Agriculture Reference
In-Depth Information
progenies derived from a cross of distinct genotypes for the trait under study.
Phenotypic values for the quantitative traits are then compared with the molecular
marker genotypes of the progeny to search for particular genomic regions showing
statistically significant associations between polymorphism and the trait variation,
which are then called QTL. QTL analysis makes use of the natural variation present
within species. Once genetic variation is found among accessions, the aim is to
identify how many loci account for it and where they are located in the genome
(Koornneef et al.
2004
).
Identifying the number and genome position of the segregating QTL in an
experimental population requires the following steps: (a) the generation of an
experimental mapping population; (b) its genotyping with markers throughout the
genome and the phenotyping for the trait of interest; (c) the association analysis
between phenotypic values of the trait and genotypic classes of the polymorphic
markers. Thus, the number and genetic position of loci that control the trait
variation in that population, their relative additive effect, the contribution of genetic
interactions between loci (epistasis) and the mode of action of each QTL (domi-
nance effects) are calculated depending on the population type (Koornneef
et al.
2004
). The number of loci identified per analysis varies from 1 to
10,
depending on the complexity of the genetic variation under study, including
parameters such as the true number of loci segregating, the relative additive effect
of each QTL, and the effect of genetic interactions. In addition, this number
depends on the heritability of the trait in the assay performed,
i.e.
the control of
the environmental uniformity, the quality and density of genotypic data, the statis-
tical method used to map QTL, and the size of the mapping population.
>
Mapping Populations
In plants, the use of “immortal” mapping populations consisting of homozygous
individuals is preferred because it allows performance of replications and multiple
analyses of the same population. Such populations known as recombinant inbred
lines (RILs) or introgression lines (ILs), also referred to as near isogenic lines
(NILs), are practically homozygous and therefore phenotypic values can be based
on multiple replicates, reducing the environmental effects and increasing the power
to detect QTL. They can be analysed in multiple environments without the need for
further genotyping, and thus, the effects of each QTL in different environments can
be precisely estimated and tested for QTL
environment interactions (Koornneef
et al.
2004
). Homozygous populations can be obtained by repeated selfing, as for
RILs, but also by induced chromosomal doubling of haploids. In contrast, NILs
consist of lines containing a single fragment or a small number of genomic
introgression fragments from a donor parent into an otherwise homogeneous
genetic background, which increases the power to detect a small-effect QTL. In
plants, RILs and NILs are the most common types of experimental populations used
