Agriculture Reference
In-Depth Information
large number of segregating recombinants and the use of new polymorphic markers
in the QTL area makes it possible to define a candidate region of less than 50 kb
which will contain about 10 ORFs (open reading frames). If the region size is not
sufficiently small for further analysis, new screening of rHIFs (possible
recombinants within a heterozygous region of a QTL) is performed. When the
desired region size contains only few genes, the QTL is considered as fine mapped
and genes within it are examined for potential clues (Ikram and Chardon
2010
). In
addition to fine mapping, several functional strategies are available for plants whose
complete genome sequence is available in order to select relevant candidate genes
for the QTL. The knowledge of the complete genome sequence allows the search of
such candidates on the bases of the predicted gene functions. Nevertheless, the
function of many ORFs remains unknown at the cellular and/or phenotypic level
and, therefore, it is not always possible to find obvious candidates from the genome
sequence (Koornneef et al.
2004
).
QTL cloning is a very efficient way to verify a new gene without
a priori
. For
instance, Calenge et al. (
2006
) were interested in two genotypes, which accumu-
lated soluble sugars at different rates in 10 and 3 mM nitrate nutrition. QTL analysis
resulted in a major QTL for fructose content in leaves. The fine mapping restricted
the QTL area to a 3 kb interval enclosing the single gene
SWEET17
(Chardon
et al.
2013
). The authors showed by functional analysis that variation in fructose
content is uncoupled from further metabolic pathways, which result from seques-
tration of fructose into the vacuole, the main compartment for soluble sugars. They
demonstrated that SWEET17 is a new vacuolar transporter of fructose in plant.
In contrast, simply resequencing a region with dozens or more genes is, on its
own, not generally informative because of the high number of polymorphisms that
distinguish an arbitrary pair of accessions, about 1 in every 200 bp (Weigel
2012
).
Fortunately, compared to other multicellular organisms in which natural variation is
studied,
Arabidopsis
has the enormous advantage that almost all accessions are
quite easily transformed by dipping flowering plants into a suspension of
Agrobacterium tumefaciens
containing a T-DNA vector with the transgene of
interest.
QTL Meta-analysis
With data on multiple populations, it useful to know whether QTL identified for a
given trait in one population correspond to those detected in other populations, or
whether QTL locations identified in one species correspond to QTL or other types
of loci detected in corresponding regions in other plant species. With this aim, a
method has been developed by Goffinet and Gerber (
2000
) to estimate the mini-
mum number of loci giving the observed QTL in individual studies and to combine
the available information to precisely give the position of each individual QTL.
Such an approach is called
and its usefulness is to pool information
when raw data are not available. Comparative analysis of QTL between species
meta-analysis
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