Plant genomics research had its beginning in December
2000, with the publication of the whole genome sequence of the model plant
species Arabidopsis thaliana. Rapid progress has since been made in this
area. The significant developments include the publication of a high-quality
rice genome sequence in August 2005, draft genome of poplar in September 2006,
whole genome sequence of two grapevine genotypes in 2007, and that of
transgenic papaya in 2008. Draft sequences of corn gene-space and those of the
genomes of Lotus japonicus and Glycine max have also become available
in 2008. Genomes of several other plant species (e.g., Sorghum bicolor, Manihot
esculenta (cassava), barley, wheat, potato, cotton, tomato, maize, Brachypodium distachyon
(a small model
grass genome), Medicago truncatula,
shepherd's purse, peach) are also currently being sequenced. Multinational
genome projects on Brassica and
Solanaceous genomes are also in progress. In still other cases (e.g., wheat,
corn, barley), where the large genome size prohibits whole genome sequencing,
the gene rich regions (GRRs) of the genomes are being identified to bring down
the sequencing work to a manageable level. The 10-year-old US National Plant
Genome Initiative (NPGI) also made a call for more plant genomes to be
sequenced. While making a choice for additional plant genomes to be sequenced, it
has also been emphasized that much of plant diversity is available in tropical
plants so that during the next decade, more genomes from tropics (e.g., Carica, Saccharum,
Psychoria, Opuntia) need to be sequenced.
The sequencing
information obtained as above will be utilized for both basic and applied
research so that while this will help in elucidating evolutionary relationships
and developing better phylogenetic classification, this will also help in the discovery
of new genes, allele-mining, and large-scale SNP genotyping. In order to
achieve these objectives, there has also been a call for sequencing genomes of
diverse cultivars of each crop like
rice. As a result, the concept of plant pan genome (initially developed for
microbial genomes), each composed of “core genome” and “dispensable
genome,” has also been introduced. The sequence information from diverse
cultivars in a crop will be utilized for molecular breeding. For instance, new
technologies have been used for the improvement of indica rice, but similar efforts
are now being made for improvement
of japonica rice also. An overview of
the present status of plant genomics research and its impact is also available
in a recent special issue of Science (April 25, 2008).
The future plant
genomics research will certainly derive benefit from the recent development of new-generation
sequencing technologies. These new technologies include improvements in
sequencing systems based on Sanger's sequencing approach, as well as a number of
non-Sanger sequencing technologies that became available during 2005–2008. The non-Sanger
technologies include both sequencing based on amplified DNA molecules, and
those based on single DNA molecules including Helicos true single molecule
sequencing (tSMS) technology commercially launched in 2008. These new-generation
sequencing technologies will certainly help in plant genomics research in a big
way and may include a variety of research projects. While more plant genomes will
be sequenced, epigenomes, transcriptomes, and metabolomes will also be worked
out with much higher speed and at a cost reduced by several orders in
magnitude. The science of plant genomics will also be influenced by the new
emerging areas of “chemogenomics” and “synthetic genomics.”
This special issue
of the International Journal of Plant Genomics is devoted to “Genomics of Major
Crops and Model Plant Species” with the aim to present an updated account
of the genomics of major crop species and the model plant species. Articles
published in this special issue involve almost all fields of genomics,
including structural genomics, functional genomics, proteomics, metabolomics,
and comparative genomics. Discussions also extend to cover phenomics,
bioinformatics, epigenetics, and organellar genomics. Translational genomics
from model plant species to cultivated crops and applications of genomics in
crop improvement are topics for several articles. Structural genomics, as a major
field for most crop plants, received a greater attention in this special issue,
compared to other fields, including various types of molecular markers from
RFLP to SNP and their use in construction of genetic, cytogenetic, and physical
maps, QTL/gene mapping, genome sequencing, and generation of genomics
resources. Functional genomics is the second field that received more
attention, and some issues addressed significantly include gene isolation
through map-based cloning and candidate gene approach, as well as functional
analysis through insertional mutagenesis, RNAi, TILLING, and transcription
profiling.
There are 14
review articles in this special issue, seven belonging to grass family, two
devoted to legumes (soybean and Medicago),
one devoted to oil-seed crop (Brassica
rapa), and one each to cotton, tomato, potato, and Citrus. The special issue starts
with several articles on genomics
of food crops including wheat, barley and rice. There is a comprehensive article
on wheat genomics written by P. K. Gupta et al. (Meerut, India) followed by an
article giving an overview on barley genomics by N. Sreenivasulu et al. from IPK (Gatersleben,
Germany). On rice
genomics, there are two articles: one with emphasis on genome sequencing
(written by T. Matsumoto et al. (Japan))
gives an account of international collaboration in sequencing rice genome and
its annotation (including structure and composition of rice centromeres and
telomeres), and the other on rice molecular breeding (written jointly by B. Collard
(Queensland, Australia) and the rice genomics group
(including D. J. Mackill) from International
Rice Research Institute (IRRI) (Manila,
Philippines)) gives a detailed account of how rice genomics resources
can be utilized for molecular breeding. A. H. Paterson has written a review on Sorghum
genomics (giving information on both
markers and whole genome sequencing) and H. Budak et al. (from Turkey and Spain)
give an updated account of the development of genomics resources for the grass
genus Brachypodium, which is being
preferred over the rice genus Oryza as a model for temperate grasses (including cereals
and forage grasses). G. M.
Souza et al. (Brazil) have written an article on sugarcane functional genomics,
outlining the development and the use of ESTs and cDNA microarrays for gene
discovery.
Among legume
species, soybean (Glycine max) is an
important crop world-wide, while Medicago
truncatula and Lotus japonicus emerged
as model systems for legume biology during the last decade. Therefore, one
article on soybean genomics and another on Medicago
truncatula have been included in this special issue. D. A. Lightfoot from The Illinois
Soybean Center (Illinois, USA)
discusses the use of Forresr cultivar for the development of genomic resources
in this crop. Similarly, Julia
Frugoli (SC, USA) with his two other
colleagues elsewhere wrote an article on Medicago truncatula giving an updated account
on the developments
of genomic resources in this model legume. C. P. Hong et al.
report the current understanding of the genome structure of Brassica rapa and
efforts for the whole-genome sequencing of the species.
Hong-Bin Zhang
from College Station (Texas, USA) and his coworkers (from University of Georgia and
China) discuss
advances on genomics research in cotton, highlighting the development of DNA
marker linkage/physical maps, QTL mapping, ESTs, and whole genome sequencing. The
last three articles deal with genomics of two related Solanaceous crops, namely,
tomato and potato, as well as a fruit-tree genus (Citrus). L. Frusciante
et al. from (Portici and Roma, Italy)
give an updated account of tomato genomics, G. J. Bryan and I. Hein from
Scottish Crop Research Institute (SCRI, Dundee, UK) give an account of potato
genomics, and M. Talon (Valencia, Spain)
with F. G. Gmitter (Citrus
Research and Education Center, University of Florida, USA) give an account for Citrus
genomics.