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Indirect Selction in Plant Breeding Using RFLP - If a RFLP locus is tightly linked with a gene of interest, indirect selection for the gene can be exercised by selecting for a particular RFLP phenotype, which is linked with the desired phenotype for the economic trait. Such an indirect selection has several advantages including the following:

(i) during backcrossing, selection for a recessive gene can be exercised even in a heterozygous plant, because RFLPs are co-dominant; this will eliminate the need of selfing after each backcross as required in conventional backcross method of plant breeding and will thus help in speeding up the process;

(ii) indirect selection may also be desirable for dominant genes in some cases during backcrossing because selection can be exercised at the seedling stage and the plants not carrying the desirable allele can be weeded out early, thus saving space and expense;
(iii)during pyramiding of genes (when it is desired to incorporate more than one gene for the same trait) for traits like disease or insect resistance, it is not possible to select for the presence of an additional gene in the presence of an existing gene for the same trait; under such a situation, RFLP markers associated with different genes will differ and can be conveniently used to follow any number of genes during the breeding programme;
(iv) selection for mapped QTLs representing several chromosome segments contributing to the quan­titative trait, can be exercised simultaneously with the help of RFLPs associated with these chromosome segments.