In this article we will discuss about the applications of RAPD marker in plants. Also learn about its demerits.
1. RAPD is used to distinguish between variety is based on difference in DNA sequence. RAPD have been used to identify nearly 15 commercial sunflower varieties. The new bean varieties (Phaseolus vulgaris) which are difficult to distinguish based on morphological trait have been used as ideal candidate for the application of RAPD marker methods when DNA was extracted from each varieties. The 12 samples were analysed using 60 primers.
This produced 296 markers and that could be scored. Almost 85% similarity was predicted. For example, DNA from plant allows the amplification of sequences a, c, d but not b. This indicates that in plant 1, primer sites for the primers used not found at sequence b. Similarly, a DNA sequence alternation at one of the primer binding site (priming) for a sequence ‘a’ has prevent it from being amplified when DNA from plant 2 is used.
RAPD have been extensively used for number of horticultural crops in variety identification, genetic purity and sex determination. A specific RAPD marker has been used to select for high and low β-glucan content between barley varieties.
2. RAPD markers are employed in the construction of genetic maps. Genetic maps of several plants including model plant Arabidopsis and tobacco have been constructed. RAPD markers have been used to construct 15 linkage groups in coffee. Both genomic and chloroplast DNA provided the source of probes.
RAPD markers are used for the selection of segregating populations more or less indirectly, during plant breeding. These markers also accelerate back crossing process and allow the selection of individually with more of recurrent genome at each generation facilitate breeding programme to be completed within few generations.
3. RAPD molecular marker used in the direct selection of desirable trait. Molecular marker linked to the trait of interest can be screened for at any stage in the breeding programme.
4. RAPD and other molecular markers have great value in the selection for desirable trait in long-lived species which takes long time for maturity and show phenotypic character. For example, avacado (Persea americana) fruit quality can be assessed in seedling itself using RAPD molecular marker.
5. RAPD markers have been used to identify several disease resistant genes in plants. The rp94 gene is responsible for resistance to stem rust (Puccinia gramnis) in barley. RAPD markers identified to link to this gene. Similarly, RAPD markers linked to heat smut resistance gene have been characterized. Controlling of height in barley plant by specific gene has been used to locate dwarfism gene by RAPD marker.
6. In tissue culture work, somatic hybrids involving protoplast fusion requires thorough screening. However, screening of somatic hybrid is cumbersome. Therefore, RAPD markers can be exploited in identifying somatic hybrids. RAPD analysis provides an important tool for the characterization of biodiversity.
Identification of areas rich in endemic genotypes helps in habitat conservative and prevents species extinction. Molecular analysis of genetic diversity using RAPD or RFLP in plant genetic germplasm collection facilitate better management especially space and resources are serious constraints.
RAPD analysis has been used for the identification of duplicates in germplasm. These duplicates are then discarded once no morphological differences were detected. RAPD analysis has been implicated in the analysis of rice genome collections held at the International Rice Research Institute, Phillipines.
Genetic diversity was carried out in a set a 63 tetraploid wheat genotype. Which comprises 24 duran land races, 18 duran cultivars and nine diococcum cultivars, two wild tetraploid species? The duran and dicoccum wheat genotypes are part of the germplasm used in Indian tetraploid wheat breeding programme.
RAPD scoring analysis reveals 78% were polymorphic in different categories of Indian tetraploid wheat. These indicate that RAPD diversity data can be used in breeding improved cultivars and maintaining genetic diversity in germplasm. Similarly RAPD markers were generated from 6 groups of 23 varieties of Tibetian barley. Nearly 23 RAPD and 29 genes loci were identified on 72 chromosomes.
RAPD have also been used in variety identification and purity in grain processing in food industry. For example, particular duran variety of wheat is used in the preparation of food products. Contamination of other variety can be identified by using these molecular markers.
Demerits of RAPD:
1. Constraints about reproducibility of results.
2. Since RAPD markers are dominant, only half the genetic informations are co-dominant markers.
3. Null alleles not directly detected.