Plant breeding improves the genetic performance of the plants. Creation of the plant variety better than previous plants. Conventional breeding is based on the phenotype and marker assisted selection breeding is based on the genotype.
Limitation of the conventional breeding
- Genotype is often interact with the environmental condition.
- phenotyping procedure is expensive and time consuming
- some phenotype characters are combine with the abiotic stress.
Phenotypic variation may be qualitative and quantitative traits.
Marker assisted breeding is based on the genotype
QTLs (Quantitative trait loci) – the region with the genome that contain genes associated with the particular quantitative traits)
Pre-requisites for an efficient Marker assisted selection
- High-throughput DNA extraction protocol (extract the DNA from the large number of small samples at reasonable short time period)
- Low cost, High throughput DNA marker technology. (highly polymorphic, co-dominance inheritance, reproducibility)
- Linkage map – Provide framework for detecting marker traits association and selection markers.
- Selection of the QTLs – Due to the cost of utilizing the several QTLs, only markers that are tightly linked to the three QTLs are typically used.
- Efficient data management – labelling, storing, retrieving, and analyzing large data sets, and producing reports useful to the breeder
Linkage maps
Arranging the markers in order to indicating the relative genetic distance between them is call mapping, linkage mapping are these markers are on the same chromosome.
If the frequency of the recombination between two markers is lower, they are located closer on the same chromosome. Recombination frequency of linked genes/markers will be < 50%, unlinked markers are located far apart on the same chromosome or on different chromosomes, recombination frequency ≈ 50%
Procedure of the Marker assisted selection
- Extraction of DNA from tissue of each individual
- Marker assay (PCR for (single sequence repeat))
- Analysis of amplified products (using agarose gel electrophoresis or SDS-PAGE)
- heterozygotes lines are removed.
- Combine the marker results with other characters (phenotypic data)
Advantages of the Marker assisted selection
- Select genotype at the early seedling stage.
- Not affected by environmental conditions – determine the plant resistance level independent of the environmental conditions.
- MAS some times cheaper and faster method than conventional breeding methods but it depends on the trait
- Recessive allele can be identified by the appropriate linked markers, if the desired trait is determine by the recessive alleles that can not be identified by the conventional phenotype base method
- Gene pyramiding (Combings multiple genes simultaneously) – gene pyramiding is difficult to identify by the conventional phenotype base method, trait of the one gene is hidden by the additional genes.
- Selection of trait that having low heritability – most of the time conventional breeding methods used plants with high heritability.
Limitation of the MSA
- Large initial cost
- Inadequate facilities and conditions for large scale practices.
- Markers that used should be breeder friendly markers
- Markers that used for one population may not be transferrable to another population.
- Imprecise estimates of the QTLs
- Recombination between the marker and the gene of interest may lead to false positive results.
- The level of integration between molecular geneticists and plant breeders
Marker Assisted Breeding Schemes
- Markers – assisted backcross (MABC) breeding
- Markers – assisted gene pyramiding
- Early generation of the markers assisted selection
- Marker – directed phenotyping
Markers – assisted backcross (MABC) breeding
Goal is to incorporate one major gene from donor parent into an elite cultivar/recurrent parent, and reducing the donor parent DNA in the recurrent parent. This can be achieve by the repeated backcrossing and selection. DNA markers are accelerate the process MABC method only takes three generation of Back cross generations, conventional backcrossing may takes 6-8 backcross for the recovery of the recurrent parent genome.
- When backcross larger number of donor chromosome (undesirable or deleterious genes) along with the beneficial gene are remain even after many back crosses this is called as linkage drag
- Markers – assisted backcross (MABC) breeding reduce the level of linkage drags
MABC involves three levels of selection
- Foreground Selection – Selection the target QTL, reduce the linkage drags, until the final backcross is completed. Use tightly linked flanking markers to the QTL of the donor parent at the target locus
- Recombinant Selection – Selection for recombination between the target locus and flanking markers, minimized the linkage drag, only feasible the position of the QTLs is well defined.
- Background selection – Selecting the Backcross progeny with the greatest proportion of recurrent genome. Breeder select the recurrent parent markers alleles in all genomic regions except the target locus (select the markers that unlinked to the QTLs of the parent genome).
Use linked flanking markers for recombinant selection and unlinked markers to select for the RP’s genome
Efficiency of MABC depends on the
- Population size of each backcross generation
- Distance between the makers and the target locus
- Number of background markers (unlinked markers to QTLs)
Marker-assisted gene pyramiding (stacking)
Combine several genes into single genotype, parents contains several genes with the desired traits, they are cross and offspring population is screening for the genes of interest.
Early generation marker-assisted selection
- Plant with the unwanted genes are discarded.
Marker-directed phenotyping
- A combination of phenotypic screening and MAS