|
|
|
|
Identification
and
Mapping
of
Quantitative
Trait
Loci
(QTLs)
Using
RFLp - Many quantitative traits of economic value are under polygenic control and are selected for, directly. Such a selection is often ineffective, since the effect of each gene is small and is also influenced by the environment. Therefore, one would welcome a procedure for indirect selection, which is not influenced by the environment.
For this purpose, linkage between quantitative traits and major marker genes should be known. Such marker genes involving morphological traits have been identified and mapped in Drosophila and in several crop plants. Isozyme marker loci linked to quantitative traits of economic value had also been earlier identified in tomato and maize.
However, in. recent years, it became possible to identify and map quantitative trait loci (QTLs) using RFLP markers, particularly in some crop plants like tomato and maize. The RFLPs arc recommended for this purpose, since these arc numerous and codominant.
|
For the study of RFLP-QTL linkage relationships, the experimental procedures differ for self pollinated and cross pollinated species, although with the availability of inbred lines in cross pollinated species, similar methods can be used in the two cases. In self pollinated genotypes and among inbred lines (in cross pollinated species), parents are first selected which differ for a number of RFLPs as well as for mean values of the quantitative traits. Once such parental lines are selected, they are crossed and F2 plants are derived.
In the F2 population, a chromosomal segment representing linkage between a RFLP marker and a QTL will be present in the background of random genetic variation due 10 independent assortment and recombination. By growing samples of F2 population in different environments, one may also study the linkage under different environments.
|
In these cases if mean values of a particular quantitative trait are determined in two groups of plants representing alternative alleles of RFLP, a significant difference in means (of two groups) for quantitative trait will indicate RFLP-QTL linkage. The observed marker associated difference in quantitative trait value will be a function of allelic effects at the QTL. Map distance between an RFLP and a QTL can also be determined.
In results of an experiment arc shown, where in tomato linkage is evident between one of the two molecular markers (A1I, A 2 ) and a QTL for high soluble solids. Two lines (cultivars VF 36 and its near isogenic line LA 1563) used in the cross had molecular markers (RFLPs) that identified L. esculentum (- 5% soluble solids) and L. chmielewskii (- 10% soluble solids), and also differed significantly for soluble solids (- 5% and 7-8%).
In F2' allele 'c' of the marker Al showed association with the QTL for high mean value of soluble solids, while the allele 'e' of A1' and both the alleles of A2 did not, suggesting that this QTL is found in the vicinity of AI' RFLPs, associated with the expression of complex traits like insect resistance and WUE, i.e. water use efficiency, have also been identified and mapped in tomato.
|
|
In the experiments like the above, if parents differ for a sufficient number of molecular markers (RFLPs,) which arc spaced out throughout the genome, a single cross can allow identification and mapping of all those QTLs for which the parents differ.
New analytical methods for the analysis of quantitative trait loci in plants using mapped RFLP markers were later suggested. These new methods included maximum likelihood method for interval mapping which was earlier used in humans. Interval mapping assesses the effects of each genome segment, located between a pair of marker loci, rather than the effect of a QTL associated with a single RFLP.
|
|
|
This provides greater precision. Lod scores (log of the score of odds for the presence, of a linkage against the odds of not having this linkage, e.g. if the Score is 100: 1 in favour of linkage, the lod score is 2) are also used in this method to reduce the probability of false positives for linkage. The results arc depicted as 'QTL likelihood maps'.
The technique of interval mapping allowed the QTLs to be mapped to intervals of 20cM, which was a poor resolution. Therefore, the technique of interval mapping was supplemented through the use of substitution mapping using selected overlapping recombinant chromosomes. This technique is analogous to the use of overlapping deletions and allowed fine mapping of QTLs.
The method has been successfully used for a study of tomato fruit characters, including mass per fruit, soluble solid concentration and fruit pH. The QTLs for these characters were mapped to intervals, as small as 3 cM.
|
In the above methods of QTL-RFLP linkage analysis, no distinction can be made between a group of tightly linked loci, each with small effect and a single locus' of large effect for a QTL. A distinction between these two situations may be important for fundamental as well as for applied studies, since selection strategies may differ in two cases, and also because studies at the molecular level are often conducted at individual gene level.
However, the success of genetic improvement based on selection of marker genes still remains to be tested, and will be effective only in specific cases. Further, it may not be necessary to use this method in cases where direct selection is more convenient and economic.
| |
