Agriculture Reference
In-Depth Information
QTL Fine Mapping
NILs have been used in various studies to confirm and fine map QTLs previously
mapped in RIL populations (Koornneef and Smeekens
2005
; Edwards et al.
2005
)
for which heterogeneous inbred families (HIFs) have also been used (Tuinstra
et al.
1997
). To construct an HIF-type NIL, a RIL is chosen that is still heterozygous
around the QTL of interest but homozygous elsewhere. In fact, even after six
generations of inbreeding, which is customary for RILs, a small percentage of the
genome remains heterozygous. This RIL is then selfed and genotyped so that each
homozygous genotype at the region of interest can be identified and studied in
detail. HIFs should not to be compared with the reference parental genotype, but
with one another within the descendants (family) of the chosen RIL. In contrast to
“conventional” NILs, the genetic background of an HIF line is not homogeneous,
but a mix of both parental genomes since these lines originate from one RIL of the
population. The ease with which NILs can be extracted from a large population of
HIFs may also allow a QTL mapped at low significance thresholds to be confirmed
by subsequent examination of NILs. Second, NILs extracted from segregating HIFs
are useful for the fine mapping of QTLs. Each segregating HIF is independent and
contains unique recombination events in genomic regions flanking the QTL. An
example of fine mapping using HIFs comes from the investigation of the four loci
identified in the Arabidopsis population Bay-0
Shahdara in low and high nitrogen
environments by Loudet et al. (
2003
). The production of homogeneous plant
material for a large number of lines was certainly the most challenging and limiting
step of this work, but the authors also remarked that uncontrolled environmental
effects can affect the evaluation of the quantitative traits and that environmental
heterogeneity can occur between two different cultivation repetitions (even in the
same growth chamber), as well as within one single growth chamber during a
repetition. For these reasons, it is recommended (a) to always study all of the lines
in the same cultivation repetition and (b) to compare different N environments in
the same cultivation repetition. One of the limitations of HIF analysis for the
evaluation of QTL is that the genetic background of NILs derived from HIFs are
unique and cannot be easily replicated. NILs are not easily developed for evaluating
the effects of more than one QTL in a single genetic background or for comparing
the effects of QTL identified in different populations.
Candidate Genes
Co-localisation with candidate genes sometimes allows rapid molecular identifica-
tion of QTL. This was the case in a study by Loudet et al. (
2007
) where QTL
mapping for sulfate content in Arabidopsis leaves resulted in the identification of
several minor QTLs and one major QTL on chromosome 1 in two contrasted N
levels (3 mM and 10 mM). The major QTL co-localised with the gene APR2 coding
