies of maize xylem sap also
found changes in levels of phenylpropanoid
compounds under drought stress (Alvarez et al.,
2008).
Genetical genomics, the integration of genetic
recombination and the raw power of genomics
(Jansen and Nap 2001), assists in the elucidation
of the genic basis of drought response traits, in
the identifi cation of candidate genes suitable for
use as markers, and in the identifi cation of regu-
latory genes controlling traits of interest. By
using structured germplasm in genomic studies,
gene expression variation is more likely to have
a genetic basis that can be subsequently exploited
in cultivar development programs (Xue et al.,
2006, 2008). Genes that are differentially
expressed in response to water stress that collo-
cate with QTLs for drought-related traits are
more likely to contribute to the expression of
that trait. Furthermore, levels of expression of
genes can be mapped; collocation with QTLs for
drought-relevant traits can indicate a genetic
role of a functional or regulatory gene in the
expression of the trait. A recent study by Jordan
et al. (2007) identifi ed both
cis
-acting (functional
Functional genomics and beyond
Water stress triggers a wide variety of plant
responses, including biochemical, physiological,
and cellular structure changes in plant cells.
High-throughput analysis of messenger RNA
expression—made possible through advances in
microarray technology—enables temporal, spatial,
and genotypic variation in levels of gene expres-
sion to be studied for a very large number of genes
in response to water stress. Knowledge of the
genes involved in the drought response is impor-
tant to understanding the underlying biochemical
and physiological basis of traits and of QTLs
involved in traits which will indirectly infl uence
breeding strategies. Candidate genes can be used
as perfect markers for the traits they infl uence,
and allelic variants of these candidate genes may
be readily converted to high-throughput, single-
nucleotide polymorphism (SNP) markers (Cogan
et al., 2006; Tuberosa and Salvi 2006). Finally,
candidate genes may have potential as transgenes;
manipulation of expression of these candidate
genes may provide enhanced drought tolerance
and increased yields of wheat in stress environ-
ments (see Umezawa et al., 2006 and references
therein).
High-throughput analysis of messenger RNA
(mRNA) expression has revealed that a large
number of genes are differentially expressed in
plants in response to water stress. Two broad
categories of genes are involved in response to
water stress: functional genes that protect against
the stress and regulatory genes that control
