Molecular Markers in Breeding Programme:
The advent of molecular techniques played a significant role in increase our knowledge of cereal genetics and behaviour of cereal genomics. While RFLP markers have been the basis for most work in crop plants, valuable markers have been generated from RAPD and AFLPs.
Recently, other improvised molecular marker such as simple sequence repeats (SSR), microsatellite marker have also been developed for major crop plants and initiate rapid advance in both marker development and implementation in breeding programme.
Conventional plant breeding is time consuming and depends on environmental conditions, for example, breeding for new variety development takes between eight and twelve years without any guarantee of variety release.
Hence, breeding is extremely enthusiastic and extremely interested in new molecular breeding technologies that could make this entire breeding exercise simple, speedy and efficient. This technology also offers selection of desirable combination of traits.
This approach can be establishing linkage between molecular marker and traits to be selected. Once this approach is completed would allow breeding process to be conducted in the laboratory without waiting for expression of the genes for particular phenotype. For example, resistant to plant pathogen can be evaluated in the absence of disease. Every stress tolerance can be analysed in the seedling stages itself.
Marker Assisted Selection (MAS):
(i) Mapping of plant genomes:
Among several important crop plant, rice has been the target plant for intense mapping studies. However, model plant, Arabidopsis thaliana has also been considered for extensive mapping study. Currently, genetic mapping for rice and Arabidopsis has also been completed.
Mapping smaller the size of genome is ideal for key strategy for the identification of gene in the complex genome. Molecular marker like RFLP marker from closely related species is good reliable markers for constructing gene map. Microsatellite is useful tool for constructing gene map to each species whereas RFLP loci can be used to map at greater degree in related taxa.
(ii) Linkage of molecular marker to desired trait:
Identification of genes responsible for useful trait may be established by a linkage analysis with markers on a genetic map of plant genome polymorphic marker is generally used to identify linked markers. Finding of linked markers can be accomplished by a certain useful technique like bulked segregate analysis (BSA). This technique is used to detect polymorphism between two DNA samples made up of bulk of individuals from the segregating populations.
For example, one bulk sample DNA from one individual contain target gene while other DNA from individual devoid of this gene. The segregating population derived sample contains both of the two bulks containing most genes.
Polymorphism between the bulks is likely to be linked to genes for the trait. The analysis of linkers for dominant (RAPD) and co-dominant marker (RFLP or microsatellite) requires separate unique analysis of mapping with F2 population.
(iii) Accelerated back crossing:
Marker assisted selection facilitate in the acceleration of whole breeding process, allowing earlier release of plant commercial. This is achieved by two important method like accelerated back crossing and selection for a desired trait. Introduction of desirable trait has been the favourite choice for plant breeders without altering other character.
This can be accomplished by repeated crossing to the plant with the genetic background required. Each and every generation requires selection of introduced trait. This requires number of crossing and more number of generation since molecular marker facilitate selection of individuals with more of the recurrent genome at each generation. It can limit breeding programme to be completed with few generation.
Selection for a Desired Trait:
Several desirable traits can be directly selected by molecular marker and can be screen at any stage in the breeding programme. In addition to the available marker for routine use, conversion of RFLP marker to PCR based marker helps significantly in the economy of molecular usage. In addition, usage of molecular marker for fruit selection in plant breeding requires availability of simple, inexpensive technique that provides rapid result in the assessment for next round of selection.
Molecular Breeding for Resistance:
PCR-based marker has been used in the breeding of desirable resistance to viral and fungal pathogen in plants. Barley yellow mosaic virus (Ba YMU) has been considered as important viral disease in Europe. Therefore, breeding for resistance to the disease is special importance. Applications of closely linked PCR-based markers for the transmission of resistance gene(s) against barley yellow mosaic virus are now successful and efficient.
Similarly breeding for resistance to fungal pathogen has been advanced. Fusarium head blight is a serious disease of wheat. Molecular markers closely liked to the major QTL involved in Fusarium head blight (FHB) resistance have been identified and raise the possibility of marker assisted selection (MAS) for introducing resistance alleles into elite wheat variety. These are some of the safety strategy in breeding. The new varieties combined high yield performance and high level of resistance to fusarium pathogen.
Identification of Breeding Lines:
In the germplasm labelling error can lead to breeding artifact because handling of large number of lines may create problem in identifying molecular marker can be used to confirm breeding lines.
Identification of Hybridity:
Molecular marker can be used to identify hybrid nature of individual especially in self- pollinating species. Production of hybrid through non-conventional hybrid method like somatic hybrid also can be identical using RAPD analysis.
Purity of Breeding Lines:
Accidental mixing of seeds or cross-contamination in seed harvested may lead to contamination of breeding lines. Molecular markers can be used to assist establishment of pure breeding lines and check contamination of breeding.
Prediction of Hybrid Performance (Heterosis):
Establishment of genetic distance between the parents used in the cross can able to ascertain the performance of hybridity. Genetic distance between possible parents can be estimated by employing molecular markers. RFLP microsatellite markers are selected as useful marker for these predictions.
Identification of several useful genetic resources of possible parents for use in breeding requires suitable molecular technique. RAPD marker is useful tool for the survey of germplasm, for example, survey of rice germplasm using RAPD shows linkage between the presence of specific marker and quantitative trait loci (QTL) for novel character.
Before the onset of molecular markers, some of the earlier experiments were carried out using biochemical markers. Certain isozymes (or isoenzymes) have been employed as biochemical markers in various aspects of plant breeding and genetics due to their significance as natural markers.
Some of the commonly known biochemical isozyme markers are esterases, peroxidases, dehydrogenases etc. Basically these markers are gene expression products and are characterised by electrophoresis and staining. By definition, isoenzymes are multiple molecular forms of the same enzyme that execute the same function.
They are the products of the different alleles of one or several genes. In several cases monomer and dimer isozymes are most often employed due to their early segregation process. Biochemical marker and assessment showed that these are co-dominant markers. Although isoenzymes are potentially a reliable marker, their polymorphism is however, exhibit relatively poor within a cultivated species.