Bioinformatic Tools in Crop Improvement - Crop Improvement: New Approaches and Modern Techniques - page 57

grapevine (Mullins et al. 2006 ; Torada et al. 2006 ; Jaillon et al. 2007 ; Heesacker
et al. 2008 ; Kota et al. 2008 ; Talon and Gmitter 2008 ; Blair et al. 2009 ; Deleu et al.
2009 ; Kaur et al. 2009 ; Li et al. 2009 ).
Some molecular markers identified this way allow the indirect selection of in-
teresting genotypes (i.e. breeding lines in crops), and these cultivars constitute an
essential tool for the development of marker-assisted selection (MAS) in plant
breeding. The use of DNA markers (and indirectly EST markers from RNA) for
direct selection offers greater potential gains in breeding for QTL and traits with
low heritability, and these can be the most difficult to work with in crop breeding.
However these low heritability traits are also amongst the most interesting and the
most difficult to develop.
When a locus has many variants, or alleles, it is referred to as being polymor-
phic. Mutation(s) at a number of loci generate multiple alleles, most of which are
eliminated from the population by genetic drift or breeding selection. Only a small
number of alleles are incorporated into the population by chance or selection. Most
polymorphisms can be genetically straightforward, with two alleles directly de-
termining two versions of the same protein (gene), however, some can be highly
complex, with multiple, related genes in a complex system of metabolic differ-
ences. Crop breeders have known the complexity of multiple alleles for decades.
However with the advent of molecular markers, genetic diversity and other forms
of genetic structure in breeding populations is possible. Listed in Table 2.2 are the
most important web-based sites for DNA markers and some of the population sta-
tistics programs and web resources commonly in use. Molecular markers fall into a
number of types listed below, each having positive and negative features, and care-
ful consideration is required before they are adopted in any type of research (Hoang
et al. 2009 ; De Filippis 2012 ).
Restriction Fragment Length Polymorphism (RFLP)
RFLP requires hydrolysis of probe DNA from samples. RFLP can provide high
quality data but has severe restrictions on throughput because large amounts of
DNA are required, and because it is not based on amplification of the target DNA
via the polymerase chain reaction (PCR).
Random Amplified Polymorphic DNA (RAPD)
RAPD is a method based on PCR but uses arbitrary short primers (10 bases long)
to identity plant DNA regions. No knowledge of the genome is needed, but by the
same token markers can target many places on the genome. Results can be inconsis-
tent and only dominant genes can be identified.