© Benaki Phytopathological Institute
Molecular Biotechnology on agricultural crop improvement
43
been reported that the Palomero genome, a
corn variety diverged from B73 about 9,000
years ago, is around 400 million nucleotides
smaller and contains about 20% less repet-
itive DNA than B732 (Vielle-Calzada
et al.,
2009). To map maize haplotypes a part of
the gene-rich region of 27 maize varieties
was sequenced. ‘HapMap’ revealed thou-
sands of genes around the centres of the
chromosomes, where they were unlikely to
be shuffled around during recombination
(Gore
et al.
, 2009). Schnable
et al.
(2011) dem-
onstrated that the maize subgenomes are
differentiated by genome dominance and
both ancient and ongoing gene loss. Most
of the economically important traits consid-
ered in maize breeding are inherited quanti-
tatively. Multiple genes or quantitative trait
loci (QTLs) affecting flowering traits, root
characteristics, cell wall traits, and toler-
ance to biotic/abiotic stresses panicle mor-
phology and grain development have been
cloned, and gene expression research has
provided new information about the na-
ture of complex genetic networks involved
in the expression of these traits (Buckler
et
al.
, 2009; Chung
et al.
, 2011; Fernandez
et
al.
, 2009; Messmer
et al.
, 2009; Poland
et al.
,
2011; Trachsel
et al.
, 2009). Ameta-analysis of
QTL associated with plant digestibility and
cell wall composition in maize identified
key chromosomal regions involved in silage
quality and potentially associated genes for
most of these regions (Truntzler
et al.
, 2010).
Association mapping (associating specif-
ic DNA polymorphisms with traits of interest
based on linkage disequilibrium).
McMullen
et al.
(2009) described the maize NAM pop-
ulation generated by crossing 25 diverse
inbred lines to a common line, inbred B73.
Sequenome-based SNP-typing assay was
used to identify 1,359 SNPs in maize tran-
scriptome and 75% of these SNPs were con-
firmed and applied in association analysis
(Liu
et al.,
2010). Currently, there are over 2
million maize ESTs in GenBank (Benson
et al.,
2009). However, the assembly of these ESTs
into gene models presents practical prob-
lems. Therefore, a full length cDNA library
has been recently constructed for
Zea mays
(http:www.maizecdna.org/) (Soderlund
et
al.,
2009). A normalized cDNA library, cov-
ering most of the developmental stages of
maize seeds, was also constructed and 57
putative transcription factors were identi-
fied (Wang
et al.,
2010). The cDNA libraries
can serve as primary resources for design-
ing microarray probes and as clone resourc-
es for genetic engineering to improve crop
efficiency.
Maize GDB (
).
Maize GDB
is a database that provides docu-
mentation and data for the microarrays pro-
duced by the Maize Gene Discovery Proj-
ect. An extensive expression atlas covering
a wide array of tissues and developmental
stages of maize using a NimbleGen microar-
ray encompassing 80 301 probe sets was
recently constructed (Sekhon
et al.,
2011).
Random-sheared, paired-end Illumina GAII
reads have been generated from 103 maize,
teosinte and maize landrace inbred lines at
a depth ranging from 4-30x (Chia
et al.,
2012;
Hufford
et al.,
2012). Microarray studies have
also been performed to study cell wall me-
tabolism in maize, with the aim of identi-
fying tissue-specific or developmentally
regulated gene expression of members of
multigene families or to obtain a better un-
derstanding of regulatory networks that are
exposed when cell wall-related genes are
mutated (Guillaumie
et al.,
2007a; Guillaumie
et al.,
2007b). The MAIZEWALL sequence da-
tabase and expression profiling resource has
been developed
-
tlse.fr/MAIZEWALL). Rajhi and co-workers
performed transcriptome analysis in maize
root cortical cells during lysigenous aeren-
chyma formation and discovered a number
of genes whose expression changed in re-
sponse to ethylene under waterlogged con-
ditions (Rajhi
et al.,
2011).
Maize small RNAs.
Small RNAs in the wild
type and in the isogenic Mediator Of Para-
mutation1 loss-of- function (mop1-1) mu-
tant have been examined by deep sequenc-
ing to analyze the size distribution of maize
small RNAs (Nobuta
et al.,
2008). Small RNAs
are playing roles as major components of
epigenetic processes and gene networks
