Agriculture Reference
In-Depth Information
for the analysis of quantitative traits. In both cases the accuracy of QTL
localisation, referred to as mapping resolution, depends on population size. The
mapping of QTL in segregating populations has limited resolution since loci
associated with the expression of a quantitative trait can be mapped with a precision
of about 5-20 cM depending on its relative effect and the quality of the QTL
mapping assay (Keurentjes et al.
2007
). The choice of one mapping population over
another depends on the plant species and the specific parents of interest. In cases
where different cultivars or wild accessions are studied, preference is often given to
RILs. However, when different species or wild and cultivated germplasm are
combined, NILs are preferred. In
Arabidopsis
for example, the ease with which
fertile RIL populations with complete genome coverage can be generated, due to its
fast generation time, has led to their extensive use in mapping quantitative traits. An
overview of the steps undertaken to generate a set of RILs is represented in Fig.
2.1
.
The population derived from a European accession and a genetically distant one
from central Asia, Bay-0 and Shahdara, is an example of a novel RIL population
suitable for the investigation of traits such as the response to nitrogen availability,
root architecture, seed germination, drought tolerance and virus resistance (Loudet
et al.
2002
). The phenotypic variation resulting from such a cross is expected to
reflect the adaptation to the specific habitat and the genetic distance between the
parental accessions. The first extensive study of N metabolism in Arabidopsis using
QTL mapping was
conducted by Loudet on 415 RILs derived from
Bay-0
Shahdara population (Loudet et al.
2003
) to describe whole plant N
physiology and growth at a vegetative stage. The study, conducted in controlled
growth conditions, aimed at comparing two different N environments (10 mM and
3 mM nitrate) and identified several loci explaining the variability of growth and
total N, nitrate, and free amino acid contents.
Other approaches involve the use of multiple parents, as in the multiple
advanced generation intercross (MAGIC) and
Arabidopsis
multiparent RIL
(AMPRIL) populations (Kover et al.
2009
; Huang et al.
2011
). The MAGIC design
is more elaborate and generates more recombination events per line than the
AMPRIL strategy, but the founder genomes are less evenly represented in the
final lines. Mapping in either population is more complex than with RILs, but
with a sufficiently high density of intermediate frequency markers, one can infer the
most likely local founder genotype. Some of the advantages of using RIL-type
populations will continue to apply in the future.
Maize is the crop species, which has traditionally been involved in QTL map-
ping, and numerous QTL studies for NUE are now available. Zhang et al. (
2010
)
has published recently a study on QTL mapping for several enzyme activities. They
detected 73 QTLs for the activity of 10 enzymes involved in carbon and nitrogen
metabolism and eight QTLs for biomass in an intermating RIL population devel-
oped by randomly intermating plants for four generations following the F2, prior to
the derivation of mapping progeny. A RIL population of rice has also been tested
for tolerance to salinity, measuring the amount of Na
+
and K
+
ions in shoots
and roots in three environmental conditions of 0, 100 and 120 mM NaCl
