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7. ROLE OF QTLs IN THE EARLY EVOLUTION...
crops in two years of cultivation. Thus, factorial analysis of variance within general linear
model (GLM) was used to check for genotype, environment (year or crop) and interaction
genotype x environment effect. Significant differences between genotypes were analysed by
the LSD test.
For each hybrid the level of heterosis was estimated as an increase over the better
parent. Heterosis was defined here, according to of G.H. Shull (Shull 1952), as the increase
in size, vigour, yield, disease resistance and other quantitative traits in F 1
hybrids in comparison
with the better parent. This definition points at the advantage of the F 1
hybrid over
each parent. Therefore, the level of heterosis with regard to a given trait should be estimated
as the increase over this parent, which exhibits the higher value of a trait. In the light of the
Shull’s definition, it is misunderstanding to measure heterosis in relation to mid-parent value
although some authors tend to do it (Polok 1996).
7.2.2. QTL mapping
Quantitative trait loci were mapped in the interspecific F 2
population derived from a cross
between L. multiflorum and L. perenne, BR3 x NZ15, for which the genetic map was previously
constructed (Chapter 6). A set of 502 genetic markers from this map was combined
with a dataset from quantitative traits. QTL mapping was done first with MAPL98 (Ukai 2004)
using interval mapping by maximum likelihood. The principle behind this method was to test
for the presence of a QTL at many positions between two mapped markers. The likehood of
the observed distributions of a QTL effect was computed and the map position of a QTL was
determined as the maximum likelihood from the distribution of likelihood values (LOD scores).
The 1 cM intervals and a minimum LOD threshold of 3.0 were selected for significance of
location of QTLs. The genetic map of L. multiflorum and L. perenne had high resolution, the
density of markers was high and they were rather equally distributed on each linkage group
with mean distance of around 2 cM thereby, the same critical LOD score could be employed
for all linkage groups. If evidence for more than one QTL peak was found on the same linkage
group, the trait was analysed by composite interval mapping with multiple regression
using Windows QTL Cartographer 2.5 (Wang et al. 2007). Similarly, to simple interval mapping,
this method tests hypothesis of a QTL presence in an interval between two adjacent
markers, however, at the same time it tests the effects of segregating QTLs elsewhere in the
genome. Additional criterion was employed for QTLs in close proximity. They were accepted
only when score dip between the QTLs peaks was bigger than 2 LODs.
The magnitude of QTL effect was estimated as the percentage of F 2
phenotypic variance
explained (PVE). An arbitrary criterion of minimum 25% PVE was used to define a major
QTL (Bradshaw et al. 1998). The additive and dominance effects of each QTLs were
tested. The sign of the effects indicated the direction of change in the phenotype. A positive
sign indicated an increase and negative sign a decrease in the trait value caused by a given
QTL.