Justifications for the development and use of MAS in plant breeding fall into four broad areas that are relevant to almost all target crops.
a. Traits that are difficult to manage through conventional phenotypic selection because they are expensive or time consuming to measure, or have low penetrance or complex inheritance.
b. Traits whose selection depends on specific environments or developmental stages that influence the expression of the target phenotype.
c. Maintenance of recessive alleles during back-crossing or for speeding up backcross breeding in general.
d. Pyramiding multiple monogenic traits such as pest and disease resistance or quality traits or several QTL for single target traits with complex inheritance.
Backcross breeding can be accelerated through MAS significantly. For most crops, over 90% of the recurrent parent genotype can be recovered within two generations when a suitable number of markers (for example one marker every 10 cM) and an adequate number of progeny is used for background selection.
This represents a substantial saving in time compared to conventional backcross breeding. Molecular markers intended for MABC can be selected based on their genomic distribution, haplotype diversity and/or polymorphic information content indices, and their association with candidate gene and other agronomic traits.
Marker assisted backcrossing has been found to be specially valuable where there are many good varieties that need to be improved for just one simply inherited trait such as certain pest or diseases or a component trait for enhancing adaptation or stress tolerance. With recent advances in high-throughput genotyping system, MABC is likely to become increasingly cost effective.
Introgression and pyramiding of multiple genes affecting the same trait poses a big challenge to the breeding programme. The target environments of many breeding programmes require a combination of diverse biotic stress resistances, agronomic and quality trait profiles and tolerance to abiotic stresses to improve performance, yield stability and acceptance by the farmers.
The success of MAS in such challenging situations will depend upon large scale genotyping for both multiple target traits and genetic background. The advantage with this type of integrated molecular breeding approach will be to achieve the same breeding progress in a much shorter time than through conventional breeding. The pyramiding of genes is achieved rather easily which is difficult through other means.
In a conventional breeding programme, there is simultaneous selection for more and more target traits leading to loss of breeding gains and increase in number of breeding cycles. MAS on the other hand, offers the potential to accumulate target traits in the same genotype more precisely with less unintentional losses and in fewer selection cycles.
The opportunities for improving more complex traits such as abiotic stress tolerances are confounded by low heritability, large number of genes involved, unpredictable effect of epistasis and the effect of various environmental factors. Under such situations, routine application of MAS still remains a challenge.