Agriculture Reference
In-Depth Information
(Rafalski
2010
). In marker assisted recurrent selection, breeders identify desirable
alleles at one or more loci, basing on the outcome of a mapping experiment, and
then use closely linked genetic markers for selecting individuals in breeding
populations (Collard and Mackill
2008
; Ribaut et al.
2010
). This approach results
in fixing the desirable allele(s) in the population(s) of interest.
Limitations
The detection power of association mapping greatly depends not only on the
magnitude of the effect that can be ascribed to a locus, relative to other loci present
in the population, but also on the allele frequency distribution. Rare alleles cannot
be detected with good confidence, unless their effect is very large. Therefore,
segregating biparental populations are more appropriate for the mapping of alleles
rare in the germplasm pool of interest (Rafalski
2010
). Genetic association mapping
enriches the repertoire of tools available for the dissection of trait architecture in
crop plants and model species. As high-density genotyping becomes increasingly
accessible, this approach will gain power to identify with high-resolution genetic
loci and in some cases causal polymorphism affecting agronomic and end-use traits
in crop plants, as long as relevant alleles are present at high frequency. Mapping in
defined biparental populations will remain the method of choice for rare alleles,
especially those with moderate effects, and for the study of epistatic interactions.
Independent validation of the associations found by both approach and evaluation
of their effects in different genetic backgrounds remains an essential, even though
sometimes neglected, aspect of a genetic experiment. Improvement in phenotyping
remains a major challenge for mapping many agronomical important traits such as
NUE or drought tolerance.
Future Perspectives
In addition to visually obvious phenotypes, natural variation has also been observed
in genetic mechanisms such as cytosine methylation (Riddle and Richards
2002
). A
recent interest concerns the exploitation of natural variation in gene expression,
leading to the first studies using expression QTL mapping (eQTL) proposed as a
valuable approach to dissect the genetic basis of transcript variation, one of the
prime causes of natural phenotypic variation. A recent study using eQTL conducted
on 191-individual pseudo-F1 progeny of grape to dissect the genetic basis of berry
colour formation (Huang et al.
2013
), led to the identification of two major QTL
explaining 20 % of genotypic variance and co-locating with a key enzyme for
anthocyanin synthesis. With available genomic tools such as the whole genome
