Principles of Plant Genetics and Breeding

238 CHAPTER 14
rDNA is that DNA is universal and hence the transfer of
DNA is possible, in theory, across biological barriers.
Eukaryotes are genetically complex organisms, and not
directly amenable to certain biotechnological procedures.
Consequently, scientists pick plants and animals
that are easy to manipulate, and invest in a thorough
genetic analysis of their genomes. The information
derived from such studies is extrapolated to more complex
organisms. Arabidopsis thaliana was the first plant
to be completely sequenced. This flowering plant has a
short life cycle of about 6 weeks from germination to
seed maturity. It produces seed profusely. Because of its
small size, Arabidopsis can be cultured in trays or pots in
a limited space. Two of the most important higher
plants used for food that are being developed as model
plants are rice (Oriza sativa) and maize (Zea mays).
There are several subspecies of rice, the most widely
eaten being O. indica, followed by O. japonica.
Through both public and private sector efforts, the
genome sequences of the two subspecies have been
developed. Genomes of all cereals (wheat, barley, rice,
corn, etc.) are structurally similar (see next Section).
Genomic colinearity and its application in
plant breeding
Genomic colinearity is a term used to refer to the
conservation (through evolutionary history) of gene
content, order, and orientation between chromosomes
of different species, or between non-homologous chromosomes
within a single species. The term is sometimes
used as synonymous with synteny, the phenomeonon of
conservation of gene order within related genomes.
Synteny has been observed in the Brassicaceae using
molecular techniques. An important discovery is the
synteny found between dicots and monocots. The
sequence information for Arabidopsis thaliana (a
Brassica species) and rice have revealed a conserved
gene order across this vast evolutionary distance. It is
estimated that about 75% of genes in dicot species
and about 40% in monocots occur in regions that have
colinearity with Arabidopsis that could be exploited by
breeders.
Synteny has also been discovered in Fabaceae involving
soybean, peanut, mungbean, lentil, common bean,
common pea, and alfalfa. Some conservation of the
genomic region in this family with Arabidopsis has been
established. Synteny in the Poaceae is one of the clearest
to be documented. Using the rice genome as the inner
circle, researchers have graphically aligned the genomes
of several cereals (sorghum, maize, wheat) by colinearity
into concentric circles such that colinear regions in
different species lie along any radius. Rice has become a
model species for comparative genomic studies of species
with large genomes (e.g., wheat, sugarcane) that are
difficult to study by traditional genetics. Another advantage
is that the so-called “orphan crops” (e.g., millet),
which would otherwise not receive significant attention
as the major cereals do, can now benefit from the
information obtained from rice.
The applications of colinearity to plant breeding
include the following:
1 The prediction of the location of genes controlling a
particular function in crop species.
2 The facilitation of genome mapping by transferring
markers from a well-mapped genome to a less studied
one.
3 Mapping will facilitate marker-assisted selection or
map-based cloning.
4 After cloning a locus of agronomic importance, colinearity
may provide opportunities for accumulating
alleles of that locus from other distantly related species.
This collection of genes may be a source for genetic
engineering applications for crop improvement.
Functional genomics
Once DNA sequences have been obtained, the next
important task is to understand their function.
Structural genomics focuses on sequencing of the
genome; functional genomics focuses on gene function.
The genome is essentially a set of instructions for
making proteins of various kinds. Because most genes
are expressed as proteins, one of the common ways of
understanding gene function is by tracking protein
expression by cells (called proteomics). Genes may provide
instructions for making specific proteins. However,
in the process of carrying out these instructions, additional
proteins can be produced, as has already been
noted. Linking gene to function is a complex undertaking.
Understanding the genome structure alone is
insufficient; it is critical to identify the proteins they
encode. Many techniques have been developed for
deciphering gene function.
Bioinformatics in plant breeding
Bioinformatics may be defined as a knowledge-based
theoretical discipline that attempts to make predictions
about biological function using data from DNA