Biology Reference
In-Depth Information
population is developed by selfing the F
1
hybrids. The major disadvantage
of using F
2
populations is that the populations are not immortal. Therefore,
the sample tissue to isolate DNA for genotyping is finite. Another problem
is that each individual plant in the F
2
population possesses one unique
genotype and cannot be replicated in measuring quantitative traits. Since
the F
2
populations are easy to develop, they were used in the construction of
the early sunflower linkage maps (Barry et al. 1995: Gentzbittel et al. 1995,
1999; Jan et al. 1998).
Recombinant inbred lines (RILs) were first constructed for the model
plant
Arabidopsis thaliana
as permanent mapping populations (Reiter et al.
1992; Lister and Dean 1993) to add more markers to the existing genome
map. RIL populations are developed by self-pollinating individual F
2
plant
followed by three additional cycles of single-seed descent (SSD) to advance
the generation to F
7
. Since each of the resulting RIL can be traced back to the
individual F
2
plants, these lines are also called F
2
-derived lines.
Sunflower
plants need large space to grow from seed to seed, generation advance in
greenhouse is not practical. Only two generations (one in growing season
and one in off-season winter nursery) can be achieved. Therefore, an RIL
population needs at least four years to develop. After several generations of
self-pollination, a RIL population becomes an eternal mapping population
since each individual line possesses a practically homozygous genotype
and can be propagated generation after generation as a clone. RILs increase
the mapping accuracy of the high-throughput, dominant markers such as
AFLP and TRAP, which cannot easily differentiate heterozygous from
homozygous genotypes in the F
2
populations. RILs are also powerful tools
for analyzing quantitative traits because lines of identical genotypes can be
used in replicated trials to generate quantitative trait data, which is used to
determine the chromosomal location of the molecular markers closely
associated with the traits of interest. There are a number of sunflower linkage
maps constructed with RIL populations (Flores Berrios et al. 2000a; Tang at
al. 2002; Yu at al. 2003; Langer et al. 2003; Hu et al. 2004a; Poormohammad
Kiani et al. 2007).
3.4.2 Mapping Software Packages
Classical linkage analysis consists of three steps. The first step is to establish
a linkage relationship between two markers by a simple statistical test such
as a Chi-square test. The second step is to calculate the genetic distance
between the two markers from the recombinant frequency of the phenotypes
in the segregating population under investigation. The third step is to
determine the order of the markers, if three or more markers are in the same
linkage group, by three-point test. These were manually done when working
with a few morphological markers. This process has been computerized
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