Molecular Breeding - Genetics, Genomics and Breeding of Crop Plants - page 246

comparison to running conventional progeny tests after each backcross.
Marker-assisted backcrossing plays an important part in many commercial
programs with markers being used for both the selection of plants carrying
the gene(s) of interest and for recurrent parent background. Hospital et al.
(1992) demonstrated that it is not possible to optimize selection for the gene
of interest and the recurrent parent background simultaneously. They
suggested that the process should be subdivided into: a) the reduction in
length of the donor segment around the gene and b) the recovery of the
recurrent parent genotype. Depending on population sizes, a single gene
can be introgressed in three backcrosses and a self with, for example, the
emphasis in the first generation on a favorable crossover on one side of the
target gene, then in the next cycle on the other side and then the final
generation and self to “clean up” the background and to fix the introgressed
region.
Marker-assisted backcross programs are dependent on the
characterization of proprietary germplasm with a set of high quality SSR
markers that give a good coverage of the sunflower genome. Each year, new
lines and hybrids are genotyped to identify DNA polymorphisms and to
assess the genetic diversity of the material available to the breeders for
crossing. As discussed earlier, it is easy to distinguish elite male and female
lines using DNA markers, but hybrid sunflower breeding only dates backs
to the late 1960s and so, as yet, no heterotic groups exist within these two
major groups of elite commercial oilseed germplasm. However, some breeders
use the genetic distance between lines as a basis for making diverse B and R
line breeding populations. They will also make some crosses between B and
R lines and in these cases markers for the branching and CMS restorer
genes are useful tools for screening the progenies.
Routine marker application in segregating breeding populations
requires: the accurate sampling of leaf discs from the field for DNA extraction
in the laboratory and high throughput, cheap diagnostic tests for the genes
of agronomic importance. Knowledge of the major gene/QTL complement
of the parental lines enables the identification of populations that will
segregate for specific loci and the breeder then prioritizes which crosses are
to be screened with markers. Marker deployment in the F 2 or F 3 generation
depends on the economic importance of the trait, the robustness of the
phenotypic screen, the codominance/dominance of the linked markers and
whether there is an opportunity within crosses to pyramid genes/QTL for
different traits. Obviously the more traits that segregate in a given cross, the
bigger the population size has to be. Rapid methodologies have been
developed for extracting DNA from thousands of plants, but PCR on a locus
by locus basis, fragment separation and data capture are still relatively
time-consuming, depending on the lab set up. The advantages of SNPs are
that it is possible to assay from 10's to 1,000's of loci in a single reaction,